From li.luo at kaust.edu.sa Sun Dec 1 02:56:42 2019 From: li.luo at kaust.edu.sa (Li Luo) Date: Sun, 1 Dec 2019 11:56:42 +0300 Subject: [petsc-users] (no subject) Message-ID: Dear Developers, I tried to use the multi-color finite-difference (MC-FD) method for constructing the Jacobians. However, I find it is very slow compared to the exact Jacobian. My implementation of MC-FD Jacobian is posted below, would you please check whether I am correct? Anything missed? Thank you! ////////// Setup phase: MatStructure flag; ISColoring iscoloring; ierr = MatGetColoring(Jac,MATCOLORINGSL,&iscoloring); ierr = MatFDColoringCreate(Jac,iscoloring,&this->matfdcoloring); ierr = MatFDColoringSetFunction(this->matfdcoloring,(PetscErrorCode (*)(void))__libmesh_petsc_snes_residual,(void *)this); ierr = MatFDColoringSetFromOptions(this->matfdcoloring); ierr = ISColoringDestroy(&iscoloring); //////////// Apply: ierr = MatZeroEntries(*jac);CHKERRQ(ierr); ierr = MatFDColoringApply(*jac,solver->matfdcoloring,x,msflag,snes); Best regards, Li Luo -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jroman at dsic.upv.es Sun Dec 1 02:59:24 2019 From: jroman at dsic.upv.es (Jose E. Roman) Date: Sun, 1 Dec 2019 09:59:24 +0100 Subject: [petsc-users] Floating point exception In-Reply-To: References: Message-ID: <60EB8B0E-5046-45FC-AD21-8B03C2D79CEE@dsic.upv.es> If you have problems with PETSc's LU, I would suggest trying with an external package such as MUMPS. See section 3.4.1 of SLEPc's users manual. On the other hand, if you know where the wanted eigenvalues are located (around a value s), use shift-and-invert: -st_type sinvert -eps_target s This will factorize matrix (A-s*B) instead of B. Jose > El 30 nov 2019, a las 22:56, baikadi pranay escribi?: > > Hello, > > The entire output is the following: > > > [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- > [0]PETSC ERROR: Floating point exception > [0]PETSC ERROR: Vec entry at local location 0 is not-a-number or infinite at end of function: Parameter number 3 > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. > [0]PETSC ERROR: Petsc Release Version 3.11.1, Apr, 12, 2019 > [0]PETSC ERROR: ./a.out on a linux-gnu-c-debug named agave1.agave.rc.asu.edu by pbaikadi Sat Nov 30 14:54:31 2019 > [0]PETSC ERROR: Configure options > [0]PETSC ERROR: #1 VecValidValues() line 28 in /packages/7x/petsc/3.11.1/petsc-3.11.1/src/vec/vec/interface/rvector.c > [0]PETSC ERROR: #2 PCApply() line 464 in /packages/7x/petsc/3.11.1/petsc-3.11.1/src/ksp/pc/interface/precon.c > [0]PETSC ERROR: #3 KSP_PCApply() line 281 in /packages/7x/petsc/3.11.1/petsc-3.11.1/include/petsc/private/kspimpl.h > [0]PETSC ERROR: #4 KSPSolve_PREONLY() line 22 in /packages/7x/petsc/3.11.1/petsc-3.11.1/src/ksp/ksp/impls/preonly/preonly.c > [0]PETSC ERROR: #5 KSPSolve() line 782 in /packages/7x/petsc/3.11.1/petsc-3.11.1/src/ksp/ksp/interface/itfunc.c > [0]PETSC ERROR: #6 STMatSolve() line 193 in /packages/7x/slepc/3.11.1/slepc-3.11.1/src/sys/classes/st/interface/stsles.c > [0]PETSC ERROR: #7 STApply_Shift() line 25 in /packages/7x/slepc/3.11.1/slepc-3.11.1/src/sys/classes/st/impls/shift/shift.c > [0]PETSC ERROR: #8 STApply() line 57 in /packages/7x/slepc/3.11.1/slepc-3.11.1/src/sys/classes/st/interface/stsolve.c > [0]PETSC ERROR: #9 EPSGetStartVector() line 797 in /packages/7x/slepc/3.11.1/slepc-3.11.1/src/eps/interface/epssolve.c > [0]PETSC ERROR: #10 EPSSolve_KrylovSchur_Symm() line 32 in /packages/7x/slepc/3.11.1/slepc-3.11.1/src/eps/impls/krylov/krylovschur/ks-symm.c > [0]PETSC ERROR: #11 EPSSolve() line 149 in /packages/7x/slepc/3.11.1/slepc-3.11.1/src/eps/interface/epssolve.c > > Regards, > Pranay. > > On Sat, Nov 30, 2019 at 2:46 PM Matthew Knepley wrote: > On Sat, Nov 30, 2019 at 3:19 PM baikadi pranay wrote: > Hello PETSc users, > > I am currently trying to build a 1-D Schrodinger solver. I have built my hamiltonian matrix (of size 121 x 121) and i'm trying to find the eigenvalues. I have the following lines of code for the solver: > > call EPSCreate(PETSC_COMM_WORLD,eps,ierr) > call EPSSetOperators(eps,ham,S,ierr) > call EPSSetProblemType(eps,EPS_GHEP,ierr) > call EPSSetFromOptions(eps,ierr) > call EPSSetDimensions(eps,10,PETSC_DEFAULT_INTEGER,PETSC_DEFAULT_INTEGER,ierr) > call EPSSolve(eps,ierr) > call EPSDestroy(eps,ierr) > > At the EPSSolve line, i get the following error: > > [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- > [0]PETSC ERROR: Floating point exception > [0]PETSC ERROR: Vec entry at local location 0 is not-a-number or infinite at end of function: Parameter number 3 > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. > [0]PETSC ERROR: Petsc Release Version 3.11.1, Apr, 12, 2019 > > You need to show the entire stack trace that is output here. > > Thanks, > > Matt > > I am using the options -st_pc_factor_shift_type NONZERO -st_pc_factor_shift_amount 1 ( else I end up getting the "zero pivot in LU factorization" error ). > > I outputted my matrix to matlab and confirmed that the null space is empty and the matrix is not singular. I am not sure why I'm getting this error. Could you provide me a hint as to how to solve this problem. > > Sincerely, > Pranay. > > > -- > What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ From mfadams at lbl.gov Sun Dec 1 06:43:09 2019 From: mfadams at lbl.gov (Mark Adams) Date: Sun, 1 Dec 2019 07:43:09 -0500 Subject: [petsc-users] (no subject) In-Reply-To: References: Message-ID: FM matrices are slow and meant for debugging mostly (I thought, although the docs just give this warning if coloring is not available). I would check the timings from -log_view and verify that the time is spent in MatFDColoringApply. Running with -info should print the number of colors (C). The cost of an FD matrix is about C x cost of an exact Jacobian. Roughly. You could check that. Mark On Sun, Dec 1, 2019 at 3:58 AM Li Luo wrote: > Dear Developers, > > I tried to use the multi-color finite-difference (MC-FD) method for > constructing the Jacobians. However, I find it is very slow compared to the > exact Jacobian. > My implementation of MC-FD Jacobian is posted below, would you please > check whether I am correct? Anything missed? Thank you! > > ////////// Setup phase: > MatStructure flag; > ISColoring iscoloring; > ierr = MatGetColoring(Jac,MATCOLORINGSL,&iscoloring); > ierr = MatFDColoringCreate(Jac,iscoloring,&this->matfdcoloring); > ierr = > MatFDColoringSetFunction(this->matfdcoloring,(PetscErrorCode > (*)(void))__libmesh_petsc_snes_residual,(void *)this); > ierr = MatFDColoringSetFromOptions(this->matfdcoloring); > ierr = ISColoringDestroy(&iscoloring); > > //////////// Apply: > ierr = MatZeroEntries(*jac);CHKERRQ(ierr); > ierr = > MatFDColoringApply(*jac,solver->matfdcoloring,x,msflag,snes); > > Best regards, > Li Luo > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jed at jedbrown.org Sun Dec 1 09:45:35 2019 From: jed at jedbrown.org (Jed Brown) Date: Sun, 01 Dec 2019 08:45:35 -0700 Subject: [petsc-users] (no subject) In-Reply-To: References: Message-ID: <8736e49hi8.fsf@jedbrown.org> Mark Adams writes: > FM matrices are slow and meant for debugging mostly (I thought, > although the docs just give this warning if coloring is not available). > > I would check the timings from -log_view and verify that the time is spent > in MatFDColoringApply. Running with -info should print the number of colors > (C). The cost of an FD matrix is about C x cost of an exact Jacobian. > Roughly. You could check that. This depends a lot on how efficient the residual and Jacobian evaluation is. We've seen examples where a colored Jacobian is less expensive than analytic, even when the analytic is not "poorly written". From knepley at gmail.com Sun Dec 1 10:33:09 2019 From: knepley at gmail.com (Matthew Knepley) Date: Sun, 1 Dec 2019 10:33:09 -0600 Subject: [petsc-users] Floating point exception In-Reply-To: References: Message-ID: On Sat, Nov 30, 2019 at 3:56 PM baikadi pranay wrote: > Hello, > > The entire output is the following: > Okay, you are definitely getting an infinity in the output vector from the LU solve, so you are giving it a singular matrix. I am guessing this is B? How can you justify using a singular B? Also, -st_pc_factor_shift_amount 1 is strange. You would normally use a very small offset like 1.0e-10 or something. Thanks, Matt > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [0]PETSC ERROR: Floating point exception > [0]PETSC ERROR: Vec entry at local location 0 is not-a-number or infinite > at end of function: Parameter number 3 > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > [0]PETSC ERROR: Petsc Release Version 3.11.1, Apr, 12, 2019 > [0]PETSC ERROR: ./a.out on a linux-gnu-c-debug named > agave1.agave.rc.asu.edu by pbaikadi Sat Nov 30 14:54:31 2019 > [0]PETSC ERROR: Configure options > [0]PETSC ERROR: #1 VecValidValues() line 28 in > /packages/7x/petsc/3.11.1/petsc-3.11.1/src/vec/vec/interface/rvector.c > [0]PETSC ERROR: #2 PCApply() line 464 in > /packages/7x/petsc/3.11.1/petsc-3.11.1/src/ksp/pc/interface/precon.c > [0]PETSC ERROR: #3 KSP_PCApply() line 281 in > /packages/7x/petsc/3.11.1/petsc-3.11.1/include/petsc/private/kspimpl.h > [0]PETSC ERROR: #4 KSPSolve_PREONLY() line 22 in > /packages/7x/petsc/3.11.1/petsc-3.11.1/src/ksp/ksp/impls/preonly/preonly.c > [0]PETSC ERROR: #5 KSPSolve() line 782 in > /packages/7x/petsc/3.11.1/petsc-3.11.1/src/ksp/ksp/interface/itfunc.c > [0]PETSC ERROR: #6 STMatSolve() line 193 in > /packages/7x/slepc/3.11.1/slepc-3.11.1/src/sys/classes/st/interface/stsles.c > [0]PETSC ERROR: #7 STApply_Shift() line 25 in > /packages/7x/slepc/3.11.1/slepc-3.11.1/src/sys/classes/st/impls/shift/shift.c > [0]PETSC ERROR: #8 STApply() line 57 in > /packages/7x/slepc/3.11.1/slepc-3.11.1/src/sys/classes/st/interface/stsolve.c > [0]PETSC ERROR: #9 EPSGetStartVector() line 797 in > /packages/7x/slepc/3.11.1/slepc-3.11.1/src/eps/interface/epssolve.c > [0]PETSC ERROR: #10 EPSSolve_KrylovSchur_Symm() line 32 in > /packages/7x/slepc/3.11.1/slepc-3.11.1/src/eps/impls/krylov/krylovschur/ks-symm.c > [0]PETSC ERROR: #11 EPSSolve() line 149 in > /packages/7x/slepc/3.11.1/slepc-3.11.1/src/eps/interface/epssolve.c > > Regards, > Pranay. > > On Sat, Nov 30, 2019 at 2:46 PM Matthew Knepley wrote: > >> On Sat, Nov 30, 2019 at 3:19 PM baikadi pranay >> wrote: >> >>> Hello PETSc users, >>> >>> I am currently trying to build a 1-D Schrodinger solver. I have built my >>> hamiltonian matrix (of size 121 x 121) and i'm trying to find the >>> eigenvalues. I have the following lines of code for the solver: >>> >>> *call EPSCreate(PETSC_COMM_WORLD,eps,ierr)* >>> >>> *call EPSSetOperators(eps,ham,S,ierr)call >>> EPSSetProblemType(eps,EPS_GHEP,ierr)* >>> >>> >>> >>> *call EPSSetFromOptions(eps,ierr)call >>> EPSSetDimensions(eps,10,PETSC_DEFAULT_INTEGER,PETSC_DEFAULT_INTEGER,ierr)call >>> EPSSolve(eps,ierr)call EPSDestroy(eps,ierr)* >>> >>> At the EPSSolve line, i get the following error: >>> >>> >>> >>> >>> >>> *[0]PETSC ERROR: --------------------- Error Message >>> --------------------------------------------------------------[0]PETSC >>> ERROR: Floating point exception[0]PETSC ERROR: Vec entry at local location >>> 0 is not-a-number or infinite at end of function: Parameter number >>> 3[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html >>> for trouble >>> shooting.[0]PETSC ERROR: Petsc Release Version 3.11.1, Apr, 12, 2019* >>> >> >> You need to show the entire stack trace that is output here. >> >> Thanks, >> >> Matt >> >> >>> I am using the options *-st_pc_factor_shift_type NONZERO >>> -st_pc_factor_shift_amount 1* ( else I end up getting the "zero >>> pivot in LU factorization" error ). >>> >>> I outputted my matrix to matlab and confirmed that the null space is >>> empty and the matrix is not singular. I am not sure why I'm getting this >>> error. Could you provide me a hint as to how to solve this problem. >>> >>> Sincerely, >>> Pranay. >>> >> >> >> -- >> What most experimenters take for granted before they begin their >> experiments is infinitely more interesting than any results to which their >> experiments lead. >> -- Norbert Wiener >> >> https://www.cse.buffalo.edu/~knepley/ >> >> > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From pranayreddy865 at gmail.com Sun Dec 1 11:21:55 2019 From: pranayreddy865 at gmail.com (baikadi pranay) Date: Sun, 1 Dec 2019 10:21:55 -0700 Subject: [petsc-users] Floating point exception In-Reply-To: References: Message-ID: Hello, I was able to fix the problem. You are correct that the matrix B is singular although that was not the intention. I am using fortran and although i knew that PETSc uses 0-based indexing for fortran, I forgot to take this into account while filling out the B matrix. This resulted in the program accessing matrix elements which are essentially zero. Also I am not using the *-st_pc_factor_shift_amount* option or the *-st_pc_factor_shift_type *and it works fine. Thank you for your time. Best wishes, Pranay. On Sun, Dec 1, 2019 at 9:33 AM Matthew Knepley wrote: > On Sat, Nov 30, 2019 at 3:56 PM baikadi pranay > wrote: > >> Hello, >> >> The entire output is the following: >> > > Okay, you are definitely getting an infinity in the output vector from the > LU solve, so you are giving it a singular matrix. > I am guessing this is B? How can you justify using a singular B? > Also, -st_pc_factor_shift_amount 1 is strange. You > would normally use a very small offset like 1.0e-10 or something. > > Thanks, > > Matt > > >> [0]PETSC ERROR: --------------------- Error Message >> -------------------------------------------------------------- >> [0]PETSC ERROR: Floating point exception >> [0]PETSC ERROR: Vec entry at local location 0 is not-a-number or infinite >> at end of function: Parameter number 3 >> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html >> for trouble shooting. >> [0]PETSC ERROR: Petsc Release Version 3.11.1, Apr, 12, 2019 >> [0]PETSC ERROR: ./a.out on a linux-gnu-c-debug named >> agave1.agave.rc.asu.edu by pbaikadi Sat Nov 30 14:54:31 2019 >> [0]PETSC ERROR: Configure options >> [0]PETSC ERROR: #1 VecValidValues() line 28 in >> /packages/7x/petsc/3.11.1/petsc-3.11.1/src/vec/vec/interface/rvector.c >> [0]PETSC ERROR: #2 PCApply() line 464 in >> /packages/7x/petsc/3.11.1/petsc-3.11.1/src/ksp/pc/interface/precon.c >> [0]PETSC ERROR: #3 KSP_PCApply() line 281 in >> /packages/7x/petsc/3.11.1/petsc-3.11.1/include/petsc/private/kspimpl.h >> [0]PETSC ERROR: #4 KSPSolve_PREONLY() line 22 in >> /packages/7x/petsc/3.11.1/petsc-3.11.1/src/ksp/ksp/impls/preonly/preonly.c >> [0]PETSC ERROR: #5 KSPSolve() line 782 in >> /packages/7x/petsc/3.11.1/petsc-3.11.1/src/ksp/ksp/interface/itfunc.c >> [0]PETSC ERROR: #6 STMatSolve() line 193 in >> /packages/7x/slepc/3.11.1/slepc-3.11.1/src/sys/classes/st/interface/stsles.c >> [0]PETSC ERROR: #7 STApply_Shift() line 25 in >> /packages/7x/slepc/3.11.1/slepc-3.11.1/src/sys/classes/st/impls/shift/shift.c >> [0]PETSC ERROR: #8 STApply() line 57 in >> /packages/7x/slepc/3.11.1/slepc-3.11.1/src/sys/classes/st/interface/stsolve.c >> [0]PETSC ERROR: #9 EPSGetStartVector() line 797 in >> /packages/7x/slepc/3.11.1/slepc-3.11.1/src/eps/interface/epssolve.c >> [0]PETSC ERROR: #10 EPSSolve_KrylovSchur_Symm() line 32 in >> /packages/7x/slepc/3.11.1/slepc-3.11.1/src/eps/impls/krylov/krylovschur/ks-symm.c >> [0]PETSC ERROR: #11 EPSSolve() line 149 in >> /packages/7x/slepc/3.11.1/slepc-3.11.1/src/eps/interface/epssolve.c >> >> Regards, >> Pranay. >> >> On Sat, Nov 30, 2019 at 2:46 PM Matthew Knepley >> wrote: >> >>> On Sat, Nov 30, 2019 at 3:19 PM baikadi pranay >>> wrote: >>> >>>> Hello PETSc users, >>>> >>>> I am currently trying to build a 1-D Schrodinger solver. I have built >>>> my hamiltonian matrix (of size 121 x 121) and i'm trying to find the >>>> eigenvalues. I have the following lines of code for the solver: >>>> >>>> *call EPSCreate(PETSC_COMM_WORLD,eps,ierr)* >>>> >>>> *call EPSSetOperators(eps,ham,S,ierr)call >>>> EPSSetProblemType(eps,EPS_GHEP,ierr)* >>>> >>>> >>>> >>>> *call EPSSetFromOptions(eps,ierr)call >>>> EPSSetDimensions(eps,10,PETSC_DEFAULT_INTEGER,PETSC_DEFAULT_INTEGER,ierr)call >>>> EPSSolve(eps,ierr)call EPSDestroy(eps,ierr)* >>>> >>>> At the EPSSolve line, i get the following error: >>>> >>>> >>>> >>>> >>>> >>>> *[0]PETSC ERROR: --------------------- Error Message >>>> --------------------------------------------------------------[0]PETSC >>>> ERROR: Floating point exception[0]PETSC ERROR: Vec entry at local location >>>> 0 is not-a-number or infinite at end of function: Parameter number >>>> 3[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html >>>> for trouble >>>> shooting.[0]PETSC ERROR: Petsc Release Version 3.11.1, Apr, 12, 2019* >>>> >>> >>> You need to show the entire stack trace that is output here. >>> >>> Thanks, >>> >>> Matt >>> >>> >>>> I am using the options *-st_pc_factor_shift_type NONZERO >>>> -st_pc_factor_shift_amount 1* ( else I end up getting the "zero >>>> pivot in LU factorization" error ). >>>> >>>> I outputted my matrix to matlab and confirmed that the null space is >>>> empty and the matrix is not singular. I am not sure why I'm getting this >>>> error. Could you provide me a hint as to how to solve this problem. >>>> >>>> Sincerely, >>>> Pranay. >>>> >>> >>> >>> -- >>> What most experimenters take for granted before they begin their >>> experiments is infinitely more interesting than any results to which their >>> experiments lead. >>> -- Norbert Wiener >>> >>> https://www.cse.buffalo.edu/~knepley/ >>> >>> >> > > -- > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Mon Dec 2 01:03:34 2019 From: bsmith at mcs.anl.gov (Smith, Barry F.) Date: Mon, 2 Dec 2019 07:03:34 +0000 Subject: [petsc-users] (no subject) In-Reply-To: References: Message-ID: How many colors is it requiring? And how long is the MatGetColoring() taking? Are you running in parallel? The MatGetColoring() MATCOLORINGSL uses a sequential coloring algorithm so if your matrix is large and parallel the coloring will take a long time. The parallel colorings are MATCOLORINGGREEDY and MATCOLORINGJP Barry > On Dec 1, 2019, at 12:56 AM, Li Luo wrote: > > Dear Developers, > > I tried to use the multi-color finite-difference (MC-FD) method for constructing the Jacobians. However, I find it is very slow compared to the exact Jacobian. > My implementation of MC-FD Jacobian is posted below, would you please check whether I am correct? Anything missed? Thank you! > > ////////// Setup phase: > MatStructure flag; > ISColoring iscoloring; > ierr = MatGetColoring(Jac,MATCOLORINGSL,&iscoloring); > ierr = MatFDColoringCreate(Jac,iscoloring,&this->matfdcoloring); > ierr = MatFDColoringSetFunction(this->matfdcoloring,(PetscErrorCode (*)(void))__libmesh_petsc_snes_residual,(void *)this); > ierr = MatFDColoringSetFromOptions(this->matfdcoloring); > ierr = ISColoringDestroy(&iscoloring); > > //////////// Apply: > ierr = MatZeroEntries(*jac);CHKERRQ(ierr); > ierr = MatFDColoringApply(*jac,solver->matfdcoloring,x,msflag,snes); > > Best regards, > Li Luo > > This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. From li.luo at kaust.edu.sa Mon Dec 2 03:02:45 2019 From: li.luo at kaust.edu.sa (Li Luo) Date: Mon, 2 Dec 2019 12:02:45 +0300 Subject: [petsc-users] (no subject) In-Reply-To: References: Message-ID: Thank you for your reply. The matrix is small with only 67500 rows, but is relatively dense since a second-order discontinuous Galerkin FEM is used, nonzeros=23,036,400. The number of colors is 539 as shown by using -mat_fd_coloring_view: MatFDColoring Object: 64 MPI processes type not yet set Error tolerance=1.49012e-08 Umin=1.49012e-06 Number of colors=539 Information for color 0 Number of columns 1 378 Number of rows 756 0 1188 1 1188 2 1188 3 1188 4 1188 5 1188 ... Is this normal? When using MCFD, is there any difference using mpiaij and mpibaij? Best, Li On Mon, Dec 2, 2019 at 10:03 AM Smith, Barry F. wrote: > > How many colors is it requiring? And how long is the MatGetColoring() > taking? Are you running in parallel? The MatGetColoring() MATCOLORINGSL > uses a sequential coloring algorithm so if your matrix is large and > parallel the coloring will take a long time. The parallel colorings are > MATCOLORINGGREEDY and MATCOLORINGJP > > Barry > > > > On Dec 1, 2019, at 12:56 AM, Li Luo wrote: > > > > Dear Developers, > > > > I tried to use the multi-color finite-difference (MC-FD) method for > constructing the Jacobians. However, I find it is very slow compared to the > exact Jacobian. > > My implementation of MC-FD Jacobian is posted below, would you please > check whether I am correct? Anything missed? Thank you! > > > > ////////// Setup phase: > > MatStructure flag; > > ISColoring iscoloring; > > ierr = MatGetColoring(Jac,MATCOLORINGSL,&iscoloring); > > ierr = > MatFDColoringCreate(Jac,iscoloring,&this->matfdcoloring); > > ierr = > MatFDColoringSetFunction(this->matfdcoloring,(PetscErrorCode > (*)(void))__libmesh_petsc_snes_residual,(void *)this); > > ierr = MatFDColoringSetFromOptions(this->matfdcoloring); > > ierr = ISColoringDestroy(&iscoloring); > > > > //////////// Apply: > > ierr = MatZeroEntries(*jac);CHKERRQ(ierr); > > ierr = > MatFDColoringApply(*jac,solver->matfdcoloring,x,msflag,snes); > > > > Best regards, > > Li Luo > > > > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > -- Postdoctoral Fellow Extreme Computing Research Center King Abdullah University of Science & Technology https://sites.google.com/site/rolyliluo/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Mon Dec 2 06:21:35 2019 From: knepley at gmail.com (Matthew Knepley) Date: Mon, 2 Dec 2019 07:21:35 -0500 Subject: [petsc-users] (no subject) In-Reply-To: References: Message-ID: On Mon, Dec 2, 2019 at 4:04 AM Li Luo wrote: > Thank you for your reply. > > The matrix is small with only 67500 rows, but is relatively dense since a > second-order discontinuous Galerkin FEM is used, nonzeros=23,036,400. > This is very dense, 0.5% fill or 340 nonzeros per row. > The number of colors is 539 as shown by using -mat_fd_coloring_view: > Coloring is not appropriate for this matrix since you have enormous dense blocks (I am guessing). It could work if you statically condense them out or had a fast analytic Jacobian. With 540 colors, it takes 540 matvecs to generate the action of the Jacobian. Thanks, Matt > MatFDColoring Object: 64 MPI processes > type not yet set > Error tolerance=1.49012e-08 > Umin=1.49012e-06 > Number of colors=539 > Information for color 0 > Number of columns 1 > 378 > Number of rows 756 > 0 1188 > 1 1188 > 2 1188 > 3 1188 > 4 1188 > 5 1188 > ... > > Is this normal? > When using MCFD, is there any difference using mpiaij and mpibaij? > > Best, > Li > > On Mon, Dec 2, 2019 at 10:03 AM Smith, Barry F. > wrote: > >> >> How many colors is it requiring? And how long is the MatGetColoring() >> taking? Are you running in parallel? The MatGetColoring() MATCOLORINGSL >> uses a sequential coloring algorithm so if your matrix is large and >> parallel the coloring will take a long time. The parallel colorings are >> MATCOLORINGGREEDY and MATCOLORINGJP >> >> Barry >> >> >> > On Dec 1, 2019, at 12:56 AM, Li Luo wrote: >> > >> > Dear Developers, >> > >> > I tried to use the multi-color finite-difference (MC-FD) method for >> constructing the Jacobians. However, I find it is very slow compared to the >> exact Jacobian. >> > My implementation of MC-FD Jacobian is posted below, would you please >> check whether I am correct? Anything missed? Thank you! >> > >> > ////////// Setup phase: >> > MatStructure flag; >> > ISColoring iscoloring; >> > ierr = MatGetColoring(Jac,MATCOLORINGSL,&iscoloring); >> > ierr = >> MatFDColoringCreate(Jac,iscoloring,&this->matfdcoloring); >> > ierr = >> MatFDColoringSetFunction(this->matfdcoloring,(PetscErrorCode >> (*)(void))__libmesh_petsc_snes_residual,(void *)this); >> > ierr = MatFDColoringSetFromOptions(this->matfdcoloring); >> > ierr = ISColoringDestroy(&iscoloring); >> > >> > //////////// Apply: >> > ierr = MatZeroEntries(*jac);CHKERRQ(ierr); >> > ierr = >> MatFDColoringApply(*jac,solver->matfdcoloring,x,msflag,snes); >> > >> > Best regards, >> > Li Luo >> > >> > This message and its contents, including attachments are intended >> solely for the original recipient. If you are not the intended recipient or >> have received this message in error, please notify me immediately and >> delete this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. >> >> > > -- > > Postdoctoral Fellow > Extreme Computing Research Center > King Abdullah University of Science & Technology > https://sites.google.com/site/rolyliluo/ > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From li.luo at kaust.edu.sa Mon Dec 2 06:30:54 2019 From: li.luo at kaust.edu.sa (Li Luo) Date: Mon, 2 Dec 2019 15:30:54 +0300 Subject: [petsc-users] (no subject) In-Reply-To: References: Message-ID: Thank you very much! It looks forming an analytic Jacobian is the only choice. Best, Li On Mon, Dec 2, 2019 at 3:21 PM Matthew Knepley wrote: > On Mon, Dec 2, 2019 at 4:04 AM Li Luo wrote: > >> Thank you for your reply. >> >> The matrix is small with only 67500 rows, but is relatively dense since a >> second-order discontinuous Galerkin FEM is used, nonzeros=23,036,400. >> > > This is very dense, 0.5% fill or 340 nonzeros per row. > > >> The number of colors is 539 as shown by using -mat_fd_coloring_view: >> > > Coloring is not appropriate for this matrix since you have enormous dense > blocks (I am guessing). It could work if you statically > condense them out or had a fast analytic Jacobian. With 540 colors, it > takes 540 matvecs to generate the action of the Jacobian. > > Thanks, > > Matt > > >> MatFDColoring Object: 64 MPI processes >> type not yet set >> Error tolerance=1.49012e-08 >> Umin=1.49012e-06 >> Number of colors=539 >> Information for color 0 >> Number of columns 1 >> 378 >> Number of rows 756 >> 0 1188 >> 1 1188 >> 2 1188 >> 3 1188 >> 4 1188 >> 5 1188 >> ... >> >> Is this normal? >> When using MCFD, is there any difference using mpiaij and mpibaij? >> >> Best, >> Li >> >> On Mon, Dec 2, 2019 at 10:03 AM Smith, Barry F. >> wrote: >> >>> >>> How many colors is it requiring? And how long is the >>> MatGetColoring() taking? Are you running in parallel? The MatGetColoring() >>> MATCOLORINGSL uses a sequential coloring algorithm so if your matrix is >>> large and parallel the coloring will take a long time. The parallel >>> colorings are MATCOLORINGGREEDY and MATCOLORINGJP >>> >>> Barry >>> >>> >>> > On Dec 1, 2019, at 12:56 AM, Li Luo wrote: >>> > >>> > Dear Developers, >>> > >>> > I tried to use the multi-color finite-difference (MC-FD) method for >>> constructing the Jacobians. However, I find it is very slow compared to the >>> exact Jacobian. >>> > My implementation of MC-FD Jacobian is posted below, would you please >>> check whether I am correct? Anything missed? Thank you! >>> > >>> > ////////// Setup phase: >>> > MatStructure flag; >>> > ISColoring iscoloring; >>> > ierr = MatGetColoring(Jac,MATCOLORINGSL,&iscoloring); >>> > ierr = >>> MatFDColoringCreate(Jac,iscoloring,&this->matfdcoloring); >>> > ierr = >>> MatFDColoringSetFunction(this->matfdcoloring,(PetscErrorCode >>> (*)(void))__libmesh_petsc_snes_residual,(void *)this); >>> > ierr = MatFDColoringSetFromOptions(this->matfdcoloring); >>> > ierr = ISColoringDestroy(&iscoloring); >>> > >>> > //////////// Apply: >>> > ierr = MatZeroEntries(*jac);CHKERRQ(ierr); >>> > ierr = >>> MatFDColoringApply(*jac,solver->matfdcoloring,x,msflag,snes); >>> > >>> > Best regards, >>> > Li Luo >>> > >>> > This message and its contents, including attachments are intended >>> solely for the original recipient. If you are not the intended recipient or >>> have received this message in error, please notify me immediately and >>> delete this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> >> >> -- >> >> Postdoctoral Fellow >> Extreme Computing Research Center >> King Abdullah University of Science & Technology >> https://sites.google.com/site/rolyliluo/ >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. > > > > -- > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ > > -- Postdoctoral Fellow Extreme Computing Research Center King Abdullah University of Science & Technology https://sites.google.com/site/rolyliluo/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Mon Dec 2 07:55:28 2019 From: bsmith at mcs.anl.gov (Smith, Barry F.) Date: Mon, 2 Dec 2019 13:55:28 +0000 Subject: [petsc-users] (no subject) In-Reply-To: References: Message-ID: <4CB643E1-BD45-405B-8703-BFBEE53C3644@mcs.anl.gov> Please send a run with optimization turned on (--with-debugging=0 in ./configure) and -log_view without the actual timing information we are just guessing where the time is spent. If your problem has a natural block size then using baij should be a bit faster than aij, but not dramatically better Barry > On Dec 2, 2019, at 4:30 AM, Li Luo wrote: > > Thank you very much! It looks forming an analytic Jacobian is the only choice. > > Best, > Li > > On Mon, Dec 2, 2019 at 3:21 PM Matthew Knepley wrote: > On Mon, Dec 2, 2019 at 4:04 AM Li Luo wrote: > Thank you for your reply. > > The matrix is small with only 67500 rows, but is relatively dense since a second-order discontinuous Galerkin FEM is used, nonzeros=23,036,400. > > This is very dense, 0.5% fill or 340 nonzeros per row. > > The number of colors is 539 as shown by using -mat_fd_coloring_view: > > Coloring is not appropriate for this matrix since you have enormous dense blocks (I am guessing). It could work if you statically > condense them out or had a fast analytic Jacobian. With 540 colors, it takes 540 matvecs to generate the action of the Jacobian. > > Thanks, > > Matt > > MatFDColoring Object: 64 MPI processes > type not yet set > Error tolerance=1.49012e-08 > Umin=1.49012e-06 > Number of colors=539 > Information for color 0 > Number of columns 1 > 378 > Number of rows 756 > 0 1188 > 1 1188 > 2 1188 > 3 1188 > 4 1188 > 5 1188 > ... > > Is this normal? > When using MCFD, is there any difference using mpiaij and mpibaij? > > Best, > Li > > On Mon, Dec 2, 2019 at 10:03 AM Smith, Barry F. wrote: > > How many colors is it requiring? And how long is the MatGetColoring() taking? Are you running in parallel? The MatGetColoring() MATCOLORINGSL uses a sequential coloring algorithm so if your matrix is large and parallel the coloring will take a long time. The parallel colorings are MATCOLORINGGREEDY and MATCOLORINGJP > > Barry > > > > On Dec 1, 2019, at 12:56 AM, Li Luo wrote: > > > > Dear Developers, > > > > I tried to use the multi-color finite-difference (MC-FD) method for constructing the Jacobians. However, I find it is very slow compared to the exact Jacobian. > > My implementation of MC-FD Jacobian is posted below, would you please check whether I am correct? Anything missed? Thank you! > > > > ////////// Setup phase: > > MatStructure flag; > > ISColoring iscoloring; > > ierr = MatGetColoring(Jac,MATCOLORINGSL,&iscoloring); > > ierr = MatFDColoringCreate(Jac,iscoloring,&this->matfdcoloring); > > ierr = MatFDColoringSetFunction(this->matfdcoloring,(PetscErrorCode (*)(void))__libmesh_petsc_snes_residual,(void *)this); > > ierr = MatFDColoringSetFromOptions(this->matfdcoloring); > > ierr = ISColoringDestroy(&iscoloring); > > > > //////////// Apply: > > ierr = MatZeroEntries(*jac);CHKERRQ(ierr); > > ierr = MatFDColoringApply(*jac,solver->matfdcoloring,x,msflag,snes); > > > > Best regards, > > Li Luo > > > > This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. > > > > -- > Postdoctoral Fellow > Extreme Computing Research Center > King Abdullah University of Science & Technology > https://sites.google.com/site/rolyliluo/ > > This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. > > > -- > What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ > > > -- > Postdoctoral Fellow > Extreme Computing Research Center > King Abdullah University of Science & Technology > https://sites.google.com/site/rolyliluo/ > > This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. From fe.wallner at gmail.com Mon Dec 2 08:55:28 2019 From: fe.wallner at gmail.com (Felipe Giacomelli) Date: Mon, 2 Dec 2019 11:55:28 -0300 Subject: [petsc-users] Weird behaviour of PCGAMG in coupled poroelasticity In-Reply-To: References: Message-ID: Thank you, Barry and Mark. The "very fast" cases indeed yield good results, that is, the numerical solution matches the analytical one. Nevertheless, the usage of PCHypre has eliminated this strange behavior. I wasn't aware of the GAMG limitations pointed out by Mark. In fact, for another classical poroelasticity problem, GAMG has performed really well, regardless of the physical properties employed. That made the observed behavior even more surprising. Regards, Felipe Em s?b., 30 de nov. de 2019 ?s 07:01, Mark Adams escreveu: > Let me add that generic AMG is not great for systems like this > (indefinite, asymmetric) so yes, check that your good cases are really good. > > GAMG uses eigenvalues, which are problematic for indefinite and > asymmetric matrices. I don't know why this is ever working well, but try > '-pc_type hypre' (and configure with --download-hypre'). Hypre is better > with asymmetric matrices. This would provide useful information to > diagnose what is going on here if not solve your problem. > > Note, the algorithms and implementations of hypre and GAMG are not very > domain decomposition dependant so it is surprising to see these huge > differences from the number of processors used. > > On Sat, Nov 30, 2019 at 1:49 AM Smith, Barry F. > wrote: > >> >> I would first run with -ksp_monitor_true_residual -ksp_converged_reason >> to make sure that those "very fast" cases are actually converging in those >> runs also use -ksp_view to see what the GMAG parameters are. Also use the >> -info option to have it print details on the solution process. >> >> Barry >> >> >> >> > On Nov 29, 2019, at 4:14 PM, Felipe Giacomelli >> wrote: >> > >> > Hello, >> > >> > I'm trying to solve Biot's poroelasticity (Cryer's sphere problem) >> through a fully coupled scheme. Thus, the solution of a single linear >> system yields both displacement and pressure fields, >> > >> > |K L | | u | = |b_u|. >> > |Q (A + H) | | p | = |b_p| >> > >> > The linear system is asymmetric, given that the discrete equations were >> obtained through the Element based Finite Volume Method (EbFVM). An >> unstructured tetrahedral grid is utilised, it has about 10000 nodal points >> (not coarse, nor too refined). Therefore, GMRES and GAMG are employed to >> solve it. >> > >> > Furthermore, the program was parallelised through a Domain >> Decomposition Method. Thus, each processor works in its subdomain only. >> > >> > So far, so good. For a given set of poroelastic properties (which are >> constant throughout time and space), the speedup increases as more >> processors are utilised: >> > >> > coupling intensity: 7.51e-01 >> > >> > proc solve time [s] >> > 1 314.23 >> > 2 171.65 >> > 3 143.21 >> > 4 149.26 (> 143.21, but ok) >> > >> > However, after making the problem MORE coupled (different poroelastic >> properties), a strange behavior is observed: >> > >> > coupling intensity: 2.29e+01 >> > >> > proc solve time [s] >> > 1 28909.35 >> > 2 192.39 >> > 3 181.29 >> > 4 14463.63 >> > >> > Recalling that GMRES and GAMG are used, KSP takes about 4300 iterations >> to converge when 1 processor is employed. On the other hand, for 2 >> processors, KSP takes around 30 iterations to reach convergence. Hence, >> explaining the difference between the solution times. >> > >> > Increasing the coupling even MORE, everything goes as expected: >> > >> > coupling intensity: 4.63e+01 >> > >> > proc solve time [s] >> > 1 229.26 >> > 2 146.04 >> > 3 121.49 >> > 4 107.80 >> > >> > Because of this, I ask: >> > >> > * What may be the source of this behavior? Can it be predicted? >> > * How can I remedy this situation? >> > >> > At last, are there better solver-pc choices for coupled poroelasticity? >> > >> > Thank you, >> > Felipe >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Mon Dec 2 15:10:49 2019 From: bsmith at mcs.anl.gov (Smith, Barry F.) Date: Mon, 2 Dec 2019 21:10:49 +0000 Subject: [petsc-users] (no subject) In-Reply-To: References: <4CB643E1-BD45-405B-8703-BFBEE53C3644@mcs.anl.gov> <909A1208-FC8F-4D21-B767-DD9A7A79F3E5@mcs.anl.gov> Message-ID: <58409C2D-97FF-48AB-8D36-F923977E959D@mcs.anl.gov> > On Dec 2, 2019, at 2:30 PM, Li Luo wrote: > > -snes_mf fails to converge in my case, but -ds_snes_mf_operator works, when the original analytic matrix is still used as the preconditioner. > The timing is several times greater than using the analytic matrix for both Jacobian and preconditioner. ok, how does -snes_mf fail to converge? -ksp_monitor ? does the linear solver just never converge? Using -snes_mf_operator will also build the Jacobian so in your case doesn't make much sense by itself since it is very expensive > > For an implicit time-stepping scheme, if using -snes_lag_jacobian -2, is the Jacobian built only twice at the first time step then it is used for all later time steps? Or it is built twice at every time step? Check the manual page for SNESSolve it should just compute the Jacobian once and reuse it forever. You can also try -snes_mf -snes_lag_jacobian -2 which should compute the Jacobian once, use that original one to build the preconditioner once and reuse the same preconditioner but use the matrix free to define the operator. Barry > > Regards, > Li > > On Mon, Dec 2, 2019 at 6:02 PM Smith, Barry F. wrote: > > Ok it is spending 99+ percent of the time computing the Jacobians. > > > MatFDColorApply 106 1.0 8.7622e+03 1.0 1.31e+08 1.1 6.9e+07 2.6e+03 1.1e+06 99 0 97 81 99 99 0 97 81 99 1 > MatFDColorFunc 60950 1.0 8.7560e+03 1.0 0.00e+00 0.0 6.9e+07 2.6e+03 1.1e+06 99 0 97 81 99 99 0 97 81 99 0 > > It is requiring on average 12 KSP iterations per linear solve so the resulting linear system appears well conditioned, this means even if you compute the Jacobian analytically likely most of the time in the run will still be computing Jacobians. > > Try using -snes_mf with the logging and see what happens. You can also try -snes_lag_jacobian_persists -snes_lag_jacobian -2 > > Note there may be other ways of avoiding the costly computation of the Jacobian at each Newton step. > > Barry > > > > On Dec 2, 2019, at 6:38 AM, Li Luo wrote: > > > > Dear Barry, > > > > Here is my log. > > Because I am using libMesh built on PETSc, there is more information from libMesh in the log file. > > I ran 13 time steps for the simulation so there are repeated snes_view info. > > The algorithm is simply NKS. > > > > Cheers, > > Li > > > > On Mon, Dec 2, 2019 at 4:55 PM Smith, Barry F. wrote: > > > > Please send a run with optimization turned on (--with-debugging=0 in ./configure) and -log_view without the actual timing information we are just guessing where the time is spent. > > > > If your problem has a natural block size then using baij should be a bit faster than aij, but not dramatically better > > > > Barry > > > > > > > On Dec 2, 2019, at 4:30 AM, Li Luo wrote: > > > > > > Thank you very much! It looks forming an analytic Jacobian is the only choice. > > > > > > Best, > > > Li > > > > > > On Mon, Dec 2, 2019 at 3:21 PM Matthew Knepley wrote: > > > On Mon, Dec 2, 2019 at 4:04 AM Li Luo wrote: > > > Thank you for your reply. > > > > > > The matrix is small with only 67500 rows, but is relatively dense since a second-order discontinuous Galerkin FEM is used, nonzeros=23,036,400. > > > > > > This is very dense, 0.5% fill or 340 nonzeros per row. > > > > > > The number of colors is 539 as shown by using -mat_fd_coloring_view: > > > > > > Coloring is not appropriate for this matrix since you have enormous dense blocks (I am guessing). It could work if you statically > > > condense them out or had a fast analytic Jacobian. With 540 colors, it takes 540 matvecs to generate the action of the Jacobian. > > > > > > Thanks, > > > > > > Matt > > > > > > MatFDColoring Object: 64 MPI processes > > > type not yet set > > > Error tolerance=1.49012e-08 > > > Umin=1.49012e-06 > > > Number of colors=539 > > > Information for color 0 > > > Number of columns 1 > > > 378 > > > Number of rows 756 > > > 0 1188 > > > 1 1188 > > > 2 1188 > > > 3 1188 > > > 4 1188 > > > 5 1188 > > > ... > > > > > > Is this normal? > > > When using MCFD, is there any difference using mpiaij and mpibaij? > > > > > > Best, > > > Li > > > > > > On Mon, Dec 2, 2019 at 10:03 AM Smith, Barry F. wrote: > > > > > > How many colors is it requiring? And how long is the MatGetColoring() taking? Are you running in parallel? The MatGetColoring() MATCOLORINGSL uses a sequential coloring algorithm so if your matrix is large and parallel the coloring will take a long time. The parallel colorings are MATCOLORINGGREEDY and MATCOLORINGJP > > > > > > Barry > > > > > > > > > > On Dec 1, 2019, at 12:56 AM, Li Luo wrote: > > > > > > > > Dear Developers, > > > > > > > > I tried to use the multi-color finite-difference (MC-FD) method for constructing the Jacobians. However, I find it is very slow compared to the exact Jacobian. > > > > My implementation of MC-FD Jacobian is posted below, would you please check whether I am correct? Anything missed? Thank you! > > > > > > > > ////////// Setup phase: > > > > MatStructure flag; > > > > ISColoring iscoloring; > > > > ierr = MatGetColoring(Jac,MATCOLORINGSL,&iscoloring); > > > > ierr = MatFDColoringCreate(Jac,iscoloring,&this->matfdcoloring); > > > > ierr = MatFDColoringSetFunction(this->matfdcoloring,(PetscErrorCode (*)(void))__libmesh_petsc_snes_residual,(void *)this); > > > > ierr = MatFDColoringSetFromOptions(this->matfdcoloring); > > > > ierr = ISColoringDestroy(&iscoloring); > > > > > > > > //////////// Apply: > > > > ierr = MatZeroEntries(*jac);CHKERRQ(ierr); > > > > ierr = MatFDColoringApply(*jac,solver->matfdcoloring,x,msflag,snes); > > > > > > > > Best regards, > > > > Li Luo > > > > > > > > This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. > > > > > > > > > > > > -- > > > Postdoctoral Fellow > > > Extreme Computing Research Center > > > King Abdullah University of Science & Technology > > > https://sites.google.com/site/rolyliluo/ > > > > > > This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. > > > > > > > > > -- > > > What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. > > > -- Norbert Wiener > > > > > > https://www.cse.buffalo.edu/~knepley/ > > > > > > > > > -- > > > Postdoctoral Fellow > > > Extreme Computing Research Center > > > King Abdullah University of Science & Technology > > > https://sites.google.com/site/rolyliluo/ > > > > > > This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. > > > > > > > > -- > > Postdoctoral Fellow > > Extreme Computing Research Center > > King Abdullah University of Science & Technology > > https://sites.google.com/site/rolyliluo/ > > > > This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. > > > > -- > Postdoctoral Fellow > Extreme Computing Research Center > King Abdullah University of Science & Technology > https://sites.google.com/site/rolyliluo/ > > This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. From mbuerkle at web.de Tue Dec 3 01:10:29 2019 From: mbuerkle at web.de (Marius Buerkle) Date: Tue, 3 Dec 2019 08:10:29 +0100 Subject: [petsc-users] MatView to disk for Elemental Message-ID: An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Tue Dec 3 02:14:19 2019 From: bsmith at mcs.anl.gov (Smith, Barry F.) Date: Tue, 3 Dec 2019 08:14:19 +0000 Subject: [petsc-users] MatView to disk for Elemental In-Reply-To: References: Message-ID: sorry about this. The numerical values between C and Fortran got out of sync. I've attached a patch file you can apply with patch -p1 < format.patch or you can use the branch https://gitlab.com/petsc/petsc/merge_requests/2346 Barry > On Dec 3, 2019, at 1:10 AM, Marius Buerkle wrote: > > Hi, > > I try to save a matrix in Elemental format to disk. I am doing, where p_matout is of type MATELEMENTAL, > > call PetscViewerCreate(PETSC_COMM_WORLD,v_file,ierr) > call PetscViewerPushFormat(v_file,PETSC_VIEWER_NATIVE,ierr) > call PetscViewerSetType(v_file,PETSCVIEWERBINARY,ierr) > call PetscViewerFileSetMode(v_file,FILE_MODE_WRITE,ierr) > call PetscViewerFileSetName(v_file,trim(filename),ierr) > call MatView(p_matout,v_file,ierr) > call PetscViewerDestroy(v_file,ierr) > > This gives the following error > [18]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- > [18]PETSC ERROR: No support for this operation for this object type > [18]PETSC ERROR: To store a parallel dense matrix you must first call PetscViewerPushFormat(viewer,PETSC_VIEWER_NATIVE) > [18]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. > [18]PETSC ERROR: Petsc Development GIT revision: v3.12.1-317-gcc59f4f82c GIT Date: 2019-11-08 00:07:59 -0600 > [18]PETSC ERROR: /home/marius/prog/ownstuff/fortran/programs/transomat_dev/save_load_fs/transomat/transomat on a named tono-hpc1 by marius Tue Dec 3 16:08:38 2019 > [18]PETSC ERROR: Configure options --prefix=/home/marius/prog/petsc/petsc_slepc_opt --with-scalar-type=complex --with-fortran-kernels=1 --with-64-bit-indices=0 --CC=mpicc --COPTFLAGS="-g -Ofast -std=c11 -qopenmmp" --CXX=mpicxx --CXXOPTFLAGS="-g -Ofast -std=c++14 -qopenmp" --FC=mpif90 --FOPTFLAGS="-g -Ofast -traceback -qopenmp" --with-mpi=1 --with-x=0 --download-parmetis=1 --download-metis=1 --download-superlu_dist=1 --download-superlu_dist-commit=f8ace664ec4ca10e96e258a764552cbda299ba6e --download-superlu_dist-cmake-arguments=-Denable_openmp:BOOL=TRUE --download-hwloc=1 --download-sowing=1 --with-openmp=1 --with-pthread=1 --download-elemental=1 --download-elemental-commit=6eb15a0da2a4998bf1cf971ae231b78e06d989d9 --download-elemental-cmake-arguments=-DEL_HYBRID:BOOL=TRUE --with-cxx-dialect=c++11 --with-debugging=0 --with-valgrind=0 --with-blaslapack-lib=" /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a -Wl,--start-group /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_intel_lp64.a /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_intel_thread.a /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_core.a /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.a -Wl,--end-group -liomp5 -lpthread -lm -ldl -lmpi_wrapper" --with-scalapack-lib=" /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a -Wl,--start-group /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_intel_lp64.a /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_intel_thread.a /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_core.a /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.a -Wl,--end-group -liomp5 -lpthread -lm -ldl -lmpi_wrapper" --with-mkl_pardiso-dir=/home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl --with-mkl_cpardiso-dir=/home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl --with-mkl_sparse-dir=/home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl --with-mkl_sparse_optimize-dir=/home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl --download-slepc=1 --download-slepc-commit=658271f --download-make=1 --download-cmake=1 > [18]PETSC ERROR: #1 MatView_MPIDense_Binary() line 682 in /home/marius/prog/petsc/git/petsc/src/mat/impls/dense/mpi/mpidense.c > [18]PETSC ERROR: #2 MatView_MPIDense() line 786 in /home/marius/prog/petsc/git/petsc/src/mat/impls/dense/mpi/mpidense.c > [18]PETSC ERROR: #3 MatView() line 1066 in /home/marius/prog/petsc/git/petsc/src/mat/interface/matrix.c > [18]PETSC ERROR: #4 MatView_Elemental() line 83 in /home/marius/prog/petsc/git/petsc/src/mat/impls/elemental/matelem.cxx > [18]PETSC ERROR: #5 MatView() line 1066 in /home/marius/prog/petsc/git/petsc/src/mat/interface/matrix.c > [19]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- > > > and on StdOut > Elemental matrix (explicit ordering) > > Any suggestions? > > Best, > Marius -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: format.patch Type: application/octet-stream Size: 1781 bytes Desc: format.patch URL: From bsmith at mcs.anl.gov Tue Dec 3 20:34:34 2019 From: bsmith at mcs.anl.gov (Smith, Barry F.) Date: Wed, 4 Dec 2019 02:34:34 +0000 Subject: [petsc-users] (no subject) In-Reply-To: References: <4CB643E1-BD45-405B-8703-BFBEE53C3644@mcs.anl.gov> <909A1208-FC8F-4D21-B767-DD9A7A79F3E5@mcs.anl.gov> <58409C2D-97FF-48AB-8D36-F923977E959D@mcs.anl.gov> Message-ID: From the code: if (snes->lagjacobian == -2) { snes->lagjacobian = -1; ierr = PetscInfo(snes,"Recomputing Jacobian/preconditioner because lag is -2 (means compute Jacobian, but then never again) \n");CHKERRQ(ierr); } else if (snes->lagjacobian == -1) { ierr = PetscInfo(snes,"Reusing Jacobian/preconditioner because lag is -1\n");CHKERRQ(ierr); ierr = PetscObjectTypeCompare((PetscObject)A,MATMFFD,&flag);CHKERRQ(ierr); if (flag) { ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); } PetscFunctionReturn(0); So it does what the manual page says. If you use -2 it will compute the Jacobian the next time it is needed but then will never compute it again,. This means it reuses the one computed for all time-steps. It can make sense depending on how much the Jacobian changes to use with -snes_mf_operator. To compute just once at the beginning of each new linear solver you can use for example 100 (this assumes that one nonlinear solver never needs more than 100 linear solvers.) This can also be used with -snes_mf_operator (or without). Barry > On Dec 3, 2019, at 6:33 AM, Li Luo wrote: > > If use -snes_mf, the linear solver just never converges. And at the second time step, it reports an error as: > [0]PETSC ERROR: No support for this operation for this object type! > [0]PETSC ERROR: Mat type mffd! > > I still don't understand "-snes_lag_jacobian -2", from the manual, it seems Jacobian is computed only once by setting -1, but it is recomputed once by -2. > For a time-stepping scheme where each step calls SNESSolve, if using -snes_lag_jacobian -2, will the following time steps reuse the Jacobian built at the first time step? > > Best, > Li > > > > On Tue, Dec 3, 2019 at 12:10 AM Smith, Barry F. wrote: > > > > On Dec 2, 2019, at 2:30 PM, Li Luo wrote: > > > > -snes_mf fails to converge in my case, but -ds_snes_mf_operator works, when the original analytic matrix is still used as the preconditioner. > > The timing is several times greater than using the analytic matrix for both Jacobian and preconditioner. > > ok, how does -snes_mf fail to converge? -ksp_monitor ? does the linear solver just never converge? > > Using -snes_mf_operator will also build the Jacobian so in your case doesn't make much sense by itself since it is very expensive > > > > > For an implicit time-stepping scheme, if using -snes_lag_jacobian -2, is the Jacobian built only twice at the first time step then it is used for all later time steps? Or it is built twice at every time step? > > Check the manual page for SNESSolve it should just compute the Jacobian once and reuse it forever. > > You can also try -snes_mf -snes_lag_jacobian -2 which should compute the Jacobian once, use that original one to build the preconditioner once and reuse the same preconditioner but use the matrix free to define the operator. > > > > Barry > > > > > Regards, > > Li > > > > On Mon, Dec 2, 2019 at 6:02 PM Smith, Barry F. wrote: > > > > Ok it is spending 99+ percent of the time computing the Jacobians. > > > > > > MatFDColorApply 106 1.0 8.7622e+03 1.0 1.31e+08 1.1 6.9e+07 2.6e+03 1.1e+06 99 0 97 81 99 99 0 97 81 99 1 > > MatFDColorFunc 60950 1.0 8.7560e+03 1.0 0.00e+00 0.0 6.9e+07 2.6e+03 1.1e+06 99 0 97 81 99 99 0 97 81 99 0 > > > > It is requiring on average 12 KSP iterations per linear solve so the resulting linear system appears well conditioned, this means even if you compute the Jacobian analytically likely most of the time in the run will still be computing Jacobians. > > > > Try using -snes_mf with the logging and see what happens. You can also try -snes_lag_jacobian_persists -snes_lag_jacobian -2 > > > > Note there may be other ways of avoiding the costly computation of the Jacobian at each Newton step. > > > > Barry > > > > > > > On Dec 2, 2019, at 6:38 AM, Li Luo wrote: > > > > > > Dear Barry, > > > > > > Here is my log. > > > Because I am using libMesh built on PETSc, there is more information from libMesh in the log file. > > > I ran 13 time steps for the simulation so there are repeated snes_view info. > > > The algorithm is simply NKS. > > > > > > Cheers, > > > Li > > > > > > On Mon, Dec 2, 2019 at 4:55 PM Smith, Barry F. wrote: > > > > > > Please send a run with optimization turned on (--with-debugging=0 in ./configure) and -log_view without the actual timing information we are just guessing where the time is spent. > > > > > > If your problem has a natural block size then using baij should be a bit faster than aij, but not dramatically better > > > > > > Barry > > > > > > > > > > On Dec 2, 2019, at 4:30 AM, Li Luo wrote: > > > > > > > > Thank you very much! It looks forming an analytic Jacobian is the only choice. > > > > > > > > Best, > > > > Li > > > > > > > > On Mon, Dec 2, 2019 at 3:21 PM Matthew Knepley wrote: > > > > On Mon, Dec 2, 2019 at 4:04 AM Li Luo wrote: > > > > Thank you for your reply. > > > > > > > > The matrix is small with only 67500 rows, but is relatively dense since a second-order discontinuous Galerkin FEM is used, nonzeros=23,036,400. > > > > > > > > This is very dense, 0.5% fill or 340 nonzeros per row. > > > > > > > > The number of colors is 539 as shown by using -mat_fd_coloring_view: > > > > > > > > Coloring is not appropriate for this matrix since you have enormous dense blocks (I am guessing). It could work if you statically > > > > condense them out or had a fast analytic Jacobian. With 540 colors, it takes 540 matvecs to generate the action of the Jacobian. > > > > > > > > Thanks, > > > > > > > > Matt > > > > > > > > MatFDColoring Object: 64 MPI processes > > > > type not yet set > > > > Error tolerance=1.49012e-08 > > > > Umin=1.49012e-06 > > > > Number of colors=539 > > > > Information for color 0 > > > > Number of columns 1 > > > > 378 > > > > Number of rows 756 > > > > 0 1188 > > > > 1 1188 > > > > 2 1188 > > > > 3 1188 > > > > 4 1188 > > > > 5 1188 > > > > ... > > > > > > > > Is this normal? > > > > When using MCFD, is there any difference using mpiaij and mpibaij? > > > > > > > > Best, > > > > Li > > > > > > > > On Mon, Dec 2, 2019 at 10:03 AM Smith, Barry F. wrote: > > > > > > > > How many colors is it requiring? And how long is the MatGetColoring() taking? Are you running in parallel? The MatGetColoring() MATCOLORINGSL uses a sequential coloring algorithm so if your matrix is large and parallel the coloring will take a long time. The parallel colorings are MATCOLORINGGREEDY and MATCOLORINGJP > > > > > > > > Barry > > > > > > > > > > > > > On Dec 1, 2019, at 12:56 AM, Li Luo wrote: > > > > > > > > > > Dear Developers, > > > > > > > > > > I tried to use the multi-color finite-difference (MC-FD) method for constructing the Jacobians. However, I find it is very slow compared to the exact Jacobian. > > > > > My implementation of MC-FD Jacobian is posted below, would you please check whether I am correct? Anything missed? Thank you! > > > > > > > > > > ////////// Setup phase: > > > > > MatStructure flag; > > > > > ISColoring iscoloring; > > > > > ierr = MatGetColoring(Jac,MATCOLORINGSL,&iscoloring); > > > > > ierr = MatFDColoringCreate(Jac,iscoloring,&this->matfdcoloring); > > > > > ierr = MatFDColoringSetFunction(this->matfdcoloring,(PetscErrorCode (*)(void))__libmesh_petsc_snes_residual,(void *)this); > > > > > ierr = MatFDColoringSetFromOptions(this->matfdcoloring); > > > > > ierr = ISColoringDestroy(&iscoloring); > > > > > > > > > > //////////// Apply: > > > > > ierr = MatZeroEntries(*jac);CHKERRQ(ierr); > > > > > ierr = MatFDColoringApply(*jac,solver->matfdcoloring,x,msflag,snes); > > > > > > > > > > Best regards, > > > > > Li Luo > > > > > > > > > > This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. > > > > > > > > > > > > > > > > -- > > > > Postdoctoral Fellow > > > > Extreme Computing Research Center > > > > King Abdullah University of Science & Technology > > > > https://sites.google.com/site/rolyliluo/ > > > > > > > > This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. > > > > > > > > > > > > -- > > > > What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. > > > > -- Norbert Wiener > > > > > > > > https://www.cse.buffalo.edu/~knepley/ > > > > > > > > > > > > -- > > > > Postdoctoral Fellow > > > > Extreme Computing Research Center > > > > King Abdullah University of Science & Technology > > > > https://sites.google.com/site/rolyliluo/ > > > > > > > > This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. > > > > > > > > > > > > -- > > > Postdoctoral Fellow > > > Extreme Computing Research Center > > > King Abdullah University of Science & Technology > > > https://sites.google.com/site/rolyliluo/ > > > > > > This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. > > > > > > > > -- > > Postdoctoral Fellow > > Extreme Computing Research Center > > King Abdullah University of Science & Technology > > https://sites.google.com/site/rolyliluo/ > > > > This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. > > > > -- > Postdoctoral Fellow > Extreme Computing Research Center > King Abdullah University of Science & Technology > https://sites.google.com/site/rolyliluo/ > > This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. From li.luo at kaust.edu.sa Wed Dec 4 01:56:38 2019 From: li.luo at kaust.edu.sa (Li Luo) Date: Wed, 4 Dec 2019 10:56:38 +0300 Subject: [petsc-users] (no subject) In-Reply-To: References: <4CB643E1-BD45-405B-8703-BFBEE53C3644@mcs.anl.gov> <909A1208-FC8F-4D21-B767-DD9A7A79F3E5@mcs.anl.gov> <58409C2D-97FF-48AB-8D36-F923977E959D@mcs.anl.gov> Message-ID: Thank you, I'll try that. Best, Li On Wed, Dec 4, 2019 at 5:34 AM Smith, Barry F. wrote: > > From the code: > > if (snes->lagjacobian == -2) { > snes->lagjacobian = -1; > > ierr = PetscInfo(snes,"Recomputing Jacobian/preconditioner because lag > is -2 (means compute Jacobian, but then never again) \n");CHKERRQ(ierr); > } else if (snes->lagjacobian == -1) { > ierr = PetscInfo(snes,"Reusing Jacobian/preconditioner because lag is > -1\n");CHKERRQ(ierr); > ierr = > PetscObjectTypeCompare((PetscObject)A,MATMFFD,&flag);CHKERRQ(ierr); > if (flag) { > ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); > ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); > } > PetscFunctionReturn(0); > > So it does what the manual page says. If you use -2 it will compute the > Jacobian the next time it is needed but then will never compute it again,. > This means it reuses the one computed for all time-steps. It can make sense > depending on how much the Jacobian changes to use with -snes_mf_operator. > > To compute just once at the beginning of each new linear solver you can > use for example 100 (this assumes that one nonlinear solver never needs > more than 100 linear solvers.) This can also be used with -snes_mf_operator > (or without). > > > Barry > > > > On Dec 3, 2019, at 6:33 AM, Li Luo wrote: > > > > If use -snes_mf, the linear solver just never converges. And at the > second time step, it reports an error as: > > [0]PETSC ERROR: No support for this operation for this object type! > > [0]PETSC ERROR: Mat type mffd! > > > > I still don't understand "-snes_lag_jacobian -2", from the manual, it > seems Jacobian is computed only once by setting -1, but it is recomputed > once by -2. > > For a time-stepping scheme where each step calls SNESSolve, if using > -snes_lag_jacobian -2, will the following time steps reuse the Jacobian > built at the first time step? > > > > Best, > > Li > > > > > > > > On Tue, Dec 3, 2019 at 12:10 AM Smith, Barry F. > wrote: > > > > > > > On Dec 2, 2019, at 2:30 PM, Li Luo wrote: > > > > > > -snes_mf fails to converge in my case, but -ds_snes_mf_operator > works, when the original analytic matrix is still used as the > preconditioner. > > > The timing is several times greater than using the analytic matrix for > both Jacobian and preconditioner. > > > > ok, how does -snes_mf fail to converge? -ksp_monitor ? does the > linear solver just never converge? > > > > Using -snes_mf_operator will also build the Jacobian so in your case > doesn't make much sense by itself since it is very expensive > > > > > > > > For an implicit time-stepping scheme, if using -snes_lag_jacobian -2, > is the Jacobian built only twice at the first time step then it is used for > all later time steps? Or it is built twice at every time step? > > > > Check the manual page for SNESSolve it should just compute the > Jacobian once and reuse it forever. > > > > You can also try -snes_mf -snes_lag_jacobian -2 which should compute > the Jacobian once, use that original one to build the preconditioner once > and reuse the same preconditioner but use the matrix free to define the > operator. > > > > > > > > Barry > > > > > > > > Regards, > > > Li > > > > > > On Mon, Dec 2, 2019 at 6:02 PM Smith, Barry F. > wrote: > > > > > > Ok it is spending 99+ percent of the time computing the Jacobians. > > > > > > > > > MatFDColorApply 106 1.0 8.7622e+03 1.0 1.31e+08 1.1 6.9e+07 > 2.6e+03 1.1e+06 99 0 97 81 99 99 0 97 81 99 1 > > > MatFDColorFunc 60950 1.0 8.7560e+03 1.0 0.00e+00 0.0 6.9e+07 > 2.6e+03 1.1e+06 99 0 97 81 99 99 0 97 81 99 0 > > > > > > It is requiring on average 12 KSP iterations per linear solve so the > resulting linear system appears well conditioned, this means even if you > compute the Jacobian analytically likely most of the time in the run will > still be computing Jacobians. > > > > > > Try using -snes_mf with the logging and see what happens. You can > also try -snes_lag_jacobian_persists -snes_lag_jacobian -2 > > > > > > Note there may be other ways of avoiding the costly computation of the > Jacobian at each Newton step. > > > > > > Barry > > > > > > > > > > On Dec 2, 2019, at 6:38 AM, Li Luo wrote: > > > > > > > > Dear Barry, > > > > > > > > Here is my log. > > > > Because I am using libMesh built on PETSc, there is more information > from libMesh in the log file. > > > > I ran 13 time steps for the simulation so there are repeated > snes_view info. > > > > The algorithm is simply NKS. > > > > > > > > Cheers, > > > > Li > > > > > > > > On Mon, Dec 2, 2019 at 4:55 PM Smith, Barry F. > wrote: > > > > > > > > Please send a run with optimization turned on (--with-debugging=0 > in ./configure) and -log_view without the actual timing information we are > just guessing where the time is spent. > > > > > > > > If your problem has a natural block size then using baij should be > a bit faster than aij, but not dramatically better > > > > > > > > Barry > > > > > > > > > > > > > On Dec 2, 2019, at 4:30 AM, Li Luo wrote: > > > > > > > > > > Thank you very much! It looks forming an analytic Jacobian is the > only choice. > > > > > > > > > > Best, > > > > > Li > > > > > > > > > > On Mon, Dec 2, 2019 at 3:21 PM Matthew Knepley > wrote: > > > > > On Mon, Dec 2, 2019 at 4:04 AM Li Luo wrote: > > > > > Thank you for your reply. > > > > > > > > > > The matrix is small with only 67500 rows, but is relatively dense > since a second-order discontinuous Galerkin FEM is used, > nonzeros=23,036,400. > > > > > > > > > > This is very dense, 0.5% fill or 340 nonzeros per row. > > > > > > > > > > The number of colors is 539 as shown by using > -mat_fd_coloring_view: > > > > > > > > > > Coloring is not appropriate for this matrix since you have > enormous dense blocks (I am guessing). It could work if you statically > > > > > condense them out or had a fast analytic Jacobian. With 540 > colors, it takes 540 matvecs to generate the action of the Jacobian. > > > > > > > > > > Thanks, > > > > > > > > > > Matt > > > > > > > > > > MatFDColoring Object: 64 MPI processes > > > > > type not yet set > > > > > Error tolerance=1.49012e-08 > > > > > Umin=1.49012e-06 > > > > > Number of colors=539 > > > > > Information for color 0 > > > > > Number of columns 1 > > > > > 378 > > > > > Number of rows 756 > > > > > 0 1188 > > > > > 1 1188 > > > > > 2 1188 > > > > > 3 1188 > > > > > 4 1188 > > > > > 5 1188 > > > > > ... > > > > > > > > > > Is this normal? > > > > > When using MCFD, is there any difference using mpiaij and mpibaij? > > > > > > > > > > Best, > > > > > Li > > > > > > > > > > On Mon, Dec 2, 2019 at 10:03 AM Smith, Barry F. < > bsmith at mcs.anl.gov> wrote: > > > > > > > > > > How many colors is it requiring? And how long is the > MatGetColoring() taking? Are you running in parallel? The MatGetColoring() > MATCOLORINGSL uses a sequential coloring algorithm so if your matrix is > large and parallel the coloring will take a long time. The parallel > colorings are MATCOLORINGGREEDY and MATCOLORINGJP > > > > > > > > > > Barry > > > > > > > > > > > > > > > > On Dec 1, 2019, at 12:56 AM, Li Luo wrote: > > > > > > > > > > > > Dear Developers, > > > > > > > > > > > > I tried to use the multi-color finite-difference (MC-FD) method > for constructing the Jacobians. However, I find it is very slow compared to > the exact Jacobian. > > > > > > My implementation of MC-FD Jacobian is posted below, would you > please check whether I am correct? Anything missed? Thank you! > > > > > > > > > > > > ////////// Setup phase: > > > > > > MatStructure flag; > > > > > > ISColoring iscoloring; > > > > > > ierr = MatGetColoring(Jac,MATCOLORINGSL,&iscoloring); > > > > > > ierr = > MatFDColoringCreate(Jac,iscoloring,&this->matfdcoloring); > > > > > > ierr = > MatFDColoringSetFunction(this->matfdcoloring,(PetscErrorCode > (*)(void))__libmesh_petsc_snes_residual,(void *)this); > > > > > > ierr = > MatFDColoringSetFromOptions(this->matfdcoloring); > > > > > > ierr = ISColoringDestroy(&iscoloring); > > > > > > > > > > > > //////////// Apply: > > > > > > ierr = MatZeroEntries(*jac);CHKERRQ(ierr); > > > > > > ierr = > MatFDColoringApply(*jac,solver->matfdcoloring,x,msflag,snes); > > > > > > > > > > > > Best regards, > > > > > > Li Luo > > > > > > > > > > > > This message and its contents, including attachments are > intended solely for the original recipient. If you are not the intended > recipient or have received this message in error, please notify me > immediately and delete this message from your computer system. Any > unauthorized use or distribution is prohibited. Please consider the > environment before printing this email. > > > > > > > > > > > > > > > > > > > > -- > > > > > Postdoctoral Fellow > > > > > Extreme Computing Research Center > > > > > King Abdullah University of Science & Technology > > > > > https://sites.google.com/site/rolyliluo/ > > > > > > > > > > This message and its contents, including attachments are intended > solely for the original recipient. If you are not the intended recipient or > have received this message in error, please notify me immediately and > delete this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > > > > > > > > > > > > > > -- > > > > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > > > > > -- Norbert Wiener > > > > > > > > > > https://www.cse.buffalo.edu/~knepley/ > > > > > > > > > > > > > > > -- > > > > > Postdoctoral Fellow > > > > > Extreme Computing Research Center > > > > > King Abdullah University of Science & Technology > > > > > https://sites.google.com/site/rolyliluo/ > > > > > > > > > > This message and its contents, including attachments are intended > solely for the original recipient. If you are not the intended recipient or > have received this message in error, please notify me immediately and > delete this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > > > > > > > > > > > > > > > -- > > > > Postdoctoral Fellow > > > > Extreme Computing Research Center > > > > King Abdullah University of Science & Technology > > > > https://sites.google.com/site/rolyliluo/ > > > > > > > > This message and its contents, including attachments are intended > solely for the original recipient. If you are not the intended recipient or > have received this message in error, please notify me immediately and > delete this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > > > > > > > > > > > -- > > > Postdoctoral Fellow > > > Extreme Computing Research Center > > > King Abdullah University of Science & Technology > > > https://sites.google.com/site/rolyliluo/ > > > > > > This message and its contents, including attachments are intended > solely for the original recipient. If you are not the intended recipient or > have received this message in error, please notify me immediately and > delete this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > > > > > > > -- > > Postdoctoral Fellow > > Extreme Computing Research Center > > King Abdullah University of Science & Technology > > https://sites.google.com/site/rolyliluo/ > > > > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > -- Postdoctoral Fellow Extreme Computing Research Center King Abdullah University of Science & Technology https://sites.google.com/site/rolyliluo/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mbuerkle at web.de Wed Dec 4 02:07:10 2019 From: mbuerkle at web.de (Marius Buerkle) Date: Wed, 4 Dec 2019 09:07:10 +0100 Subject: [petsc-users] MatView to disk for Elemental In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: From eda.oktay at metu.edu.tr Wed Dec 4 02:47:54 2019 From: eda.oktay at metu.edu.tr (Eda Oktay) Date: Wed, 4 Dec 2019 11:47:54 +0300 Subject: [petsc-users] Drawing partitioned graphs via PETSc Message-ID: Hello all, I am partitioning some graphs and I need to visualize them. I was wondering if I can do it in PETSc. I know that there is some Draw routines but most of them are for line graphs. ? didn't use PETSc for drawing before so I don't know how and what to do. Thanks! Eda -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Wed Dec 4 06:05:59 2019 From: knepley at gmail.com (Matthew Knepley) Date: Wed, 4 Dec 2019 07:05:59 -0500 Subject: [petsc-users] Drawing partitioned graphs via PETSc In-Reply-To: References: Message-ID: On Wed, Dec 4, 2019 at 3:48 AM Eda Oktay wrote: > Hello all, > > I am partitioning some graphs and I need to visualize them. I was > wondering if I can do it in PETSc. I know that there is some Draw routines > but most of them are for line graphs. ? didn't use PETSc for drawing before > so I don't know how and what to do. > If it is 2D, we have a very simple X drawing with -dm_view draw, but for anything complicated you want either VTK or HDF5 output. If you use HDF5, then you run lib/petsc/bin/petsc_gen_xmdf.py mesh.h5 to get XDMF and then load that in ParaView. Thanks, Matt > Thanks! > > Eda > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From colin.cotter at imperial.ac.uk Wed Dec 4 07:17:42 2019 From: colin.cotter at imperial.ac.uk (Cotter, Colin J) Date: Wed, 4 Dec 2019 13:17:42 +0000 Subject: [petsc-users] -pc_fieldsplit_schur_precondition Message-ID: Dear PETSc users, I'm curious: how does PETSc compute the Schur complement matrix under the option pc_fieldsplit_schur_precondition full? Does it use sparse linear algebra? all the best --Colin -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Wed Dec 4 07:32:48 2019 From: knepley at gmail.com (Matthew Knepley) Date: Wed, 4 Dec 2019 08:32:48 -0500 Subject: [petsc-users] -pc_fieldsplit_schur_precondition In-Reply-To: References: Message-ID: On Wed, Dec 4, 2019 at 8:20 AM Cotter, Colin J wrote: > Dear PETSc users, > I'm curious: how does PETSc compute the Schur complement matrix under > the option pc_fieldsplit_schur_precondition full? Does it use sparse linear > algebra? > The action of the Schur complement is always MatMult() KSPSolve() MatMult(). The precondition matrix can be formed several different ways: https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/PC/PCFieldSplitSetSchurPre.html Thanks, Matt > all the best > --Colin > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From colin.cotter at imperial.ac.uk Wed Dec 4 07:36:06 2019 From: colin.cotter at imperial.ac.uk (Cotter, Colin J) Date: Wed, 4 Dec 2019 13:36:06 +0000 Subject: [petsc-users] -pc_fieldsplit_schur_precondition In-Reply-To: References: , Message-ID: >The action of the Schur complement is always MatMult() KSPSolve() MatMult(). OK, so when pc_fieldsplit_schur_precondition is set to full, what actually happens? -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Wed Dec 4 07:57:44 2019 From: knepley at gmail.com (Matthew Knepley) Date: Wed, 4 Dec 2019 08:57:44 -0500 Subject: [petsc-users] -pc_fieldsplit_schur_precondition In-Reply-To: References: Message-ID: On Wed, Dec 4, 2019 at 8:38 AM Cotter, Colin J wrote: > >The action of the Schur complement is always MatMult() KSPSolve() > MatMult(). > > OK, so when pc_fieldsplit_schur_precondition is set to full, what actually > happens? > It computes the operator explicitly: https://gitlab.com/petsc/petsc/blob/master/src/ksp/ksp/utils/schurm/schurm.c#L491 Usually you use LU, which means making B dense, then doing MatMatSolve(), and then MatMatMult() for sparse. Thanks, Matt -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Wed Dec 4 08:07:14 2019 From: bsmith at mcs.anl.gov (Smith, Barry F.) Date: Wed, 4 Dec 2019 14:07:14 +0000 Subject: [petsc-users] MatView to disk for Elemental In-Reply-To: References: Message-ID: <75260EC0-091E-4635-AF17-9CDB72A6CA3F@mcs.anl.gov> Agreed, the fix for the bug you found is now in maint I will try to do another MR that fixes this; but lots to do today so may take a while. Barry > On Dec 4, 2019, at 1:02 AM, Marius Buerkle wrote: > > thanks for the swift fix it works now. One more question though. It still outputs "Elemental matrix (explicit ordering)" to StdOut which is kinda annoying, is there anyway to turn this off? > > > Von: "Smith, Barry F." > An: "Marius Buerkle" > Cc: "petsc-users at mcs.anl.gov" > Betreff: Re: [petsc-users] MatView to disk for Elemental > > sorry about this. The numerical values between C and Fortran got out of sync. I've attached a patch file you can apply with > > patch -p1 < format.patch > > > or you can use the branch https://gitlab.com/petsc/petsc/merge_requests/2346 > > Barry > > > > On Dec 3, 2019, at 1:10 AM, Marius Buerkle wrote: > > > > Hi, > > > > I try to save a matrix in Elemental format to disk. I am doing, where p_matout is of type MATELEMENTAL, > > > > call PetscViewerCreate(PETSC_COMM_WORLD,v_file,ierr) > > call PetscViewerPushFormat(v_file,PETSC_VIEWER_NATIVE,ierr) > > call PetscViewerSetType(v_file,PETSCVIEWERBINARY,ierr) > > call PetscViewerFileSetMode(v_file,FILE_MODE_WRITE,ierr) > > call PetscViewerFileSetName(v_file,trim(filename),ierr) > > call MatView(p_matout,v_file,ierr) > > call PetscViewerDestroy(v_file,ierr) > > > > This gives the following error > > [18]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- > > [18]PETSC ERROR: No support for this operation for this object type > > [18]PETSC ERROR: To store a parallel dense matrix you must first call PetscViewerPushFormat(viewer,PETSC_VIEWER_NATIVE) > > [18]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. > > [18]PETSC ERROR: Petsc Development GIT revision: v3.12.1-317-gcc59f4f82c GIT Date: 2019-11-08 00:07:59 -0600 > > [18]PETSC ERROR: /home/marius/prog/ownstuff/fortran/programs/transomat_dev/save_load_fs/transomat/transomat on a named tono-hpc1 by marius Tue Dec 3 16:08:38 2019 > > [18]PETSC ERROR: Configure options --prefix=/home/marius/prog/petsc/petsc_slepc_opt --with-scalar-type=complex --with-fortran-kernels=1 --with-64-bit-indices=0 --CC=mpicc --COPTFLAGS="-g -Ofast -std=c11 -qopenmmp" --CXX=mpicxx --CXXOPTFLAGS="-g -Ofast -std=c++14 -qopenmp" --FC=mpif90 --FOPTFLAGS="-g -Ofast -traceback -qopenmp" --with-mpi=1 --with-x=0 --download-parmetis=1 --download-metis=1 --download-superlu_dist=1 --download-superlu_dist-commit=f8ace664ec4ca10e96e258a764552cbda299ba6e --download-superlu_dist-cmake-arguments=-Denable_openmp:BOOL=TRUE --download-hwloc=1 --download-sowing=1 --with-openmp=1 --with-pthread=1 --download-elemental=1 --download-elemental-commit=6eb15a0da2a4998bf1cf971ae231b78e06d989d9 --download-elemental-cmake-arguments=-DEL_HYBRID:BOOL=TRUE --with-cxx-dialect=c++11 --with-debugging=0 --with-valgrind=0 --with-blaslapack-lib=" /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a -Wl,--start-group /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_intel_lp64.a /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_intel_thread.a /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_core.a /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.a -Wl,--end-group -liomp5 -lpthread -lm -ldl -lmpi_wrapper" --with-scalapack-lib=" /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a -Wl,--start-group /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_intel_lp64.a /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_intel_thread.a /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_core.a /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.a -Wl,--end-group -liomp5 -lpthread -lm -ldl -lmpi_wrapper" --with-mkl_pardiso-dir=/home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl --with-mkl_cpardiso-dir=/home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl --with-mkl_sparse-dir=/home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl --with-mkl_sparse_optimize-dir=/home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl --download-slepc=1 --download-slepc-commit=658271f --download-make=1 --download-cmake=1 > > [18]PETSC ERROR: #1 MatView_MPIDense_Binary() line 682 in /home/marius/prog/petsc/git/petsc/src/mat/impls/dense/mpi/mpidense.c > > [18]PETSC ERROR: #2 MatView_MPIDense() line 786 in /home/marius/prog/petsc/git/petsc/src/mat/impls/dense/mpi/mpidense.c > > [18]PETSC ERROR: #3 MatView() line 1066 in /home/marius/prog/petsc/git/petsc/src/mat/interface/matrix.c > > [18]PETSC ERROR: #4 MatView_Elemental() line 83 in /home/marius/prog/petsc/git/petsc/src/mat/impls/elemental/matelem.cxx > > [18]PETSC ERROR: #5 MatView() line 1066 in /home/marius/prog/petsc/git/petsc/src/mat/interface/matrix.c > > [19]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- > > > > > > and on StdOut > > Elemental matrix (explicit ordering) > > > > Any suggestions? > > > > Best, > > Marius > From colin.cotter at imperial.ac.uk Wed Dec 4 08:07:36 2019 From: colin.cotter at imperial.ac.uk (Cotter, Colin J) Date: Wed, 4 Dec 2019 14:07:36 +0000 Subject: [petsc-users] -pc_fieldsplit_schur_precondition In-Reply-To: References: , Message-ID: >Usually you use LU, which means making B dense, then doing MatMatSolve(), >and then MatMatMult() for sparse. Gotcha, thanks. It is really nice to have this for debugging! all the best --cjc -------------- next part -------------- An HTML attachment was scrubbed... URL: From yjwu16 at gmail.com Wed Dec 4 09:14:17 2019 From: yjwu16 at gmail.com (Yingjie Wu) Date: Wed, 4 Dec 2019 23:14:17 +0800 Subject: [petsc-users] CMake error in PETSc Message-ID: Dear Petsc developers Hi, Because I use some external library files, I want to compile the PETSc program with CMake. I follow the library search program https://github.com/CoolProp/CoolProp/blob/b493de51a44078e4f5bbb8712e89305fd91f8b85/CMakeLists.txt recommended on GitHub. And wrote a cmakelist.txt: cmake_minimum_required(VERSION 2.8.11) project(example01cmke) add_executable(example01cmke ex1.cpp) set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake/modules) find_package(PETSc) include_directories(${PETSC_INCLUDE_DIR}) target_link_libraries(example01cmke ${PETSC_LIBRARIES}) My document relationships are: yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake$ tree . ??? build ??? cmake ? ??? modules ? ??? CorrectWindowsPaths.cmake ? ??? FindFFTW.cmake ? ??? FindGit.cmake ? ??? FindGSL.cmake ? ??? FindITAPS.cmake ? ??? FindNetCDF.cmake ? ??? FindPackageMultipass.cmake ? ??? FindPETSc.cmake ? ??? LICENSE ? ??? README ? ??? ResolveCompilerPaths.cmake ??? CMakeLists.txt ??? ex1.cpp After compiling with cmake.. and make, there is an error message: yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake/build$ cmake .. -- The C compiler identification is GNU 5.4.0 -- The CXX compiler identification is GNU 5.4.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- petsc_lib_dir /home/yjwu/petsc-3.10.1/arch-linux2-c-debug/lib -- Recognized PETSc install with single library for all packages -- Performing Test MULTIPASS_TEST_1_petsc_works_minimal -- Performing Test MULTIPASS_TEST_1_petsc_works_minimal - Success -- Minimal PETSc includes and libraries work. This probably means we are building with shared libs. -- Found PETSc: /home/yjwu/petsc-3.10.1/arch-linux2-c-debug/include;/home/yjwu/petsc-3.10.1/include (found version "3.10.1") -- Configuring done -- Generating done -- Build files have been written to: /home/yjwu/PETSctest/Testcmake/build yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake/build$ make Scanning dependencies of target example01cmke [ 50%] Building CXX object CMakeFiles/example01cmke.dir/ex1.cpp.o In file included from /home/yjwu/petsc-3.10.1/include/petscis.h:7:0, from /home/yjwu/petsc-3.10.1/include/petscvec.h:9, from /home/yjwu/petsc-3.10.1/include/petscmat.h:6, from /home/yjwu/petsc-3.10.1/include/petscpc.h:6, from /home/yjwu/petsc-3.10.1/include/petscksp.h:6, from /home/yjwu/petsc-3.10.1/include/petscsnes.h:6, from /home/yjwu/PETSctest/Testcmake/ex1.cpp:29: /home/yjwu/petsc-3.10.1/include/petscsys.h:14:23: fatal error: petscconf.h: No such file or directory compilation terminated. CMakeFiles/example01cmke.dir/build.make:62: recipe for target 'CMakeFiles/example01cmke.dir/ex1.cpp.o' failed make[2]: *** [CMakeFiles/example01cmke.dir/ex1.cpp.o] Error 1 CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/example01cmke.dir/all' failed make[1]: *** [CMakeFiles/example01cmke.dir/all] Error 2 Makefile:83: recipe for target 'all' failed make: *** [all] Error 2 I don't know how to solve this problem,ex1.cpp is the first example in SNES tutorial, please give me some advice. Best regards, Yingjie -------------- next part -------------- An HTML attachment was scrubbed... URL: From yjwu16 at gmail.com Wed Dec 4 09:18:08 2019 From: yjwu16 at gmail.com (Yingjie Wu) Date: Wed, 4 Dec 2019 23:18:08 +0800 Subject: [petsc-users] CMake error in PETSc In-Reply-To: References: Message-ID: Hi, I feel very sorry because I sent the wrong site. I fork the module: https://github.com/jedbrown/cmake-modules Thanks, Yingjie Yingjie Wu ?2019?12?4??? ??11:14??? > Dear Petsc developers > Hi, > Because I use some external library files, I want to compile the PETSc > program with CMake. I follow the library search program > https://github.com/CoolProp/CoolProp/blob/b493de51a44078e4f5bbb8712e89305fd91f8b85/CMakeLists.txt recommended > on GitHub. And wrote a cmakelist.txt: > > cmake_minimum_required(VERSION 2.8.11) > project(example01cmke) > add_executable(example01cmke ex1.cpp) > set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake/modules) > find_package(PETSc) > include_directories(${PETSC_INCLUDE_DIR}) > target_link_libraries(example01cmke ${PETSC_LIBRARIES}) > > My document relationships are: > > yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake$ tree > . > ??? build > ??? cmake > ? ??? modules > ? ??? CorrectWindowsPaths.cmake > ? ??? FindFFTW.cmake > ? ??? FindGit.cmake > ? ??? FindGSL.cmake > ? ??? FindITAPS.cmake > ? ??? FindNetCDF.cmake > ? ??? FindPackageMultipass.cmake > ? ??? FindPETSc.cmake > ? ??? LICENSE > ? ??? README > ? ??? ResolveCompilerPaths.cmake > ??? CMakeLists.txt > ??? ex1.cpp > > After compiling with cmake.. and make, there is an error message: > > > yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake/build$ cmake .. > -- The C compiler identification is GNU 5.4.0 > -- The CXX compiler identification is GNU 5.4.0 > -- Check for working C compiler: /usr/bin/cc > -- Check for working C compiler: /usr/bin/cc -- works > -- Detecting C compiler ABI info > -- Detecting C compiler ABI info - done > -- Detecting C compile features > -- Detecting C compile features - done > -- Check for working CXX compiler: /usr/bin/c++ > -- Check for working CXX compiler: /usr/bin/c++ -- works > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > -- Detecting CXX compile features > -- Detecting CXX compile features - done > -- petsc_lib_dir /home/yjwu/petsc-3.10.1/arch-linux2-c-debug/lib > -- Recognized PETSc install with single library for all packages > -- Performing Test MULTIPASS_TEST_1_petsc_works_minimal > -- Performing Test MULTIPASS_TEST_1_petsc_works_minimal - Success > -- Minimal PETSc includes and libraries work. This probably means we are > building with shared libs. > -- Found PETSc: > /home/yjwu/petsc-3.10.1/arch-linux2-c-debug/include;/home/yjwu/petsc-3.10.1/include > (found version "3.10.1") > -- Configuring done > -- Generating done > -- Build files have been written to: /home/yjwu/PETSctest/Testcmake/build > yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake/build$ make > Scanning dependencies of target example01cmke > [ 50%] Building CXX object CMakeFiles/example01cmke.dir/ex1.cpp.o > In file included from /home/yjwu/petsc-3.10.1/include/petscis.h:7:0, > from /home/yjwu/petsc-3.10.1/include/petscvec.h:9, > from /home/yjwu/petsc-3.10.1/include/petscmat.h:6, > from /home/yjwu/petsc-3.10.1/include/petscpc.h:6, > from /home/yjwu/petsc-3.10.1/include/petscksp.h:6, > from /home/yjwu/petsc-3.10.1/include/petscsnes.h:6, > from /home/yjwu/PETSctest/Testcmake/ex1.cpp:29: > /home/yjwu/petsc-3.10.1/include/petscsys.h:14:23: fatal error: > petscconf.h: No such file or directory > compilation terminated. > CMakeFiles/example01cmke.dir/build.make:62: recipe for target > 'CMakeFiles/example01cmke.dir/ex1.cpp.o' failed > make[2]: *** [CMakeFiles/example01cmke.dir/ex1.cpp.o] Error 1 > CMakeFiles/Makefile2:67: recipe for target > 'CMakeFiles/example01cmke.dir/all' failed > make[1]: *** [CMakeFiles/example01cmke.dir/all] Error 2 > Makefile:83: recipe for target 'all' failed > make: *** [all] Error 2 > > I don't know how to solve this problem,ex1.cpp is the first example in > SNES tutorial, please give me some advice. > > Best regards, > Yingjie > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jed at jedbrown.org Wed Dec 4 09:31:00 2019 From: jed at jedbrown.org (Jed Brown) Date: Wed, 04 Dec 2019 08:31:00 -0700 Subject: [petsc-users] CMake error in PETSc In-Reply-To: References: Message-ID: <875ziwkszv.fsf@jedbrown.org> Yingjie Wu writes: > Dear Petsc developers > Hi, > Because I use some external library files, I want to compile the PETSc > program with CMake. I follow the library search program > https://github.com/CoolProp/CoolProp/blob/b493de51a44078e4f5bbb8712e89305fd91f8b85/CMakeLists.txt > recommended > on GitHub. And wrote a cmakelist.txt: > > cmake_minimum_required(VERSION 2.8.11) > project(example01cmke) > add_executable(example01cmke ex1.cpp) > set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake/modules) > find_package(PETSc) > include_directories(${PETSC_INCLUDE_DIR}) This needs to be spelled PETSC_INCLUDES, as stated in FindPETSc.cmake. These days, I usually recommend that people use https://cmake.org/cmake/help/latest/module/FindPkgConfig.html instead of my FindPETSc.cmake because its simpler and doesn't require the script (which was developed before we added pkg-config support to PETSc). From yjwu16 at gmail.com Wed Dec 4 10:02:23 2019 From: yjwu16 at gmail.com (Yingjie Wu) Date: Thu, 5 Dec 2019 00:02:23 +0800 Subject: [petsc-users] CMake error in PETSc In-Reply-To: <875ziwkszv.fsf@jedbrown.org> References: <875ziwkszv.fsf@jedbrown.org> Message-ID: Thank you for your response. I have two questions about using FindPkgConfig: 1. Is there any requirement for petsc version using FindPkgConfig? I'm using an older version 3.10.1. 2. Does the use of FindPkgConfig only require the following commands and does not require any scripts? find_package(PkgConfig REQUIRED) pkg_search_module (PETSC REQUIRED PETSc) target_link_libraries(testapp ${PETSC_LIBRARIES}) target_link_includes(testapp ${PETSC_INCLUDE_DIRS}) Since I just came into contact with cmake, I really need some help. Thanks, Yingjie Jed Brown ?2019?12?4??? ??11:31??? > Yingjie Wu writes: > > > Dear Petsc developers > > Hi, > > Because I use some external library files, I want to compile the PETSc > > program with CMake. I follow the library search program > > > https://github.com/CoolProp/CoolProp/blob/b493de51a44078e4f5bbb8712e89305fd91f8b85/CMakeLists.txt > > recommended > > on GitHub. And wrote a cmakelist.txt: > > > > cmake_minimum_required(VERSION 2.8.11) > > project(example01cmke) > > add_executable(example01cmke ex1.cpp) > > set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake/modules) > > find_package(PETSc) > > include_directories(${PETSC_INCLUDE_DIR}) > > This needs to be spelled PETSC_INCLUDES, as stated in FindPETSc.cmake. > > These days, I usually recommend that people use > > https://cmake.org/cmake/help/latest/module/FindPkgConfig.html > > instead of my FindPETSc.cmake because its simpler and doesn't require > the script (which was developed before we added pkg-config support to > PETSc). > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jed at jedbrown.org Wed Dec 4 10:05:30 2019 From: jed at jedbrown.org (Jed Brown) Date: Wed, 04 Dec 2019 09:05:30 -0700 Subject: [petsc-users] CMake error in PETSc In-Reply-To: References: <875ziwkszv.fsf@jedbrown.org> Message-ID: <87zhg8jctx.fsf@jedbrown.org> Yingjie Wu writes: > Thank you for your response. > > I have two questions about using FindPkgConfig: > > > 1. Is there any requirement for petsc version using FindPkgConfig? I'm > using an older version 3.10.1. 3.10 should be sufficient (though we recommend upgrading). > 2. Does the use of FindPkgConfig only require the following commands and > does not require any scripts? Correct, no scripts. > find_package(PkgConfig REQUIRED) > > pkg_search_module (PETSC REQUIRED PETSc) > > target_link_libraries(testapp ${PETSC_LIBRARIES}) > > target_link_includes(testapp ${PETSC_INCLUDE_DIRS}) > > Since I just came into contact with cmake, I really need some help. > > > Thanks, > > Yingjie > > > Jed Brown ?2019?12?4??? ??11:31??? > >> Yingjie Wu writes: >> >> > Dear Petsc developers >> > Hi, >> > Because I use some external library files, I want to compile the PETSc >> > program with CMake. I follow the library search program >> > >> https://github.com/CoolProp/CoolProp/blob/b493de51a44078e4f5bbb8712e89305fd91f8b85/CMakeLists.txt >> > recommended >> > on GitHub. And wrote a cmakelist.txt: >> > >> > cmake_minimum_required(VERSION 2.8.11) >> > project(example01cmke) >> > add_executable(example01cmke ex1.cpp) >> > set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake/modules) >> > find_package(PETSc) >> > include_directories(${PETSC_INCLUDE_DIR}) >> >> This needs to be spelled PETSC_INCLUDES, as stated in FindPETSc.cmake. >> >> These days, I usually recommend that people use >> >> https://cmake.org/cmake/help/latest/module/FindPkgConfig.html >> >> instead of my FindPETSc.cmake because its simpler and doesn't require >> the script (which was developed before we added pkg-config support to >> PETSc). >> From alexlindsay239 at gmail.com Wed Dec 4 13:40:57 2019 From: alexlindsay239 at gmail.com (Alexander Lindsay) Date: Wed, 4 Dec 2019 11:40:57 -0800 Subject: [petsc-users] Could not find a CXX preprocessor on Catalina Message-ID: I'm currently unable to build superlu_dist during configuration because of "Could not find a CXX preprocessor". From configure.log it looks like CXXPP is getting deleted after errors executing `mpicxx -E` and then `mpicxx --use cpp32`. Attached is configure.log. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: configure.log Type: application/octet-stream Size: 1130139 bytes Desc: not available URL: From alexlindsay239 at gmail.com Wed Dec 4 14:10:01 2019 From: alexlindsay239 at gmail.com (Alexander Lindsay) Date: Wed, 4 Dec 2019 12:10:01 -0800 Subject: [petsc-users] Could not find a CXX preprocessor on Catalina In-Reply-To: References: Message-ID: Is this regarded as failing just because of the unused option warning? The `mpicxx` wrapper specifies `-Wl,-flat_namespace` which is indeed going to be unused during preprocessing... On Wed, Dec 4, 2019 at 11:40 AM Alexander Lindsay wrote: > I'm currently unable to build superlu_dist during configuration because of > "Could not find a CXX preprocessor". From configure.log it looks like CXXPP > is getting deleted after errors executing `mpicxx -E` and then `mpicxx > --use cpp32`. Attached is configure.log. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Wed Dec 4 14:18:43 2019 From: balay at mcs.anl.gov (Balay, Satish) Date: Wed, 4 Dec 2019 20:18:43 +0000 Subject: [petsc-users] Could not find a CXX preprocessor on Catalina In-Reply-To: References: Message-ID: Yes - this is a link time option - and somehow your build of mpich is using at compile/preprocess time. You can try rebuilding this mpich - or use --download-mpich with petsc configure Satish On Wed, 4 Dec 2019, Alexander Lindsay wrote: > Is this regarded as failing just because of the unused option warning? The > `mpicxx` wrapper specifies `-Wl,-flat_namespace` which is indeed going to > be unused during preprocessing... > > On Wed, Dec 4, 2019 at 11:40 AM Alexander Lindsay > wrote: > > > I'm currently unable to build superlu_dist during configuration because of > > "Could not find a CXX preprocessor". From configure.log it looks like CXXPP > > is getting deleted after errors executing `mpicxx -E` and then `mpicxx > > --use cpp32`. Attached is configure.log. > > > From mbuerkle at web.de Wed Dec 4 16:45:35 2019 From: mbuerkle at web.de (Marius Buerkle) Date: Wed, 4 Dec 2019 23:45:35 +0100 Subject: [petsc-users] MatView to disk for Elemental In-Reply-To: <75260EC0-091E-4635-AF17-9CDB72A6CA3F@mcs.anl.gov> References: <75260EC0-091E-4635-AF17-9CDB72A6CA3F@mcs.anl.gov> Message-ID: An HTML attachment was scrubbed... URL: From yjwu16 at gmail.com Wed Dec 4 21:48:49 2019 From: yjwu16 at gmail.com (Yingjie Wu) Date: Thu, 5 Dec 2019 11:48:49 +0800 Subject: [petsc-users] CMake error in PETSc In-Reply-To: <87zhg8jctx.fsf@jedbrown.org> References: <875ziwkszv.fsf@jedbrown.org> <87zhg8jctx.fsf@jedbrown.org> Message-ID: Hi, I tried to use PKG to find the library file of PETSc, but there were some errors. Because I am not very familiar with cmake, I refer to different PKG tutorials. My CMakeList.txt is as follows. I don't know how to solve this error message, please give me some suggestions. yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake$ cat CMakeLists.txt #This is a CMake makefile. cmake_minimum_required(VERSION 2.8.11) project(example01cmke) add_executable(example01cmke ex1.cpp) find_package(PkgConfig REQUIRED) message("petsc directories: ${PETSC_DIR}") message("petsc arch: ${PETSC_ARCH}") set(ENV{PKG_CONFIG_PATH} /home/yjwu/petsc-3.10.1/arch-linux2-c-debug/lib/pkgconfig) pkg_search_module(PETSC REQUIRED PETSc) message("pkg include dirs: ${PETSC_INCLUDE_DIRS}") message("pkg include libs: ${PETSC_LIBRARIES}") message("pkg ldflags: ${PETSC_LDFLAGS}") include_directories(${PETSC_INCLUDE_DIRS}) target_link_libraries(example01cmke ${PETSC_LDFLAGS}) yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake$ cd build/ yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake/build$ cmake .. -- The C compiler identification is GNU 5.4.0 -- The CXX compiler identification is GNU 5.4.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") petsc directories: petsc arch: -- Checking for one of the modules 'PETSc' pkg include dirs: /home/yjwu/petsc-3.10.1/include;/home/yjwu/petsc-3.10.1/arch-linux2-c-debug/include pkg include libs: petsc pkg ldflags: -L/home/yjwu/petsc-3.10.1/lib;-lpetsc -- Configuring done -- Generating done -- Build files have been written to: /home/yjwu/PETSctest/Testcmake/build yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake/build$ make Scanning dependencies of target example01cmke [ 50%] Building CXX object CMakeFiles/example01cmke.dir/ex1.cpp.o [100%] Linking CXX executable example01cmke /usr/bin/ld: cannot find -lpetsc collect2: error: ld returned 1 exit status CMakeFiles/example01cmke.dir/build.make:94: recipe for target 'example01cmke' failed make[2]: *** [example01cmke] Error 1 CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/example01cmke.dir/all' failed make[1]: *** [CMakeFiles/example01cmke.dir/all] Error 2 Makefile:83: recipe for target 'all' failed make: *** [all] Error 2 Thanks, Yingjie Jed Brown ?2019?12?5??? ??12:05??? > Yingjie Wu writes: > > > Thank you for your response. > > > > I have two questions about using FindPkgConfig: > > > > > > 1. Is there any requirement for petsc version using FindPkgConfig? I'm > > using an older version 3.10.1. > > 3.10 should be sufficient (though we recommend upgrading). > > > 2. Does the use of FindPkgConfig only require the following commands > and > > does not require any scripts? > > Correct, no scripts. > > > find_package(PkgConfig REQUIRED) > > > > pkg_search_module (PETSC REQUIRED PETSc) > > > > target_link_libraries(testapp ${PETSC_LIBRARIES}) > > > > target_link_includes(testapp ${PETSC_INCLUDE_DIRS}) > > > > Since I just came into contact with cmake, I really need some help. > > > > > > Thanks, > > > > Yingjie > > > > > > Jed Brown ?2019?12?4??? ??11:31??? > > > >> Yingjie Wu writes: > >> > >> > Dear Petsc developers > >> > Hi, > >> > Because I use some external library files, I want to compile the PETSc > >> > program with CMake. I follow the library search program > >> > > >> > https://github.com/CoolProp/CoolProp/blob/b493de51a44078e4f5bbb8712e89305fd91f8b85/CMakeLists.txt > >> > recommended > >> > on GitHub. And wrote a cmakelist.txt: > >> > > >> > cmake_minimum_required(VERSION 2.8.11) > >> > project(example01cmke) > >> > add_executable(example01cmke ex1.cpp) > >> > set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake/modules) > >> > find_package(PETSc) > >> > include_directories(${PETSC_INCLUDE_DIR}) > >> > >> This needs to be spelled PETSC_INCLUDES, as stated in FindPETSc.cmake. > >> > >> These days, I usually recommend that people use > >> > >> https://cmake.org/cmake/help/latest/module/FindPkgConfig.html > >> > >> instead of my FindPETSc.cmake because its simpler and doesn't require > >> the script (which was developed before we added pkg-config support to > >> PETSc). > >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bhatiamanav at gmail.com Wed Dec 4 22:04:26 2019 From: bhatiamanav at gmail.com (Manav Bhatia) Date: Wed, 4 Dec 2019 22:04:26 -0600 Subject: [petsc-users] Eigensolution with matrices from mixed formulation problems Message-ID: <160887C1-23D6-4435-84B9-8405EFFB072F@gmail.com> Hi, I am working on mixed form finite element discretization which leads to eigenvalues of the form A x = lambda B x With the matrices defined in a block structure as A = [ K D^T ] [ D 0 ] B = [ M 0 ] [ 0 0 ] The second row of equations come from Lagrange multipliers in our discretization scheme. A system with m Lagrange multiplier is expected to have m Inf eigenvalues. We are testing the standard eigensolvers in Matlab and as the system size increases the eigensolves are stopping with larger residuals, || r_i ||, of the eigensystem: r_i = A x_i - lambda_i B x_i I am working towards setting this up in SLEPc. In the meantime I am curious about the following: 1. Is the eigensolution of such systems known to be problematic? 2. Are there standard tricks in SLEPc or elsewhere that are geared towards more robust solutions of such systems? I would appreciate guidance on this. Regards, Manav From jed at jedbrown.org Wed Dec 4 23:16:59 2019 From: jed at jedbrown.org (Jed Brown) Date: Wed, 04 Dec 2019 22:16:59 -0700 Subject: [petsc-users] CMake error in PETSc In-Reply-To: References: <875ziwkszv.fsf@jedbrown.org> <87zhg8jctx.fsf@jedbrown.org> Message-ID: <87r21jjqr8.fsf@jedbrown.org> Yingjie Wu writes: > Hi, > I tried to use PKG to find the library file of PETSc, but there were some > errors. Because I am not very familiar with cmake, I refer to different PKG > tutorials. My CMakeList.txt is as follows. I don't know how to solve this > error message, please give me some suggestions. > > yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake$ cat CMakeLists.txt > #This is a CMake makefile. > cmake_minimum_required(VERSION 2.8.11) > > project(example01cmke) > > add_executable(example01cmke ex1.cpp) > > find_package(PkgConfig REQUIRED) > > message("petsc directories: ${PETSC_DIR}") > > message("petsc arch: ${PETSC_ARCH}") > > set(ENV{PKG_CONFIG_PATH} > /home/yjwu/petsc-3.10.1/arch-linux2-c-debug/lib/pkgconfig) > > pkg_search_module(PETSC REQUIRED PETSc) > > message("pkg include dirs: ${PETSC_INCLUDE_DIRS}") > > message("pkg include libs: ${PETSC_LIBRARIES}") > > message("pkg ldflags: ${PETSC_LDFLAGS}") > > include_directories(${PETSC_INCLUDE_DIRS}) > > target_link_libraries(example01cmke ${PETSC_LDFLAGS}) > > yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake$ cd build/ > yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake/build$ cmake .. > -- The C compiler identification is GNU 5.4.0 > -- The CXX compiler identification is GNU 5.4.0 > -- Check for working C compiler: /usr/bin/cc > -- Check for working C compiler: /usr/bin/cc -- works > -- Detecting C compiler ABI info > -- Detecting C compiler ABI info - done > -- Detecting C compile features > -- Detecting C compile features - done > -- Check for working CXX compiler: /usr/bin/c++ > -- Check for working CXX compiler: /usr/bin/c++ -- works > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > -- Detecting CXX compile features > -- Detecting CXX compile features - done > -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") > petsc directories: > petsc arch: > -- Checking for one of the modules 'PETSc' > pkg include dirs: > /home/yjwu/petsc-3.10.1/include;/home/yjwu/petsc-3.10.1/arch-linux2-c-debug/include > pkg include libs: petsc > pkg ldflags: -L/home/yjwu/petsc-3.10.1/lib;-lpetsc > -- Configuring done > -- Generating done > -- Build files have been written to: /home/yjwu/PETSctest/Testcmake/build > yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake/build$ make > Scanning dependencies of target example01cmke > [ 50%] Building CXX object CMakeFiles/example01cmke.dir/ex1.cpp.o > [100%] Linking CXX executable example01cmke > /usr/bin/ld: cannot find -lpetsc > collect2: error: ld returned 1 exit status Is your PETSc fully built/installed, or just configured? I just tested with this simplified file cmake_minimum_required(VERSION 2.8.11) project(example01cmke) add_executable(example01cmke ex1.cpp) find_package(PkgConfig REQUIRED) pkg_search_module(PETSC REQUIRED PETSc) message("pkg include dirs: ${PETSC_INCLUDE_DIRS}") message("pkg include libs: ${PETSC_LIBRARIES}") message("pkg ldflags: ${PETSC_LDFLAGS}") include_directories(${PETSC_INCLUDE_DIRS}) target_link_libraries(example01cmke ${PETSC_LDFLAGS}) $ PKG_CONFIG_PATH=$PETSC_DIR/$PETSC_ARCH/lib/pkgconfig cmake .. -- The C compiler identification is GNU 9.2.0 -- The CXX compiler identification is GNU 9.2.0 -- Check for working C compiler: /bin/cc -- Check for working C compiler: /bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /bin/c++ -- Check for working CXX compiler: /bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PkgConfig: /bin/pkg-config (found version "1.6.3") -- Checking for one of the modules 'PETSc' pkg include dirs: /home/jed/petsc/ompi-optg/include;/home/jed/petsc/include pkg include libs: petsc pkg ldflags: -L/home/jed/petsc/ompi-optg/lib;-lpetsc -- Configuring done -- Generating done -- Build files have been written to: /tmp/jed/build 22:12 jedjoule12 /tmp/jed/build$ make Scanning dependencies of target example01cmke [ 50%] Building CXX object CMakeFiles/example01cmke.dir/ex1.cpp.o [100%] Linking CXX executable example01cmke [100%] Built target example01cmke Note that you may need to set RPATH (in CMake) or export a suitable LD_LIBRARY_PATH if your PETSc is in a non-standard location. From jroman at dsic.upv.es Thu Dec 5 01:54:17 2019 From: jroman at dsic.upv.es (Jose E. Roman) Date: Thu, 5 Dec 2019 08:54:17 +0100 Subject: [petsc-users] Eigensolution with matrices from mixed formulation problems In-Reply-To: <160887C1-23D6-4435-84B9-8405EFFB072F@gmail.com> References: <160887C1-23D6-4435-84B9-8405EFFB072F@gmail.com> Message-ID: In symmetric problems (GHEP) you might have large residuals due to B being singular. The explanation is the following. By default, in SLEPc GHEPs are solved via a B-Lanczos recurrence, that is, using the inner product induced by B. If B is singular this is not a true inner product and numerical problems may arise, in particular, the computed eigenvectors may be corrupted with components in the null space of B. This is easily solved by a small computation called 'eigenvector purification' which is on by default in SLEPc, see EPSSetPurify(). This is described with a bit more detail in section 3.4.4 of the manual. In non-symmetric problems (GNHEP) you should not see this problem. The only precaution is not to solve systems with matrix B, e.g., using shift-and-invert. Jose > El 5 dic 2019, a las 5:04, Manav Bhatia escribi?: > > Hi, > > I am working on mixed form finite element discretization which leads to eigenvalues of the form > > A x = lambda B x > > With the matrices defined in a block structure as > > A = [ K D^T ] > [ D 0 ] > > B = [ M 0 ] > [ 0 0 ] > > The second row of equations come from Lagrange multipliers in our discretization scheme. A system with m Lagrange multiplier is expected to have m Inf eigenvalues. We are testing the standard eigensolvers in Matlab and as the system size increases the eigensolves are stopping with larger residuals, || r_i ||, of the eigensystem: > > r_i = A x_i - lambda_i B x_i > > I am working towards setting this up in SLEPc. In the meantime I am curious about the following: > > 1. Is the eigensolution of such systems known to be problematic? > 2. Are there standard tricks in SLEPc or elsewhere that are geared towards more robust solutions of such systems? > > I would appreciate guidance on this. > > Regards, > Manav > > From bsmith at mcs.anl.gov Thu Dec 5 02:32:24 2019 From: bsmith at mcs.anl.gov (Smith, Barry F.) Date: Thu, 5 Dec 2019 08:32:24 +0000 Subject: [petsc-users] Could not find a CXX preprocessor on Catalina In-Reply-To: References: Message-ID: Hmm, MPICH and OpenMPI have also passed this info in there compilers; perhaps this is a newer version clang that no longer tolerates these options I think we need to strip out those options as a guess > On Dec 4, 2019, at 2:18 PM, Balay, Satish wrote: > > Yes - this is a link time option - and somehow your build of mpich is > using at compile/preprocess time. > > You can try rebuilding this mpich - or use --download-mpich with petsc configure > > Satish > > On Wed, 4 Dec 2019, Alexander Lindsay wrote: > >> Is this regarded as failing just because of the unused option warning? The >> `mpicxx` wrapper specifies `-Wl,-flat_namespace` which is indeed going to >> be unused during preprocessing... >> >> On Wed, Dec 4, 2019 at 11:40 AM Alexander Lindsay >> wrote: >> >>> I'm currently unable to build superlu_dist during configuration because of >>> "Could not find a CXX preprocessor". From configure.log it looks like CXXPP >>> is getting deleted after errors executing `mpicxx -E` and then `mpicxx >>> --use cpp32`. Attached is configure.log. >>> >> > From yjwu16 at gmail.com Thu Dec 5 07:25:12 2019 From: yjwu16 at gmail.com (Yingjie Wu) Date: Thu, 5 Dec 2019 21:25:12 +0800 Subject: [petsc-users] CMake error in PETSc In-Reply-To: <87r21jjqr8.fsf@jedbrown.org> References: <875ziwkszv.fsf@jedbrown.org> <87zhg8jctx.fsf@jedbrown.org> <87r21jjqr8.fsf@jedbrown.org> Message-ID: Hi, I installed the latest version of petsc, and compiled the example using cmke as described above. Compilation can be done, but there is a new problem while the program is running, as if the program could not find the shared library libpetsc.so.3.12. How can I solve this problem? The details are as follows: lerui at yu1994-ThinkPad-W520:~/tem$ cat CMakeLists.txt #This is a CMake makefile. cmake_minimum_required(VERSION 2.8.11) project(example01cmke) add_executable(example01cmke ex1.cpp) find_package(PkgConfig REQUIRED) set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) pkg_search_module(PETSC REQUIRED PETSc) message("pkg include dirs: ${PETSC_INCLUDE_DIRS}") message("pkg include libs: ${PETSC_LIBRARIES}") message("pkg ldflags: ${PETSC_LDFLAGS}") include_directories(${PETSC_INCLUDE_DIRS}) target_link_libraries(example01cmke ${PETSC_LDFLAGS}) lerui at yu1994-ThinkPad-W520:~/tem$ mkdir build lerui at yu1994-ThinkPad-W520:~/tem$ cd build/ lerui at yu1994-ThinkPad-W520:~/tem/build$ PKG_CONFIG_PATH=$PETSC_DIR/$PETSC_ARCH/lib/pkgconfig cmake ..-- The C compiler identification is GNU 5.4.0 -- The CXX compiler identification is GNU 5.4.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") -- Checking for one of the modules 'PETSc' pkg include dirs: /home/lerui/petsc-3.12.2/arch-linux2-c-debug/include;/home/lerui/petsc-3.12.2/include pkg include libs: petsc pkg ldflags: -L/home/lerui/petsc-3.12.2/arch-linux2-c-debug/lib;-lpetsc -- Configuring done -- Generating done -- Build files have been written to: /home/lerui/tem/build lerui at yu1994-ThinkPad-W520:~/tem/build$ make Scanning dependencies of target example01cmke [ 50%] Building CXX object CMakeFiles/example01cmke.dir/ex1.cpp.o [100%] Linking CXX executable example01cmke [100%] Built target example01cmke lerui at yu1994-ThinkPad-W520:~/tem/build$ mpiexec -n 1 ./example01cmke -snes_monitor ./example01cmke: error while loading shared libraries: libpetsc.so.3.12: cannot open shared object file: No such file or directory ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- -------------------------------------------------------------------------- mpiexec detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[6716,1],0] Exit code: 127 -------------------------------------------------------------------------- Thanks, Yingjie Jed Brown ?2019?12?5??? ??1:17??? > Yingjie Wu writes: > > > Hi, > > I tried to use PKG to find the library file of PETSc, but there were some > > errors. Because I am not very familiar with cmake, I refer to different > PKG > > tutorials. My CMakeList.txt is as follows. I don't know how to solve this > > error message, please give me some suggestions. > > > > yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake$ cat CMakeLists.txt > > #This is a CMake makefile. > > cmake_minimum_required(VERSION 2.8.11) > > > > project(example01cmke) > > > > add_executable(example01cmke ex1.cpp) > > > > find_package(PkgConfig REQUIRED) > > > > message("petsc directories: ${PETSC_DIR}") > > > > message("petsc arch: ${PETSC_ARCH}") > > > > set(ENV{PKG_CONFIG_PATH} > > /home/yjwu/petsc-3.10.1/arch-linux2-c-debug/lib/pkgconfig) > > > > pkg_search_module(PETSC REQUIRED PETSc) > > > > message("pkg include dirs: ${PETSC_INCLUDE_DIRS}") > > > > message("pkg include libs: ${PETSC_LIBRARIES}") > > > > message("pkg ldflags: ${PETSC_LDFLAGS}") > > > > include_directories(${PETSC_INCLUDE_DIRS}) > > > > target_link_libraries(example01cmke ${PETSC_LDFLAGS}) > > > > yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake$ cd build/ > > yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake/build$ cmake .. > > -- The C compiler identification is GNU 5.4.0 > > -- The CXX compiler identification is GNU 5.4.0 > > -- Check for working C compiler: /usr/bin/cc > > -- Check for working C compiler: /usr/bin/cc -- works > > -- Detecting C compiler ABI info > > -- Detecting C compiler ABI info - done > > -- Detecting C compile features > > -- Detecting C compile features - done > > -- Check for working CXX compiler: /usr/bin/c++ > > -- Check for working CXX compiler: /usr/bin/c++ -- works > > -- Detecting CXX compiler ABI info > > -- Detecting CXX compiler ABI info - done > > -- Detecting CXX compile features > > -- Detecting CXX compile features - done > > -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") > > petsc directories: > > petsc arch: > > -- Checking for one of the modules 'PETSc' > > pkg include dirs: > > > /home/yjwu/petsc-3.10.1/include;/home/yjwu/petsc-3.10.1/arch-linux2-c-debug/include > > pkg include libs: petsc > > pkg ldflags: -L/home/yjwu/petsc-3.10.1/lib;-lpetsc > > -- Configuring done > > -- Generating done > > -- Build files have been written to: /home/yjwu/PETSctest/Testcmake/build > > yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake/build$ make > > Scanning dependencies of target example01cmke > > [ 50%] Building CXX object CMakeFiles/example01cmke.dir/ex1.cpp.o > > [100%] Linking CXX executable example01cmke > > /usr/bin/ld: cannot find -lpetsc > > collect2: error: ld returned 1 exit status > > Is your PETSc fully built/installed, or just configured? > > I just tested with this simplified file > > cmake_minimum_required(VERSION 2.8.11) > project(example01cmke) > > add_executable(example01cmke ex1.cpp) > > find_package(PkgConfig REQUIRED) > pkg_search_module(PETSC REQUIRED PETSc) > message("pkg include dirs: ${PETSC_INCLUDE_DIRS}") > message("pkg include libs: ${PETSC_LIBRARIES}") > message("pkg ldflags: ${PETSC_LDFLAGS}") > > include_directories(${PETSC_INCLUDE_DIRS}) > target_link_libraries(example01cmke ${PETSC_LDFLAGS}) > > > $ PKG_CONFIG_PATH=$PETSC_DIR/$PETSC_ARCH/lib/pkgconfig cmake .. > -- The C compiler identification is GNU 9.2.0 > -- The CXX compiler identification is GNU 9.2.0 > -- Check for working C compiler: /bin/cc > -- Check for working C compiler: /bin/cc -- works > -- Detecting C compiler ABI info > -- Detecting C compiler ABI info - done > -- Detecting C compile features > -- Detecting C compile features - done > -- Check for working CXX compiler: /bin/c++ > -- Check for working CXX compiler: /bin/c++ -- works > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > -- Detecting CXX compile features > -- Detecting CXX compile features - done > -- Found PkgConfig: /bin/pkg-config (found version "1.6.3") > -- Checking for one of the modules 'PETSc' > pkg include dirs: /home/jed/petsc/ompi-optg/include;/home/jed/petsc/include > pkg include libs: petsc > pkg ldflags: -L/home/jed/petsc/ompi-optg/lib;-lpetsc > -- Configuring done > -- Generating done > -- Build files have been written to: /tmp/jed/build > 22:12 jedjoule12 /tmp/jed/build$ make > Scanning dependencies of target example01cmke > [ 50%] Building CXX object CMakeFiles/example01cmke.dir/ex1.cpp.o > [100%] Linking CXX executable example01cmke > [100%] Built target example01cmke > > > Note that you may need to set RPATH (in CMake) or export a suitable > LD_LIBRARY_PATH if your PETSc is in a non-standard location. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bhatiamanav at gmail.com Thu Dec 5 08:12:59 2019 From: bhatiamanav at gmail.com (Manav Bhatia) Date: Thu, 5 Dec 2019 08:12:59 -0600 Subject: [petsc-users] Eigensolution with matrices from mixed formulation problems In-Reply-To: References: <160887C1-23D6-4435-84B9-8405EFFB072F@gmail.com> Message-ID: <409AFDA0-EE6A-495A-B468-F0FF7D74E52D@gmail.com> Thanks! Does the purify option only changes the eigenvector without influencing the eigenvalue? -Manav > On Dec 5, 2019, at 1:54 AM, Jose E. Roman wrote: > > In symmetric problems (GHEP) you might have large residuals due to B being singular. The explanation is the following. By default, in SLEPc GHEPs are solved via a B-Lanczos recurrence, that is, using the inner product induced by B. If B is singular this is not a true inner product and numerical problems may arise, in particular, the computed eigenvectors may be corrupted with components in the null space of B. This is easily solved by a small computation called 'eigenvector purification' which is on by default in SLEPc, see EPSSetPurify(). This is described with a bit more detail in section 3.4.4 of the manual. > > In non-symmetric problems (GNHEP) you should not see this problem. The only precaution is not to solve systems with matrix B, e.g., using shift-and-invert. > > Jose > > >> El 5 dic 2019, a las 5:04, Manav Bhatia escribi?: >> >> Hi, >> >> I am working on mixed form finite element discretization which leads to eigenvalues of the form >> >> A x = lambda B x >> >> With the matrices defined in a block structure as >> >> A = [ K D^T ] >> [ D 0 ] >> >> B = [ M 0 ] >> [ 0 0 ] >> >> The second row of equations come from Lagrange multipliers in our discretization scheme. A system with m Lagrange multiplier is expected to have m Inf eigenvalues. We are testing the standard eigensolvers in Matlab and as the system size increases the eigensolves are stopping with larger residuals, || r_i ||, of the eigensystem: >> >> r_i = A x_i - lambda_i B x_i >> >> I am working towards setting this up in SLEPc. In the meantime I am curious about the following: >> >> 1. Is the eigensolution of such systems known to be problematic? >> 2. Are there standard tricks in SLEPc or elsewhere that are geared towards more robust solutions of such systems? >> >> I would appreciate guidance on this. >> >> Regards, >> Manav >> >> > From yjwu16 at gmail.com Thu Dec 5 08:19:48 2019 From: yjwu16 at gmail.com (Yingjie Wu) Date: Thu, 5 Dec 2019 22:19:48 +0800 Subject: [petsc-users] CMake error in PETSc In-Reply-To: References: <875ziwkszv.fsf@jedbrown.org> <87zhg8jctx.fsf@jedbrown.org> <87r21jjqr8.fsf@jedbrown.org> Message-ID: I'm so sorry that I've ignored your previous advices. I added a global variable that seems works: export LD_LIBRARY_PATH=/home/lerui/petcs-3.12.2/arch-linux2-c-debug/lib:$LD_LIBRARY_PATH How should I make petsc in a standard position?This eliminates the need to set global variables. It seems that some of the options before running fit become unavailable: mpiexec -n 1 ./example01cmke -snes_view Options-snes _ view are not used and how should I solve this problem? Thank you for your response. Yingjie Yingjie Wu ?2019?12?5??? ??9:25??? > Hi, > > I installed the latest version of petsc, and compiled the example using > cmke as described above. Compilation can be done, but there is a new > problem while the program is running, as if the program could not find the > shared library libpetsc.so.3.12. How can I solve this problem? The details > are as follows: > > lerui at yu1994-ThinkPad-W520:~/tem$ cat CMakeLists.txt > #This is a CMake makefile. > cmake_minimum_required(VERSION 2.8.11) > > project(example01cmke) > > add_executable(example01cmke ex1.cpp) > > find_package(PkgConfig REQUIRED) > > set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) > > pkg_search_module(PETSC REQUIRED PETSc) > > message("pkg include dirs: ${PETSC_INCLUDE_DIRS}") > > message("pkg include libs: ${PETSC_LIBRARIES}") > > message("pkg ldflags: ${PETSC_LDFLAGS}") > > include_directories(${PETSC_INCLUDE_DIRS}) > > target_link_libraries(example01cmke ${PETSC_LDFLAGS}) > > lerui at yu1994-ThinkPad-W520:~/tem$ mkdir build > lerui at yu1994-ThinkPad-W520:~/tem$ cd build/ > lerui at yu1994-ThinkPad-W520:~/tem/build$ > PKG_CONFIG_PATH=$PETSC_DIR/$PETSC_ARCH/lib/pkgconfig cmake ..-- The C > compiler identification is GNU 5.4.0 > -- The CXX compiler identification is GNU 5.4.0 > -- Check for working C compiler: /usr/bin/cc > -- Check for working C compiler: /usr/bin/cc -- works > -- Detecting C compiler ABI info > -- Detecting C compiler ABI info - done > -- Detecting C compile features > -- Detecting C compile features - done > -- Check for working CXX compiler: /usr/bin/c++ > -- Check for working CXX compiler: /usr/bin/c++ -- works > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > -- Detecting CXX compile features > -- Detecting CXX compile features - done > -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") > -- Checking for one of the modules 'PETSc' > pkg include dirs: > /home/lerui/petsc-3.12.2/arch-linux2-c-debug/include;/home/lerui/petsc-3.12.2/include > pkg include libs: petsc > pkg ldflags: -L/home/lerui/petsc-3.12.2/arch-linux2-c-debug/lib;-lpetsc > -- Configuring done > -- Generating done > -- Build files have been written to: /home/lerui/tem/build > lerui at yu1994-ThinkPad-W520:~/tem/build$ make > Scanning dependencies of target example01cmke > [ 50%] Building CXX object CMakeFiles/example01cmke.dir/ex1.cpp.o > [100%] Linking CXX executable example01cmke > [100%] Built target example01cmke > lerui at yu1994-ThinkPad-W520:~/tem/build$ mpiexec -n 1 ./example01cmke > -snes_monitor > ./example01cmke: error while loading shared libraries: libpetsc.so.3.12: > cannot open shared object file: No such file or directory > ------------------------------------------------------- > Primary job terminated normally, but 1 process returned > a non-zero exit code.. Per user-direction, the job has been aborted. > ------------------------------------------------------- > -------------------------------------------------------------------------- > mpiexec detected that one or more processes exited with non-zero status, > thus causing > the job to be terminated. The first process to do so was: > > Process name: [[6716,1],0] > Exit code: 127 > -------------------------------------------------------------------------- > > Thanks, > Yingjie > > Jed Brown ?2019?12?5??? ??1:17??? > >> Yingjie Wu writes: >> >> > Hi, >> > I tried to use PKG to find the library file of PETSc, but there were >> some >> > errors. Because I am not very familiar with cmake, I refer to different >> PKG >> > tutorials. My CMakeList.txt is as follows. I don't know how to solve >> this >> > error message, please give me some suggestions. >> > >> > yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake$ cat CMakeLists.txt >> > #This is a CMake makefile. >> > cmake_minimum_required(VERSION 2.8.11) >> > >> > project(example01cmke) >> > >> > add_executable(example01cmke ex1.cpp) >> > >> > find_package(PkgConfig REQUIRED) >> > >> > message("petsc directories: ${PETSC_DIR}") >> > >> > message("petsc arch: ${PETSC_ARCH}") >> > >> > set(ENV{PKG_CONFIG_PATH} >> > /home/yjwu/petsc-3.10.1/arch-linux2-c-debug/lib/pkgconfig) >> > >> > pkg_search_module(PETSC REQUIRED PETSc) >> > >> > message("pkg include dirs: ${PETSC_INCLUDE_DIRS}") >> > >> > message("pkg include libs: ${PETSC_LIBRARIES}") >> > >> > message("pkg ldflags: ${PETSC_LDFLAGS}") >> > >> > include_directories(${PETSC_INCLUDE_DIRS}) >> > >> > target_link_libraries(example01cmke ${PETSC_LDFLAGS}) >> > >> > yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake$ cd build/ >> > yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake/build$ cmake .. >> > -- The C compiler identification is GNU 5.4.0 >> > -- The CXX compiler identification is GNU 5.4.0 >> > -- Check for working C compiler: /usr/bin/cc >> > -- Check for working C compiler: /usr/bin/cc -- works >> > -- Detecting C compiler ABI info >> > -- Detecting C compiler ABI info - done >> > -- Detecting C compile features >> > -- Detecting C compile features - done >> > -- Check for working CXX compiler: /usr/bin/c++ >> > -- Check for working CXX compiler: /usr/bin/c++ -- works >> > -- Detecting CXX compiler ABI info >> > -- Detecting CXX compiler ABI info - done >> > -- Detecting CXX compile features >> > -- Detecting CXX compile features - done >> > -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") >> > petsc directories: >> > petsc arch: >> > -- Checking for one of the modules 'PETSc' >> > pkg include dirs: >> > >> /home/yjwu/petsc-3.10.1/include;/home/yjwu/petsc-3.10.1/arch-linux2-c-debug/include >> > pkg include libs: petsc >> > pkg ldflags: -L/home/yjwu/petsc-3.10.1/lib;-lpetsc >> > -- Configuring done >> > -- Generating done >> > -- Build files have been written to: >> /home/yjwu/PETSctest/Testcmake/build >> > yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake/build$ make >> > Scanning dependencies of target example01cmke >> > [ 50%] Building CXX object CMakeFiles/example01cmke.dir/ex1.cpp.o >> > [100%] Linking CXX executable example01cmke >> > /usr/bin/ld: cannot find -lpetsc >> > collect2: error: ld returned 1 exit status >> >> Is your PETSc fully built/installed, or just configured? >> >> I just tested with this simplified file >> >> cmake_minimum_required(VERSION 2.8.11) >> project(example01cmke) >> >> add_executable(example01cmke ex1.cpp) >> >> find_package(PkgConfig REQUIRED) >> pkg_search_module(PETSC REQUIRED PETSc) >> message("pkg include dirs: ${PETSC_INCLUDE_DIRS}") >> message("pkg include libs: ${PETSC_LIBRARIES}") >> message("pkg ldflags: ${PETSC_LDFLAGS}") >> >> include_directories(${PETSC_INCLUDE_DIRS}) >> target_link_libraries(example01cmke ${PETSC_LDFLAGS}) >> >> >> $ PKG_CONFIG_PATH=$PETSC_DIR/$PETSC_ARCH/lib/pkgconfig cmake .. >> -- The C compiler identification is GNU 9.2.0 >> -- The CXX compiler identification is GNU 9.2.0 >> -- Check for working C compiler: /bin/cc >> -- Check for working C compiler: /bin/cc -- works >> -- Detecting C compiler ABI info >> -- Detecting C compiler ABI info - done >> -- Detecting C compile features >> -- Detecting C compile features - done >> -- Check for working CXX compiler: /bin/c++ >> -- Check for working CXX compiler: /bin/c++ -- works >> -- Detecting CXX compiler ABI info >> -- Detecting CXX compiler ABI info - done >> -- Detecting CXX compile features >> -- Detecting CXX compile features - done >> -- Found PkgConfig: /bin/pkg-config (found version "1.6.3") >> -- Checking for one of the modules 'PETSc' >> pkg include dirs: >> /home/jed/petsc/ompi-optg/include;/home/jed/petsc/include >> pkg include libs: petsc >> pkg ldflags: -L/home/jed/petsc/ompi-optg/lib;-lpetsc >> -- Configuring done >> -- Generating done >> -- Build files have been written to: /tmp/jed/build >> 22:12 jedjoule12 /tmp/jed/build$ make >> Scanning dependencies of target example01cmke >> [ 50%] Building CXX object CMakeFiles/example01cmke.dir/ex1.cpp.o >> [100%] Linking CXX executable example01cmke >> [100%] Built target example01cmke >> >> >> Note that you may need to set RPATH (in CMake) or export a suitable >> LD_LIBRARY_PATH if your PETSc is in a non-standard location. >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jroman at dsic.upv.es Thu Dec 5 08:31:03 2019 From: jroman at dsic.upv.es (Jose E. Roman) Date: Thu, 5 Dec 2019 15:31:03 +0100 Subject: [petsc-users] Eigensolution with matrices from mixed formulation problems In-Reply-To: <409AFDA0-EE6A-495A-B468-F0FF7D74E52D@gmail.com> References: <160887C1-23D6-4435-84B9-8405EFFB072F@gmail.com> <409AFDA0-EE6A-495A-B468-F0FF7D74E52D@gmail.com> Message-ID: <95F837A5-B776-41F1-B95F-9FA0CDBEB24F@dsic.upv.es> > El 5 dic 2019, a las 15:12, Manav Bhatia escribi?: > > Thanks! > > Does the purify option only changes the eigenvector without influencing the eigenvalue? Yes. > > -Manav > >> On Dec 5, 2019, at 1:54 AM, Jose E. Roman wrote: >> >> In symmetric problems (GHEP) you might have large residuals due to B being singular. The explanation is the following. By default, in SLEPc GHEPs are solved via a B-Lanczos recurrence, that is, using the inner product induced by B. If B is singular this is not a true inner product and numerical problems may arise, in particular, the computed eigenvectors may be corrupted with components in the null space of B. This is easily solved by a small computation called 'eigenvector purification' which is on by default in SLEPc, see EPSSetPurify(). This is described with a bit more detail in section 3.4.4 of the manual. >> >> In non-symmetric problems (GNHEP) you should not see this problem. The only precaution is not to solve systems with matrix B, e.g., using shift-and-invert. >> >> Jose >> >> >>> El 5 dic 2019, a las 5:04, Manav Bhatia escribi?: >>> >>> Hi, >>> >>> I am working on mixed form finite element discretization which leads to eigenvalues of the form >>> >>> A x = lambda B x >>> >>> With the matrices defined in a block structure as >>> >>> A = [ K D^T ] >>> [ D 0 ] >>> >>> B = [ M 0 ] >>> [ 0 0 ] >>> >>> The second row of equations come from Lagrange multipliers in our discretization scheme. A system with m Lagrange multiplier is expected to have m Inf eigenvalues. We are testing the standard eigensolvers in Matlab and as the system size increases the eigensolves are stopping with larger residuals, || r_i ||, of the eigensystem: >>> >>> r_i = A x_i - lambda_i B x_i >>> >>> I am working towards setting this up in SLEPc. In the meantime I am curious about the following: >>> >>> 1. Is the eigensolution of such systems known to be problematic? >>> 2. Are there standard tricks in SLEPc or elsewhere that are geared towards more robust solutions of such systems? >>> >>> I would appreciate guidance on this. >>> >>> Regards, >>> Manav >>> >>> >> > From yann.jobic at univ-amu.fr Thu Dec 5 09:50:36 2019 From: yann.jobic at univ-amu.fr (Yann Jobic) Date: Thu, 5 Dec 2019 16:50:36 +0100 Subject: [petsc-users] dof of DMDA & DMPlex Message-ID: Hello, I read in the email archive (from 2016) that, at that time, the number of synchronized dof (in MPI/ghost cells sense) is 3 or 4. Is that still the case ? I would like to use PETSc for solving the Boltzmann equation (via Discreet velocity method, which means a lot of dof per node). Is it the same for DMPlex ? Thanks, best regards, Yann From ellen.price at cfa.harvard.edu Thu Dec 5 10:00:11 2019 From: ellen.price at cfa.harvard.edu (Ellen M. Price) Date: Thu, 5 Dec 2019 11:00:11 -0500 Subject: [petsc-users] Updating TS solution outside PETSc Message-ID: <44237f2b-358c-e201-1121-7a6c09782705@cfa.harvard.edu> Hi PETSc users, I am working with a code that solves a set of PDEs on a rectangular domain with Neumann boundary conditions. My understanding of implementing the boundary condition is that I should set the boundary value to be the value that makes the finite difference derivative go to zero (or some other prescribed value) on that boundary. I was attempting to update the solution from TS using a pre- or post-step/stage function and TSGetSolution, but this does not appear to work as expected. What would be the correct way to prescribe the boundary condition, given that I'm using TSRK for timestepping and a DMDA for discretization? Looking forward to any help! Ellen Price From bsmith at mcs.anl.gov Thu Dec 5 10:16:31 2019 From: bsmith at mcs.anl.gov (Smith, Barry F.) Date: Thu, 5 Dec 2019 16:16:31 +0000 Subject: [petsc-users] Updating TS solution outside PETSc In-Reply-To: <44237f2b-358c-e201-1121-7a6c09782705@cfa.harvard.edu> References: <44237f2b-358c-e201-1121-7a6c09782705@cfa.harvard.edu> Message-ID: <878A14D0-7623-4C06-BD8F-CFDDAA89378F@anl.gov> Are you using cell-centered or vertex centered discretization ( makes a slight difference)? Our model is to use DM_BOUNDARY_MIRROR DMBoundaryType. This means that u_first_real_grid_point - u_its_ghost_point = 0 (since DMGlobalToLocal will automatically put into the physical ghost location the appropriate mirror values) thus u_n is zero along the edge; zero Neumann conditions, for non-zero Neuman you need to put something in the "local rhs" to represent that, I'm not sure it is clear, but think about it in one dimension for the non-zero Neumann case. Bad news not yet implemented for 3d. If you are using 3d we should fix this for you (or you fix it and make a MR because we should have this support). If you have a 2d version of your code I would test with 3d your model etc and then let us know and request how we can get the 3d mirror written. Others may have alternative advice for Neumann with DMDA, Barry > On Dec 5, 2019, at 10:00 AM, Ellen M. Price wrote: > > Hi PETSc users, > > I am working with a code that solves a set of PDEs on a rectangular > domain with Neumann boundary conditions. My understanding of > implementing the boundary condition is that I should set the boundary > value to be the value that makes the finite difference derivative go to > zero (or some other prescribed value) on that boundary. > > I was attempting to update the solution from TS using a pre- or > post-step/stage function and TSGetSolution, but this does not appear to > work as expected. What would be the correct way to prescribe the > boundary condition, given that I'm using TSRK for timestepping and a > DMDA for discretization? > > Looking forward to any help! > > Ellen Price From eda.oktay at metu.edu.tr Thu Dec 5 10:20:08 2019 From: eda.oktay at metu.edu.tr (Eda Oktay) Date: Thu, 5 Dec 2019 19:20:08 +0300 Subject: [petsc-users] Edge-cut information for CHACO Message-ID: Hello all, I am trying to find edge cut information of ParMETIS and CHACO. When I use ParMETIS, MatPartitioningViewImbalance(part,partitioning) works and it gives also number of cuts. However, when I used CHACO, it only gives imbalance information, not edge cut. I have index sets but I couldn't find how to calculate edge cut. Also, does ParMETIS calculate edge cuts according to the values of weights or number of weights? Thanks! Eda -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Thu Dec 5 10:22:11 2019 From: bsmith at mcs.anl.gov (Smith, Barry F.) Date: Thu, 5 Dec 2019 16:22:11 +0000 Subject: [petsc-users] dof of DMDA & DMPlex In-Reply-To: References: Message-ID: Hmm, for DMDA and DMStag is should not have a limit (certain ranges of values are better optimized than others but more optimizations may be done). For DMPLEX in theory again it should be what ever you like (again larger values may require more optimization in our code to get really great performance) Barry > On Dec 5, 2019, at 9:50 AM, Yann Jobic wrote: > > Hello, > I read in the email archive (from 2016) that, at that time, the number of synchronized dof (in MPI/ghost cells sense) is 3 or 4. > Is that still the case ? I would like to use PETSc for solving the Boltzmann equation (via Discreet velocity method, which means a lot of dof per node). > Is it the same for DMPlex ? > Thanks, > best regards, > Yann From ellen.price at cfa.harvard.edu Thu Dec 5 11:30:44 2019 From: ellen.price at cfa.harvard.edu (Ellen M. Price) Date: Thu, 5 Dec 2019 12:30:44 -0500 Subject: [petsc-users] Updating TS solution outside PETSc In-Reply-To: <878A14D0-7623-4C06-BD8F-CFDDAA89378F@anl.gov> References: <44237f2b-358c-e201-1121-7a6c09782705@cfa.harvard.edu> <878A14D0-7623-4C06-BD8F-CFDDAA89378F@anl.gov> Message-ID: <2eb5c2d2-f555-02c5-a3d8-1b54ac84e766@cfa.harvard.edu> I think I'm still unclear on exactly how this should work. Suppose, in my RHS function for TS, I'm processing the grid to compute its time derivative and get to an edge. What do I do? If I set the derivative there to zero, the value will never change, but it *should* change so that the spatial derivative there is zero. If I set it to the value it would get if it wasn't an edge, then the derivative isn't preserved anymore. This is where I get stuck. Ellen On 12/5/19 10:16 AM, Smith, Barry F. wrote: > > Are you using cell-centered or vertex centered discretization ( makes a slight difference)? > > Our model is to use DM_BOUNDARY_MIRROR DMBoundaryType. This means that u_first_real_grid_point - u_its_ghost_point = 0 (since DMGlobalToLocal will automatically put into the physical ghost location the appropriate mirror values) thus u_n is zero along the edge; zero Neumann conditions, for non-zero Neuman you need to put something in the "local rhs" to represent that, I'm not sure it is clear, but think about it in one dimension for the non-zero Neumann case. > > Bad news not yet implemented for 3d. > > If you are using 3d we should fix this for you (or you fix it and make a MR because we should have this support). > > If you have a 2d version of your code I would test with 3d your model etc and then let us know and request how we can get the 3d mirror written. > > Others may have alternative advice for Neumann with DMDA, > > Barry > > >> On Dec 5, 2019, at 10:00 AM, Ellen M. Price wrote: >> >> Hi PETSc users, >> >> I am working with a code that solves a set of PDEs on a rectangular >> domain with Neumann boundary conditions. My understanding of >> implementing the boundary condition is that I should set the boundary >> value to be the value that makes the finite difference derivative go to >> zero (or some other prescribed value) on that boundary. >> >> I was attempting to update the solution from TS using a pre- or >> post-step/stage function and TSGetSolution, but this does not appear to >> work as expected. What would be the correct way to prescribe the >> boundary condition, given that I'm using TSRK for timestepping and a >> DMDA for discretization? >> >> Looking forward to any help! >> >> Ellen Price > From knepley at gmail.com Thu Dec 5 12:48:04 2019 From: knepley at gmail.com (Matthew Knepley) Date: Thu, 5 Dec 2019 13:48:04 -0500 Subject: [petsc-users] Updating TS solution outside PETSc In-Reply-To: <2eb5c2d2-f555-02c5-a3d8-1b54ac84e766@cfa.harvard.edu> References: <44237f2b-358c-e201-1121-7a6c09782705@cfa.harvard.edu> <878A14D0-7623-4C06-BD8F-CFDDAA89378F@anl.gov> <2eb5c2d2-f555-02c5-a3d8-1b54ac84e766@cfa.harvard.edu> Message-ID: On Thu, Dec 5, 2019 at 12:34 PM Ellen M. Price wrote: > I think I'm still unclear on exactly how this should work. Suppose, in > my RHS function for TS, I'm processing the grid to compute its time > derivative and get to an edge. What do I do? > The idea here, I think, is that you keeping using your normal stencil. If you tell PETSc that the edge is a mirror boundary, it will have automatically put a value in the ghost location that will force a 0 spatial derivative. Thanks, Matt > If I set the derivative there to zero, the value will never change, but > it *should* change so that the spatial derivative there is zero. > > If I set it to the value it would get if it wasn't an edge, then the > derivative isn't preserved anymore. > > This is where I get stuck. > > Ellen > > > On 12/5/19 10:16 AM, Smith, Barry F. wrote: > > > > Are you using cell-centered or vertex centered discretization ( makes > a slight difference)? > > > > Our model is to use DM_BOUNDARY_MIRROR DMBoundaryType. This means > that u_first_real_grid_point - u_its_ghost_point = 0 (since DMGlobalToLocal > will automatically put into the physical ghost location the appropriate > mirror values) thus u_n is zero along the edge; zero Neumann conditions, > for non-zero Neuman you need to put something in the "local rhs" to > represent that, I'm not sure it is clear, but think about it in one > dimension for the non-zero Neumann case. > > > > Bad news not yet implemented for 3d. > > > > If you are using 3d we should fix this for you (or you fix it and > make a MR because we should have this support). > > > > If you have a 2d version of your code I would test with 3d your model > etc and then let us know and request how we can get the 3d mirror written. > > > > Others may have alternative advice for Neumann with DMDA, > > > > Barry > > > > > >> On Dec 5, 2019, at 10:00 AM, Ellen M. Price < > ellen.price at cfa.harvard.edu> wrote: > >> > >> Hi PETSc users, > >> > >> I am working with a code that solves a set of PDEs on a rectangular > >> domain with Neumann boundary conditions. My understanding of > >> implementing the boundary condition is that I should set the boundary > >> value to be the value that makes the finite difference derivative go to > >> zero (or some other prescribed value) on that boundary. > >> > >> I was attempting to update the solution from TS using a pre- or > >> post-step/stage function and TSGetSolution, but this does not appear to > >> work as expected. What would be the correct way to prescribe the > >> boundary condition, given that I'm using TSRK for timestepping and a > >> DMDA for discretization? > >> > >> Looking forward to any help! > >> > >> Ellen Price > > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From mfadams at lbl.gov Thu Dec 5 13:34:37 2019 From: mfadams at lbl.gov (Mark Adams) Date: Thu, 5 Dec 2019 14:34:37 -0500 Subject: [petsc-users] Edge-cut information for CHACO In-Reply-To: References: Message-ID: On Thu, Dec 5, 2019 at 11:20 AM Eda Oktay wrote: > Hello all, > > I am trying to find edge cut information of ParMETIS and CHACO. When I use > ParMETIS, > MatPartitioningViewImbalance(part,partitioning) > works and it gives also number of cuts. > > However, when I used CHACO, it only gives imbalance information, not edge > cut. I have index sets but I couldn't find how to calculate edge cut. > I've never heard of edge-cuts wrt Chaco. I'm sure it does not collect that information but you could look at the code. > > Also, does ParMETIS calculate edge cuts according to the values of weights > or number of weights? > Good question, I would assume this is an integer, the number of edge cuts, and not the sum of the weights. If it prints and integer then that would be a hint. > > Thanks! > > Eda > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Thu Dec 5 13:38:39 2019 From: bsmith at mcs.anl.gov (Smith, Barry F.) Date: Thu, 5 Dec 2019 19:38:39 +0000 Subject: [petsc-users] Updating TS solution outside PETSc In-Reply-To: <2eb5c2d2-f555-02c5-a3d8-1b54ac84e766@cfa.harvard.edu> References: <44237f2b-358c-e201-1121-7a6c09782705@cfa.harvard.edu> <878A14D0-7623-4C06-BD8F-CFDDAA89378F@anl.gov> <2eb5c2d2-f555-02c5-a3d8-1b54ac84e766@cfa.harvard.edu> Message-ID: <3B62F892-EC48-43C8-90A7-86F4E3D52D71@mcs.anl.gov> Let's look at the 1d case with vertex centered differencing | | u-1* u0 u1 ... u-1* is the ghost value, u0 the edge value etc. Say you are solving u_n on boundary is g(t), u inside satisfies u_t = U_xx Then if you provide a function of TSSetRHSFunction() it would be something like DMGetLocalVector(DM,&ulocal); DMGlobalToLocal(dm, U, ulocal) ; DMDAGetArray(ulocal,&u) DMDAGetArray(fglobal,&f) for (i=0,.... f[i] = (u[i+1] - 2*u[i] + u[i-1])/h f[0] += g(t) Note that f[0] = (u[i+1] - 2*u[i] + u[i-1])/h^2 = (u[1] - u[0])/h + g(t) So you are satisfying the PDE inside the domain and on the boundary you are using one-sided differencing to approximate the Neumann boundary conditions. I may have some details wrong. Barry > On Dec 5, 2019, at 11:30 AM, Ellen M. Price wrote: > > I think I'm still unclear on exactly how this should work. Suppose, in > my RHS function for TS, I'm processing the grid to compute its time > derivative and get to an edge. What do I do? > > If I set the derivative there to zero, the value will never change, but > it *should* change so that the spatial derivative there is zero. > > If I set it to the value it would get if it wasn't an edge, then the > derivative isn't preserved anymore. > > This is where I get stuck. > > Ellen > > > On 12/5/19 10:16 AM, Smith, Barry F. wrote: >> >> Are you using cell-centered or vertex centered discretization ( makes a slight difference)? >> >> Our model is to use DM_BOUNDARY_MIRROR DMBoundaryType. This means that u_first_real_grid_point - u_its_ghost_point = 0 (since DMGlobalToLocal will automatically put into the physical ghost location the appropriate mirror values) thus u_n is zero along the edge; zero Neumann conditions, for non-zero Neuman you need to put something in the "local rhs" to represent that, I'm not sure it is clear, but think about it in one dimension for the non-zero Neumann case. >> >> Bad news not yet implemented for 3d. >> >> If you are using 3d we should fix this for you (or you fix it and make a MR because we should have this support). >> >> If you have a 2d version of your code I would test with 3d your model etc and then let us know and request how we can get the 3d mirror written. >> >> Others may have alternative advice for Neumann with DMDA, >> >> Barry >> >> >>> On Dec 5, 2019, at 10:00 AM, Ellen M. Price wrote: >>> >>> Hi PETSc users, >>> >>> I am working with a code that solves a set of PDEs on a rectangular >>> domain with Neumann boundary conditions. My understanding of >>> implementing the boundary condition is that I should set the boundary >>> value to be the value that makes the finite difference derivative go to >>> zero (or some other prescribed value) on that boundary. >>> >>> I was attempting to update the solution from TS using a pre- or >>> post-step/stage function and TSGetSolution, but this does not appear to >>> work as expected. What would be the correct way to prescribe the >>> boundary condition, given that I'm using TSRK for timestepping and a >>> DMDA for discretization? >>> >>> Looking forward to any help! >>> >>> Ellen Price >> From stefano.zampini at gmail.com Thu Dec 5 13:38:50 2019 From: stefano.zampini at gmail.com (Stefano Zampini) Date: Thu, 5 Dec 2019 22:38:50 +0300 Subject: [petsc-users] Edge-cut information for CHACO In-Reply-To: References: Message-ID: <6C1EA9C3-972A-494B-A3FF-D74CF383F4B1@gmail.com> In DMPLEX, we compute the unweighted edge cut with this code https://gitlab.com/petsc/petsc/blob/master/src/dm/impls/plex/plex.c#L955 You may reuse most of this code to compute the edge cut in your case > On Dec 5, 2019, at 10:34 PM, Mark Adams wrote: > > > > On Thu, Dec 5, 2019 at 11:20 AM Eda Oktay > wrote: > Hello all, > > I am trying to find edge cut information of ParMETIS and CHACO. When I use ParMETIS, > MatPartitioningViewImbalance(part,partitioning) > works and it gives also number of cuts. > > However, when I used CHACO, it only gives imbalance information, not edge cut. I have index sets but I couldn't find how to calculate edge cut. > > I've never heard of edge-cuts wrt Chaco. I'm sure it does not collect that information but you could look at the code. > > > Also, does ParMETIS calculate edge cuts according to the values of weights or number of weights? > > Good question, I would assume this is an integer, the number of edge cuts, and not the sum of the weights. If it prints and integer then that would be a hint. > > > Thanks! > > Eda -------------- next part -------------- An HTML attachment was scrubbed... URL: From fdkong.jd at gmail.com Thu Dec 5 13:41:15 2019 From: fdkong.jd at gmail.com (Fande Kong) Date: Thu, 5 Dec 2019 12:41:15 -0700 Subject: [petsc-users] Edge-cut information for CHACO In-Reply-To: References: Message-ID: On Thu, Dec 5, 2019 at 12:34 PM Mark Adams wrote: > > > On Thu, Dec 5, 2019 at 11:20 AM Eda Oktay wrote: > >> Hello all, >> >> I am trying to find edge cut information of ParMETIS and CHACO. When I >> use ParMETIS, >> MatPartitioningViewImbalance(part,partitioning) >> works and it gives also number of cuts. >> >> However, when I used CHACO, it only gives imbalance information, not edge >> cut. I have index sets but I couldn't find how to calculate edge cut. >> > > I've never heard of edge-cuts wrt Chaco. I'm sure it does not collect that > information but you could look at the code. > Not sure chaco supports this or not, but we do not collect edge cuts from Chaco. If you want, it is actually very easy to collect all these data at the PETSc side. > > >> >> Also, does ParMETIS calculate edge cuts according to the values of >> weights or number of weights? >> > > Good question, I would assume this is an integer, the number of edge cuts, > and not the sum of the weights. If it prints and integer then that would be > a hint. > The edge-cuts in ParMETIS take the edge weights into account. For example, if you have an edge along which the domain is partitioned. If the weight of that edge is 10, and the number of edge-cuts is 10 instead of 1. Fande, > >> >> Thanks! >> >> Eda >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jed at jedbrown.org Thu Dec 5 08:23:23 2019 From: jed at jedbrown.org (Jed Brown) Date: Thu, 05 Dec 2019 07:23:23 -0700 Subject: [petsc-users] CMake error in PETSc In-Reply-To: References: <875ziwkszv.fsf@jedbrown.org> <87zhg8jctx.fsf@jedbrown.org> <87r21jjqr8.fsf@jedbrown.org> Message-ID: <87zhg6j1gk.fsf@jedbrown.org> Yingjie Wu writes: > I'm so sorry that I've ignored your previous advices. > > I added a global variable that seems works: > > > export > LD_LIBRARY_PATH=/home/lerui/petcs-3.12.2/arch-linux2-c-debug/lib:$LD_LIBRARY_PATH > > > How should I make petsc in a standard position?This eliminates the need to > set global variables. You can configure PETSc with --prefix=/your/standard/path, then make install. > It seems that some of the options before running fit become unavailable: > > > mpiexec -n 1 ./example01cmke -snes_view > > > Options-snes _ view are not used and how should I solve this problem? I don't have your ex1.cpp, but presumably you didn't SNESSetFromOptions? From jed at jedbrown.org Thu Dec 5 08:07:14 2019 From: jed at jedbrown.org (Jed Brown) Date: Thu, 05 Dec 2019 07:07:14 -0700 Subject: [petsc-users] CMake error in PETSc In-Reply-To: References: <875ziwkszv.fsf@jedbrown.org> <87zhg8jctx.fsf@jedbrown.org> <87r21jjqr8.fsf@jedbrown.org> Message-ID: <8736dykgrx.fsf@jedbrown.org> Yingjie Wu writes: > Hi, > > I installed the latest version of petsc, and compiled the example using > cmke as described above. Compilation can be done, but there is a new > problem while the program is running, as if the program could not find the > shared library libpetsc.so.3.12. How can I solve this problem? Either export LD_LIBRARY_PATH=$PETSC_DIR/$PETSC_ARCH/lib or set RPATH in CMake: https://gitlab.kitware.com/cmake/community/wikis/doc/cmake/RPATH-handling CMake's FindPkgConfig punts on this front (and it's sadly complicated, but they broke their own conventions to get here). It's been 10 years and they've had no interest in fixing some of the problems that my modules were created to handle. I stopped using CMake by choice long ago so I'd prefer to gently steer people toward something (FindPkgConfig) that I'm not on the hook to maintain. From jed at jedbrown.org Thu Dec 5 10:23:45 2019 From: jed at jedbrown.org (Jed Brown) Date: Thu, 05 Dec 2019 09:23:45 -0700 Subject: [petsc-users] dof of DMDA & DMPlex In-Reply-To: References: Message-ID: <87tv6eivvy.fsf@jedbrown.org> I don't understand the question. There has never been a limit to the number of dofs per grid point. Was the email thread referring to spatial dimension? Yann Jobic writes: > Hello, > I read in the email archive (from 2016) that, at that time, the number > of synchronized dof (in MPI/ghost cells sense) is 3 or 4. > Is that still the case ? I would like to use PETSc for solving the > Boltzmann equation (via Discreet velocity method, which means a lot of > dof per node). > Is it the same for DMPlex ? > Thanks, > best regards, > Yann From jed at jedbrown.org Thu Dec 5 12:32:50 2019 From: jed at jedbrown.org (Jed Brown) Date: Thu, 05 Dec 2019 11:32:50 -0700 Subject: [petsc-users] Updating TS solution outside PETSc In-Reply-To: <2eb5c2d2-f555-02c5-a3d8-1b54ac84e766@cfa.harvard.edu> References: <44237f2b-358c-e201-1121-7a6c09782705@cfa.harvard.edu> <878A14D0-7623-4C06-BD8F-CFDDAA89378F@anl.gov> <2eb5c2d2-f555-02c5-a3d8-1b54ac84e766@cfa.harvard.edu> Message-ID: <87a786ipwt.fsf@jedbrown.org> "Ellen M. Price" writes: > I think I'm still unclear on exactly how this should work. Suppose, in > my RHS function for TS, I'm processing the grid to compute its time > derivative and get to an edge. What do I do? > > If I set the derivative there to zero, the value will never change, but > it *should* change so that the spatial derivative there is zero. This can be implemented by creating algebraic constraints (which yields a DAE) or by formulating the problem in terms of ghost cells. Note that it is not required that a given one-sided difference equation be satisfied at a boundary. Indeed, if you enforce (u[1] - u[0])/h = 0 you'll see only first order accuracy. The DAE formulation (even if you use a high-order difference formula) can also lead to order reduction in time, depending on the time integrator. It's often preferable to use ghost points u[-1] = u[1] and then discretize your internal equations, e.g., udot[0] + (-u[-1] + 2*u[0] - u[1])/h2 = 0 which often reduces to incorporating a transient term with the one-sided algebraic formula up top udot[0] * h/2 - (u[1] - u[0])/h = 0 but this yields an ODE and retains second order accuracy. > If I set it to the value it would get if it wasn't an edge, then the > derivative isn't preserved anymore. > > This is where I get stuck. > > Ellen > > > On 12/5/19 10:16 AM, Smith, Barry F. wrote: >> >> Are you using cell-centered or vertex centered discretization ( makes a slight difference)? >> >> Our model is to use DM_BOUNDARY_MIRROR DMBoundaryType. This means that u_first_real_grid_point - u_its_ghost_point = 0 (since DMGlobalToLocal will automatically put into the physical ghost location the appropriate mirror values) thus u_n is zero along the edge; zero Neumann conditions, for non-zero Neuman you need to put something in the "local rhs" to represent that, I'm not sure it is clear, but think about it in one dimension for the non-zero Neumann case. >> >> Bad news not yet implemented for 3d. >> >> If you are using 3d we should fix this for you (or you fix it and make a MR because we should have this support). >> >> If you have a 2d version of your code I would test with 3d your model etc and then let us know and request how we can get the 3d mirror written. >> >> Others may have alternative advice for Neumann with DMDA, >> >> Barry >> >> >>> On Dec 5, 2019, at 10:00 AM, Ellen M. Price wrote: >>> >>> Hi PETSc users, >>> >>> I am working with a code that solves a set of PDEs on a rectangular >>> domain with Neumann boundary conditions. My understanding of >>> implementing the boundary condition is that I should set the boundary >>> value to be the value that makes the finite difference derivative go to >>> zero (or some other prescribed value) on that boundary. >>> >>> I was attempting to update the solution from TS using a pre- or >>> post-step/stage function and TSGetSolution, but this does not appear to >>> work as expected. What would be the correct way to prescribe the >>> boundary condition, given that I'm using TSRK for timestepping and a >>> DMDA for discretization? >>> >>> Looking forward to any help! >>> >>> Ellen Price >> From jed at jedbrown.org Thu Dec 5 13:47:03 2019 From: jed at jedbrown.org (Jed Brown) Date: Thu, 05 Dec 2019 12:47:03 -0700 Subject: [petsc-users] Updating TS solution outside PETSc In-Reply-To: <3B62F892-EC48-43C8-90A7-86F4E3D52D71@mcs.anl.gov> References: <44237f2b-358c-e201-1121-7a6c09782705@cfa.harvard.edu> <878A14D0-7623-4C06-BD8F-CFDDAA89378F@anl.gov> <2eb5c2d2-f555-02c5-a3d8-1b54ac84e766@cfa.harvard.edu> <3B62F892-EC48-43C8-90A7-86F4E3D52D71@mcs.anl.gov> Message-ID: <8736dyimh4.fsf@jedbrown.org> "Smith, Barry F." writes: > Let's look at the 1d case with vertex centered differencing > > | | > u-1* u0 u1 ... > > > u-1* is the ghost value, u0 the edge value etc. > > Say you are solving u_n on boundary is g(t), u inside satisfies u_t = U_xx > > Then if you provide a function of TSSetRHSFunction() it would be something like > > DMGetLocalVector(DM,&ulocal); > DMGlobalToLocal(dm, U, ulocal) ; > > DMDAGetArray(ulocal,&u) > DMDAGetArray(fglobal,&f) > > for (i=0,.... > f[i] = (u[i+1] - 2*u[i] + u[i-1])/h > > > f[0] += g(t) > > Note that f[0] = (u[i+1] - 2*u[i] + u[i-1])/h^2 = (u[1] - u[0])/h + g(t) Better to reflect with bias, e.g., u[-1] = u[1] + 2*h*g(t) and apply the standard differencing rule. Note that f[0] means u_t[0] = f[0] so you can't drop factors of h, etc., > So you are satisfying the PDE inside the domain and on the boundary you are using one-sided differencing to approximate the Neumann boundary conditions. Only by accident in a sense is a one-sided differencing. Yes, it reduces to some one-sided formula once you eliminate the ghost points, but the interpretation is less clear when using higher order methods, non-uniform spacing, or upwinding in the volumetric discretization. From mpovolot at purdue.edu Thu Dec 5 21:19:56 2019 From: mpovolot at purdue.edu (Povolotskyi, Mykhailo) Date: Fri, 6 Dec 2019 03:19:56 +0000 Subject: [petsc-users] petsc under cygwin Message-ID: <91825cc3-ee60-ab37-a577-56e02ddfe7be@purdue.edu> Dear Petsc support team, for some reasons I have to build petsc under Windows. I have installed Cygwin with GNU compilers and OpenMPI. Unfortunately, the configuration fails with the following message: TESTING: checkCxxCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:814) ******************************************************************************* ???????? UNABLE to CONFIGURE with GIVEN OPTIONS??? (see configure.log for details): ------------------------------------------------------------------------------- C++ compiler you provided with -with-cxx=mpicxx does not work. Cannot compile/link Cxx with mpicxx. I'm attaching the *.log file. Please advise, Michael. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: configure.log URL: From bsmith at mcs.anl.gov Thu Dec 5 22:53:14 2019 From: bsmith at mcs.anl.gov (Smith, Barry F.) Date: Fri, 6 Dec 2019 04:53:14 +0000 Subject: [petsc-users] petsc under cygwin In-Reply-To: <91825cc3-ee60-ab37-a577-56e02ddfe7be@purdue.edu> References: <91825cc3-ee60-ab37-a577-56e02ddfe7be@purdue.edu> Message-ID: <6746E426-D354-44F4-BC50-FD2C023DBD6E@anl.gov> Can you actually build and run C++ programs with the MPI? Executing: mpicxx -o /tmp/petsc-Llvze6/config.setCompilers/conftest.exe -fopenmp -fPIC /tmp/petsc-Llvze6/config.setCompilers/conftest.o Possible ERROR while running linker: exit code 1 stderr: /usr/lib/gcc/x86_64-pc-cygwin/7.4.0/../../../../x86_64-pc-cygwin/bin/ld: cannot find -lmpi_cxx collect2: error: ld returned 1 exit status Error testing C++ compiler: Cannot compile/link Cxx with mpicxx. MPI installation mpicxx is likely incorrect. Use --with-mpi-dir to indicate an alternate MPI. Also you have --with-fortran=0 but --download-fblaslapack and FOPTFLAGS=-O3 and why do you have --with-log=0 it costs no overhead if you do not use it and is always useful for tracking performance. Barry > On Dec 5, 2019, at 9:19 PM, Povolotskyi, Mykhailo wrote: > > Dear Petsc support team, > > for some reasons I have to build petsc under Windows. > > I have installed Cygwin with GNU compilers and OpenMPI. > > Unfortunately, the configuration fails with the following message: > > TESTING: checkCxxCompiler from > config.setCompilers(config/BuildSystem/config/setCompilers.py:814) > ******************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log > for details): > ------------------------------------------------------------------------------- > C++ compiler you provided with -with-cxx=mpicxx does not work. > Cannot compile/link Cxx with mpicxx. > > I'm attaching the *.log file. > > Please advise, > > Michael. > > From mpovolot at purdue.edu Thu Dec 5 23:39:46 2019 From: mpovolot at purdue.edu (Povolotskyi, Mykhailo) Date: Fri, 6 Dec 2019 05:39:46 +0000 Subject: [petsc-users] petsc under cygwin In-Reply-To: <6746E426-D354-44F4-BC50-FD2C023DBD6E@anl.gov> References: <91825cc3-ee60-ab37-a577-56e02ddfe7be@purdue.edu> <6746E426-D354-44F4-BC50-FD2C023DBD6E@anl.gov> Message-ID: <13a0e1d6-1e81-fd01-f4d8-2c356f49c280@purdue.edu> I checked: I cannot build C++ programs with MPI, but I can build and run C programs with MPI. I have -with-log=0 because there is an overhead if many small objects are created, which is my case. As for the fortran, I will remove? --with-fortran=0 On 12/5/2019 11:53 PM, Smith, Barry F. wrote: > Can you actually build and run C++ programs with the MPI? > > Executing: mpicxx -o /tmp/petsc-Llvze6/config.setCompilers/conftest.exe -fopenmp -fPIC /tmp/petsc-Llvze6/config.setCompilers/conftest.o > Possible ERROR while running linker: exit code 1 > stderr: > /usr/lib/gcc/x86_64-pc-cygwin/7.4.0/../../../../x86_64-pc-cygwin/bin/ld: cannot find -lmpi_cxx > collect2: error: ld returned 1 exit status > Error testing C++ compiler: Cannot compile/link Cxx with mpicxx. > MPI installation mpicxx is likely incorrect. > Use --with-mpi-dir to indicate an alternate MPI. > > Also you have --with-fortran=0 > > but --download-fblaslapack and FOPTFLAGS=-O3 > > and why do you have --with-log=0 it costs no overhead if you do not use it and is always useful for tracking performance. > > Barry > > >> On Dec 5, 2019, at 9:19 PM, Povolotskyi, Mykhailo wrote: >> >> Dear Petsc support team, >> >> for some reasons I have to build petsc under Windows. >> >> I have installed Cygwin with GNU compilers and OpenMPI. >> >> Unfortunately, the configuration fails with the following message: >> >> TESTING: checkCxxCompiler from >> config.setCompilers(config/BuildSystem/config/setCompilers.py:814) >> ******************************************************************************* >> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log >> for details): >> ------------------------------------------------------------------------------- >> C++ compiler you provided with -with-cxx=mpicxx does not work. >> Cannot compile/link Cxx with mpicxx. >> >> I'm attaching the *.log file. >> >> Please advise, >> >> Michael. >> >> From bsmith at mcs.anl.gov Thu Dec 5 23:57:46 2019 From: bsmith at mcs.anl.gov (Smith, Barry F.) Date: Fri, 6 Dec 2019 05:57:46 +0000 Subject: [petsc-users] petsc under cygwin In-Reply-To: <13a0e1d6-1e81-fd01-f4d8-2c356f49c280@purdue.edu> References: <91825cc3-ee60-ab37-a577-56e02ddfe7be@purdue.edu> <6746E426-D354-44F4-BC50-FD2C023DBD6E@anl.gov> <13a0e1d6-1e81-fd01-f4d8-2c356f49c280@purdue.edu> Message-ID: <9B4EFA47-D11D-4BA7-9BF4-19EADA5AE4A9@mcs.anl.gov> Ok, run configure with --with-cxx=0 and without --with-clanguage=c++ but note that certain external packages such as SuperLU_DIST require C++. > On Dec 5, 2019, at 11:39 PM, Povolotskyi, Mykhailo wrote: > > I checked: > > I cannot build C++ programs with MPI, but I can build and run C programs > with MPI. > > I have -with-log=0 because there is an overhead if many small objects > are created, which is my case. > > As for the fortran, I will remove --with-fortran=0 > > On 12/5/2019 11:53 PM, Smith, Barry F. wrote: >> Can you actually build and run C++ programs with the MPI? >> >> Executing: mpicxx -o /tmp/petsc-Llvze6/config.setCompilers/conftest.exe -fopenmp -fPIC /tmp/petsc-Llvze6/config.setCompilers/conftest.o >> Possible ERROR while running linker: exit code 1 >> stderr: >> /usr/lib/gcc/x86_64-pc-cygwin/7.4.0/../../../../x86_64-pc-cygwin/bin/ld: cannot find -lmpi_cxx >> collect2: error: ld returned 1 exit status >> Error testing C++ compiler: Cannot compile/link Cxx with mpicxx. >> MPI installation mpicxx is likely incorrect. >> Use --with-mpi-dir to indicate an alternate MPI. >> >> Also you have --with-fortran=0 >> >> but --download-fblaslapack and FOPTFLAGS=-O3 >> >> and why do you have --with-log=0 it costs no overhead if you do not use it and is always useful for tracking performance. >> >> Barry >> >> >>> On Dec 5, 2019, at 9:19 PM, Povolotskyi, Mykhailo wrote: >>> >>> Dear Petsc support team, >>> >>> for some reasons I have to build petsc under Windows. >>> >>> I have installed Cygwin with GNU compilers and OpenMPI. >>> >>> Unfortunately, the configuration fails with the following message: >>> >>> TESTING: checkCxxCompiler from >>> config.setCompilers(config/BuildSystem/config/setCompilers.py:814) >>> ******************************************************************************* >>> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log >>> for details): >>> ------------------------------------------------------------------------------- >>> C++ compiler you provided with -with-cxx=mpicxx does not work. >>> Cannot compile/link Cxx with mpicxx. >>> >>> I'm attaching the *.log file. >>> >>> Please advise, >>> >>> Michael. >>> >>> From yann.jobic at univ-amu.fr Fri Dec 6 04:46:29 2019 From: yann.jobic at univ-amu.fr (Yann Jobic) Date: Fri, 6 Dec 2019 11:46:29 +0100 Subject: [petsc-users] dof of DMDA & DMPlex In-Reply-To: <87tv6eivvy.fsf@jedbrown.org> References: <87tv6eivvy.fsf@jedbrown.org> Message-ID: <1a4288ac-a471-22e4-bd4c-bc6eda7c5a3e@univ-amu.fr> I think i may have misunderstood this discussion : https://lists.mcs.anl.gov/mailman/htdig/petsc-users/2017-October/033620.html best regards, Yann Le 05/12/2019 ? 17:23, Jed Brown a ?crit?: > I don't understand the question. There has never been a limit to the > number of dofs per grid point. Was the email thread referring to > spatial dimension? > > Yann Jobic writes: > >> Hello, >> I read in the email archive (from 2016) that, at that time, the number >> of synchronized dof (in MPI/ghost cells sense) is 3 or 4. >> Is that still the case ? I would like to use PETSc for solving the >> Boltzmann equation (via Discreet velocity method, which means a lot of >> dof per node). >> Is it the same for DMPlex ? >> Thanks, >> best regards, >> Yann -- ___________________________ Yann JOBIC HPC engineer IUSTI-CNRS UMR 7343 - Polytech Marseille Technop?le de Ch?teau Gombert 5 rue Enrico Fermi 13453 Marseille cedex 13 Tel : (33) 4 91 10 69 43 Fax : (33) 4 91 10 69 69 From knepley at gmail.com Fri Dec 6 06:29:58 2019 From: knepley at gmail.com (Matthew Knepley) Date: Fri, 6 Dec 2019 07:29:58 -0500 Subject: [petsc-users] dof of DMDA & DMPlex In-Reply-To: <1a4288ac-a471-22e4-bd4c-bc6eda7c5a3e@univ-amu.fr> References: <87tv6eivvy.fsf@jedbrown.org> <1a4288ac-a471-22e4-bd4c-bc6eda7c5a3e@univ-amu.fr> Message-ID: On Fri, Dec 6, 2019 at 5:46 AM Yann Jobic wrote: > I think i may have misunderstood this discussion : > > https://lists.mcs.anl.gov/mailman/htdig/petsc-users/2017-October/033620.html > That discussion is about the dimensionality of the problem rather than the number of dofs at a point. Regular grids suffer from the "curse of dimensionality". Thanks, Matt > best regards, > Yann > > Le 05/12/2019 ? 17:23, Jed Brown a ?crit : > > I don't understand the question. There has never been a limit to the > > number of dofs per grid point. Was the email thread referring to > > spatial dimension? > > > > Yann Jobic writes: > > > >> Hello, > >> I read in the email archive (from 2016) that, at that time, the number > >> of synchronized dof (in MPI/ghost cells sense) is 3 or 4. > >> Is that still the case ? I would like to use PETSc for solving the > >> Boltzmann equation (via Discreet velocity method, which means a lot of > >> dof per node). > >> Is it the same for DMPlex ? > >> Thanks, > >> best regards, > >> Yann > > > -- > ___________________________ > > Yann JOBIC > HPC engineer > IUSTI-CNRS UMR 7343 - Polytech Marseille > Technop?le de Ch?teau Gombert > 5 rue Enrico Fermi > 13453 Marseille cedex 13 > Tel : (33) 4 91 10 69 43 > Fax : (33) 4 91 10 69 69 > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Fri Dec 6 07:58:48 2019 From: balay at mcs.anl.gov (Balay, Satish) Date: Fri, 6 Dec 2019 13:58:48 +0000 Subject: [petsc-users] petsc under cygwin In-Reply-To: <13a0e1d6-1e81-fd01-f4d8-2c356f49c280@purdue.edu> References: <91825cc3-ee60-ab37-a577-56e02ddfe7be@purdue.edu> <6746E426-D354-44F4-BC50-FD2C023DBD6E@anl.gov> <13a0e1d6-1e81-fd01-f4d8-2c356f49c280@purdue.edu> Message-ID: Are you sure this is cygwin from OpenMPI? I don't see it refer to -lmpi_cxx balay at ps5 ~/petsc $ which mpicxx /usr/bin/mpicxx balay at ps5 ~/petsc $ mpicxx -show g++ -L/usr/lib -lmpi -lopen-rte -lopen-pal -lm -lgdi32 -lz Here is what I get with cygwin/openmpi,lapack,blas Satish ------- balay at ps5 ~/petsc $ ./configure --with-scalar-type=real --with-x=0 --with-hdf5 --download-hdf5=1 --with-single-library=1 --with-shared-libraries=0 --with-log=0 --with-clanguage=C++ --with-cxx-d ialect=C++11 --CXXFLAGS="-fopenmp -fPIC" --CFLAGS="-fopenmp -fPIC" --with-fortran=0 --FFLAGS="-fopenmp -fPIC" --with-64-bit-indices=0 --with-debugging=0 --with-cc=mpicc --with -fc=mpif77 --with-cxx=mpicxx COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 --with-fortran-kernels=0 =============================================================================== Configuring PETSc to compile on your system =============================================================================== =============================================================================== WARNING -with-clanguage=C++ is a developer feature and is *not* required for regular usage of PETSc either from C or C++ =============================================================================== =============================================================================== Trying to download git://https://bitbucket.org/petsc/pkg-sowing.git for SOWING =============================================================================== =============================================================================== Running configure on SOWING; this may take several minutes =============================================================================== =============================================================================== Running make on SOWING; this may take several minutes =============================================================================== =============================================================================== Running make install on SOWING; this may take several minutes =============================================================================== =============================================================================== Trying to download https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5.tar.gz for HDF5 =============================================================================== =============================================================================== Running configure on HDF5; this may take several minutes =============================================================================== =============================================================================== Running make on HDF5; this may take several minutes =============================================================================== =============================================================================== Running make install on HDF5; this may take several minutes =============================================================================== Compilers: C Compiler: mpicc -fopenmp -fPIC -O3 Version: gcc (GCC) 7.4.0 C++ Compiler: mpicxx -fopenmp -fPIC -O3 Version: g++ (GCC) 7.4.0 Fortran Compiler: mpif77 -fopenmp -fPIC -O3 Version: GNU Fortran (GCC) 7.4.0 Linkers: Static linker: /usr/bin/ar cr Dynamic linker: /usr/bin/ar Libraries linked against: -lgdi32 -luser32 -ladvapi32 -lkernel32 -lquadmath -lstdc++ -ldl make: Version: 4.2 /usr/bin/make BlasLapack: Library: -llapack -lblas uses 4 byte integers MPI: Version: 3 Mpiexec: mpiexec --oversubscribe OMPI_VERSION: 3.1.3 pthread: hdf5: Version: 1.10.5 Includes: -I/home/balay/petsc/arch-mswin-cxx-opt/include Library: -Wl,-rpath,/home/balay/petsc/arch-mswin-cxx-opt/lib -L/home/balay/petsc/arch-mswin-cxx-opt/lib -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 cmake: Version: 3.14.5 /usr/bin/cmake sowing: Version: 1.1.25 /home/balay/petsc/arch-mswin-cxx-opt/bin/bfort Language used to compile PETSc: Cxx PETSc: PETSC_ARCH: arch-mswin-cxx-opt PETSC_DIR: /home/balay/petsc Scalar type: real Precision: double Support for __float128 Integer size: 4 bytes shared libraries: disabled Memory alignment from malloc(): 16 bytes xxx=========================================================================xxx Configure stage complete. Now build PETSc libraries with: make PETSC_DIR=/home/balay/petsc PETSC_ARCH=arch-mswin-cxx-opt all xxx=========================================================================xxx balay at ps5 ~/petsc $ On Fri, 6 Dec 2019, Povolotskyi, Mykhailo wrote: > I checked: > > I cannot build C++ programs with MPI, but I can build and run C programs > with MPI. > > I have -with-log=0 because there is an overhead if many small objects > are created, which is my case. > > As for the fortran, I will remove? --with-fortran=0 > > On 12/5/2019 11:53 PM, Smith, Barry F. wrote: > > Can you actually build and run C++ programs with the MPI? > > > > Executing: mpicxx -o /tmp/petsc-Llvze6/config.setCompilers/conftest.exe -fopenmp -fPIC /tmp/petsc-Llvze6/config.setCompilers/conftest.o > > Possible ERROR while running linker: exit code 1 > > stderr: > > /usr/lib/gcc/x86_64-pc-cygwin/7.4.0/../../../../x86_64-pc-cygwin/bin/ld: cannot find -lmpi_cxx > > collect2: error: ld returned 1 exit status > > Error testing C++ compiler: Cannot compile/link Cxx with mpicxx. > > MPI installation mpicxx is likely incorrect. > > Use --with-mpi-dir to indicate an alternate MPI. > > > > Also you have --with-fortran=0 > > > > but --download-fblaslapack and FOPTFLAGS=-O3 > > > > and why do you have --with-log=0 it costs no overhead if you do not use it and is always useful for tracking performance. > > > > Barry > > > > > >> On Dec 5, 2019, at 9:19 PM, Povolotskyi, Mykhailo wrote: > >> > >> Dear Petsc support team, > >> > >> for some reasons I have to build petsc under Windows. > >> > >> I have installed Cygwin with GNU compilers and OpenMPI. > >> > >> Unfortunately, the configuration fails with the following message: > >> > >> TESTING: checkCxxCompiler from > >> config.setCompilers(config/BuildSystem/config/setCompilers.py:814) > >> ******************************************************************************* > >> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log > >> for details): > >> ------------------------------------------------------------------------------- > >> C++ compiler you provided with -with-cxx=mpicxx does not work. > >> Cannot compile/link Cxx with mpicxx. > >> > >> I'm attaching the *.log file. > >> > >> Please advise, > >> > >> Michael. > >> > >> > From balay at mcs.anl.gov Fri Dec 6 08:04:14 2019 From: balay at mcs.anl.gov (Balay, Satish) Date: Fri, 6 Dec 2019 14:04:14 +0000 Subject: [petsc-users] petsc under cygwin In-Reply-To: References: <91825cc3-ee60-ab37-a577-56e02ddfe7be@purdue.edu> <6746E426-D354-44F4-BC50-FD2C023DBD6E@anl.gov> <13a0e1d6-1e81-fd01-f4d8-2c356f49c280@purdue.edu> Message-ID: Its likely my cygwin is slightly old [as its not updated in the past few months]. balay at ps5 ~/petsc $ cygcheck.exe -f /usr/bin/mpicxx openmpi-3.1.3-1 Satish On Fri, 6 Dec 2019, Balay, Satish wrote: > Are you sure this is cygwin from OpenMPI? I don't see it refer to -lmpi_cxx > > balay at ps5 ~/petsc > $ which mpicxx > /usr/bin/mpicxx > > balay at ps5 ~/petsc > $ mpicxx -show > g++ -L/usr/lib -lmpi -lopen-rte -lopen-pal -lm -lgdi32 -lz > > Here is what I get with cygwin/openmpi,lapack,blas > > Satish > > ------- > > balay at ps5 ~/petsc > $ ./configure --with-scalar-type=real --with-x=0 --with-hdf5 --download-hdf5=1 --with-single-library=1 --with-shared-libraries=0 --with-log=0 --with-clanguage=C++ --with-cxx-d > ialect=C++11 --CXXFLAGS="-fopenmp -fPIC" --CFLAGS="-fopenmp -fPIC" --with-fortran=0 --FFLAGS="-fopenmp -fPIC" --with-64-bit-indices=0 --with-debugging=0 --with-cc=mpicc --with > -fc=mpif77 --with-cxx=mpicxx COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 --with-fortran-kernels=0 > =============================================================================== > Configuring PETSc to compile on your system > =============================================================================== > =============================================================================== WARNING -with-clanguage=C++ is a developer feature and is *not* required for regular usage of PETSc either from C or C++ =============================================================================== =============================================================================== Trying to download git://https://bitbucket.org/petsc/pkg-sowing.git for SOWING =============================================================================== =============================================================================== Running configure on SOWING; this may take several minutes =============================================================================== =============================================================================== Running make on SOWING; this may take several minutes =============================================================================== =============================================================================== Running make install on SOWING; this may take several minutes =============================================================================== =============================================================================== Trying to download https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5.tar.gz for HDF5 =============================================================================== =============================================================================== Running configure on HDF5; this may take several minutes =============================================================================== =============================================================================== Running make on HDF5; this may take several minutes =============================================================================== =============================================================================== Running make install on HDF5; this may take several minutes =============================================================================== Compilers: > C Compiler: mpicc -fopenmp -fPIC -O3 > Version: gcc (GCC) 7.4.0 > C++ Compiler: mpicxx -fopenmp -fPIC -O3 > Version: g++ (GCC) 7.4.0 > Fortran Compiler: mpif77 -fopenmp -fPIC -O3 > Version: GNU Fortran (GCC) 7.4.0 > Linkers: > Static linker: /usr/bin/ar cr > Dynamic linker: /usr/bin/ar > Libraries linked against: -lgdi32 -luser32 -ladvapi32 -lkernel32 -lquadmath -lstdc++ -ldl > make: > Version: 4.2 > /usr/bin/make > BlasLapack: > Library: -llapack -lblas > uses 4 byte integers > MPI: > Version: 3 > Mpiexec: mpiexec --oversubscribe > OMPI_VERSION: 3.1.3 > pthread: > hdf5: > Version: 1.10.5 > Includes: -I/home/balay/petsc/arch-mswin-cxx-opt/include > Library: -Wl,-rpath,/home/balay/petsc/arch-mswin-cxx-opt/lib -L/home/balay/petsc/arch-mswin-cxx-opt/lib -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 > cmake: > Version: 3.14.5 > /usr/bin/cmake > sowing: > Version: 1.1.25 > /home/balay/petsc/arch-mswin-cxx-opt/bin/bfort > Language used to compile PETSc: Cxx > PETSc: > PETSC_ARCH: arch-mswin-cxx-opt > PETSC_DIR: /home/balay/petsc > Scalar type: real > Precision: double > Support for __float128 > Integer size: 4 bytes > shared libraries: disabled > Memory alignment from malloc(): 16 bytes > xxx=========================================================================xxx > Configure stage complete. Now build PETSc libraries with: > make PETSC_DIR=/home/balay/petsc PETSC_ARCH=arch-mswin-cxx-opt all > xxx=========================================================================xxx > > balay at ps5 ~/petsc > $ > > > > > > > On Fri, 6 Dec 2019, Povolotskyi, Mykhailo wrote: > > > I checked: > > > > I cannot build C++ programs with MPI, but I can build and run C programs > > with MPI. > > > > I have -with-log=0 because there is an overhead if many small objects > > are created, which is my case. > > > > As for the fortran, I will remove? --with-fortran=0 > > > > On 12/5/2019 11:53 PM, Smith, Barry F. wrote: > > > Can you actually build and run C++ programs with the MPI? > > > > > > Executing: mpicxx -o /tmp/petsc-Llvze6/config.setCompilers/conftest.exe -fopenmp -fPIC /tmp/petsc-Llvze6/config.setCompilers/conftest.o > > > Possible ERROR while running linker: exit code 1 > > > stderr: > > > /usr/lib/gcc/x86_64-pc-cygwin/7.4.0/../../../../x86_64-pc-cygwin/bin/ld: cannot find -lmpi_cxx > > > collect2: error: ld returned 1 exit status > > > Error testing C++ compiler: Cannot compile/link Cxx with mpicxx. > > > MPI installation mpicxx is likely incorrect. > > > Use --with-mpi-dir to indicate an alternate MPI. > > > > > > Also you have --with-fortran=0 > > > > > > but --download-fblaslapack and FOPTFLAGS=-O3 > > > > > > and why do you have --with-log=0 it costs no overhead if you do not use it and is always useful for tracking performance. > > > > > > Barry > > > > > > > > >> On Dec 5, 2019, at 9:19 PM, Povolotskyi, Mykhailo wrote: > > >> > > >> Dear Petsc support team, > > >> > > >> for some reasons I have to build petsc under Windows. > > >> > > >> I have installed Cygwin with GNU compilers and OpenMPI. > > >> > > >> Unfortunately, the configuration fails with the following message: > > >> > > >> TESTING: checkCxxCompiler from > > >> config.setCompilers(config/BuildSystem/config/setCompilers.py:814) > > >> ******************************************************************************* > > >> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log > > >> for details): > > >> ------------------------------------------------------------------------------- > > >> C++ compiler you provided with -with-cxx=mpicxx does not work. > > >> Cannot compile/link Cxx with mpicxx. > > >> > > >> I'm attaching the *.log file. > > >> > > >> Please advise, > > >> > > >> Michael. > > >> > > >> > > From mpovolot at purdue.edu Fri Dec 6 09:21:24 2019 From: mpovolot at purdue.edu (Povolotskyi, Mykhailo) Date: Fri, 6 Dec 2019 15:21:24 +0000 Subject: [petsc-users] petsc under cygwin In-Reply-To: References: <91825cc3-ee60-ab37-a577-56e02ddfe7be@purdue.edu> <6746E426-D354-44F4-BC50-FD2C023DBD6E@anl.gov> <13a0e1d6-1e81-fd01-f4d8-2c356f49c280@purdue.edu> Message-ID: <7ee2bd95-207f-4290-57f0-a38e655e547a@purdue.edu> Hi Satish, I have installed cygwin yesterday, and this is the output I have: cygcheck.exe -f /usr/bin/mpicxx openmpi-3.1.3-1 mpicxx -show g++ -fexceptions -L/usr/lib -lmpi_cxx -lmpi -lopen-rte -lopen-pal -lm -lgdi32 As you can see, my installation for some reasons requires libmpi_cxx. Do you have an idea how can this be solved? Michael. On 12/6/2019 9:04 AM, Balay, Satish wrote: > Its likely my cygwin is slightly old [as its not updated in the past few months]. > > balay at ps5 ~/petsc > $ cygcheck.exe -f /usr/bin/mpicxx > openmpi-3.1.3-1 > > Satish > > On Fri, 6 Dec 2019, Balay, Satish wrote: > >> Are you sure this is cygwin from OpenMPI? I don't see it refer to -lmpi_cxx >> >> balay at ps5 ~/petsc >> $ which mpicxx >> /usr/bin/mpicxx >> >> balay at ps5 ~/petsc >> $ mpicxx -show >> g++ -L/usr/lib -lmpi -lopen-rte -lopen-pal -lm -lgdi32 -lz >> >> Here is what I get with cygwin/openmpi,lapack,blas >> >> Satish >> >> ------- >> >> balay at ps5 ~/petsc >> $ ./configure --with-scalar-type=real --with-x=0 --with-hdf5 --download-hdf5=1 --with-single-library=1 --with-shared-libraries=0 --with-log=0 --with-clanguage=C++ --with-cxx-d >> ialect=C++11 --CXXFLAGS="-fopenmp -fPIC" --CFLAGS="-fopenmp -fPIC" --with-fortran=0 --FFLAGS="-fopenmp -fPIC" --with-64-bit-indices=0 --with-debugging=0 --with-cc=mpicc --with >> -fc=mpif77 --with-cxx=mpicxx COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 --with-fortran-kernels=0 >> =============================================================================== >> Configuring PETSc to compile on your system >> =============================================================================== >> =============================================================================== WARNING -with-clanguage=C++ is a developer feature and is *not* required for regular usage of PETSc either from C or C++ =============================================================================== =============================================================================== Trying to download git://https://bitbucket.org/petsc/pkg-sowing.git for SOWING =============================================================================== =============================================================================== Running configure on SOWING; this may take several minutes =============================================================================== =============================================================================== Running make on SOWING; this may take several minutes =============================================================================== =============================================================================== Running make install on SOWING; this may take several minutes =============================================================================== =============================================================================== Trying to download https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5.tar.gz for HDF5 =============================================================================== =============================================================================== Running configure on HDF5; this may take several minutes =============================================================================== =============================================================================== Running make on HDF5; this may take several minutes =============================================================================== =============================================================================== Running make install on HDF5; this may take several minutes =============================================================================== Compilers: >> C Compiler: mpicc -fopenmp -fPIC -O3 >> Version: gcc (GCC) 7.4.0 >> C++ Compiler: mpicxx -fopenmp -fPIC -O3 >> Version: g++ (GCC) 7.4.0 >> Fortran Compiler: mpif77 -fopenmp -fPIC -O3 >> Version: GNU Fortran (GCC) 7.4.0 >> Linkers: >> Static linker: /usr/bin/ar cr >> Dynamic linker: /usr/bin/ar >> Libraries linked against: -lgdi32 -luser32 -ladvapi32 -lkernel32 -lquadmath -lstdc++ -ldl >> make: >> Version: 4.2 >> /usr/bin/make >> BlasLapack: >> Library: -llapack -lblas >> uses 4 byte integers >> MPI: >> Version: 3 >> Mpiexec: mpiexec --oversubscribe >> OMPI_VERSION: 3.1.3 >> pthread: >> hdf5: >> Version: 1.10.5 >> Includes: -I/home/balay/petsc/arch-mswin-cxx-opt/include >> Library: -Wl,-rpath,/home/balay/petsc/arch-mswin-cxx-opt/lib -L/home/balay/petsc/arch-mswin-cxx-opt/lib -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 >> cmake: >> Version: 3.14.5 >> /usr/bin/cmake >> sowing: >> Version: 1.1.25 >> /home/balay/petsc/arch-mswin-cxx-opt/bin/bfort >> Language used to compile PETSc: Cxx >> PETSc: >> PETSC_ARCH: arch-mswin-cxx-opt >> PETSC_DIR: /home/balay/petsc >> Scalar type: real >> Precision: double >> Support for __float128 >> Integer size: 4 bytes >> shared libraries: disabled >> Memory alignment from malloc(): 16 bytes >> xxx=========================================================================xxx >> Configure stage complete. Now build PETSc libraries with: >> make PETSC_DIR=/home/balay/petsc PETSC_ARCH=arch-mswin-cxx-opt all >> xxx=========================================================================xxx >> >> balay at ps5 ~/petsc >> $ >> >> >> >> >> >> >> On Fri, 6 Dec 2019, Povolotskyi, Mykhailo wrote: >> >>> I checked: >>> >>> I cannot build C++ programs with MPI, but I can build and run C programs >>> with MPI. >>> >>> I have -with-log=0 because there is an overhead if many small objects >>> are created, which is my case. >>> >>> As for the fortran, I will remove? --with-fortran=0 >>> >>> On 12/5/2019 11:53 PM, Smith, Barry F. wrote: >>>> Can you actually build and run C++ programs with the MPI? >>>> >>>> Executing: mpicxx -o /tmp/petsc-Llvze6/config.setCompilers/conftest.exe -fopenmp -fPIC /tmp/petsc-Llvze6/config.setCompilers/conftest.o >>>> Possible ERROR while running linker: exit code 1 >>>> stderr: >>>> /usr/lib/gcc/x86_64-pc-cygwin/7.4.0/../../../../x86_64-pc-cygwin/bin/ld: cannot find -lmpi_cxx >>>> collect2: error: ld returned 1 exit status >>>> Error testing C++ compiler: Cannot compile/link Cxx with mpicxx. >>>> MPI installation mpicxx is likely incorrect. >>>> Use --with-mpi-dir to indicate an alternate MPI. >>>> >>>> Also you have --with-fortran=0 >>>> >>>> but --download-fblaslapack and FOPTFLAGS=-O3 >>>> >>>> and why do you have --with-log=0 it costs no overhead if you do not use it and is always useful for tracking performance. >>>> >>>> Barry >>>> >>>> >>>>> On Dec 5, 2019, at 9:19 PM, Povolotskyi, Mykhailo wrote: >>>>> >>>>> Dear Petsc support team, >>>>> >>>>> for some reasons I have to build petsc under Windows. >>>>> >>>>> I have installed Cygwin with GNU compilers and OpenMPI. >>>>> >>>>> Unfortunately, the configuration fails with the following message: >>>>> >>>>> TESTING: checkCxxCompiler from >>>>> config.setCompilers(config/BuildSystem/config/setCompilers.py:814) >>>>> ******************************************************************************* >>>>> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log >>>>> for details): >>>>> ------------------------------------------------------------------------------- >>>>> C++ compiler you provided with -with-cxx=mpicxx does not work. >>>>> Cannot compile/link Cxx with mpicxx. >>>>> >>>>> I'm attaching the *.log file. >>>>> >>>>> Please advise, >>>>> >>>>> Michael. >>>>> >>>>> From mpovolot at purdue.edu Fri Dec 6 09:28:14 2019 From: mpovolot at purdue.edu (Povolotskyi, Mykhailo) Date: Fri, 6 Dec 2019 15:28:14 +0000 Subject: [petsc-users] petsc under cygwin In-Reply-To: References: <91825cc3-ee60-ab37-a577-56e02ddfe7be@purdue.edu> <6746E426-D354-44F4-BC50-FD2C023DBD6E@anl.gov> <13a0e1d6-1e81-fd01-f4d8-2c356f49c280@purdue.edu> Message-ID: Hi Satish, I looked into cygwin mail list https://sourceware.org/ml/cygwin/2018-08/msg00349.html It seem that they have removed something, so probably -lmpi_cxx is not needed, but it keeps looking for it. Michael. On 12/6/2019 9:04 AM, Balay, Satish wrote: > Its likely my cygwin is slightly old [as its not updated in the past few months]. > > balay at ps5 ~/petsc > $ cygcheck.exe -f /usr/bin/mpicxx > openmpi-3.1.3-1 > > Satish > > On Fri, 6 Dec 2019, Balay, Satish wrote: > >> Are you sure this is cygwin from OpenMPI? I don't see it refer to -lmpi_cxx >> >> balay at ps5 ~/petsc >> $ which mpicxx >> /usr/bin/mpicxx >> >> balay at ps5 ~/petsc >> $ mpicxx -show >> g++ -L/usr/lib -lmpi -lopen-rte -lopen-pal -lm -lgdi32 -lz >> >> Here is what I get with cygwin/openmpi,lapack,blas >> >> Satish >> >> ------- >> >> balay at ps5 ~/petsc >> $ ./configure --with-scalar-type=real --with-x=0 --with-hdf5 --download-hdf5=1 --with-single-library=1 --with-shared-libraries=0 --with-log=0 --with-clanguage=C++ --with-cxx-d >> ialect=C++11 --CXXFLAGS="-fopenmp -fPIC" --CFLAGS="-fopenmp -fPIC" --with-fortran=0 --FFLAGS="-fopenmp -fPIC" --with-64-bit-indices=0 --with-debugging=0 --with-cc=mpicc --with >> -fc=mpif77 --with-cxx=mpicxx COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 --with-fortran-kernels=0 >> =============================================================================== >> Configuring PETSc to compile on your system >> =============================================================================== >> =============================================================================== WARNING -with-clanguage=C++ is a developer feature and is *not* required for regular usage of PETSc either from C or C++ =============================================================================== =============================================================================== Trying to download git://https://bitbucket.org/petsc/pkg-sowing.git for SOWING =============================================================================== =============================================================================== Running configure on SOWING; this may take several minutes =============================================================================== =============================================================================== Running make on SOWING; this may take several minutes =============================================================================== =============================================================================== Running make install on SOWING; this may take several minutes =============================================================================== =============================================================================== Trying to download https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5.tar.gz for HDF5 =============================================================================== =============================================================================== Running configure on HDF5; this may take several minutes =============================================================================== =============================================================================== Running make on HDF5; this may take several minutes =============================================================================== =============================================================================== Running make install on HDF5; this may take several minutes =============================================================================== Compilers: >> C Compiler: mpicc -fopenmp -fPIC -O3 >> Version: gcc (GCC) 7.4.0 >> C++ Compiler: mpicxx -fopenmp -fPIC -O3 >> Version: g++ (GCC) 7.4.0 >> Fortran Compiler: mpif77 -fopenmp -fPIC -O3 >> Version: GNU Fortran (GCC) 7.4.0 >> Linkers: >> Static linker: /usr/bin/ar cr >> Dynamic linker: /usr/bin/ar >> Libraries linked against: -lgdi32 -luser32 -ladvapi32 -lkernel32 -lquadmath -lstdc++ -ldl >> make: >> Version: 4.2 >> /usr/bin/make >> BlasLapack: >> Library: -llapack -lblas >> uses 4 byte integers >> MPI: >> Version: 3 >> Mpiexec: mpiexec --oversubscribe >> OMPI_VERSION: 3.1.3 >> pthread: >> hdf5: >> Version: 1.10.5 >> Includes: -I/home/balay/petsc/arch-mswin-cxx-opt/include >> Library: -Wl,-rpath,/home/balay/petsc/arch-mswin-cxx-opt/lib -L/home/balay/petsc/arch-mswin-cxx-opt/lib -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 >> cmake: >> Version: 3.14.5 >> /usr/bin/cmake >> sowing: >> Version: 1.1.25 >> /home/balay/petsc/arch-mswin-cxx-opt/bin/bfort >> Language used to compile PETSc: Cxx >> PETSc: >> PETSC_ARCH: arch-mswin-cxx-opt >> PETSC_DIR: /home/balay/petsc >> Scalar type: real >> Precision: double >> Support for __float128 >> Integer size: 4 bytes >> shared libraries: disabled >> Memory alignment from malloc(): 16 bytes >> xxx=========================================================================xxx >> Configure stage complete. Now build PETSc libraries with: >> make PETSC_DIR=/home/balay/petsc PETSC_ARCH=arch-mswin-cxx-opt all >> xxx=========================================================================xxx >> >> balay at ps5 ~/petsc >> $ >> >> >> >> >> >> >> On Fri, 6 Dec 2019, Povolotskyi, Mykhailo wrote: >> >>> I checked: >>> >>> I cannot build C++ programs with MPI, but I can build and run C programs >>> with MPI. >>> >>> I have -with-log=0 because there is an overhead if many small objects >>> are created, which is my case. >>> >>> As for the fortran, I will remove? --with-fortran=0 >>> >>> On 12/5/2019 11:53 PM, Smith, Barry F. wrote: >>>> Can you actually build and run C++ programs with the MPI? >>>> >>>> Executing: mpicxx -o /tmp/petsc-Llvze6/config.setCompilers/conftest.exe -fopenmp -fPIC /tmp/petsc-Llvze6/config.setCompilers/conftest.o >>>> Possible ERROR while running linker: exit code 1 >>>> stderr: >>>> /usr/lib/gcc/x86_64-pc-cygwin/7.4.0/../../../../x86_64-pc-cygwin/bin/ld: cannot find -lmpi_cxx >>>> collect2: error: ld returned 1 exit status >>>> Error testing C++ compiler: Cannot compile/link Cxx with mpicxx. >>>> MPI installation mpicxx is likely incorrect. >>>> Use --with-mpi-dir to indicate an alternate MPI. >>>> >>>> Also you have --with-fortran=0 >>>> >>>> but --download-fblaslapack and FOPTFLAGS=-O3 >>>> >>>> and why do you have --with-log=0 it costs no overhead if you do not use it and is always useful for tracking performance. >>>> >>>> Barry >>>> >>>> >>>>> On Dec 5, 2019, at 9:19 PM, Povolotskyi, Mykhailo wrote: >>>>> >>>>> Dear Petsc support team, >>>>> >>>>> for some reasons I have to build petsc under Windows. >>>>> >>>>> I have installed Cygwin with GNU compilers and OpenMPI. >>>>> >>>>> Unfortunately, the configuration fails with the following message: >>>>> >>>>> TESTING: checkCxxCompiler from >>>>> config.setCompilers(config/BuildSystem/config/setCompilers.py:814) >>>>> ******************************************************************************* >>>>> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log >>>>> for details): >>>>> ------------------------------------------------------------------------------- >>>>> C++ compiler you provided with -with-cxx=mpicxx does not work. >>>>> Cannot compile/link Cxx with mpicxx. >>>>> >>>>> I'm attaching the *.log file. >>>>> >>>>> Please advise, >>>>> >>>>> Michael. >>>>> >>>>> From balay at mcs.anl.gov Fri Dec 6 09:32:24 2019 From: balay at mcs.anl.gov (Balay, Satish) Date: Fri, 6 Dec 2019 15:32:24 +0000 Subject: [petsc-users] petsc under cygwin In-Reply-To: <7ee2bd95-207f-4290-57f0-a38e655e547a@purdue.edu> References: <91825cc3-ee60-ab37-a577-56e02ddfe7be@purdue.edu> <6746E426-D354-44F4-BC50-FD2C023DBD6E@anl.gov> <13a0e1d6-1e81-fd01-f4d8-2c356f49c280@purdue.edu> <7ee2bd95-207f-4290-57f0-a38e655e547a@purdue.edu> Message-ID: Are you sure /usr/bin/mpicxx is the one in your PATH? which mpicxx I don't have an explanation for this behavior. Alternative suggestion is --download-mpich Satish On Fri, 6 Dec 2019, Povolotskyi, Mykhailo wrote: > Hi Satish, > > I have installed cygwin yesterday, and this is the output I have: > > cygcheck.exe -f /usr/bin/mpicxx > openmpi-3.1.3-1 > > mpicxx -show > g++ -fexceptions -L/usr/lib -lmpi_cxx -lmpi -lopen-rte -lopen-pal -lm > -lgdi32 > > As you can see, my installation for some reasons requires libmpi_cxx. > > Do you have an idea how can this be solved? > > Michael. > > On 12/6/2019 9:04 AM, Balay, Satish wrote: > > Its likely my cygwin is slightly old [as its not updated in the past few months]. > > > > balay at ps5 ~/petsc > > $ cygcheck.exe -f /usr/bin/mpicxx > > openmpi-3.1.3-1 > > > > Satish > > > > On Fri, 6 Dec 2019, Balay, Satish wrote: > > > >> Are you sure this is cygwin from OpenMPI? I don't see it refer to -lmpi_cxx > >> > >> balay at ps5 ~/petsc > >> $ which mpicxx > >> /usr/bin/mpicxx > >> > >> balay at ps5 ~/petsc > >> $ mpicxx -show > >> g++ -L/usr/lib -lmpi -lopen-rte -lopen-pal -lm -lgdi32 -lz > >> > >> Here is what I get with cygwin/openmpi,lapack,blas > >> > >> Satish > >> > >> ------- > >> > >> balay at ps5 ~/petsc > >> $ ./configure --with-scalar-type=real --with-x=0 --with-hdf5 --download-hdf5=1 --with-single-library=1 --with-shared-libraries=0 --with-log=0 --with-clanguage=C++ --with-cxx-d > >> ialect=C++11 --CXXFLAGS="-fopenmp -fPIC" --CFLAGS="-fopenmp -fPIC" --with-fortran=0 --FFLAGS="-fopenmp -fPIC" --with-64-bit-indices=0 --with-debugging=0 --with-cc=mpicc --with > >> -fc=mpif77 --with-cxx=mpicxx COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 --with-fortran-kernels=0 > >> =============================================================================== > >> Configuring PETSc to compile on your system > >> =============================================================================== > >> =============================================================================== WARNING -with-clanguage=C++ is a developer feature and is *not* required for regular usage of PETSc either from C or C++ =============================================================================== =============================================================================== Trying to download git://https://bitbucket.org/petsc/pkg-sowing.git for SOWING =============================================================================== =============================================================================== Running configure on SOWING; this may take several minutes =============================================================================== =============================================================================== Running make on SOWING; this may take several minutes =============================================================================== =============================================================================== Running make install on SOWING; this may take several minutes =============================================================================== =============================================================================== Trying to download https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5.tar.gz for HDF5 =============================================================================== =============================================================================== Running configure on HDF5; this may take several minutes =============================================================================== =============================================================================== Running make on HDF5; this may take several minutes =============================================================================== =============================================================================== Running make install on HDF5; this may take several minutes =============================================================================== Compilers: > >> C Compiler: mpicc -fopenmp -fPIC -O3 > >> Version: gcc (GCC) 7.4.0 > >> C++ Compiler: mpicxx -fopenmp -fPIC -O3 > >> Version: g++ (GCC) 7.4.0 > >> Fortran Compiler: mpif77 -fopenmp -fPIC -O3 > >> Version: GNU Fortran (GCC) 7.4.0 > >> Linkers: > >> Static linker: /usr/bin/ar cr > >> Dynamic linker: /usr/bin/ar > >> Libraries linked against: -lgdi32 -luser32 -ladvapi32 -lkernel32 -lquadmath -lstdc++ -ldl > >> make: > >> Version: 4.2 > >> /usr/bin/make > >> BlasLapack: > >> Library: -llapack -lblas > >> uses 4 byte integers > >> MPI: > >> Version: 3 > >> Mpiexec: mpiexec --oversubscribe > >> OMPI_VERSION: 3.1.3 > >> pthread: > >> hdf5: > >> Version: 1.10.5 > >> Includes: -I/home/balay/petsc/arch-mswin-cxx-opt/include > >> Library: -Wl,-rpath,/home/balay/petsc/arch-mswin-cxx-opt/lib -L/home/balay/petsc/arch-mswin-cxx-opt/lib -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 > >> cmake: > >> Version: 3.14.5 > >> /usr/bin/cmake > >> sowing: > >> Version: 1.1.25 > >> /home/balay/petsc/arch-mswin-cxx-opt/bin/bfort > >> Language used to compile PETSc: Cxx > >> PETSc: > >> PETSC_ARCH: arch-mswin-cxx-opt > >> PETSC_DIR: /home/balay/petsc > >> Scalar type: real > >> Precision: double > >> Support for __float128 > >> Integer size: 4 bytes > >> shared libraries: disabled > >> Memory alignment from malloc(): 16 bytes > >> xxx=========================================================================xxx > >> Configure stage complete. Now build PETSc libraries with: > >> make PETSC_DIR=/home/balay/petsc PETSC_ARCH=arch-mswin-cxx-opt all > >> xxx=========================================================================xxx > >> > >> balay at ps5 ~/petsc > >> $ > >> > >> > >> > >> > >> > >> > >> On Fri, 6 Dec 2019, Povolotskyi, Mykhailo wrote: > >> > >>> I checked: > >>> > >>> I cannot build C++ programs with MPI, but I can build and run C programs > >>> with MPI. > >>> > >>> I have -with-log=0 because there is an overhead if many small objects > >>> are created, which is my case. > >>> > >>> As for the fortran, I will remove? --with-fortran=0 > >>> > >>> On 12/5/2019 11:53 PM, Smith, Barry F. wrote: > >>>> Can you actually build and run C++ programs with the MPI? > >>>> > >>>> Executing: mpicxx -o /tmp/petsc-Llvze6/config.setCompilers/conftest.exe -fopenmp -fPIC /tmp/petsc-Llvze6/config.setCompilers/conftest.o > >>>> Possible ERROR while running linker: exit code 1 > >>>> stderr: > >>>> /usr/lib/gcc/x86_64-pc-cygwin/7.4.0/../../../../x86_64-pc-cygwin/bin/ld: cannot find -lmpi_cxx > >>>> collect2: error: ld returned 1 exit status > >>>> Error testing C++ compiler: Cannot compile/link Cxx with mpicxx. > >>>> MPI installation mpicxx is likely incorrect. > >>>> Use --with-mpi-dir to indicate an alternate MPI. > >>>> > >>>> Also you have --with-fortran=0 > >>>> > >>>> but --download-fblaslapack and FOPTFLAGS=-O3 > >>>> > >>>> and why do you have --with-log=0 it costs no overhead if you do not use it and is always useful for tracking performance. > >>>> > >>>> Barry > >>>> > >>>> > >>>>> On Dec 5, 2019, at 9:19 PM, Povolotskyi, Mykhailo wrote: > >>>>> > >>>>> Dear Petsc support team, > >>>>> > >>>>> for some reasons I have to build petsc under Windows. > >>>>> > >>>>> I have installed Cygwin with GNU compilers and OpenMPI. > >>>>> > >>>>> Unfortunately, the configuration fails with the following message: > >>>>> > >>>>> TESTING: checkCxxCompiler from > >>>>> config.setCompilers(config/BuildSystem/config/setCompilers.py:814) > >>>>> ******************************************************************************* > >>>>> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log > >>>>> for details): > >>>>> ------------------------------------------------------------------------------- > >>>>> C++ compiler you provided with -with-cxx=mpicxx does not work. > >>>>> Cannot compile/link Cxx with mpicxx. > >>>>> > >>>>> I'm attaching the *.log file. > >>>>> > >>>>> Please advise, > >>>>> > >>>>> Michael. > >>>>> > >>>>> > From yjwu16 at gmail.com Fri Dec 6 09:43:10 2019 From: yjwu16 at gmail.com (Yingjie Wu) Date: Fri, 6 Dec 2019 23:43:10 +0800 Subject: [petsc-users] CMake error in PETSc In-Reply-To: <87zhg6j1gk.fsf@jedbrown.org> References: <875ziwkszv.fsf@jedbrown.org> <87zhg8jctx.fsf@jedbrown.org> <87r21jjqr8.fsf@jedbrown.org> <87zhg6j1gk.fsf@jedbrown.org> Message-ID: Hi, Thank you for your email. The error in the previous program was indeed due to the missing "SNESSetFromOptions". I use the /snes/example/tutorial/ex1.cpp as test case. However, I found that some of the statements in the program were not compiled and deleted the statements containing "MPI_Comm_size", but I don't know how to solve this problem. lerui at yu1994-ThinkPad-W520:~/tem2/build2$ cmake .. -- The C compiler identification is GNU 5.4.0 -- The CXX compiler identification is GNU 5.4.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") -- Checking for one of the modules 'PETSc' pkg include dirs: /home/lerui/petsc-3.12.2/arch-linux2-c-debug/include;/home/lerui/petsc-3.12.2/include pkg include libs: petsc pkg ldflags: -L/home/lerui/petsc-3.12.2/arch-linux2-c-debug/lib;-lpetsc -- Configuring done -- Generating done -- Build files have been written to: /home/lerui/tem2/build2 lerui at yu1994-ThinkPad-W520:~/tem2/build2$ make Scanning dependencies of target main [ 50%] Building CXX object CMakeFiles/main.dir/ex1.cpp.o [100%] Linking CXX executable main /usr/bin/ld: CMakeFiles/main.dir/ex1.cpp.o: undefined reference to symbol 'MPI_Comm_size' /home/lerui/petsc-3.12.2/arch-linux2-c-debug/lib/libmpi.so.12: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status CMakeFiles/main.dir/build.make:94: recipe for target 'main' failed make[2]: *** [main] Error 1 CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/main.dir/all' failed make[1]: *** [CMakeFiles/main.dir/all] Error 2 Makefile:83: recipe for target 'all' failed make: *** [all] Error 2 Thanks, Yingjie Jed Brown ?2019?12?6??? ??10:54??? > Yingjie Wu writes: > > > I'm so sorry that I've ignored your previous advices. > > > > I added a global variable that seems works: > > > > > > export > > > LD_LIBRARY_PATH=/home/lerui/petcs-3.12.2/arch-linux2-c-debug/lib:$LD_LIBRARY_PATH > > > > > > How should I make petsc in a standard position?This eliminates the need > to > > set global variables. > > You can configure PETSc with --prefix=/your/standard/path, then make > install. > > > It seems that some of the options before running fit become unavailable: > > > > > > mpiexec -n 1 ./example01cmke -snes_view > > > > > > Options-snes _ view are not used and how should I solve this problem? > > I don't have your ex1.cpp, but presumably you didn't SNESSetFromOptions? > -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Fri Dec 6 09:46:21 2019 From: knepley at gmail.com (Matthew Knepley) Date: Fri, 6 Dec 2019 10:46:21 -0500 Subject: [petsc-users] CMake error in PETSc In-Reply-To: References: <875ziwkszv.fsf@jedbrown.org> <87zhg8jctx.fsf@jedbrown.org> <87r21jjqr8.fsf@jedbrown.org> <87zhg6j1gk.fsf@jedbrown.org> Message-ID: It sounds like your C++ compiler is name mangling the symbol, but the library has no mangling. Why are you using C++. Thanks, Matt On Fri, Dec 6, 2019 at 10:44 AM Yingjie Wu wrote: > Hi, > Thank you for your email. > > The error in the previous program was indeed due to the missing > "SNESSetFromOptions". > I use the /snes/example/tutorial/ex1.cpp as test case. However, I found > that some of the statements in the program were not compiled and deleted > the statements containing "MPI_Comm_size", but I don't know how to solve > this problem. > > lerui at yu1994-ThinkPad-W520:~/tem2/build2$ cmake .. > -- The C compiler identification is GNU 5.4.0 > -- The CXX compiler identification is GNU 5.4.0 > -- Check for working C compiler: /usr/bin/cc > -- Check for working C compiler: /usr/bin/cc -- works > -- Detecting C compiler ABI info > -- Detecting C compiler ABI info - done > -- Detecting C compile features > -- Detecting C compile features - done > -- Check for working CXX compiler: /usr/bin/c++ > -- Check for working CXX compiler: /usr/bin/c++ -- works > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > -- Detecting CXX compile features > -- Detecting CXX compile features - done > -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") > -- Checking for one of the modules 'PETSc' > pkg include dirs: > /home/lerui/petsc-3.12.2/arch-linux2-c-debug/include;/home/lerui/petsc-3.12.2/include > pkg include libs: petsc > pkg ldflags: -L/home/lerui/petsc-3.12.2/arch-linux2-c-debug/lib;-lpetsc > -- Configuring done > -- Generating done > -- Build files have been written to: /home/lerui/tem2/build2 > lerui at yu1994-ThinkPad-W520:~/tem2/build2$ make > Scanning dependencies of target main > [ 50%] Building CXX object CMakeFiles/main.dir/ex1.cpp.o > [100%] Linking CXX executable main > /usr/bin/ld: CMakeFiles/main.dir/ex1.cpp.o: undefined reference to symbol > 'MPI_Comm_size' > /home/lerui/petsc-3.12.2/arch-linux2-c-debug/lib/libmpi.so.12: error > adding symbols: DSO missing from command line > collect2: error: ld returned 1 exit status > CMakeFiles/main.dir/build.make:94: recipe for target 'main' failed > make[2]: *** [main] Error 1 > CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/main.dir/all' failed > make[1]: *** [CMakeFiles/main.dir/all] Error 2 > Makefile:83: recipe for target 'all' failed > make: *** [all] Error 2 > > Thanks, > Yingjie > > Jed Brown ?2019?12?6??? ??10:54??? > >> Yingjie Wu writes: >> >> > I'm so sorry that I've ignored your previous advices. >> > >> > I added a global variable that seems works: >> > >> > >> > export >> > >> LD_LIBRARY_PATH=/home/lerui/petcs-3.12.2/arch-linux2-c-debug/lib:$LD_LIBRARY_PATH >> > >> > >> > How should I make petsc in a standard position?This eliminates the need >> to >> > set global variables. >> >> You can configure PETSc with --prefix=/your/standard/path, then make >> install. >> >> > It seems that some of the options before running fit become unavailable: >> > >> > >> > mpiexec -n 1 ./example01cmke -snes_view >> > >> > >> > Options-snes _ view are not used and how should I solve this problem? >> >> I don't have your ex1.cpp, but presumably you didn't SNESSetFromOptions? >> > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Fri Dec 6 09:48:23 2019 From: balay at mcs.anl.gov (Balay, Satish) Date: Fri, 6 Dec 2019 15:48:23 +0000 Subject: [petsc-users] petsc under cygwin In-Reply-To: References: <91825cc3-ee60-ab37-a577-56e02ddfe7be@purdue.edu> <6746E426-D354-44F4-BC50-FD2C023DBD6E@anl.gov> <13a0e1d6-1e81-fd01-f4d8-2c356f49c280@purdue.edu> Message-ID: To be sure - I would rerun cygwin setup again [without any active running cygwin processes - i.e after a reboot] - to make sure all dependencies are installed correctly. Another thing to do is check if the install is broken cygcheck -c Here is the following packages I have: balay at ps5 ~ $ cygcheck -c |grep openmpi libopenmpi-devel 3.1.3-1 OK libopenmpi40 3.1.3-1 OK libopenmpifh40 3.1.3-1 OK libopenmpiusef08_40 3.1.3-1 OK libopenmpiusetkr40 3.1.3-1 OK openmpi 3.1.3-1 OK However its strange that 'mpicxx -show' is so different for you from what I have. g++ -fexceptions -L/usr/lib -lmpi_cxx -lmpi -lopen-rte -lopen-pal -lm -lgdi32 vs g++ -L/usr/lib -lmpi -lopen-rte -lopen-pal -lm -lgdi32 -lz Satish On Fri, 6 Dec 2019, Povolotskyi, Mykhailo wrote: > Hi Satish, > > I looked into cygwin mail list > > https://sourceware.org/ml/cygwin/2018-08/msg00349.html > > It seem that they have removed something, so probably -lmpi_cxx is not > needed, but it keeps looking for it. > > Michael. > > On 12/6/2019 9:04 AM, Balay, Satish wrote: > > Its likely my cygwin is slightly old [as its not updated in the past few months]. > > > > balay at ps5 ~/petsc > > $ cygcheck.exe -f /usr/bin/mpicxx > > openmpi-3.1.3-1 > > > > Satish > > > > On Fri, 6 Dec 2019, Balay, Satish wrote: > > > >> Are you sure this is cygwin from OpenMPI? I don't see it refer to -lmpi_cxx > >> > >> balay at ps5 ~/petsc > >> $ which mpicxx > >> /usr/bin/mpicxx > >> > >> balay at ps5 ~/petsc > >> $ mpicxx -show > >> g++ -L/usr/lib -lmpi -lopen-rte -lopen-pal -lm -lgdi32 -lz > >> > >> Here is what I get with cygwin/openmpi,lapack,blas > >> > >> Satish > >> > >> ------- > >> > >> balay at ps5 ~/petsc > >> $ ./configure --with-scalar-type=real --with-x=0 --with-hdf5 --download-hdf5=1 --with-single-library=1 --with-shared-libraries=0 --with-log=0 --with-clanguage=C++ --with-cxx-d > >> ialect=C++11 --CXXFLAGS="-fopenmp -fPIC" --CFLAGS="-fopenmp -fPIC" --with-fortran=0 --FFLAGS="-fopenmp -fPIC" --with-64-bit-indices=0 --with-debugging=0 --with-cc=mpicc --with > >> -fc=mpif77 --with-cxx=mpicxx COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 --with-fortran-kernels=0 > >> =============================================================================== > >> Configuring PETSc to compile on your system > >> =============================================================================== > >> =============================================================================== WARNING -with-clanguage=C++ is a developer feature and is *not* required for regular usage of PETSc either from C or C++ =============================================================================== =============================================================================== Trying to download git://https://bitbucket.org/petsc/pkg-sowing.git for SOWING =============================================================================== =============================================================================== Running configure on SOWING; this may take several minutes =============================================================================== =============================================================================== Running make on SOWING; this may take several minutes =============================================================================== =============================================================================== Running make install on SOWING; this may take several minutes =============================================================================== =============================================================================== Trying to download https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5.tar.gz for HDF5 =============================================================================== =============================================================================== Running configure on HDF5; this may take several minutes =============================================================================== =============================================================================== Running make on HDF5; this may take several minutes =============================================================================== =============================================================================== Running make install on HDF5; this may take several minutes =============================================================================== Compilers: > >> C Compiler: mpicc -fopenmp -fPIC -O3 > >> Version: gcc (GCC) 7.4.0 > >> C++ Compiler: mpicxx -fopenmp -fPIC -O3 > >> Version: g++ (GCC) 7.4.0 > >> Fortran Compiler: mpif77 -fopenmp -fPIC -O3 > >> Version: GNU Fortran (GCC) 7.4.0 > >> Linkers: > >> Static linker: /usr/bin/ar cr > >> Dynamic linker: /usr/bin/ar > >> Libraries linked against: -lgdi32 -luser32 -ladvapi32 -lkernel32 -lquadmath -lstdc++ -ldl > >> make: > >> Version: 4.2 > >> /usr/bin/make > >> BlasLapack: > >> Library: -llapack -lblas > >> uses 4 byte integers > >> MPI: > >> Version: 3 > >> Mpiexec: mpiexec --oversubscribe > >> OMPI_VERSION: 3.1.3 > >> pthread: > >> hdf5: > >> Version: 1.10.5 > >> Includes: -I/home/balay/petsc/arch-mswin-cxx-opt/include > >> Library: -Wl,-rpath,/home/balay/petsc/arch-mswin-cxx-opt/lib -L/home/balay/petsc/arch-mswin-cxx-opt/lib -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 > >> cmake: > >> Version: 3.14.5 > >> /usr/bin/cmake > >> sowing: > >> Version: 1.1.25 > >> /home/balay/petsc/arch-mswin-cxx-opt/bin/bfort > >> Language used to compile PETSc: Cxx > >> PETSc: > >> PETSC_ARCH: arch-mswin-cxx-opt > >> PETSC_DIR: /home/balay/petsc > >> Scalar type: real > >> Precision: double > >> Support for __float128 > >> Integer size: 4 bytes > >> shared libraries: disabled > >> Memory alignment from malloc(): 16 bytes > >> xxx=========================================================================xxx > >> Configure stage complete. Now build PETSc libraries with: > >> make PETSC_DIR=/home/balay/petsc PETSC_ARCH=arch-mswin-cxx-opt all > >> xxx=========================================================================xxx > >> > >> balay at ps5 ~/petsc > >> $ > >> > >> > >> > >> > >> > >> > >> On Fri, 6 Dec 2019, Povolotskyi, Mykhailo wrote: > >> > >>> I checked: > >>> > >>> I cannot build C++ programs with MPI, but I can build and run C programs > >>> with MPI. > >>> > >>> I have -with-log=0 because there is an overhead if many small objects > >>> are created, which is my case. > >>> > >>> As for the fortran, I will remove? --with-fortran=0 > >>> > >>> On 12/5/2019 11:53 PM, Smith, Barry F. wrote: > >>>> Can you actually build and run C++ programs with the MPI? > >>>> > >>>> Executing: mpicxx -o /tmp/petsc-Llvze6/config.setCompilers/conftest.exe -fopenmp -fPIC /tmp/petsc-Llvze6/config.setCompilers/conftest.o > >>>> Possible ERROR while running linker: exit code 1 > >>>> stderr: > >>>> /usr/lib/gcc/x86_64-pc-cygwin/7.4.0/../../../../x86_64-pc-cygwin/bin/ld: cannot find -lmpi_cxx > >>>> collect2: error: ld returned 1 exit status > >>>> Error testing C++ compiler: Cannot compile/link Cxx with mpicxx. > >>>> MPI installation mpicxx is likely incorrect. > >>>> Use --with-mpi-dir to indicate an alternate MPI. > >>>> > >>>> Also you have --with-fortran=0 > >>>> > >>>> but --download-fblaslapack and FOPTFLAGS=-O3 > >>>> > >>>> and why do you have --with-log=0 it costs no overhead if you do not use it and is always useful for tracking performance. > >>>> > >>>> Barry > >>>> > >>>> > >>>>> On Dec 5, 2019, at 9:19 PM, Povolotskyi, Mykhailo wrote: > >>>>> > >>>>> Dear Petsc support team, > >>>>> > >>>>> for some reasons I have to build petsc under Windows. > >>>>> > >>>>> I have installed Cygwin with GNU compilers and OpenMPI. > >>>>> > >>>>> Unfortunately, the configuration fails with the following message: > >>>>> > >>>>> TESTING: checkCxxCompiler from > >>>>> config.setCompilers(config/BuildSystem/config/setCompilers.py:814) > >>>>> ******************************************************************************* > >>>>> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log > >>>>> for details): > >>>>> ------------------------------------------------------------------------------- > >>>>> C++ compiler you provided with -with-cxx=mpicxx does not work. > >>>>> Cannot compile/link Cxx with mpicxx. > >>>>> > >>>>> I'm attaching the *.log file. > >>>>> > >>>>> Please advise, > >>>>> > >>>>> Michael. > >>>>> > >>>>> > From yjwu16 at gmail.com Sun Dec 8 22:06:29 2019 From: yjwu16 at gmail.com (Yingjie Wu) Date: Mon, 9 Dec 2019 12:06:29 +0800 Subject: [petsc-users] CMake error in PETSc In-Reply-To: References: <875ziwkszv.fsf@jedbrown.org> <87zhg8jctx.fsf@jedbrown.org> <87r21jjqr8.fsf@jedbrown.org> <87zhg6j1gk.fsf@jedbrown.org> Message-ID: Hi, Thank you for your response. This problem has not been solved. I've been reporting errors in the process of 'make'. The test example I used comes from: /snes /example /tutorials/ex3.c by modifying the suffix of ex3, there will be different error messages as following. I checked a lot of DSO problems on the Internet and installed a lot of libraries, but the error still haven't been solved. I was wondering if I was missing any prefix during the configure of PETSc(I use the simplest recommended installation), but there was no problem when the program was compiled with the 'makefile' which is recommended. Because I need some extra libraries, I have to use cmake. with ex3.c: yjwu at yjwu-XPS-8910:~/tem/build2$ make Scanning dependencies of target Test1 [ 50%] Building C object CMakeFiles/Test1.dir/ex3.c.o [100%] Linking C executable Test1 /usr/bin/ld: CMakeFiles/Test1.dir/ex3.c.o: undefined reference to symbol 'pow@@GLIBC_2.2.5' //lib/x86_64-linux-gnu/libm.so.6: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status CMakeFiles/Test1.dir/build.make:94: recipe for target 'Test1' failed make[2]: *** [Test1] Error 1 CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/Test1.dir/all' failed make[1]: *** [CMakeFiles/Test1.dir/all] Error 2 Makefile:83: recipe for target 'all' failed make: *** [all] Error 2 with ex3.cpp: yjwu at yjwu-XPS-8910:~/tem/build2$ make Scanning dependencies of target Test1 [ 50%] Building CXX object CMakeFiles/Test1.dir/ex3.cpp.o [100%] Linking CXX executable Test1 /usr/bin/ld: CMakeFiles/Test1.dir/ex3.cpp.o: undefined reference to symbol 'MPI_Comm_rank' /home/yjwu/petsc-3.12.2/arch-linux2-c-debug/lib/libmpi.so.12: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status CMakeFiles/Test1.dir/build.make:94: recipe for target 'Test1' failed make[2]: *** [Test1] Error 1 CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/Test1.dir/all' failed make[1]: *** [CMakeFiles/Test1.dir/all] Error 2 Makefile:83: recipe for target 'all' failed make: *** [all] Error 2 Thanks, Yingjie Matthew Knepley ?2019?12?6??? ??11:46??? > It sounds like your C++ compiler is name mangling the symbol, but the > library has no mangling. > Why are you using C++. > > Thanks, > > Matt > > On Fri, Dec 6, 2019 at 10:44 AM Yingjie Wu wrote: > >> Hi, >> Thank you for your email. >> >> The error in the previous program was indeed due to the missing >> "SNESSetFromOptions". >> I use the /snes/example/tutorial/ex1.cpp as test case. However, I found >> that some of the statements in the program were not compiled and deleted >> the statements containing "MPI_Comm_size", but I don't know how to solve >> this problem. >> >> lerui at yu1994-ThinkPad-W520:~/tem2/build2$ cmake .. >> -- The C compiler identification is GNU 5.4.0 >> -- The CXX compiler identification is GNU 5.4.0 >> -- Check for working C compiler: /usr/bin/cc >> -- Check for working C compiler: /usr/bin/cc -- works >> -- Detecting C compiler ABI info >> -- Detecting C compiler ABI info - done >> -- Detecting C compile features >> -- Detecting C compile features - done >> -- Check for working CXX compiler: /usr/bin/c++ >> -- Check for working CXX compiler: /usr/bin/c++ -- works >> -- Detecting CXX compiler ABI info >> -- Detecting CXX compiler ABI info - done >> -- Detecting CXX compile features >> -- Detecting CXX compile features - done >> -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") >> -- Checking for one of the modules 'PETSc' >> pkg include dirs: >> /home/lerui/petsc-3.12.2/arch-linux2-c-debug/include;/home/lerui/petsc-3.12.2/include >> pkg include libs: petsc >> pkg ldflags: -L/home/lerui/petsc-3.12.2/arch-linux2-c-debug/lib;-lpetsc >> -- Configuring done >> -- Generating done >> -- Build files have been written to: /home/lerui/tem2/build2 >> lerui at yu1994-ThinkPad-W520:~/tem2/build2$ make >> Scanning dependencies of target main >> [ 50%] Building CXX object CMakeFiles/main.dir/ex1.cpp.o >> [100%] Linking CXX executable main >> /usr/bin/ld: CMakeFiles/main.dir/ex1.cpp.o: undefined reference to symbol >> 'MPI_Comm_size' >> /home/lerui/petsc-3.12.2/arch-linux2-c-debug/lib/libmpi.so.12: error >> adding symbols: DSO missing from command line >> collect2: error: ld returned 1 exit status >> CMakeFiles/main.dir/build.make:94: recipe for target 'main' failed >> make[2]: *** [main] Error 1 >> CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/main.dir/all' >> failed >> make[1]: *** [CMakeFiles/main.dir/all] Error 2 >> Makefile:83: recipe for target 'all' failed >> make: *** [all] Error 2 >> >> Thanks, >> Yingjie >> >> Jed Brown ?2019?12?6??? ??10:54??? >> >>> Yingjie Wu writes: >>> >>> > I'm so sorry that I've ignored your previous advices. >>> > >>> > I added a global variable that seems works: >>> > >>> > >>> > export >>> > >>> LD_LIBRARY_PATH=/home/lerui/petcs-3.12.2/arch-linux2-c-debug/lib:$LD_LIBRARY_PATH >>> > >>> > >>> > How should I make petsc in a standard position?This eliminates the >>> need to >>> > set global variables. >>> >>> You can configure PETSc with --prefix=/your/standard/path, then make >>> install. >>> >>> > It seems that some of the options before running fit become >>> unavailable: >>> > >>> > >>> > mpiexec -n 1 ./example01cmke -snes_view >>> > >>> > >>> > Options-snes _ view are not used and how should I solve this problem? >>> >>> I don't have your ex1.cpp, but presumably you didn't SNESSetFromOptions? >>> >> > > -- > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Sun Dec 8 22:29:08 2019 From: bsmith at mcs.anl.gov (Smith, Barry F.) Date: Mon, 9 Dec 2019 04:29:08 +0000 Subject: [petsc-users] CMake error in PETSc In-Reply-To: References: <875ziwkszv.fsf@jedbrown.org> <87zhg8jctx.fsf@jedbrown.org> <87r21jjqr8.fsf@jedbrown.org> <87zhg6j1gk.fsf@jedbrown.org> Message-ID: There is something missing in the cmake process that is causing needed libraries not to be linked. Please email your program and your CMake stuff (files you use) so we can reproduce the problem and find a fix. Barry > On Dec 8, 2019, at 10:06 PM, Yingjie Wu wrote: > > Hi, > Thank you for your response. > This problem has not been solved. I've been reporting errors in the process of 'make'. The test example I used comes from: /snes /example /tutorials/ex3.c by modifying the suffix of ex3, there will be different error messages as following. I checked a lot of DSO problems on the Internet and installed a lot of libraries, but the error still haven't been solved. I was wondering if I was missing any prefix during the configure of PETSc(I use the simplest recommended installation), but there was no problem when the program was compiled with the 'makefile' which is recommended. Because I need some extra libraries, I have to use cmake. > with ex3.c: > yjwu at yjwu-XPS-8910:~/tem/build2$ make > Scanning dependencies of target Test1 > [ 50%] Building C object CMakeFiles/Test1.dir/ex3.c.o > [100%] Linking C executable Test1 > /usr/bin/ld: CMakeFiles/Test1.dir/ex3.c.o: undefined reference to symbol 'pow@@GLIBC_2.2.5' > //lib/x86_64-linux-gnu/libm.so.6: error adding symbols: DSO missing from command line > collect2: error: ld returned 1 exit status > CMakeFiles/Test1.dir/build.make:94: recipe for target 'Test1' failed > make[2]: *** [Test1] Error 1 > CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/Test1.dir/all' failed > make[1]: *** [CMakeFiles/Test1.dir/all] Error 2 > Makefile:83: recipe for target 'all' failed > make: *** [all] Error 2 > with ex3.cpp: > yjwu at yjwu-XPS-8910:~/tem/build2$ make > Scanning dependencies of target Test1 > [ 50%] Building CXX object CMakeFiles/Test1.dir/ex3.cpp.o > [100%] Linking CXX executable Test1 > /usr/bin/ld: CMakeFiles/Test1.dir/ex3.cpp.o: undefined reference to symbol 'MPI_Comm_rank' > /home/yjwu/petsc-3.12.2/arch-linux2-c-debug/lib/libmpi.so.12: error adding symbols: DSO missing from command line > collect2: error: ld returned 1 exit status > CMakeFiles/Test1.dir/build.make:94: recipe for target 'Test1' failed > make[2]: *** [Test1] Error 1 > CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/Test1.dir/all' failed > make[1]: *** [CMakeFiles/Test1.dir/all] Error 2 > Makefile:83: recipe for target 'all' failed > make: *** [all] Error 2 > Thanks, > Yingjie > > Matthew Knepley ?2019?12?6??? ??11:46??? > It sounds like your C++ compiler is name mangling the symbol, but the library has no mangling. > Why are you using C++. > > Thanks, > > Matt > > On Fri, Dec 6, 2019 at 10:44 AM Yingjie Wu wrote: > Hi, > Thank you for your email. > The error in the previous program was indeed due to the missing "SNESSetFromOptions". > I use the /snes/example/tutorial/ex1.cpp as test case. However, I found that some of the statements in the program were not compiled and deleted the statements containing "MPI_Comm_size", but I don't know how to solve this problem. > lerui at yu1994-ThinkPad-W520:~/tem2/build2$ cmake .. > -- The C compiler identification is GNU 5.4.0 > -- The CXX compiler identification is GNU 5.4.0 > -- Check for working C compiler: /usr/bin/cc > -- Check for working C compiler: /usr/bin/cc -- works > -- Detecting C compiler ABI info > -- Detecting C compiler ABI info - done > -- Detecting C compile features > -- Detecting C compile features - done > -- Check for working CXX compiler: /usr/bin/c++ > -- Check for working CXX compiler: /usr/bin/c++ -- works > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > -- Detecting CXX compile features > -- Detecting CXX compile features - done > -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") > -- Checking for one of the modules 'PETSc' > pkg include dirs: /home/lerui/petsc-3.12.2/arch-linux2-c-debug/include;/home/lerui/petsc-3.12.2/include > pkg include libs: petsc > pkg ldflags: -L/home/lerui/petsc-3.12.2/arch-linux2-c-debug/lib;-lpetsc > -- Configuring done > -- Generating done > -- Build files have been written to: /home/lerui/tem2/build2 > lerui at yu1994-ThinkPad-W520:~/tem2/build2$ make > Scanning dependencies of target main > [ 50%] Building CXX object CMakeFiles/main.dir/ex1.cpp.o > [100%] Linking CXX executable main > /usr/bin/ld: CMakeFiles/main.dir/ex1.cpp.o: undefined reference to symbol 'MPI_Comm_size' > /home/lerui/petsc-3.12.2/arch-linux2-c-debug/lib/libmpi.so.12: error adding symbols: DSO missing from command line > collect2: error: ld returned 1 exit status > CMakeFiles/main.dir/build.make:94: recipe for target 'main' failed > make[2]: *** [main] Error 1 > CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/main.dir/all' failed > make[1]: *** [CMakeFiles/main.dir/all] Error 2 > Makefile:83: recipe for target 'all' failed > make: *** [all] Error 2 > Thanks, > Yingjie > > Jed Brown ?2019?12?6??? ??10:54??? > Yingjie Wu writes: > > > I'm so sorry that I've ignored your previous advices. > > > > I added a global variable that seems works: > > > > > > export > > LD_LIBRARY_PATH=/home/lerui/petcs-3.12.2/arch-linux2-c-debug/lib:$LD_LIBRARY_PATH > > > > > > How should I make petsc in a standard position?This eliminates the need to > > set global variables. > > You can configure PETSc with --prefix=/your/standard/path, then make install. > > > It seems that some of the options before running fit become unavailable: > > > > > > mpiexec -n 1 ./example01cmke -snes_view > > > > > > Options-snes _ view are not used and how should I solve this problem? > > I don't have your ex1.cpp, but presumably you didn't SNESSetFromOptions? > > > -- > What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ From yjwu16 at gmail.com Sun Dec 8 22:38:04 2019 From: yjwu16 at gmail.com (Yingjie Wu) Date: Mon, 9 Dec 2019 12:38:04 +0800 Subject: [petsc-users] CMake error in PETSc In-Reply-To: References: <875ziwkszv.fsf@jedbrown.org> <87zhg8jctx.fsf@jedbrown.org> <87r21jjqr8.fsf@jedbrown.org> <87zhg6j1gk.fsf@jedbrown.org> Message-ID: Thank you very much for your help. My programs are as follows. Smith, Barry F. ?2019?12?9??? ??12:29??? > > There is something missing in the cmake process that is causing needed > libraries not to be linked. > > Please email your program and your CMake stuff (files you use) so we > can reproduce the problem and find a fix. > > Barry > > > > On Dec 8, 2019, at 10:06 PM, Yingjie Wu wrote: > > > > Hi, > > Thank you for your response. > > This problem has not been solved. I've been reporting errors in the > process of 'make'. The test example I used comes from: /snes /example > /tutorials/ex3.c by modifying the suffix of ex3, there will be different > error messages as following. I checked a lot of DSO problems on the > Internet and installed a lot of libraries, but the error still haven't been > solved. I was wondering if I was missing any prefix during the configure of > PETSc(I use the simplest recommended installation), but there was no > problem when the program was compiled with the 'makefile' which is > recommended. Because I need some extra libraries, I have to use cmake. > > with ex3.c: > > yjwu at yjwu-XPS-8910:~/tem/build2$ make > > Scanning dependencies of target Test1 > > [ 50%] Building C object CMakeFiles/Test1.dir/ex3.c.o > > [100%] Linking C executable Test1 > > /usr/bin/ld: CMakeFiles/Test1.dir/ex3.c.o: undefined reference to symbol > 'pow@@GLIBC_2.2.5' > > //lib/x86_64-linux-gnu/libm.so.6: error adding symbols: DSO missing from > command line > > collect2: error: ld returned 1 exit status > > CMakeFiles/Test1.dir/build.make:94: recipe for target 'Test1' failed > > make[2]: *** [Test1] Error 1 > > CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/Test1.dir/all' > failed > > make[1]: *** [CMakeFiles/Test1.dir/all] Error 2 > > Makefile:83: recipe for target 'all' failed > > make: *** [all] Error 2 > > with ex3.cpp: > > yjwu at yjwu-XPS-8910:~/tem/build2$ make > > Scanning dependencies of target Test1 > > [ 50%] Building CXX object CMakeFiles/Test1.dir/ex3.cpp.o > > [100%] Linking CXX executable Test1 > > /usr/bin/ld: CMakeFiles/Test1.dir/ex3.cpp.o: undefined reference to > symbol 'MPI_Comm_rank' > > /home/yjwu/petsc-3.12.2/arch-linux2-c-debug/lib/libmpi.so.12: error > adding symbols: DSO missing from command line > > collect2: error: ld returned 1 exit status > > CMakeFiles/Test1.dir/build.make:94: recipe for target 'Test1' failed > > make[2]: *** [Test1] Error 1 > > CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/Test1.dir/all' > failed > > make[1]: *** [CMakeFiles/Test1.dir/all] Error 2 > > Makefile:83: recipe for target 'all' failed > > make: *** [all] Error 2 > > Thanks, > > Yingjie > > > > Matthew Knepley ?2019?12?6??? ??11:46??? > > It sounds like your C++ compiler is name mangling the symbol, but the > library has no mangling. > > Why are you using C++. > > > > Thanks, > > > > Matt > > > > On Fri, Dec 6, 2019 at 10:44 AM Yingjie Wu wrote: > > Hi, > > Thank you for your email. > > The error in the previous program was indeed due to the missing > "SNESSetFromOptions". > > I use the /snes/example/tutorial/ex1.cpp as test case. However, I found > that some of the statements in the program were not compiled and deleted > the statements containing "MPI_Comm_size", but I don't know how to solve > this problem. > > lerui at yu1994-ThinkPad-W520:~/tem2/build2$ cmake .. > > -- The C compiler identification is GNU 5.4.0 > > -- The CXX compiler identification is GNU 5.4.0 > > -- Check for working C compiler: /usr/bin/cc > > -- Check for working C compiler: /usr/bin/cc -- works > > -- Detecting C compiler ABI info > > -- Detecting C compiler ABI info - done > > -- Detecting C compile features > > -- Detecting C compile features - done > > -- Check for working CXX compiler: /usr/bin/c++ > > -- Check for working CXX compiler: /usr/bin/c++ -- works > > -- Detecting CXX compiler ABI info > > -- Detecting CXX compiler ABI info - done > > -- Detecting CXX compile features > > -- Detecting CXX compile features - done > > -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") > > -- Checking for one of the modules 'PETSc' > > pkg include dirs: > /home/lerui/petsc-3.12.2/arch-linux2-c-debug/include;/home/lerui/petsc-3.12.2/include > > pkg include libs: petsc > > pkg ldflags: -L/home/lerui/petsc-3.12.2/arch-linux2-c-debug/lib;-lpetsc > > -- Configuring done > > -- Generating done > > -- Build files have been written to: /home/lerui/tem2/build2 > > lerui at yu1994-ThinkPad-W520:~/tem2/build2$ make > > Scanning dependencies of target main > > [ 50%] Building CXX object CMakeFiles/main.dir/ex1.cpp.o > > [100%] Linking CXX executable main > > /usr/bin/ld: CMakeFiles/main.dir/ex1.cpp.o: undefined reference to > symbol 'MPI_Comm_size' > > /home/lerui/petsc-3.12.2/arch-linux2-c-debug/lib/libmpi.so.12: error > adding symbols: DSO missing from command line > > collect2: error: ld returned 1 exit status > > CMakeFiles/main.dir/build.make:94: recipe for target 'main' failed > > make[2]: *** [main] Error 1 > > CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/main.dir/all' > failed > > make[1]: *** [CMakeFiles/main.dir/all] Error 2 > > Makefile:83: recipe for target 'all' failed > > make: *** [all] Error 2 > > Thanks, > > Yingjie > > > > Jed Brown ?2019?12?6??? ??10:54??? > > Yingjie Wu writes: > > > > > I'm so sorry that I've ignored your previous advices. > > > > > > I added a global variable that seems works: > > > > > > > > > export > > > > LD_LIBRARY_PATH=/home/lerui/petcs-3.12.2/arch-linux2-c-debug/lib:$LD_LIBRARY_PATH > > > > > > > > > How should I make petsc in a standard position?This eliminates the > need to > > > set global variables. > > > > You can configure PETSc with --prefix=/your/standard/path, then make > install. > > > > > It seems that some of the options before running fit become > unavailable: > > > > > > > > > mpiexec -n 1 ./example01cmke -snes_view > > > > > > > > > Options-snes _ view are not used and how should I solve this problem? > > > > I don't have your ex1.cpp, but presumably you didn't SNESSetFromOptions? > > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- #This is a CMake makefile. cmake_minimum_required(VERSION 2.8.11) project(Test1) add_executable(Test1 ex3.cpp) find_package(PkgConfig REQUIRED) set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) set(ENV{PKG_CONFIG_PATH} /home/yjwu/petsc-3.12.2/arch-linux2-c-debug/lib/pkgconfig) pkg_search_module(PETSC REQUIRED PETSc) message("pkg include dirs: ${PETSC_INCLUDE_DIRS}") message("pkg include libs: ${PETSC_LIBRARIES}") message("pkg ldflags: ${PETSC_LDFLAGS}") include_directories(${PETSC_INCLUDE_DIRS}) target_link_libraries(Test1 ${PETSC_LDFLAGS} pthread) #set(COOLPROP_STATIC_LIBRARY true CACHE BOOL "Use CoolProp") #add_subdirectory("${CMAKE_SOURCE_DIR}/externals/CoolProp" "CoolProp") #target_link_libraries (Test1 CoolProp) #if (UNIX) # target_link_libraries (Test1 ${CMAKE_DL_LIBS}) #endif() -------------- next part -------------- static char help[] = "Newton methods to solve u'' + u^{2} = f in parallel.\n\ This example employs a user-defined monitoring routine and optionally a user-defined\n\ routine to check candidate iterates produced by line search routines.\n\ The command line options include:\n\ -pre_check_iterates : activate checking of iterates\n\ -post_check_iterates : activate checking of iterates\n\ -check_tol : set tolerance for iterate checking\n\ -user_precond : activate a (trivial) user-defined preconditioner\n\n"; /*T Concepts: SNES^basic parallel example Concepts: SNES^setting a user-defined monitoring routine Processors: n T*/ /* Include "petscdm.h" so that we can use data management objects (DMs) Include "petscdmda.h" so that we can use distributed arrays (DMDAs). Include "petscsnes.h" so that we can use SNES solvers. Note that this file automatically includes: petscsys.h - base PETSc routines petscvec.h - vectors petscmat.h - matrices petscis.h - index sets petscksp.h - Krylov subspace methods petscviewer.h - viewers petscpc.h - preconditioners petscksp.h - linear solvers */ #include #include #include /* User-defined routines. */ PetscErrorCode FormJacobian(SNES,Vec,Mat,Mat,void*); PetscErrorCode FormFunction(SNES,Vec,Vec,void*); PetscErrorCode FormInitialGuess(Vec); PetscErrorCode Monitor(SNES,PetscInt,PetscReal,void*); PetscErrorCode PreCheck(SNESLineSearch,Vec,Vec,PetscBool*,void*); PetscErrorCode PostCheck(SNESLineSearch,Vec,Vec,Vec,PetscBool*,PetscBool*,void*); PetscErrorCode PostSetSubKSP(SNESLineSearch,Vec,Vec,Vec,PetscBool*,PetscBool*,void*); PetscErrorCode MatrixFreePreconditioner(PC,Vec,Vec); /* User-defined application context */ typedef struct { DM da; /* distributed array */ Vec F; /* right-hand-side of PDE */ PetscMPIInt rank; /* rank of processor */ PetscMPIInt size; /* size of communicator */ PetscReal h; /* mesh spacing */ PetscBool sjerr; /* if or not to test jacobian domain error */ } ApplicationCtx; /* User-defined context for monitoring */ typedef struct { PetscViewer viewer; } MonitorCtx; /* User-defined context for checking candidate iterates that are determined by line search methods */ typedef struct { Vec last_step; /* previous iterate */ PetscReal tolerance; /* tolerance for changes between successive iterates */ ApplicationCtx *user; } StepCheckCtx; typedef struct { PetscInt its0; /* num of prevous outer KSP iterations */ } SetSubKSPCtx; int main(int argc,char **argv) { SNES snes; /* SNES context */ SNESLineSearch linesearch; /* SNESLineSearch context */ Mat J; /* Jacobian matrix */ ApplicationCtx ctx; /* user-defined context */ Vec x,r,U,F; /* vectors */ MonitorCtx monP; /* monitoring context */ StepCheckCtx checkP; /* step-checking context */ SetSubKSPCtx checkP1; PetscBool pre_check,post_check,post_setsubksp; /* flag indicating whether we're checking candidate iterates */ PetscScalar xp,*FF,*UU,none = -1.0; PetscErrorCode ierr; PetscInt its,N = 5,i,maxit,maxf,xs,xm; PetscReal abstol,rtol,stol,norm; PetscBool flg; ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&ctx.rank);CHKERRQ(ierr); ierr = MPI_Comm_size(PETSC_COMM_WORLD,&ctx.size);CHKERRQ(ierr); ctx.rank=1; ctx.size=1; ierr = PetscOptionsGetInt(NULL,NULL,"-n",&N,NULL);CHKERRQ(ierr); ctx.h = 1.0/(N-1); ctx.sjerr = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,NULL,"-test_jacobian_domain_error",&ctx.sjerr,NULL);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create nonlinear solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = SNESCreate(PETSC_COMM_WORLD,&snes);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create vector data structures; set function evaluation routine - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ /* Create distributed array (DMDA) to manage parallel grid and vectors */ ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,N,1,1,NULL,&ctx.da);CHKERRQ(ierr); ierr = DMSetFromOptions(ctx.da);CHKERRQ(ierr); ierr = DMSetUp(ctx.da);CHKERRQ(ierr); /* Extract global and local vectors from DMDA; then duplicate for remaining vectors that are the same types */ ierr = DMCreateGlobalVector(ctx.da,&x);CHKERRQ(ierr); ierr = VecDuplicate(x,&r);CHKERRQ(ierr); ierr = VecDuplicate(x,&F);CHKERRQ(ierr); ctx.F = F; ierr = VecDuplicate(x,&U);CHKERRQ(ierr); /* Set function evaluation routine and vector. Whenever the nonlinear solver needs to compute the nonlinear function, it will call this routine. - Note that the final routine argument is the user-defined context that provides application-specific data for the function evaluation routine. */ ierr = SNESSetFunction(snes,r,FormFunction,&ctx);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create matrix data structure; set Jacobian evaluation routine - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = MatCreate(PETSC_COMM_WORLD,&J);CHKERRQ(ierr); ierr = MatSetSizes(J,PETSC_DECIDE,PETSC_DECIDE,N,N);CHKERRQ(ierr); ierr = MatSetFromOptions(J);CHKERRQ(ierr); ierr = MatSeqAIJSetPreallocation(J,3,NULL);CHKERRQ(ierr); ierr = MatMPIAIJSetPreallocation(J,3,NULL,3,NULL);CHKERRQ(ierr); /* Set Jacobian matrix data structure and default Jacobian evaluation routine. Whenever the nonlinear solver needs to compute the Jacobian matrix, it will call this routine. - Note that the final routine argument is the user-defined context that provides application-specific data for the Jacobian evaluation routine. */ ierr = SNESSetJacobian(snes,J,J,FormJacobian,&ctx);CHKERRQ(ierr); /* Optionally allow user-provided preconditioner */ ierr = PetscOptionsHasName(NULL,NULL,"-user_precond",&flg);CHKERRQ(ierr); if (flg) { KSP ksp; PC pc; ierr = SNESGetKSP(snes,&ksp);CHKERRQ(ierr); ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr); ierr = PCSetType(pc,PCSHELL);CHKERRQ(ierr); ierr = PCShellSetApply(pc,MatrixFreePreconditioner);CHKERRQ(ierr); } /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Customize nonlinear solver; set runtime options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ /* Set an optional user-defined monitoring routine */ ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,0,0,0,400,400,&monP.viewer);CHKERRQ(ierr); ierr = SNESMonitorSet(snes,Monitor,&monP,0);CHKERRQ(ierr); /* Set names for some vectors to facilitate monitoring (optional) */ ierr = PetscObjectSetName((PetscObject)x,"Approximate Solution");CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)U,"Exact Solution");CHKERRQ(ierr); /* Set SNES/KSP/KSP/PC runtime options, e.g., -snes_view -snes_monitor -ksp_type -pc_type */ ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); /* Set an optional user-defined routine to check the validity of candidate iterates that are determined by line search methods */ ierr = SNESGetLineSearch(snes, &linesearch);CHKERRQ(ierr); ierr = PetscOptionsHasName(NULL,NULL,"-post_check_iterates",&post_check);CHKERRQ(ierr); if (post_check) { ierr = PetscPrintf(PETSC_COMM_WORLD,"Activating post step checking routine\n");CHKERRQ(ierr); ierr = SNESLineSearchSetPostCheck(linesearch,PostCheck,&checkP);CHKERRQ(ierr); ierr = VecDuplicate(x,&(checkP.last_step));CHKERRQ(ierr); checkP.tolerance = 1.0; checkP.user = &ctx; ierr = PetscOptionsGetReal(NULL,NULL,"-check_tol",&checkP.tolerance,NULL);CHKERRQ(ierr); } ierr = PetscOptionsHasName(NULL,NULL,"-post_setsubksp",&post_setsubksp);CHKERRQ(ierr); if (post_setsubksp) { ierr = PetscPrintf(PETSC_COMM_WORLD,"Activating post setsubksp\n");CHKERRQ(ierr); ierr = SNESLineSearchSetPostCheck(linesearch,PostSetSubKSP,&checkP1);CHKERRQ(ierr); } ierr = PetscOptionsHasName(NULL,NULL,"-pre_check_iterates",&pre_check);CHKERRQ(ierr); if (pre_check) { ierr = PetscPrintf(PETSC_COMM_WORLD,"Activating pre step checking routine\n");CHKERRQ(ierr); ierr = SNESLineSearchSetPreCheck(linesearch,PreCheck,&checkP);CHKERRQ(ierr); } /* Print parameters used for convergence testing (optional) ... just to demonstrate this routine; this information is also printed with the option -snes_view */ ierr = SNESGetTolerances(snes,&abstol,&rtol,&stol,&maxit,&maxf);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"atol=%g, rtol=%g, stol=%g, maxit=%D, maxf=%D\n",(double)abstol,(double)rtol,(double)stol,maxit,maxf);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Initialize application: Store right-hand-side of PDE and exact solution - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ /* Get local grid boundaries (for 1-dimensional DMDA): xs, xm - starting grid index, width of local grid (no ghost points) */ ierr = DMDAGetCorners(ctx.da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr); /* Get pointers to vector data */ ierr = DMDAVecGetArray(ctx.da,F,&FF);CHKERRQ(ierr); ierr = DMDAVecGetArray(ctx.da,U,&UU);CHKERRQ(ierr); /* Compute local vector entries */ xp = ctx.h*xs; for (i=xs; ida; PetscScalar *xx,*ff,*FF,d; PetscErrorCode ierr; PetscInt i,M,xs,xm; Vec xlocal; PetscFunctionBeginUser; ierr = DMGetLocalVector(da,&xlocal);CHKERRQ(ierr); /* Scatter ghost points to local vector, using the 2-step process DMGlobalToLocalBegin(), DMGlobalToLocalEnd(). By placing code between these two statements, computations can be done while messages are in transition. */ ierr = DMGlobalToLocalBegin(da,x,INSERT_VALUES,xlocal);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(da,x,INSERT_VALUES,xlocal);CHKERRQ(ierr); /* Get pointers to vector data. - The vector xlocal includes ghost point; the vectors x and f do NOT include ghost points. - Using DMDAVecGetArray() allows accessing the values using global ordering */ ierr = DMDAVecGetArray(da,xlocal,&xx);CHKERRQ(ierr); ierr = DMDAVecGetArray(da,f,&ff);CHKERRQ(ierr); ierr = DMDAVecGetArray(da,user->F,&FF);CHKERRQ(ierr); /* Get local grid boundaries (for 1-dimensional DMDA): xs, xm - starting grid index, width of local grid (no ghost points) */ ierr = DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr); ierr = DMDAGetInfo(da,NULL,&M,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);CHKERRQ(ierr); /* Set function values for boundary points; define local interior grid point range: xsi - starting interior grid index xei - ending interior grid index */ if (xs == 0) { /* left boundary */ ff[0] = xx[0]; xs++;xm--; } if (xs+xm == M) { /* right boundary */ ff[xs+xm-1] = xx[xs+xm-1] - 1.0; xm--; } /* Compute function over locally owned part of the grid (interior points only) */ d = 1.0/(user->h*user->h); for (i=xs; iF,&FF);CHKERRQ(ierr); ierr = DMRestoreLocalVector(da,&xlocal);CHKERRQ(ierr); PetscFunctionReturn(0); } /* ------------------------------------------------------------------- */ /* FormJacobian - Evaluates Jacobian matrix. Input Parameters: . snes - the SNES context . x - input vector . dummy - optional user-defined context (not used here) Output Parameters: . jac - Jacobian matrix . B - optionally different preconditioning matrix . flag - flag indicating matrix structure */ PetscErrorCode FormJacobian(SNES snes,Vec x,Mat jac,Mat B,void *ctx) { ApplicationCtx *user = (ApplicationCtx*) ctx; PetscScalar *xx,d,A[3]; PetscErrorCode ierr; PetscInt i,j[3],M,xs,xm; DM da = user->da; PetscFunctionBeginUser; if (user->sjerr) { ierr = SNESSetJacobianDomainError(snes);CHKERRQ(ierr); PetscFunctionReturn(0); } /* Get pointer to vector data */ ierr = DMDAVecGetArrayRead(da,x,&xx);CHKERRQ(ierr); ierr = DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr); /* Get range of locally owned matrix */ ierr = DMDAGetInfo(da,NULL,&M,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);CHKERRQ(ierr); /* Determine starting and ending local indices for interior grid points. Set Jacobian entries for boundary points. */ if (xs == 0) { /* left boundary */ i = 0; A[0] = 1.0; ierr = MatSetValues(jac,1,&i,1,&i,A,INSERT_VALUES);CHKERRQ(ierr); xs++;xm--; } if (xs+xm == M) { /* right boundary */ i = M-1; A[0] = 1.0; ierr = MatSetValues(jac,1,&i,1,&i,A,INSERT_VALUES);CHKERRQ(ierr); xm--; } /* Interior grid points - Note that in this case we set all elements for a particular row at once. */ d = 1.0/(user->h*user->h); for (i=xs; iviewer);CHKERRQ(ierr); PetscFunctionReturn(0); } /* ------------------------------------------------------------------- */ /* PreCheck - Optional user-defined routine that checks the validity of candidate steps of a line search method. Set by SNESLineSearchSetPreCheck(). Input Parameters: snes - the SNES context xcurrent - current solution y - search direction and length Output Parameters: y - proposed step (search direction and length) (possibly changed) changed_y - tells if the step has changed or not */ PetscErrorCode PreCheck(SNESLineSearch linesearch,Vec xcurrent,Vec y, PetscBool *changed_y, void * ctx) { PetscFunctionBeginUser; *changed_y = PETSC_FALSE; PetscFunctionReturn(0); } /* ------------------------------------------------------------------- */ /* PostCheck - Optional user-defined routine that checks the validity of candidate steps of a line search method. Set by SNESLineSearchSetPostCheck(). Input Parameters: snes - the SNES context ctx - optional user-defined context for private data for the monitor routine, as set by SNESLineSearchSetPostCheck() xcurrent - current solution y - search direction and length x - the new candidate iterate Output Parameters: y - proposed step (search direction and length) (possibly changed) x - current iterate (possibly modified) */ PetscErrorCode PostCheck(SNESLineSearch linesearch,Vec xcurrent,Vec y,Vec x,PetscBool *changed_y,PetscBool *changed_x, void * ctx) { PetscErrorCode ierr; PetscInt i,iter,xs,xm; StepCheckCtx *check; ApplicationCtx *user; PetscScalar *xa,*xa_last,tmp; PetscReal rdiff; DM da; SNES snes; PetscFunctionBeginUser; *changed_x = PETSC_FALSE; *changed_y = PETSC_FALSE; ierr = SNESLineSearchGetSNES(linesearch, &snes);CHKERRQ(ierr); check = (StepCheckCtx*)ctx; user = check->user; ierr = SNESGetIterationNumber(snes,&iter);CHKERRQ(ierr); /* iteration 1 indicates we are working on the second iteration */ if (iter > 0) { da = user->da; ierr = PetscPrintf(PETSC_COMM_WORLD,"Checking candidate step at iteration %D with tolerance %g\n",iter,(double)check->tolerance);CHKERRQ(ierr); /* Access local array data */ ierr = DMDAVecGetArray(da,check->last_step,&xa_last);CHKERRQ(ierr); ierr = DMDAVecGetArray(da,x,&xa);CHKERRQ(ierr); ierr = DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr); /* If we fail the user-defined check for validity of the candidate iterate, then modify the iterate as we like. (Note that the particular modification below is intended simply to demonstrate how to manipulate this data, not as a meaningful or appropriate choice.) */ for (i=xs; itolerance; else rdiff = PetscAbsScalar((xa[i] - xa_last[i])/xa[i]); if (rdiff > check->tolerance) { tmp = xa[i]; xa[i] = .5*(xa[i] + xa_last[i]); *changed_x = PETSC_TRUE; ierr = PetscPrintf(PETSC_COMM_WORLD," Altering entry %D: x=%g, x_last=%g, diff=%g, x_new=%g\n",i,(double)PetscAbsScalar(tmp),(double)PetscAbsScalar(xa_last[i]),(double)rdiff,(double)PetscAbsScalar(xa[i]));CHKERRQ(ierr); } } ierr = DMDAVecRestoreArray(da,check->last_step,&xa_last);CHKERRQ(ierr); ierr = DMDAVecRestoreArray(da,x,&xa);CHKERRQ(ierr); } ierr = VecCopy(x,check->last_step);CHKERRQ(ierr); PetscFunctionReturn(0); } /* ------------------------------------------------------------------- */ /* PostSetSubKSP - Optional user-defined routine that reset SubKSP options when hierarchical bjacobi PC is used e.g, mpiexec -n 8 ./ex3 -nox -n 10000 -ksp_type fgmres -pc_type bjacobi -pc_bjacobi_blocks 4 -sub_ksp_type gmres -sub_ksp_max_it 3 -post_setsubksp -sub_ksp_rtol 1.e-16 Set by SNESLineSearchSetPostCheck(). Input Parameters: linesearch - the LineSearch context xcurrent - current solution y - search direction and length x - the new candidate iterate Output Parameters: y - proposed step (search direction and length) (possibly changed) x - current iterate (possibly modified) */ PetscErrorCode PostSetSubKSP(SNESLineSearch linesearch,Vec xcurrent,Vec y,Vec x,PetscBool *changed_y,PetscBool *changed_x, void * ctx) { PetscErrorCode ierr; SetSubKSPCtx *check; PetscInt iter,its,sub_its,maxit; KSP ksp,sub_ksp,*sub_ksps; PC pc; PetscReal ksp_ratio; SNES snes; PetscFunctionBeginUser; ierr = SNESLineSearchGetSNES(linesearch, &snes);CHKERRQ(ierr); check = (SetSubKSPCtx*)ctx; ierr = SNESGetIterationNumber(snes,&iter);CHKERRQ(ierr); ierr = SNESGetKSP(snes,&ksp);CHKERRQ(ierr); ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr); ierr = PCBJacobiGetSubKSP(pc,NULL,NULL,&sub_ksps);CHKERRQ(ierr); sub_ksp = sub_ksps[0]; ierr = KSPGetIterationNumber(ksp,&its);CHKERRQ(ierr); /* outer KSP iteration number */ ierr = KSPGetIterationNumber(sub_ksp,&sub_its);CHKERRQ(ierr); /* inner KSP iteration number */ if (iter) { ierr = PetscPrintf(PETSC_COMM_WORLD," ...PostCheck snes iteration %D, ksp_it %D %D, subksp_it %D\n",iter,check->its0,its,sub_its);CHKERRQ(ierr); ksp_ratio = ((PetscReal)(its))/check->its0; maxit = (PetscInt)(ksp_ratio*sub_its + 0.5); if (maxit < 2) maxit = 2; ierr = KSPSetTolerances(sub_ksp,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,maxit);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD," ...ksp_ratio %g, new maxit %D\n\n",(double)ksp_ratio,maxit);CHKERRQ(ierr); } check->its0 = its; /* save current outer KSP iteration number */ PetscFunctionReturn(0); } /* ------------------------------------------------------------------- */ /* MatrixFreePreconditioner - This routine demonstrates the use of a user-provided preconditioner. This code implements just the null preconditioner, which of course is not recommended for general use. Input Parameters: + pc - preconditioner - x - input vector Output Parameter: . y - preconditioned vector */ PetscErrorCode MatrixFreePreconditioner(PC pc,Vec x,Vec y) { PetscErrorCode ierr; ierr = VecCopy(x,y);CHKERRQ(ierr); return 0; } /*TEST test: args: -nox -snes_monitor_cancel -snes_monitor_short -ksp_gmres_cgs_refinement_type refine_always test: suffix: 2 nsize: 3 args: -nox -pc_type asm -mat_type mpiaij -snes_monitor_cancel -snes_monitor_short -ksp_gmres_cgs_refinement_type refine_always test: suffix: 3 nsize: 2 args: -nox -snes_monitor_cancel -snes_monitor_short -ksp_gmres_cgs_refinement_type refine_always test: suffix: 4 args: -nox -pre_check_iterates -post_check_iterates test: suffix: 5 requires: double !complex !single nsize: 2 args: -nox -snes_test_jacobian -snes_test_jacobian_view test: suffix: 6 requires: double !complex !single nsize: 4 args: -test_jacobian_domain_error -snes_converged_reason -snes_check_jacobian_domain_error 1 test: suffix: 7 requires: double !complex !single nsize: 4 args: -test_jacobian_domain_error -snes_converged_reason -snes_type newtontr -snes_check_jacobian_domain_error 1 test: suffix: 8 requires: double !complex !single nsize: 4 args: -test_jacobian_domain_error -snes_converged_reason -snes_type vinewtonrsls -snes_check_jacobian_domain_error 1 test: suffix: 9 requires: double !complex !single nsize: 4 args: -test_jacobian_domain_error -snes_converged_reason -snes_type vinewtonssls -snes_check_jacobian_domain_error 1 test: suffix: 10 requires: double !complex !single nsize: 4 args: -test_jacobian_domain_error -snes_converged_reason -snes_type qn -snes_qn_scale_type jacobian -snes_check_jacobian_domain_error 1 test: suffix: 11 requires: double !complex !single nsize: 4 args: -test_jacobian_domain_error -snes_converged_reason -snes_type ms -snes_check_jacobian_domain_error 1 TEST*/ From bsmith at mcs.anl.gov Mon Dec 9 07:56:34 2019 From: bsmith at mcs.anl.gov (Smith, Barry F.) Date: Mon, 9 Dec 2019 13:56:34 +0000 Subject: [petsc-users] CMake error in PETSc In-Reply-To: References: <875ziwkszv.fsf@jedbrown.org> <87zhg8jctx.fsf@jedbrown.org> <87r21jjqr8.fsf@jedbrown.org> <87zhg6j1gk.fsf@jedbrown.org> Message-ID: <63433CEA-54BF-43E8-8FC5-FB9AFA7B294E@mcs.anl.gov> The problem is that your Cmake file knows nothing about the MPI compilers that are required and hence just selects some random compilers it found in the path which do not support MPI. I have attached a new CMakeList.txt for you to try. I uses the environmental variables PETSC_DIR and PETSC_ARCH to find the configuration file AND use the compilers from the configuration file. It works for me, please let me know if you have trouble. Barry > On Dec 8, 2019, at 10:38 PM, Yingjie Wu wrote: > > Thank you very much for your help. > My programs are as follow > Smith, Barry F. ?2019?12?9??? ??12:29??? > > There is something missing in the cmake process that is causing needed libraries not to be linked. > > Please email your program and your CMake stuff (files you use) so we can reproduce the problem and find a fix. > > Barry > > > > On Dec 8, 2019, at 10:06 PM, Yingjie Wu wrote: > > > > Hi, > > Thank you for your response. > > This problem has not been solved. I've been reporting errors in the process of 'make'. The test example I used comes from: /snes /example /tutorials/ex3.c by modifying the suffix of ex3, there will be different error messages as following. I checked a lot of DSO problems on the Internet and installed a lot of libraries, but the error still haven't been solved. I was wondering if I was missing any prefix during the configure of PETSc(I use the simplest recommended installation), but there was no problem when the program was compiled with the 'makefile' which is recommended. Because I need some extra libraries, I have to use cmake. > > with ex3.c: > > yjwu at yjwu-XPS-8910:~/tem/build2$ make > > Scanning dependencies of target Test1 > > [ 50%] Building C object CMakeFiles/Test1.dir/ex3.c.o > > [100%] Linking C executable Test1 > > /usr/bin/ld: CMakeFiles/Test1.dir/ex3.c.o: undefined reference to symbol 'pow@@GLIBC_2.2.5' > > //lib/x86_64-linux-gnu/libm.so.6: error adding symbols: DSO missing from command line > > collect2: error: ld returned 1 exit status > > CMakeFiles/Test1.dir/build.make:94: recipe for target 'Test1' failed > > make[2]: *** [Test1] Error 1 > > CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/Test1.dir/all' failed > > make[1]: *** [CMakeFiles/Test1.dir/all] Error 2 > > Makefile:83: recipe for target 'all' failed > > make: *** [all] Error 2 > > with ex3.cpp: > > yjwu at yjwu-XPS-8910:~/tem/build2$ make > > Scanning dependencies of target Test1 > > [ 50%] Building CXX object CMakeFiles/Test1.dir/ex3.cpp.o > > [100%] Linking CXX executable Test1 > > /usr/bin/ld: CMakeFiles/Test1.dir/ex3.cpp.o: undefined reference to symbol 'MPI_Comm_rank' > > /home/yjwu/petsc-3.12.2/arch-linux2-c-debug/lib/libmpi.so.12: error adding symbols: DSO missing from command line > > collect2: error: ld returned 1 exit status > > CMakeFiles/Test1.dir/build.make:94: recipe for target 'Test1' failed > > make[2]: *** [Test1] Error 1 > > CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/Test1.dir/all' failed > > make[1]: *** [CMakeFiles/Test1.dir/all] Error 2 > > Makefile:83: recipe for target 'all' failed > > make: *** [all] Error 2 > > Thanks, > > Yingjie > > > > Matthew Knepley ?2019?12?6??? ??11:46??? > > It sounds like your C++ compiler is name mangling the symbol, but the library has no mangling. > > Why are you using C++. > > > > Thanks, > > > > Matt > > > > On Fri, Dec 6, 2019 at 10:44 AM Yingjie Wu wrote: > > Hi, > > Thank you for your email. > > The error in the previous program was indeed due to the missing "SNESSetFromOptions". > > I use the /snes/example/tutorial/ex1.cpp as test case. However, I found that some of the statements in the program were not compiled and deleted the statements containing "MPI_Comm_size", but I don't know how to solve this problem. > > lerui at yu1994-ThinkPad-W520:~/tem2/build2$ cmake .. > > -- The C compiler identification is GNU 5.4.0 > > -- The CXX compiler identification is GNU 5.4.0 > > -- Check for working C compiler: /usr/bin/cc > > -- Check for working C compiler: /usr/bin/cc -- works > > -- Detecting C compiler ABI info > > -- Detecting C compiler ABI info - done > > -- Detecting C compile features > > -- Detecting C compile features - done > > -- Check for working CXX compiler: /usr/bin/c++ > > -- Check for working CXX compiler: /usr/bin/c++ -- works > > -- Detecting CXX compiler ABI info > > -- Detecting CXX compiler ABI info - done > > -- Detecting CXX compile features > > -- Detecting CXX compile features - done > > -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") > > -- Checking for one of the modules 'PETSc' > > pkg include dirs: /home/lerui/petsc-3.12.2/arch-linux2-c-debug/include;/home/lerui/petsc-3.12.2/include > > pkg include libs: petsc > > pkg ldflags: -L/home/lerui/petsc-3.12.2/arch-linux2-c-debug/lib;-lpetsc > > -- Configuring done > > -- Generating done > > -- Build files have been written to: /home/lerui/tem2/build2 > > lerui at yu1994-ThinkPad-W520:~/tem2/build2$ make > > Scanning dependencies of target main > > [ 50%] Building CXX object CMakeFiles/main.dir/ex1.cpp.o > > [100%] Linking CXX executable main > > /usr/bin/ld: CMakeFiles/main.dir/ex1.cpp.o: undefined reference to symbol 'MPI_Comm_size' > > /home/lerui/petsc-3.12.2/arch-linux2-c-debug/lib/libmpi.so.12: error adding symbols: DSO missing from command line > > collect2: error: ld returned 1 exit status > > CMakeFiles/main.dir/build.make:94: recipe for target 'main' failed > > make[2]: *** [main] Error 1 > > CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/main.dir/all' failed > > make[1]: *** [CMakeFiles/main.dir/all] Error 2 > > Makefile:83: recipe for target 'all' failed > > make: *** [all] Error 2 > > Thanks, > > Yingjie > > > > Jed Brown ?2019?12?6??? ??10:54??? > > Yingjie Wu writes: > > > > > I'm so sorry that I've ignored your previous advices. > > > > > > I added a global variable that seems works: > > > > > > > > > export > > > LD_LIBRARY_PATH=/home/lerui/petcs-3.12.2/arch-linux2-c-debug/lib:$LD_LIBRARY_PATH > > > > > > > > > How should I make petsc in a standard position?This eliminates the need to > > > set global variables. > > > > You can configure PETSc with --prefix=/your/standard/path, then make install. > > > > > It seems that some of the options before running fit become unavailable: > > > > > > > > > mpiexec -n 1 ./example01cmke -snes_view > > > > > > > > > Options-snes _ view are not used and how should I solve this problem? > > > > I don't have your ex1.cpp, but presumably you didn't SNESSetFromOptions? > > > > > > -- > > What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. > > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: CMakeLists.txt URL: From yjwu16 at gmail.com Mon Dec 9 08:37:02 2019 From: yjwu16 at gmail.com (Yingjie Wu) Date: Mon, 9 Dec 2019 22:37:02 +0800 Subject: [petsc-users] CMake error in PETSc In-Reply-To: <63433CEA-54BF-43E8-8FC5-FB9AFA7B294E@mcs.anl.gov> References: <875ziwkszv.fsf@jedbrown.org> <87zhg8jctx.fsf@jedbrown.org> <87r21jjqr8.fsf@jedbrown.org> <87zhg6j1gk.fsf@jedbrown.org> <63433CEA-54BF-43E8-8FC5-FB9AFA7B294E@mcs.anl.gov> Message-ID: Thank you for your response, Barry It works for me! I made some minor changes. I found that there was no petsc.pc in my pkgconfig folder, but PETSc.pc. So I rewrote it to: execute_process ( COMMAND pkg-config PETSc ......... And the program can run and will not report an DSO error. Thanks again for your help. Yingjie Smith, Barry F. ?2019?12?9??? ??9:56??? > > The problem is that your Cmake file knows nothing about the MPI > compilers that are required and hence just selects some random compilers it > found in the path which do not support MPI. > > I have attached a new CMakeList.txt for you to try. > > I uses the environmental variables PETSC_DIR and PETSC_ARCH to find the > configuration file AND use the compilers from the configuration file. It > works for me, please let me know if you have trouble. > > Barry > > > > > On Dec 8, 2019, at 10:38 PM, Yingjie Wu wrote: > > > > Thank you very much for your help. > > My programs are as follow > > Smith, Barry F. ?2019?12?9??? ??12:29??? > > > > There is something missing in the cmake process that is causing > needed libraries not to be linked. > > > > Please email your program and your CMake stuff (files you use) so we > can reproduce the problem and find a fix. > > > > Barry > > > > > > > On Dec 8, 2019, at 10:06 PM, Yingjie Wu wrote: > > > > > > Hi, > > > Thank you for your response. > > > This problem has not been solved. I've been reporting errors in the > process of 'make'. The test example I used comes from: /snes /example > /tutorials/ex3.c by modifying the suffix of ex3, there will be different > error messages as following. I checked a lot of DSO problems on the > Internet and installed a lot of libraries, but the error still haven't been > solved. I was wondering if I was missing any prefix during the configure of > PETSc(I use the simplest recommended installation), but there was no > problem when the program was compiled with the 'makefile' which is > recommended. Because I need some extra libraries, I have to use cmake. > > > with ex3.c: > > > yjwu at yjwu-XPS-8910:~/tem/build2$ make > > > Scanning dependencies of target Test1 > > > [ 50%] Building C object CMakeFiles/Test1.dir/ex3.c.o > > > [100%] Linking C executable Test1 > > > /usr/bin/ld: CMakeFiles/Test1.dir/ex3.c.o: undefined reference to > symbol 'pow@@GLIBC_2.2.5' > > > //lib/x86_64-linux-gnu/libm.so.6: error adding symbols: DSO missing > from command line > > > collect2: error: ld returned 1 exit status > > > CMakeFiles/Test1.dir/build.make:94: recipe for target 'Test1' failed > > > make[2]: *** [Test1] Error 1 > > > CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/Test1.dir/all' > failed > > > make[1]: *** [CMakeFiles/Test1.dir/all] Error 2 > > > Makefile:83: recipe for target 'all' failed > > > make: *** [all] Error 2 > > > with ex3.cpp: > > > yjwu at yjwu-XPS-8910:~/tem/build2$ make > > > Scanning dependencies of target Test1 > > > [ 50%] Building CXX object CMakeFiles/Test1.dir/ex3.cpp.o > > > [100%] Linking CXX executable Test1 > > > /usr/bin/ld: CMakeFiles/Test1.dir/ex3.cpp.o: undefined reference to > symbol 'MPI_Comm_rank' > > > /home/yjwu/petsc-3.12.2/arch-linux2-c-debug/lib/libmpi.so.12: error > adding symbols: DSO missing from command line > > > collect2: error: ld returned 1 exit status > > > CMakeFiles/Test1.dir/build.make:94: recipe for target 'Test1' failed > > > make[2]: *** [Test1] Error 1 > > > CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/Test1.dir/all' > failed > > > make[1]: *** [CMakeFiles/Test1.dir/all] Error 2 > > > Makefile:83: recipe for target 'all' failed > > > make: *** [all] Error 2 > > > Thanks, > > > Yingjie > > > > > > Matthew Knepley ?2019?12?6??? ??11:46??? > > > It sounds like your C++ compiler is name mangling the symbol, but the > library has no mangling. > > > Why are you using C++. > > > > > > Thanks, > > > > > > Matt > > > > > > On Fri, Dec 6, 2019 at 10:44 AM Yingjie Wu wrote: > > > Hi, > > > Thank you for your email. > > > The error in the previous program was indeed due to the missing > "SNESSetFromOptions". > > > I use the /snes/example/tutorial/ex1.cpp as test case. However, I > found that some of the statements in the program were not compiled and > deleted the statements containing "MPI_Comm_size", but I don't know how to > solve this problem. > > > lerui at yu1994-ThinkPad-W520:~/tem2/build2$ cmake .. > > > -- The C compiler identification is GNU 5.4.0 > > > -- The CXX compiler identification is GNU 5.4.0 > > > -- Check for working C compiler: /usr/bin/cc > > > -- Check for working C compiler: /usr/bin/cc -- works > > > -- Detecting C compiler ABI info > > > -- Detecting C compiler ABI info - done > > > -- Detecting C compile features > > > -- Detecting C compile features - done > > > -- Check for working CXX compiler: /usr/bin/c++ > > > -- Check for working CXX compiler: /usr/bin/c++ -- works > > > -- Detecting CXX compiler ABI info > > > -- Detecting CXX compiler ABI info - done > > > -- Detecting CXX compile features > > > -- Detecting CXX compile features - done > > > -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") > > > -- Checking for one of the modules 'PETSc' > > > pkg include dirs: > /home/lerui/petsc-3.12.2/arch-linux2-c-debug/include;/home/lerui/petsc-3.12.2/include > > > pkg include libs: petsc > > > pkg ldflags: -L/home/lerui/petsc-3.12.2/arch-linux2-c-debug/lib;-lpetsc > > > -- Configuring done > > > -- Generating done > > > -- Build files have been written to: /home/lerui/tem2/build2 > > > lerui at yu1994-ThinkPad-W520:~/tem2/build2$ make > > > Scanning dependencies of target main > > > [ 50%] Building CXX object CMakeFiles/main.dir/ex1.cpp.o > > > [100%] Linking CXX executable main > > > /usr/bin/ld: CMakeFiles/main.dir/ex1.cpp.o: undefined reference to > symbol 'MPI_Comm_size' > > > /home/lerui/petsc-3.12.2/arch-linux2-c-debug/lib/libmpi.so.12: error > adding symbols: DSO missing from command line > > > collect2: error: ld returned 1 exit status > > > CMakeFiles/main.dir/build.make:94: recipe for target 'main' failed > > > make[2]: *** [main] Error 1 > > > CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/main.dir/all' > failed > > > make[1]: *** [CMakeFiles/main.dir/all] Error 2 > > > Makefile:83: recipe for target 'all' failed > > > make: *** [all] Error 2 > > > Thanks, > > > Yingjie > > > > > > Jed Brown ?2019?12?6??? ??10:54??? > > > Yingjie Wu writes: > > > > > > > I'm so sorry that I've ignored your previous advices. > > > > > > > > I added a global variable that seems works: > > > > > > > > > > > > export > > > > > LD_LIBRARY_PATH=/home/lerui/petcs-3.12.2/arch-linux2-c-debug/lib:$LD_LIBRARY_PATH > > > > > > > > > > > > How should I make petsc in a standard position?This eliminates the > need to > > > > set global variables. > > > > > > You can configure PETSc with --prefix=/your/standard/path, then make > install. > > > > > > > It seems that some of the options before running fit become > unavailable: > > > > > > > > > > > > mpiexec -n 1 ./example01cmke -snes_view > > > > > > > > > > > > Options-snes _ view are not used and how should I solve this problem? > > > > > > I don't have your ex1.cpp, but presumably you didn't > SNESSetFromOptions? > > > > > > > > > -- > > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > > > -- Norbert Wiener > > > > > > https://www.cse.buffalo.edu/~knepley/ > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hgbk2008 at gmail.com Mon Dec 9 09:55:40 2019 From: hgbk2008 at gmail.com (hg) Date: Mon, 9 Dec 2019 16:55:40 +0100 Subject: [petsc-users] MatGetDiagonal In-Reply-To: References: Message-ID: I think the manual is also insufficient in this case. The vector must be VECMPI and contains only the portion in the local process. Is that correct? Giang On Wed, Jan 23, 2013 at 5:24 PM Nachiket Gokhale wrote: > Thanks, I guess I misinterpreted the manual. > > -Nachiket > > On Wed, Jan 23, 2013 at 11:20 AM, Jed Brown wrote: > > It works in serial. In parallel, it currently gives the diagonal of the > > "diagonal blocks" induced by the row and column distributions. That only > > matches the true diagonal for square matrices, though an actual diagonal > > doesn't typically make algorithmic sense for a non-square parallel > matrix. > > > > > > On Wed, Jan 23, 2013 at 10:16 AM, Nachiket Gokhale > > wrote: > >> > >> Any chance of making this work in serial? > >> > >> > >> > http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatGetDiagonal.html > >> > >> Not a show stopper, I am trying to get the diagonal of some small > >> projected, dense matrices (which come from large sparse matrices). I > >> am running in serial because 1) Since my projected matrices are small, > >> and 2) PETSc does not do certain matrix multiplications involving a > >> dense matrix in parallel, > >> > >> -Nachiket > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mfadams at lbl.gov Mon Dec 9 11:31:00 2019 From: mfadams at lbl.gov (Mark Adams) Date: Mon, 9 Dec 2019 12:31:00 -0500 Subject: [petsc-users] MatGetDiagonal In-Reply-To: References: Message-ID: On Mon, Dec 9, 2019 at 10:57 AM hg wrote: > I think the manual is also insufficient in this case. The vector must be > VECMPI and contains only the portion in the local process. Is that correct? > The vector and matrix (row) maps must match. This is assumed for any method that I can think of that takes a matrix and a vector(s). This will dictate if its MPI and the data layout. Perhaps there is some ambiguity as to whether it is the row or column map, but they are usually the same for a square matrix and MatGetDiagonal makes no sense for a rectangular matrix. > > Giang > > > On Wed, Jan 23, 2013 at 5:24 PM Nachiket Gokhale > wrote: > >> Thanks, I guess I misinterpreted the manual. >> >> -Nachiket >> >> On Wed, Jan 23, 2013 at 11:20 AM, Jed Brown wrote: >> > It works in serial. In parallel, it currently gives the diagonal of the >> > "diagonal blocks" induced by the row and column distributions. That only >> > matches the true diagonal for square matrices, though an actual diagonal >> > doesn't typically make algorithmic sense for a non-square parallel >> matrix. >> > >> > >> > On Wed, Jan 23, 2013 at 10:16 AM, Nachiket Gokhale >> > wrote: >> >> >> >> Any chance of making this work in serial? >> >> >> >> >> >> >> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatGetDiagonal.html >> >> >> >> Not a show stopper, I am trying to get the diagonal of some small >> >> projected, dense matrices (which come from large sparse matrices). I >> >> am running in serial because 1) Since my projected matrices are small, >> >> and 2) PETSc does not do certain matrix multiplications involving a >> >> dense matrix in parallel, >> >> >> >> -Nachiket >> > >> > >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hgbk2008 at gmail.com Mon Dec 9 11:51:24 2019 From: hgbk2008 at gmail.com (hg) Date: Mon, 9 Dec 2019 18:51:24 +0100 Subject: [petsc-users] MatGetDiagonal In-Reply-To: References: Message-ID: Dear Mark Yes, that is correct. I'm working on square matrix all the time. My point is that looking initially in the manual page of MatGetDiagonal: https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatGetDiagonal.html one does not automatically know what is the resultant vector is. After some investigation (coding + printing) I know that would be a VECMPI if the matrix is MPIAIJ. In my case I would like to get an image of the global diagonal in the local proc, subsequently I have to use VecScatter to get it. Giang On Mon, Dec 9, 2019 at 6:31 PM Mark Adams wrote: > > > On Mon, Dec 9, 2019 at 10:57 AM hg wrote: > >> I think the manual is also insufficient in this case. The vector must be >> VECMPI and contains only the portion in the local process. Is that correct? >> > > The vector and matrix (row) maps must match. This is assumed for any > method that I can think of that takes a matrix and a vector(s). This will > dictate if its MPI and the data layout. > > Perhaps there is some ambiguity as to whether it is the row or column map, > but they are usually the same for a square matrix and MatGetDiagonal makes > no sense for a rectangular matrix. > > >> >> Giang >> >> >> On Wed, Jan 23, 2013 at 5:24 PM Nachiket Gokhale >> wrote: >> >>> Thanks, I guess I misinterpreted the manual. >>> >>> -Nachiket >>> >>> On Wed, Jan 23, 2013 at 11:20 AM, Jed Brown >>> wrote: >>> > It works in serial. In parallel, it currently gives the diagonal of the >>> > "diagonal blocks" induced by the row and column distributions. That >>> only >>> > matches the true diagonal for square matrices, though an actual >>> diagonal >>> > doesn't typically make algorithmic sense for a non-square parallel >>> matrix. >>> > >>> > >>> > On Wed, Jan 23, 2013 at 10:16 AM, Nachiket Gokhale >> > >>> > wrote: >>> >> >>> >> Any chance of making this work in serial? >>> >> >>> >> >>> >> >>> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatGetDiagonal.html >>> >> >>> >> Not a show stopper, I am trying to get the diagonal of some small >>> >> projected, dense matrices (which come from large sparse matrices). I >>> >> am running in serial because 1) Since my projected matrices are small, >>> >> and 2) PETSc does not do certain matrix multiplications involving a >>> >> dense matrix in parallel, >>> >> >>> >> -Nachiket >>> > >>> > >>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Tue Dec 10 07:56:58 2019 From: bsmith at mcs.anl.gov (Smith, Barry F.) Date: Tue, 10 Dec 2019 13:56:58 +0000 Subject: [petsc-users] MatView to disk for Elemental In-Reply-To: References: <75260EC0-091E-4635-AF17-9CDB72A6CA3F@mcs.anl.gov> Message-ID: <3D4AF666-F7CB-4BC0-9287-2A7DF590704F@mcs.anl.gov> What went wrong. Since you don't have write access to the repository you will need to make a fork and then make a MR off the fork. Send all details including screen shots of what fails, we've had other people do it in the past Barry > On Dec 9, 2019, at 7:59 PM, Marius Buerkle wrote: > > Hi, > > Is it actually possible to submit a pull (merge) request ? I followed the petsc wiki but this didn't work. > > Best > Marius > > > Gesendet: Donnerstag, 05. Dezember 2019 um 07:45 Uhr > Von: "Marius Buerkle" > An: "Smith, Barry F." > Cc: "PETSc users list" > Betreff: Re: [petsc-users] MatView to disk for Elemental > Doesn't look difficult to fix, I can do it and create a pull request. > > > Von: "Smith, Barry F." > An: "Marius Buerkle" > Cc: "PETSc users list" > Betreff: Re: [petsc-users] MatView to disk for Elemental > > Agreed, the fix for the bug you found is now in maint I will try to do another MR that fixes this; but lots to do today so may take a while. > > Barry > > > > > On Dec 4, 2019, at 1:02 AM, Marius Buerkle wrote: > > > > thanks for the swift fix it works now. One more question though. It still outputs "Elemental matrix (explicit ordering)" to StdOut which is kinda annoying, is there anyway to turn this off? > > > > > > Von: "Smith, Barry F." > > An: "Marius Buerkle" > > Cc: "petsc-users at mcs.anl.gov" > > Betreff: Re: [petsc-users] MatView to disk for Elemental > > > > sorry about this. The numerical values between C and Fortran got out of sync. I've attached a patch file you can apply with > > > > patch -p1 < format.patch > > > > > > or you can use the branch https://gitlab.com/petsc/petsc/merge_requests/2346 > > > > Barry > > > > > > > On Dec 3, 2019, at 1:10 AM, Marius Buerkle wrote: > > > > > > Hi, > > > > > > I try to save a matrix in Elemental format to disk. I am doing, where p_matout is of type MATELEMENTAL, > > > > > > call PetscViewerCreate(PETSC_COMM_WORLD,v_file,ierr) > > > call PetscViewerPushFormat(v_file,PETSC_VIEWER_NATIVE,ierr) > > > call PetscViewerSetType(v_file,PETSCVIEWERBINARY,ierr) > > > call PetscViewerFileSetMode(v_file,FILE_MODE_WRITE,ierr) > > > call PetscViewerFileSetName(v_file,trim(filename),ierr) > > > call MatView(p_matout,v_file,ierr) > > > call PetscViewerDestroy(v_file,ierr) > > > > > > This gives the following error > > > [18]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- > > > [18]PETSC ERROR: No support for this operation for this object type > > > [18]PETSC ERROR: To store a parallel dense matrix you must first call PetscViewerPushFormat(viewer,PETSC_VIEWER_NATIVE) > > > [18]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. > > > [18]PETSC ERROR: Petsc Development GIT revision: v3.12.1-317-gcc59f4f82c GIT Date: 2019-11-08 00:07:59 -0600 > > > [18]PETSC ERROR: /home/marius/prog/ownstuff/fortran/programs/transomat_dev/save_load_fs/transomat/transomat on a named tono-hpc1 by marius Tue Dec 3 16:08:38 2019 > > > [18]PETSC ERROR: Configure options --prefix=/home/marius/prog/petsc/petsc_slepc_opt --with-scalar-type=complex --with-fortran-kernels=1 --with-64-bit-indices=0 --CC=mpicc --COPTFLAGS="-g -Ofast -std=c11 -qopenmmp" --CXX=mpicxx --CXXOPTFLAGS="-g -Ofast -std=c++14 -qopenmp" --FC=mpif90 --FOPTFLAGS="-g -Ofast -traceback -qopenmp" --with-mpi=1 --with-x=0 --download-parmetis=1 --download-metis=1 --download-superlu_dist=1 --download-superlu_dist-commit=f8ace664ec4ca10e96e258a764552cbda299ba6e --download-superlu_dist-cmake-arguments=-Denable_openmp:BOOL=TRUE --download-hwloc=1 --download-sowing=1 --with-openmp=1 --with-pthread=1 --download-elemental=1 --download-elemental-commit=6eb15a0da2a4998bf1cf971ae231b78e06d989d9 --download-elemental-cmake-arguments=-DEL_HYBRID:BOOL=TRUE --with-cxx-dialect=c++11 --with-debugging=0 --with-valgrind=0 --with-blaslapack-lib=" /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a -Wl,--start-group /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_intel_lp64.a /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_intel_thread.a /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_core.a /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.a -Wl,--end-group -liomp5 -lpthread -lm -ldl -lmpi_wrapper" --with-scalapack-lib=" /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a -Wl,--start-group /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_intel_lp64.a /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_intel_thread.a /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_core.a /home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.a -Wl,--end-group -liomp5 -lpthread -lm -ldl -lmpi_wrapper" --with-mkl_pardiso-dir=/home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl --with-mkl_cpardiso-dir=/home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl --with-mkl_sparse-dir=/home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl --with-mkl_sparse_optimize-dir=/home/marius/intel/compilers_and_libraries_2019.5.281/linux/mkl --download-slepc=1 --download-slepc-commit=658271f --download-make=1 --download-cmake=1 > > > [18]PETSC ERROR: #1 MatView_MPIDense_Binary() line 682 in /home/marius/prog/petsc/git/petsc/src/mat/impls/dense/mpi/mpidense.c > > > [18]PETSC ERROR: #2 MatView_MPIDense() line 786 in /home/marius/prog/petsc/git/petsc/src/mat/impls/dense/mpi/mpidense.c > > > [18]PETSC ERROR: #3 MatView() line 1066 in /home/marius/prog/petsc/git/petsc/src/mat/interface/matrix.c > > > [18]PETSC ERROR: #4 MatView_Elemental() line 83 in /home/marius/prog/petsc/git/petsc/src/mat/impls/elemental/matelem.cxx > > > [18]PETSC ERROR: #5 MatView() line 1066 in /home/marius/prog/petsc/git/petsc/src/mat/interface/matrix.c > > > [19]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- > > > > > > > > > and on StdOut > > > Elemental matrix (explicit ordering) > > > > > > Any suggestions? > > > > > > Best, > > > Marius > > > From perceval.desforges at polytechnique.edu Tue Dec 10 11:36:04 2019 From: perceval.desforges at polytechnique.edu (Perceval Desforges) Date: Tue, 10 Dec 2019 18:36:04 +0100 Subject: [petsc-users] Memory optimization In-Reply-To: References: <7e97478cd26eb88d653bfd7617e92f18@polytechnique.edu> <852862500ebf52db0edde47a63ce8ae7@polytechnique.edu> <9177FF06-92F4-40E4-8CF6-4A2995C17072@dsic.upv.es> <792624a5b70858444b7e529ce3624395@polytechnique.edu> <0007da7378494d3bdb15c219872d3359@polytechnique.edu> Message-ID: <512643d3fb3ab2128cc1e6978af1c7e3@polytechnique.edu> Hello again, I have tried following your advice to use preconditioned iterative solvers for my 3D systems, and have been encountering some difficulties. I have been following the recommendations of section 3.4.1 of the slepc user's manual, setting the following options: -st_ksp_type gmres -ksp_gmres_modifiedgramschmidt -st_pc_type asm -st_sub_pc_type lu -st_ksp_rtol 1e-9 -st_ksp_converged_reason -st_ksp_monitor_true_residual. The problem is that the code converges quite rapidly for the first eigenvalues (at around 0.4 in my case, and in about 20 iterations for each). The last eigenvalue obtained is a bit higher than 0,5. However, when I set the shift to 0.5, it does not converge even after 10000 iterations, and the residual norm is still at around 0,01. This only seems to be happening when my matrix is large enough (10^6 by 10^6). Is there something obvious I am doing wrong? Thanks for your time, Regards, Perceval, > In 3D problems it is recommended to use preconditioned iterative solvers. Unfortunately the spectrum slicing technique requires the full factorization (because it uses matrix inertia). > > El 25 nov 2019, a las 18:44, Perceval Desforges escribi?: > > I am basically trying to solve a finite element problem, which is why in 3D I have 7 non-zero diagonals that are quite farm apart from one another. In 2D I only have 5 non-zero diagonals that are less far apart. So is it normal that the set up time is around 400 times greater in the 3D case? Is there nothing to be done? > > I will try setting up only one partition. > > Thanks, > > Perceval, > > Probably it is not a preallocation issue, as it shows "total number of mallocs used during MatSetValues calls =0". > > Adding new diagonals may increase fill-in a lot, if the new diagonals are displaced with respect to the other ones. > > The partitions option is intended for running several nodes. If you are using just one node probably it is better to set one partition only. > > Jose > > El 25 nov 2019, a las 18:25, Matthew Knepley escribi?: > > On Mon, Nov 25, 2019 at 11:20 AM Perceval Desforges wrote: > Hi, > > So I'm loading two matrices from files, both 1000000 by 10000000. I ran the program with -mat_view::ascii_info and I got: > > Mat Object: 1 MPI processes > type: seqaij > rows=1000000, cols=1000000 > total: nonzeros=7000000, allocated nonzeros=7000000 > total number of mallocs used during MatSetValues calls =0 > not using I-node routines > > 20 times, and then > > Mat Object: 1 MPI processes > type: seqaij > rows=1000000, cols=1000000 > total: nonzeros=1000000, allocated nonzeros=1000000 > total number of mallocs used during MatSetValues calls =0 > not using I-node routines > > 20 times as well, and then > > Mat Object: 1 MPI processes > type: seqaij > rows=1000000, cols=1000000 > total: nonzeros=7000000, allocated nonzeros=7000000 > total number of mallocs used during MatSetValues calls =0 > not using I-node routines > > 20 times as well before crashing. > > I realized it might be because I am setting up 20 krylov schur partitions which may be too much. I tried running the code again with only 2 partitions and now the code runs but I have speed issues. > > I have one version of the code where my first matrix has 5 non-zero diagonals (so 5000000 non-zero entries), and the set up time is quite fast (8 seconds) and solving is also quite fast. The second version is the same but I have two extra non-zero diagonals (7000000 non-zero entries) and the set up time is a lot slower (2900 seconds ~ 50 minutes) and solving is also a lot slower. Is it normal that adding two extra diagonals increases solve and set up time so much? > > I can't see the rest of your code, but I am guessing your preallocation statement has "5", so it does no mallocs when you create > your first matrix, but mallocs for every row when you create your second matrix. When you load them from disk, we do all the > preallocation correctly. > > Thanks, > > Matt > Thanks again, > > Best regards, > > Perceval, > > Then I guess it is the factorization that is failing. How many nonzero entries do you have? Run with > -mat_view ::ascii_info > > Jose > > El 22 nov 2019, a las 19:56, Perceval Desforges escribi?: > > Hi, > > Thanks for your answer. I tried looking at the inertias before solving, but the problem is that the program crashes when I call EPSSetUp with this error: > > slurmstepd: error: Step 2140.0 exceeded virtual memory limit (313526508 > 107317760), being killed > > I get this error even when there are no eigenvalues in the interval. > > I've started using BVMAT instead of BVVECS by the way. > > Thanks, > > Perceval, > > Don't use -mat_mumps_icntl_14 to reduce the memory used by MUMPS. > > Most likely the problem is that the interval you gave is too large and contains too many eigenvalues (SLEPc needs to allocate at least one vector per each eigenvalue). You can count the eigenvalues in the interval with the inertias, which are available at EPSSetUp (no need to call EPSSolve). See this example: > http://slepc.upv.es/documentation/current/src/eps/examples/tutorials/ex25.c.html > You can comment out the call to EPSSolve() and run with the option -show_inertias > For example, the output > Shift 0.1 Inertia 3 > Shift 0.35 Inertia 11 > means that the interval [0.1,0.35] contains 8 eigenvalues (=11-3). > > By the way, I would suggest using BVMAT instead of BVVECS (the latter is slower). > > Jose > > El 21 nov 2019, a las 18:13, Perceval Desforges via petsc-users escribi?: > > Hello all, > > I am trying to obtain all the eigenvalues in a certain interval for a fairly large matrix (1000000 * 1000000). I therefore use the spectrum slicing method detailed in section 3.4.5 of the manual. The calculations are run on a processor with 20 cores and 96 Go of RAM. > > The options I use are : > > -bv_type vecs -eps_krylovschur_detect_zeros 1 -mat_mumps_icntl_13 1 -mat_mumps_icntl_24 1 -mat_mumps_cntl_3 1e-12 > > However the program quickly crashes with this error: > > slurmstepd: error: Step 2115.0 exceeded virtual memory limit (312121084 > 107317760), being killed > > I've tried reducing the amount of memory used by slepc with the -mat_mumps_icntl_14 option by setting it at -70 for example but then I get this error: > > [1]PETSC ERROR: Error in external library > [1]PETSC ERROR: Error reported by MUMPS in numerical factorization phase: INFOG(1)=-9, INFO(2)=82733614 > > which is an error due to setting the mumps icntl option so low from what I've gathered. > > Is there any other way I can reduce memory usage? > > Thanks, > > Regards, > > Perceval, > > P.S. I sent the same email a few minutes ago but I think I made a mistake in the address, I'm sorry if I've sent it twice. -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jroman at dsic.upv.es Tue Dec 10 11:42:39 2019 From: jroman at dsic.upv.es (Jose E. Roman) Date: Tue, 10 Dec 2019 18:42:39 +0100 Subject: [petsc-users] Memory optimization In-Reply-To: <512643d3fb3ab2128cc1e6978af1c7e3@polytechnique.edu> References: <7e97478cd26eb88d653bfd7617e92f18@polytechnique.edu> <852862500ebf52db0edde47a63ce8ae7@polytechnique.edu> <9177FF06-92F4-40E4-8CF6-4A2995C17072@dsic.upv.es> <792624a5b70858444b7e529ce3624395@polytechnique.edu> <0007da7378494d3bdb15c219872d3359@polytechnique.edu> <512643d3fb3ab2128cc1e6978af1c7e3@polytechnique.edu> Message-ID: <6ECC30F8-CBDD-4068-8822-A5A15141A56F@dsic.upv.es> I guess conditioning is getting worse. I would try using MUMPS for the sub_pc LU. Jose > El 10 dic 2019, a las 18:36, Perceval Desforges escribi?: > > Hello again, > > I have tried following your advice to use preconditioned iterative solvers for my 3D systems, and have been encountering some difficulties. > I have been following the recommendations of section 3.4.1 of the slepc user's manual, setting the following options: -st_ksp_type gmres -ksp_gmres_modifiedgramschmidt -st_pc_type asm -st_sub_pc_type lu -st_ksp_rtol 1e-9 -st_ksp_converged_reason -st_ksp_monitor_true_residual. > > The problem is that the code converges quite rapidly for the first eigenvalues (at around 0.4 in my case, and in about 20 iterations for each). The last eigenvalue obtained is a bit higher than 0,5. However, when I set the shift to 0.5, it does not converge even after 10000 iterations, and the residual norm is still at around 0,01. > > This only seems to be happening when my matrix is large enough (10^6 by 10^6). > > Is there something obvious I am doing wrong? > > Thanks for your time, > > Regards, > > Perceval, > > > >> In 3D problems it is recommended to use preconditioned iterative solvers. Unfortunately the spectrum slicing technique requires the full factorization (because it uses matrix inertia). >> >> >>> El 25 nov 2019, a las 18:44, Perceval Desforges escribi?: >>> >>> I am basically trying to solve a finite element problem, which is why in 3D I have 7 non-zero diagonals that are quite farm apart from one another. In 2D I only have 5 non-zero diagonals that are less far apart. So is it normal that the set up time is around 400 times greater in the 3D case? Is there nothing to be done? >>> >>> I will try setting up only one partition. >>> >>> Thanks, >>> >>> Perceval, >>> >>>> Probably it is not a preallocation issue, as it shows "total number of mallocs used during MatSetValues calls =0". >>>> >>>> Adding new diagonals may increase fill-in a lot, if the new diagonals are displaced with respect to the other ones. >>>> >>>> The partitions option is intended for running several nodes. If you are using just one node probably it is better to set one partition only. >>>> >>>> Jose >>>> >>>> >>>>> El 25 nov 2019, a las 18:25, Matthew Knepley escribi?: >>>>> >>>>> On Mon, Nov 25, 2019 at 11:20 AM Perceval Desforges wrote: >>>>> Hi, >>>>> >>>>> So I'm loading two matrices from files, both 1000000 by 10000000. I ran the program with -mat_view::ascii_info and I got: >>>>> >>>>> Mat Object: 1 MPI processes >>>>> type: seqaij >>>>> rows=1000000, cols=1000000 >>>>> total: nonzeros=7000000, allocated nonzeros=7000000 >>>>> total number of mallocs used during MatSetValues calls =0 >>>>> not using I-node routines >>>>> >>>>> 20 times, and then >>>>> >>>>> Mat Object: 1 MPI processes >>>>> type: seqaij >>>>> rows=1000000, cols=1000000 >>>>> total: nonzeros=1000000, allocated nonzeros=1000000 >>>>> total number of mallocs used during MatSetValues calls =0 >>>>> not using I-node routines >>>>> >>>>> 20 times as well, and then >>>>> >>>>> Mat Object: 1 MPI processes >>>>> type: seqaij >>>>> rows=1000000, cols=1000000 >>>>> total: nonzeros=7000000, allocated nonzeros=7000000 >>>>> total number of mallocs used during MatSetValues calls =0 >>>>> not using I-node routines >>>>> >>>>> 20 times as well before crashing. >>>>> >>>>> I realized it might be because I am setting up 20 krylov schur partitions which may be too much. I tried running the code again with only 2 partitions and now the code runs but I have speed issues. >>>>> >>>>> I have one version of the code where my first matrix has 5 non-zero diagonals (so 5000000 non-zero entries), and the set up time is quite fast (8 seconds) and solving is also quite fast. The second version is the same but I have two extra non-zero diagonals (7000000 non-zero entries) and the set up time is a lot slower (2900 seconds ~ 50 minutes) and solving is also a lot slower. Is it normal that adding two extra diagonals increases solve and set up time so much? >>>>> >>>>> >>>>> I can't see the rest of your code, but I am guessing your preallocation statement has "5", so it does no mallocs when you create >>>>> your first matrix, but mallocs for every row when you create your second matrix. When you load them from disk, we do all the >>>>> preallocation correctly. >>>>> >>>>> Thanks, >>>>> >>>>> Matt >>>>> Thanks again, >>>>> >>>>> Best regards, >>>>> >>>>> Perceval, >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>> Then I guess it is the factorization that is failing. How many nonzero entries do you have? Run with >>>>>> -mat_view ::ascii_info >>>>>> >>>>>> Jose >>>>>> >>>>>> >>>>>>> El 22 nov 2019, a las 19:56, Perceval Desforges escribi?: >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> Thanks for your answer. I tried looking at the inertias before solving, but the problem is that the program crashes when I call EPSSetUp with this error: >>>>>>> >>>>>>> slurmstepd: error: Step 2140.0 exceeded virtual memory limit (313526508 > 107317760), being killed >>>>>>> >>>>>>> I get this error even when there are no eigenvalues in the interval. >>>>>>> >>>>>>> I've started using BVMAT instead of BVVECS by the way. >>>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> Perceval, >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>> Don't use -mat_mumps_icntl_14 to reduce the memory used by MUMPS. >>>>>>>> >>>>>>>> Most likely the problem is that the interval you gave is too large and contains too many eigenvalues (SLEPc needs to allocate at least one vector per each eigenvalue). You can count the eigenvalues in the interval with the inertias, which are available at EPSSetUp (no need to call EPSSolve). See this example: >>>>>>>> http://slepc.upv.es/documentation/current/src/eps/examples/tutorials/ex25.c.html >>>>>>>> You can comment out the call to EPSSolve() and run with the option -show_inertias >>>>>>>> For example, the output >>>>>>>> Shift 0.1 Inertia 3 >>>>>>>> Shift 0.35 Inertia 11 >>>>>>>> means that the interval [0.1,0.35] contains 8 eigenvalues (=11-3). >>>>>>>> >>>>>>>> By the way, I would suggest using BVMAT instead of BVVECS (the latter is slower). >>>>>>>> >>>>>>>> Jose >>>>>>>> >>>>>>>> >>>>>>>>> El 21 nov 2019, a las 18:13, Perceval Desforges via petsc-users escribi?: >>>>>>>>> >>>>>>>>> Hello all, >>>>>>>>> >>>>>>>>> I am trying to obtain all the eigenvalues in a certain interval for a fairly large matrix (1000000 * 1000000). I therefore use the spectrum slicing method detailed in section 3.4.5 of the manual. The calculations are run on a processor with 20 cores and 96 Go of RAM. >>>>>>>>> >>>>>>>>> The options I use are : >>>>>>>>> >>>>>>>>> -bv_type vecs -eps_krylovschur_detect_zeros 1 -mat_mumps_icntl_13 1 -mat_mumps_icntl_24 1 -mat_mumps_cntl_3 1e-12 >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> However the program quickly crashes with this error: >>>>>>>>> >>>>>>>>> slurmstepd: error: Step 2115.0 exceeded virtual memory limit (312121084 > 107317760), being killed >>>>>>>>> >>>>>>>>> I've tried reducing the amount of memory used by slepc with the -mat_mumps_icntl_14 option by setting it at -70 for example but then I get this error: >>>>>>>>> >>>>>>>>> [1]PETSC ERROR: Error in external library >>>>>>>>> [1]PETSC ERROR: Error reported by MUMPS in numerical factorization phase: INFOG(1)=-9, INFO(2)=82733614 >>>>>>>>> >>>>>>>>> which is an error due to setting the mumps icntl option so low from what I've gathered. >>>>>>>>> >>>>>>>>> Is there any other way I can reduce memory usage? >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> >>>>>>>>> Regards, >>>>>>>>> >>>>>>>>> Perceval, >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> P.S. I sent the same email a few minutes ago but I think I made a mistake in the address, I'm sorry if I've sent it twice. >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. >>>>> -- Norbert Wiener >>>>> >>>>> https://www.cse.buffalo.edu/~knepley/ >>> > > From griesser.jan at googlemail.com Mon Dec 16 10:08:10 2019 From: griesser.jan at googlemail.com (=?UTF-8?B?SmFuIEdyaWXDn2Vy?=) Date: Mon, 16 Dec 2019 17:08:10 +0100 Subject: [petsc-users] Corrrect usage of MatMumpsGetInverse() Message-ID: Hello, everybody, I am using PETSc version 3.12 together with MUMPS to calculate a part of an inverse from a matrix A. For this I used the example mat/examples/tests/ex214.c as suggested here in the forum. For test purposes I read a matrix with the dimension 10x10, which only has entries on the main diagonal, because I know the inverse of it. But now I have a problem using the MatMumpsGetInverse() function. I get the error message: Error reported by MUMPS in solve phase: INFOG(1)=-47 INFO(2)=1 ACcording to the MUMPS Docu this message tells me that I would ignored the constraint NRHS= N. I checked the shape of spRHST but they appear to be correct. Does anyone see the error? My code is appended below. static char help[] ="Compute a part of the inverse of a sparse matrix. This code requires that PETSc was configured with MUMPS since we are dealing with large matrices \ and therefore use a parallel LU factorization. We compute the inverse by solving the equation A*X=RHS. Where A is our Matrix, X is the inverse and RHS is the identity matrix.\ Note that the number of columns nrhs of X can be chosen smaller than the number of columns N in A. Therefore only a part of the inverse is computed in X. \n \ In this code we use a sparse representation of the RHS matrix in MUMPS in csr format. Computation of selected entries in inv(A) is done using MatMumpsGetInverse. \n \ Input parameters: \n\ -fin : file to load \n \ -fout : file to load \n \ -nrhs : Number of columns to compute \n \ -displ : Print matrices to terminal \n\ Example usage: \n \ mpiexec -np 2 ./compute_inverse_sparse_rhs -fin ../../convert_to_binary_petsc_matrix/identity_matrix_prefactor3_ncols10 -nrhs 5 -displ"; #include #include #include int main(int argc, char **args){ PetscErrorCode ierr; // Datatype used for return error code PetscMPIInt size,rank; // Datatype used to represent 'int' parameters to MPI functions. #if defined(PETSC_HAVE_MUMPS) Mat A,F,spRHST; // Abstract PETSc matrix object used to manage all linear operators in PETSc PetscViewer fd; // Abstract PETSc object that helps view (in ASCII, binary, graphically etc) other PETSc objects PetscBool flg1,flg2; // Logical variable. Actually an int in C. PetscBool displ=PETSC_FALSE; // Display matrices PetscInt M,N,m,n,rstart,rend,nrhs,i; // PETSc type that represents an integer, used primarily to represent size of arrays and indexing into arrays. PetscScalar v; // PETSc type that represents either a double precision real number,... char inputfile[1][PETSC_MAX_PATH_LEN]; // Input file name // char outputfile[1][PETSC_MAX_PATH_LEN]; // Outputfile file name #endif // Initializes PETSc and MPI. Get size and rank of MPI. ierr = PetscInitialize(&argc, &args, (char*)0, help);if (ierr){return ierr;} ierr = MPI_Comm_size(PETSC_COMM_WORLD, &size);CHKERRQ(ierr); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); //Check if PETSc was configured with MUMPS. If not print error message and exit #if !defined(PETSC_HAVE_MUMPS) if (!=rank){ierr = PetscPrintf(PETSC_COMM_SELF, "This code requires MUMPS, exit...\n");CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; } #else // Check if displ is set. If True the matrices are printed to the terminal ierr = PetscOptionsGetBool(NULL, NULL, "-displ", &displ, NULL);CHKERRQ(ierr); // Load matrix A from file ierr = PetscOptionsGetString(NULL, NULL, "-fin" ,inputfile[0], PETSC_MAX_PATH_LEN, &flg1);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Load matrix in: %s \n", inputfile[0]);CHKERRQ(ierr); ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD, inputfile[0], FILE_MODE_READ, &fd);CHKERRQ(ierr); ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr); ierr = MatSetType(A, MATAIJ);CHKERRQ(ierr); ierr = MatLoad(A, fd);CHKERRQ(ierr); // Print matrix A if (displ){ ierr = PetscPrintf(PETSC_COMM_WORLD, "\n---------------\n");CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"Matrix A from file:\n", nrhs); ierr = MatView(A, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "\n");CHKERRQ(ierr); } // Check if matrix is quadratic ierr = MatGetSize(A, &M, &N);CHKERRQ(ierr); ierr = MatGetLocalSize(A, &m, &n);CHKERRQ(ierr); if (M != N){ //Macro that is called when an error has been detected. SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Detected a rectangular matrix: (%d, %d)", M, N); } ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "---------------\n");CHKERRQ(ierr); ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD, "Ownership ranges for Matrix A, rank: %i, size: %i, rstart: %i, rend: %i \n", rank, size, rstart, rend);CHKERRQ(ierr); ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD, PETSC_STDOUT);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "---------------\n");CHKERRQ(ierr); // Set the number of columns of the inverse to be computed. nrhs = N; ierr = PetscOptionsGetInt(NULL, NULL, "-nrhs", &nrhs, &flg2);CHKERRQ(ierr); // Create SpRHST for inv(A) with sparse RHS stored in the host. // PETSc does not support compressed column format which is required by MUMPS for sparse RHS matrix, // thus user must create spRHST=spRHS^T and call MatMatTransposeSolve() // User must create B^T in sparse compressed row format on the host processor and call MatMatTransposeSolve() to implement MUMPS' MatMatSolve(). // MUMPS requires nrhs = N ierr = MatCreate(PETSC_COMM_WORLD, &spRHST);CHKERRQ(ierr); if (!rank){ ierr = MatSetSizes(spRHST,N,M,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); } else{ ierr = MatSetSizes(spRHST,0,0,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); } ierr = MatSetType(spRHST,MATAIJ);CHKERRQ(ierr); ierr = MatSetFromOptions(spRHST);CHKERRQ(ierr); ierr = MatSetUp(spRHST);CHKERRQ(ierr); if (!rank){ v = 1.0; for(i=0;i From hzhang at mcs.anl.gov Mon Dec 16 15:57:17 2019 From: hzhang at mcs.anl.gov (Zhang, Hong) Date: Mon, 16 Dec 2019 21:57:17 +0000 Subject: [petsc-users] Corrrect usage of MatMumpsGetInverse() In-Reply-To: References: Message-ID: Jan: You found a bug in our interface. I pushed a fix https://gitlab.com/petsc/petsc/commit/6fa4709e1488f7c58b0a4ecbdf34b75ae4ac64d2 in branch hzhang/fix-mumps-GetInverse. You may give it a try by 'git checkout hzhang/fix-mumps-GetInverse' at PETSC_DIR and rebuild petsc. Let me know if it fixes the issue. Hong Hello, everybody, I am using PETSc version 3.12 together with MUMPS to calculate a part of an inverse from a matrix A. For this I used the example mat/examples/tests/ex214.c as suggested here in the forum. For test purposes I read a matrix with the dimension 10x10, which only has entries on the main diagonal, because I know the inverse of it. But now I have a problem using the MatMumpsGetInverse() function. I get the error message: Error reported by MUMPS in solve phase: INFOG(1)=-47 INFO(2)=1 ACcording to the MUMPS Docu this message tells me that I would ignored the constraint NRHS= N. I checked the shape of spRHST but they appear to be correct. Does anyone see the error? My code is appended below. static char help[] ="Compute a part of the inverse of a sparse matrix. This code requires that PETSc was configured with MUMPS since we are dealing with large matrices \ and therefore use a parallel LU factorization. We compute the inverse by solving the equation A*X=RHS. Where A is our Matrix, X is the inverse and RHS is the identity matrix.\ Note that the number of columns nrhs of X can be chosen smaller than the number of columns N in A. Therefore only a part of the inverse is computed in X. \n \ In this code we use a sparse representation of the RHS matrix in MUMPS in csr format. Computation of selected entries in inv(A) is done using MatMumpsGetInverse. \n \ Input parameters: \n\ -fin : file to load \n \ -fout : file to load \n \ -nrhs : Number of columns to compute \n \ -displ : Print matrices to terminal \n\ Example usage: \n \ mpiexec -np 2 ./compute_inverse_sparse_rhs -fin ../../convert_to_binary_petsc_matrix/identity_matrix_prefactor3_ncols10 -nrhs 5 -displ"; #include #include #include int main(int argc, char **args){ PetscErrorCode ierr; // Datatype used for return error code PetscMPIInt size,rank; // Datatype used to represent 'int' parameters to MPI functions. #if defined(PETSC_HAVE_MUMPS) Mat A,F,spRHST; // Abstract PETSc matrix object used to manage all linear operators in PETSc PetscViewer fd; // Abstract PETSc object that helps view (in ASCII, binary, graphically etc) other PETSc objects PetscBool flg1,flg2; // Logical variable. Actually an int in C. PetscBool displ=PETSC_FALSE; // Display matrices PetscInt M,N,m,n,rstart,rend,nrhs,i; // PETSc type that represents an integer, used primarily to represent size of arrays and indexing into arrays. PetscScalar v; // PETSc type that represents either a double precision real number,... char inputfile[1][PETSC_MAX_PATH_LEN]; // Input file name // char outputfile[1][PETSC_MAX_PATH_LEN]; // Outputfile file name #endif // Initializes PETSc and MPI. Get size and rank of MPI. ierr = PetscInitialize(&argc, &args, (char*)0, help);if (ierr){return ierr;} ierr = MPI_Comm_size(PETSC_COMM_WORLD, &size);CHKERRQ(ierr); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); //Check if PETSc was configured with MUMPS. If not print error message and exit #if !defined(PETSC_HAVE_MUMPS) if (!=rank){ierr = PetscPrintf(PETSC_COMM_SELF, "This code requires MUMPS, exit...\n");CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; } #else // Check if displ is set. If True the matrices are printed to the terminal ierr = PetscOptionsGetBool(NULL, NULL, "-displ", &displ, NULL);CHKERRQ(ierr); // Load matrix A from file ierr = PetscOptionsGetString(NULL, NULL, "-fin" ,inputfile[0], PETSC_MAX_PATH_LEN, &flg1);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Load matrix in: %s \n", inputfile[0]);CHKERRQ(ierr); ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD, inputfile[0], FILE_MODE_READ, &fd);CHKERRQ(ierr); ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr); ierr = MatSetType(A, MATAIJ);CHKERRQ(ierr); ierr = MatLoad(A, fd);CHKERRQ(ierr); // Print matrix A if (displ){ ierr = PetscPrintf(PETSC_COMM_WORLD, "\n---------------\n");CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"Matrix A from file:\n", nrhs); ierr = MatView(A, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "\n");CHKERRQ(ierr); } // Check if matrix is quadratic ierr = MatGetSize(A, &M, &N);CHKERRQ(ierr); ierr = MatGetLocalSize(A, &m, &n);CHKERRQ(ierr); if (M != N){ //Macro that is called when an error has been detected. SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Detected a rectangular matrix: (%d, %d)", M, N); } ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "---------------\n");CHKERRQ(ierr); ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD, "Ownership ranges for Matrix A, rank: %i, size: %i, rstart: %i, rend: %i \n", rank, size, rstart, rend);CHKERRQ(ierr); ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD, PETSC_STDOUT);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "---------------\n");CHKERRQ(ierr); // Set the number of columns of the inverse to be computed. nrhs = N; ierr = PetscOptionsGetInt(NULL, NULL, "-nrhs", &nrhs, &flg2);CHKERRQ(ierr); // Create SpRHST for inv(A) with sparse RHS stored in the host. // PETSc does not support compressed column format which is required by MUMPS for sparse RHS matrix, // thus user must create spRHST=spRHS^T and call MatMatTransposeSolve() // User must create B^T in sparse compressed row format on the host processor and call MatMatTransposeSolve() to implement MUMPS' MatMatSolve(). // MUMPS requires nrhs = N ierr = MatCreate(PETSC_COMM_WORLD, &spRHST);CHKERRQ(ierr); if (!rank){ ierr = MatSetSizes(spRHST,N,M,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); } else{ ierr = MatSetSizes(spRHST,0,0,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); } ierr = MatSetType(spRHST,MATAIJ);CHKERRQ(ierr); ierr = MatSetFromOptions(spRHST);CHKERRQ(ierr); ierr = MatSetUp(spRHST);CHKERRQ(ierr); if (!rank){ v = 1.0; for(i=0;i From sam.guo at cd-adapco.com Mon Dec 16 17:56:14 2019 From: sam.guo at cd-adapco.com (Sam Guo) Date: Mon, 16 Dec 2019 18:56:14 -0500 Subject: [petsc-users] win32fe icl won't work Message-ID: Dear PETSc dev team, I tried to compile petsc using intel compiler win32fe icl on cygwin but encountered error. By the way, I am able to compile using visual studio compiler win32fe cl. =============================================================================== Configuring PETSc to compile on your system =============================================================================== =============================================================================== Warning: "with-clean" is specified. Removing all build files from arch-starccmplus_s=============================================================================== TESTING: checkCCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- C compiler you provided with -with-cc=win32fe icl does not work. Cannot compile/link C with /home/xianzhongg/dev/star/petsc/lib/petsc/bin/win32fe/win32fe icl. ******************************************************************************* BR, Sam -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: configure.log Type: application/octet-stream Size: 118 bytes Desc: not available URL: From balay at mcs.anl.gov Mon Dec 16 18:03:50 2019 From: balay at mcs.anl.gov (Balay, Satish) Date: Tue, 17 Dec 2019 00:03:50 +0000 Subject: [petsc-users] win32fe icl won't work In-Reply-To: References: Message-ID: The attached configure.log is a link file. Can you resend the log from PETSC_ARCH/lib/petsc/conf Also can you verify that you followed instructions from https://www.mcs.anl.gov/petsc/documentation/installation.html#windows [its not explicitly specified - but you need to run the correct cmd that sets up Intel compiler - instead of the MS compiler] i.e verify 'icl' works from cygwin/bash - before attempting configure. Satish On Mon, 16 Dec 2019, Sam Guo wrote: > Dear PETSc dev team, > I tried to compile petsc using intel compiler win32fe icl on cygwin but > encountered error. By the way, I am able to compile using visual studio > compiler win32fe cl. > > =============================================================================== > Configuring PETSc to compile on your system > =============================================================================== > =============================================================================== > Warning: "with-clean" is specified. Removing all build files from > arch-starccmplus_s=============================================================================== > TESTING: checkCCompiler from > config.setCompilers(config/BuildSystem/config/setCompilers.py******************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > details): > ------------------------------------------------------------------------------- > C compiler you provided with -with-cc=win32fe icl does not work. > Cannot compile/link C with > /home/xianzhongg/dev/star/petsc/lib/petsc/bin/win32fe/win32fe icl. > ******************************************************************************* > > BR, > Sam > From sam.guo at cd-adapco.com Mon Dec 16 18:41:08 2019 From: sam.guo at cd-adapco.com (Sam Guo) Date: Mon, 16 Dec 2019 19:41:08 -0500 Subject: [petsc-users] win32fe icl won't work In-Reply-To: References: Message-ID: Thanks for the quick response. I attach the configure.log again. icl is found $ icl Intel(R) C++ Intel(R) 64 Compiler for applications running on Intel(R) 64, Version 18.0.3.210 Build 20180410 Copyright (C) 1985-2018 Intel Corporation. All rights reserved. icl: command line error: no files specified; for help type "icl /help" On Mon, Dec 16, 2019 at 7:03 PM Balay, Satish wrote: > The attached configure.log is a link file. Can you resend the log from > PETSC_ARCH/lib/petsc/conf > > Also can you verify that you followed instructions from > https://www.mcs.anl.gov/petsc/documentation/installation.html#windows > [its not explicitly specified - but you need to run the correct cmd that > sets up Intel compiler - instead of the MS compiler] > > i.e verify 'icl' works from cygwin/bash - before attempting configure. > > Satish > > On Mon, 16 Dec 2019, Sam Guo wrote: > > > Dear PETSc dev team, > > I tried to compile petsc using intel compiler win32fe icl on cygwin > but > > encountered error. By the way, I am able to compile using visual studio > > compiler win32fe cl. > > > > > =============================================================================== > > Configuring PETSc to compile on your system > > > =============================================================================== > > > =============================================================================== > > Warning: "with-clean" is specified. Removing all build files from > > > arch-starccmplus_s=============================================================================== > > TESTING: checkCCompiler from > > > config.setCompilers(config/BuildSystem/config/setCompilers.py******************************************************************************* > > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > > details): > > > ------------------------------------------------------------------------------- > > C compiler you provided with -with-cc=win32fe icl does not work. > > Cannot compile/link C with > > /home/xianzhongg/dev/star/petsc/lib/petsc/bin/win32fe/win32fe icl. > > > ******************************************************************************* > > > > BR, > > Sam > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: configure.log Type: application/octet-stream Size: 50173 bytes Desc: not available URL: From balay at mcs.anl.gov Mon Dec 16 19:30:27 2019 From: balay at mcs.anl.gov (Balay, Satish) Date: Tue, 17 Dec 2019 01:30:27 +0000 Subject: [petsc-users] win32fe icl won't work In-Reply-To: References: Message-ID: Try: mv /usr/bin/link.exe /usr/bin/link-cygwin.exe And rerun configure Satish ------ On Mon, 16 Dec 2019, Sam Guo wrote: > Thanks for the quick response. I attach the configure.log again. > > icl is found > $ icl > Intel(R) C++ Intel(R) 64 Compiler for applications running on Intel(R) 64, > Version 18.0.3.210 Build 20180410 > Copyright (C) 1985-2018 Intel Corporation. All rights reserved. > icl: command line error: no files specified; for help type "icl /help" > > On Mon, Dec 16, 2019 at 7:03 PM Balay, Satish wrote: > > > The attached configure.log is a link file. Can you resend the log from > > PETSC_ARCH/lib/petsc/conf > > > > Also can you verify that you followed instructions from > > https://www.mcs.anl.gov/petsc/documentation/installation.html#windows > > [its not explicitly specified - but you need to run the correct cmd that > > sets up Intel compiler - instead of the MS compiler] > > > > i.e verify 'icl' works from cygwin/bash - before attempting configure. > > > > Satish > > > > On Mon, 16 Dec 2019, Sam Guo wrote: > > > > > Dear PETSc dev team, > > > I tried to compile petsc using intel compiler win32fe icl on cygwin > > but > > > encountered error. By the way, I am able to compile using visual studio > > > compiler win32fe cl. > > > > > > > > =============================================================================== > > > Configuring PETSc to compile on your system > > > > > =============================================================================== > > > > > =============================================================================== > > > Warning: "with-clean" is specified. Removing all build files from > > > > > arch-starccmplus_s=============================================================================== > > > TESTING: checkCCompiler from > > > > > config.setCompilers(config/BuildSystem/config/setCompilers.py******************************************************************************* > > > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > > > details): > > > > > ------------------------------------------------------------------------------- > > > C compiler you provided with -with-cc=win32fe icl does not work. > > > Cannot compile/link C with > > > /home/xianzhongg/dev/star/petsc/lib/petsc/bin/win32fe/win32fe icl. > > > > > ******************************************************************************* > > > > > > BR, > > > Sam > > > > > > > > From balay at mcs.anl.gov Mon Dec 16 19:40:10 2019 From: balay at mcs.anl.gov (Balay, Satish) Date: Tue, 17 Dec 2019 01:40:10 +0000 Subject: [petsc-users] win32fe icl won't work In-Reply-To: References: Message-ID: BTW: You can try the branch 'balay/update-win32-link-check/maint' to check if you get an appropriate warning message for this usage. Satish On Tue, 17 Dec 2019, Balay, Satish wrote: > Try: > > mv /usr/bin/link.exe /usr/bin/link-cygwin.exe > > And rerun configure > > Satish > > ------ > > > On Mon, 16 Dec 2019, Sam Guo wrote: > > > Thanks for the quick response. I attach the configure.log again. > > > > icl is found > > $ icl > > Intel(R) C++ Intel(R) 64 Compiler for applications running on Intel(R) 64, > > Version 18.0.3.210 Build 20180410 > > Copyright (C) 1985-2018 Intel Corporation. All rights reserved. > > icl: command line error: no files specified; for help type "icl /help" > > > > On Mon, Dec 16, 2019 at 7:03 PM Balay, Satish wrote: > > > > > The attached configure.log is a link file. Can you resend the log from > > > PETSC_ARCH/lib/petsc/conf > > > > > > Also can you verify that you followed instructions from > > > https://www.mcs.anl.gov/petsc/documentation/installation.html#windows > > > [its not explicitly specified - but you need to run the correct cmd that > > > sets up Intel compiler - instead of the MS compiler] > > > > > > i.e verify 'icl' works from cygwin/bash - before attempting configure. > > > > > > Satish > > > > > > On Mon, 16 Dec 2019, Sam Guo wrote: > > > > > > > Dear PETSc dev team, > > > > I tried to compile petsc using intel compiler win32fe icl on cygwin > > > but > > > > encountered error. By the way, I am able to compile using visual studio > > > > compiler win32fe cl. > > > > > > > > > > > =============================================================================== > > > > Configuring PETSc to compile on your system > > > > > > > =============================================================================== > > > > > > > =============================================================================== > > > > Warning: "with-clean" is specified. Removing all build files from > > > > > > > arch-starccmplus_s=============================================================================== > > > > TESTING: checkCCompiler from > > > > > > > config.setCompilers(config/BuildSystem/config/setCompilers.py******************************************************************************* > > > > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > > > > details): > > > > > > > ------------------------------------------------------------------------------- > > > > C compiler you provided with -with-cc=win32fe icl does not work. > > > > Cannot compile/link C with > > > > /home/xianzhongg/dev/star/petsc/lib/petsc/bin/win32fe/win32fe icl. > > > > > > > ******************************************************************************* > > > > > > > > BR, > > > > Sam > > > > > > > > > > > > > From sam.guo at cd-adapco.com Tue Dec 17 00:40:58 2019 From: sam.guo at cd-adapco.com (Sam Guo) Date: Tue, 17 Dec 2019 01:40:58 -0500 Subject: [petsc-users] win32fe icl won't work In-Reply-To: References: Message-ID: I cannot move link.exe: $ mv link.exe link_cyg.exe mv: cannot move 'link.exe' to 'link_cyg.exe': Permission denied I figure I need admin privilege. On Mon, Dec 16, 2019 at 8:30 PM Balay, Satish wrote: > Try: > > mv /usr/bin/link.exe /usr/bin/link-cygwin.exe > > And rerun configure > > Satish > > ------ > > > On Mon, 16 Dec 2019, Sam Guo wrote: > > > Thanks for the quick response. I attach the configure.log again. > > > > icl is found > > $ icl > > Intel(R) C++ Intel(R) 64 Compiler for applications running on Intel(R) > 64, > > Version 18.0.3.210 Build 20180410 > > Copyright (C) 1985-2018 Intel Corporation. All rights reserved. > > icl: command line error: no files specified; for help type "icl /help" > > > > On Mon, Dec 16, 2019 at 7:03 PM Balay, Satish wrote: > > > > > The attached configure.log is a link file. Can you resend the log from > > > PETSC_ARCH/lib/petsc/conf > > > > > > Also can you verify that you followed instructions from > > > https://www.mcs.anl.gov/petsc/documentation/installation.html#windows > > > [its not explicitly specified - but you need to run the correct cmd > that > > > sets up Intel compiler - instead of the MS compiler] > > > > > > i.e verify 'icl' works from cygwin/bash - before attempting configure. > > > > > > Satish > > > > > > On Mon, 16 Dec 2019, Sam Guo wrote: > > > > > > > Dear PETSc dev team, > > > > I tried to compile petsc using intel compiler win32fe icl on > cygwin > > > but > > > > encountered error. By the way, I am able to compile using visual > studio > > > > compiler win32fe cl. > > > > > > > > > > > > =============================================================================== > > > > Configuring PETSc to compile on your system > > > > > > > > =============================================================================== > > > > > > > > =============================================================================== > > > > Warning: "with-clean" is specified. Removing all build files from > > > > > > > > arch-starccmplus_s=============================================================================== > > > > TESTING: checkCCompiler from > > > > > > > > config.setCompilers(config/BuildSystem/config/setCompilers.py******************************************************************************* > > > > UNABLE to CONFIGURE with GIVEN OPTIONS (see > configure.log for > > > > details): > > > > > > > > ------------------------------------------------------------------------------- > > > > C compiler you provided with -with-cc=win32fe icl does not work. > > > > Cannot compile/link C with > > > > /home/xianzhongg/dev/star/petsc/lib/petsc/bin/win32fe/win32fe icl. > > > > > > > > ******************************************************************************* > > > > > > > > BR, > > > > Sam > > > > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Tue Dec 17 07:42:38 2019 From: balay at mcs.anl.gov (Balay, Satish) Date: Tue, 17 Dec 2019 13:42:38 +0000 Subject: [petsc-users] win32fe icl won't work In-Reply-To: References: Message-ID: Alternative is to update PATH so that link.exe from compiler is before the one from cygwin. I have it at '/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 14.0/VC/BIN/amd64/link.exe' so would do: export PATH='/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 14.0/VC/BIN/amd64':$PATH And verify with: balay at ps4 ~ $ which link.exe /cygdrive/c/Program Files (x86)/Microsoft Visual Studio 14.0/VC/BIN/amd64/link.exe balay at ps4 ~ $ Satish On Tue, 17 Dec 2019, Sam Guo wrote: > I cannot move link.exe: > $ mv link.exe link_cyg.exe > mv: cannot move 'link.exe' to 'link_cyg.exe': Permission denied > > I figure I need admin privilege. > > On Mon, Dec 16, 2019 at 8:30 PM Balay, Satish wrote: > > > Try: > > > > mv /usr/bin/link.exe /usr/bin/link-cygwin.exe > > > > And rerun configure > > > > Satish > > > > ------ > > > > > > On Mon, 16 Dec 2019, Sam Guo wrote: > > > > > Thanks for the quick response. I attach the configure.log again. > > > > > > icl is found > > > $ icl > > > Intel(R) C++ Intel(R) 64 Compiler for applications running on Intel(R) > > 64, > > > Version 18.0.3.210 Build 20180410 > > > Copyright (C) 1985-2018 Intel Corporation. All rights reserved. > > > icl: command line error: no files specified; for help type "icl /help" > > > > > > On Mon, Dec 16, 2019 at 7:03 PM Balay, Satish wrote: > > > > > > > The attached configure.log is a link file. Can you resend the log from > > > > PETSC_ARCH/lib/petsc/conf > > > > > > > > Also can you verify that you followed instructions from > > > > https://www.mcs.anl.gov/petsc/documentation/installation.html#windows > > > > [its not explicitly specified - but you need to run the correct cmd > > that > > > > sets up Intel compiler - instead of the MS compiler] > > > > > > > > i.e verify 'icl' works from cygwin/bash - before attempting configure. > > > > > > > > Satish > > > > > > > > On Mon, 16 Dec 2019, Sam Guo wrote: > > > > > > > > > Dear PETSc dev team, > > > > > I tried to compile petsc using intel compiler win32fe icl on > > cygwin > > > > but > > > > > encountered error. By the way, I am able to compile using visual > > studio > > > > > compiler win32fe cl. > > > > > > > > > > > > > > > > =============================================================================== > > > > > Configuring PETSc to compile on your system > > > > > > > > > > > =============================================================================== > > > > > > > > > > > =============================================================================== > > > > > Warning: "with-clean" is specified. Removing all build files from > > > > > > > > > > > arch-starccmplus_s=============================================================================== > > > > > TESTING: checkCCompiler from > > > > > > > > > > > config.setCompilers(config/BuildSystem/config/setCompilers.py******************************************************************************* > > > > > UNABLE to CONFIGURE with GIVEN OPTIONS (see > > configure.log for > > > > > details): > > > > > > > > > > > ------------------------------------------------------------------------------- > > > > > C compiler you provided with -with-cc=win32fe icl does not work. > > > > > Cannot compile/link C with > > > > > /home/xianzhongg/dev/star/petsc/lib/petsc/bin/win32fe/win32fe icl. > > > > > > > > > > > ******************************************************************************* > > > > > > > > > > BR, > > > > > Sam > > > > > > > > > > > > > > > > > > > > > From fdkong.jd at gmail.com Tue Dec 17 10:11:05 2019 From: fdkong.jd at gmail.com (Fande Kong) Date: Tue, 17 Dec 2019 09:11:05 -0700 Subject: [petsc-users] Running moose/scripts/update_and_rebuild_petsc.sh on HPC In-Reply-To: References: <277eb13a-0590-4b1a-a089-09a7c35efd83@googlegroups.com> Message-ID: Are you able to run your MPI code using " mpiexec_mpt -n 1 ./yourbinary"? You need to use --with-mpiexec to specify what exactly command lines you can run, e.g., --with-mpiexec="mpirun -n 1". I am also CCing the email to PETSc guys who may know the answer to these questions. Thanks, Fande, On Mon, Dec 16, 2019 at 3:52 PM Tomas Mondragon < tom.alex.mondragon at gmail.com> wrote: > I have attached the configure.log file from when I ran > update_and_rebuild_petsc.sh on both machines. In the log from jim is from > an attempt to rebuild after adding --with-mpiexec=mpiexec_mpt to the call > to pets/configure in the update and rebuild script > > -- > You received this message because you are subscribed to the Google Groups > "moose-users" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to moose-users+unsubscribe at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/moose-users/edd3a169-5012-4e46-a060-5088a199603c%40googlegroups.com > > . > -------------- next part -------------- An HTML attachment was scrubbed... URL: From fdkong.jd at gmail.com Tue Dec 17 10:40:42 2019 From: fdkong.jd at gmail.com (Fande Kong) Date: Tue, 17 Dec 2019 09:40:42 -0700 Subject: [petsc-users] Fwd: Running moose/scripts/update_and_rebuild_petsc.sh on HPC In-Reply-To: References: <277eb13a-0590-4b1a-a089-09a7c35efd83@googlegroups.com> Message-ID: Just want to make sure the log files were forward to the PETSc list correctly. Fande, ---------- Forwarded message --------- From: Tomas Mondragon Date: Mon, Dec 16, 2019 at 3:52 PM Subject: Re: Running moose/scripts/update_and_rebuild_petsc.sh on HPC To: moose-users I have attached the configure.log file from when I ran update_and_rebuild_petsc.sh on both machines. In the log from jim is from an attempt to rebuild after adding --with-mpiexec=mpiexec_mpt to the call to pets/configure in the update and rebuild script -- You received this message because you are subscribed to the Google Groups "moose-users" group. To unsubscribe from this group and stop receiving emails from it, send an email to moose-users+unsubscribe at googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/moose-users/edd3a169-5012-4e46-a060-5088a199603c%40googlegroups.com . -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- ================================================================================ ================================================================================ Starting configure run at Mon, 16 Dec 2019 16:05:58 -0600 Configure Options: --configModules=PETSc.Configure --optionsModule=config.compilerOptions --download-hypre=1 --with-debugging=no --with-shared-libraries=1 --download-fblaslapack=1 --download-metis=1 --download-ptscotch=1 --download-parmetis=1 --download-superlu_dist=1 --download-mumps=1 --download-scalapack=1 --download-slepc=git://https://gitlab.com/slepc/slepc.git --download-slepc-commit= 59ff81b --with-mpi=1 --with-mpiexec=mpiexec_mpt --with-cxx-dialect=C++11 --with-fortran-bindings=0 --with-sowing=0 Working directory: /p/work2/tmondrag/moose/petsc Machine platform: ('Linux', 'jim07.erdc.hpc.mil', '4.12.14-94.41-default', '#1 SMP Wed Oct 31 12:25:04 UTC 2018 (3090901)', 'x86_64', 'x86_64') Python version: 2.7.13 (default, Jan 11 2017, 10:56:06) [GCC] ================================================================================ ================================================================================ TEST configureExternalPackagesDir from config.framework(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/framework.py:911) TESTING: configureExternalPackagesDir from config.framework(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/framework.py:911) ================================================================================ TEST configureDebuggers from config.utilities.debuggers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/debuggers.py:21) TESTING: configureDebuggers from config.utilities.debuggers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/debuggers.py:21) Find a default debugger and determine its arguments Executing: uname -s stdout: Linux Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/gdb...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/gdb...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/gdb...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/gdb...not found Checking for program /usr/local/krb5/bin/gdb...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/gdb...not found Checking for program /p/home/apps/gnu_compiler/7.3.0/bin/gdb...not found Checking for program /opt/clmgr/sbin/gdb...not found Checking for program /opt/clmgr/bin/gdb...not found Checking for program /opt/sgi/sbin/gdb...not found Checking for program /opt/sgi/bin/gdb...not found Checking for program /usr/local/krb5/bin/gdb...not found Checking for program /usr/local/krb5/libexec/gdb...not found Checking for program /usr/local/bin/gdb...not found Checking for program /usr/bin/gdb...found Defined make macro "GDB" to "/usr/bin/gdb" Defined "USE_DEBUGGER" to ""gdb"" Executing: uname -s stdout: Linux Defined make macro "DSYMUTIL" to "true" child config.utilities.debuggers 0.046537 ================================================================================ TEST configureDirectories from PETSc.options.petscdir(/p/work2/tmondrag/moose/petsc/config/PETSc/options/petscdir.py:23) TESTING: configureDirectories from PETSc.options.petscdir(/p/work2/tmondrag/moose/petsc/config/PETSc/options/petscdir.py:23) Checks PETSC_DIR and sets if not set Version Information: #define PETSC_VERSION_RELEASE 1 #define PETSC_VERSION_MAJOR 3 #define PETSC_VERSION_MINOR 12 #define PETSC_VERSION_SUBMINOR 1 #define PETSC_VERSION_PATCH 0 #define PETSC_VERSION_DATE "unknown" #define PETSC_VERSION_GIT "unknown" #define PETSC_VERSION_DATE_GIT "unknown" #define PETSC_VERSION_EQ(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_ PETSC_VERSION_EQ #define PETSC_VERSION_LT(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_LE(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_GT(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_GE(MAJOR,MINOR,SUBMINOR) \ child PETSc.options.petscdir 0.045620 ================================================================================ TEST getDatafilespath from PETSc.options.dataFilesPath(/p/work2/tmondrag/moose/petsc/config/PETSc/options/dataFilesPath.py:29) TESTING: getDatafilespath from PETSc.options.dataFilesPath(/p/work2/tmondrag/moose/petsc/config/PETSc/options/dataFilesPath.py:29) Checks what DATAFILESPATH should be child PETSc.options.dataFilesPath 0.011436 ================================================================================ TEST configureGit from config.sourceControl(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/sourceControl.py:24) TESTING: configureGit from config.sourceControl(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/sourceControl.py:24) Find the Git executable Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/git...found Defined make macro "GIT" to "git" Executing: git --version stdout: git version 2.4.4 child config.sourceControl 0.022918 ================================================================================ TEST configureInstallationMethod from PETSc.options.petscclone(/p/work2/tmondrag/moose/petsc/config/PETSc/options/petscclone.py:20) TESTING: configureInstallationMethod from PETSc.options.petscclone(/p/work2/tmondrag/moose/petsc/config/PETSc/options/petscclone.py:20) lib/petsc/bin/maint exists. This appears to be a repository clone .git directory exists Executing: ['git', 'describe', '--match=v*'] stdout: v3.12.1-23-g5ea3abf Executing: ['git', 'log', '-1', '--pretty=format:%H'] stdout: 5ea3abfa7fe8791a5f316416921daa28f47703d9 Executing: ['git', 'log', '-1', '--pretty=format:%ci'] stdout: 2019-10-29 13:35:52 +0000 Executing: ['git', 'branch'] stdout: * (HEAD detached at 5ea3abf) master Defined "VERSION_GIT" to ""v3.12.1-23-g5ea3abf"" Defined "VERSION_DATE_GIT" to ""2019-10-29 13:35:52 +0000"" Defined "VERSION_BRANCH_GIT" to ""(HEAD detached at 5ea3abf)"" child PETSc.options.petscclone 1.206299 ================================================================================ TEST setNativeArchitecture from PETSc.options.arch(/p/work2/tmondrag/moose/petsc/config/PETSc/options/arch.py:31) TESTING: setNativeArchitecture from PETSc.options.arch(/p/work2/tmondrag/moose/petsc/config/PETSc/options/arch.py:31) ================================================================================ TEST configureArchitecture from PETSc.options.arch(/p/work2/tmondrag/moose/petsc/config/PETSc/options/arch.py:43) TESTING: configureArchitecture from PETSc.options.arch(/p/work2/tmondrag/moose/petsc/config/PETSc/options/arch.py:43) Checks PETSC_ARCH and sets if not set No previous hashfile found Setting hashfile: arch-moose/lib/petsc/conf/configure-hash Deleting configure hash file: arch-moose/lib/petsc/conf/configure-hash Unable to delete configure hash file: arch-moose/lib/petsc/conf/configure-hash child PETSc.options.arch 3.472163 ================================================================================ TEST setInstallDir from PETSc.options.installDir(/p/work2/tmondrag/moose/petsc/config/PETSc/options/installDir.py:35) TESTING: setInstallDir from PETSc.options.installDir(/p/work2/tmondrag/moose/petsc/config/PETSc/options/installDir.py:35) setup installDir to either prefix or if that is not set to PETSC_DIR/PETSC_ARCH Defined make macro "PREFIXDIR" to "/p/home/tmondrag/WORK/moose/petsc/arch-moose" ================================================================================ TEST saveReconfigure from PETSc.options.installDir(/p/work2/tmondrag/moose/petsc/config/PETSc/options/installDir.py:79) TESTING: saveReconfigure from PETSc.options.installDir(/p/work2/tmondrag/moose/petsc/config/PETSc/options/installDir.py:79) ================================================================================ TEST cleanConfDir from PETSc.options.installDir(/p/work2/tmondrag/moose/petsc/config/PETSc/options/installDir.py:72) TESTING: cleanConfDir from PETSc.options.installDir(/p/work2/tmondrag/moose/petsc/config/PETSc/options/installDir.py:72) ================================================================================ TEST configureInstallDir from PETSc.options.installDir(/p/work2/tmondrag/moose/petsc/config/PETSc/options/installDir.py:56) TESTING: configureInstallDir from PETSc.options.installDir(/p/work2/tmondrag/moose/petsc/config/PETSc/options/installDir.py:56) Makes installDir subdirectories if it does not exist for both prefix install location and PETSc work install location Changed persistence directory to /p/home/tmondrag/WORK/moose/petsc/arch-moose/lib/petsc/conf ================================================================================ TEST restoreReconfigure from PETSc.options.installDir(/p/work2/tmondrag/moose/petsc/config/PETSc/options/installDir.py:92) TESTING: restoreReconfigure from PETSc.options.installDir(/p/work2/tmondrag/moose/petsc/config/PETSc/options/installDir.py:92) child PETSc.options.installDir 0.008305 ================================================================================ TEST setExternalPackagesDir from PETSc.options.externalpackagesdir(/p/work2/tmondrag/moose/petsc/config/PETSc/options/externalpackagesdir.py:15) TESTING: setExternalPackagesDir from PETSc.options.externalpackagesdir(/p/work2/tmondrag/moose/petsc/config/PETSc/options/externalpackagesdir.py:15) ================================================================================ TEST cleanExternalpackagesDir from PETSc.options.externalpackagesdir(/p/work2/tmondrag/moose/petsc/config/PETSc/options/externalpackagesdir.py:22) TESTING: cleanExternalpackagesDir from PETSc.options.externalpackagesdir(/p/work2/tmondrag/moose/petsc/config/PETSc/options/externalpackagesdir.py:22) child PETSc.options.externalpackagesdir 0.001212 ================================================================================ TEST configureCLanguage from PETSc.options.languages(/p/work2/tmondrag/moose/petsc/config/PETSc/options/languages.py:27) TESTING: configureCLanguage from PETSc.options.languages(/p/work2/tmondrag/moose/petsc/config/PETSc/options/languages.py:27) Choose whether to compile the PETSc library using a C or C++ compiler C language is C Defined "CLANGUAGE_C" to "1" child PETSc.options.languages 0.001919 ================================================================================ TEST printEnvVariables from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1715) TESTING: printEnvVariables from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1715) **** printenv **** CPPFLAGS=-I/app/unsupported/COST/tcltk/8.6.4/gnu//include -I/app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//include -I/app/unsupported/COST/valgrind/3.12.0/gnu//include I_MPI_CC=gcc ARCHIVE_HOST=gold.erdc.hpc.mil LESS=-M -I -R XKEYSYMDB=/usr/X11R6/lib/X11/XKeysymDB BASH_FUNC_module%%=() { eval `/usr/share/Modules/$MODULE_VERSION/bin/modulecmd bash $*` } BC_ACCELERATOR_NODE_CORES=28 KRB5HOME=/usr/local/krb5 SHELL=/bin/bash MPI_LAUNCH_TIMEOUT=300 BC_STANDARD_NODE_CORES=36 XDG_DATA_DIRS=/usr/share BC_NODE_TYPE=LOGIN HISTSIZE=1000 CSI_HOME=/app LESS_ADVANCED_PREPROCESSOR=no MANPATH=/app/unsupported/COST/tcltk/8.6.4/gnu//man:/usr/local/krb5/share/man:/p/home/apps/hpe/mpt-2.19/man:/p/home/apps/gnu_compiler/7.3.0/share/man:/usr/local/krb5/share/man:/usr/local/krb5/ssl/man:/usr/local/man:/usr/share/man:/opt/c3/man:/opt/pbs/default/share/man:/opt/clmgr/man:/opt/sgi/share/man:/app/unsupported/local/man:/usr/share/catman:/usr/catman:/usr/man BC_BIGMEM_NODE_CORES=32 JAVA_HOME=/usr/lib64/jvm/java PROFILEREAD=true XDG_RUNTIME_DIR=/run/user/905790 ARCHIVE_HOME=/erdc1/tmondrag FPATH=/p/home/apps/hpe/mpt-2.19/include MPIF90_F90=gfortran MPSCP_BLOCKED_FILE=/app/unsupported/local/etc/mpscp_blocked_ports XDG_SESSION_ID=2479 SDK_HOME=/usr/lib64/jvm/java SSH_CONNECTION=134.164.188.51 49744 140.31.13.248 22 CXX=g++ HOSTNAME=jim07.erdc.hpc.mil PETSC_ARCH=arch-moose MAIL=/var/mail/tmondrag LS_COLORS=no=00:fi=00:di=01;34:ln=00;36:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=41;33;01:ex=00;32:*.cmd=00;32:*.exe=01;32:*.com=01;32:*.bat=01;32:*.btm=01;32:*.dll=01;32:*.tar=00;31:*.tbz=00;31:*.tgz=00;31:*.rpm=00;31:*.deb=00;31:*.arj=00;31:*.taz=00;31:*.lzh=00;31:*.lzma=00;31:*.zip=00;31:*.zoo=00;31:*.z=00;31:*.Z=00;31:*.gz=00;31:*.bz2=00;31:*.tb2=00;31:*.tz2=00;31:*.tbz2=00;31:*.xz=00;31:*.avi=01;35:*.bmp=01;35:*.fli=01;35:*.gif=01;35:*.jpg=01;35:*.jpeg=01;35:*.mng=01;35:*.mov=01;35:*.mpg=01;35:*.pcx=01;35:*.pbm=01;35:*.pgm=01;35:*.png=01;35:*.ppm=01;35:*.tga=01;35:*.tif=01;35:*.xbm=01;35:*.xpm=01;35:*.dl=01;35:*.gl=01;35:*.wmv=01;35:*.aiff=00;32:*.au=00;32:*.mid=00;32:*.mp3=00;32:*.ogg=00;32:*.voc=00;32:*.wav=00;32: BC_PHI_NODE_CORES=0 JAVA_ROOT=/usr/lib64/jvm/java MINICOM=-c on OSCAR_HOME=/opt/oscar CSHEDIT=emacs LESSOPEN=lessopen.sh %s CPATH=/p/home/apps/hpe/mpt-2.19/include:/p/home/apps/gnu_compiler/7.3.0/include USER=tmondrag INPUTRC=/etc/inputrc I_MPI_F77=gfortran PET_HOME=/app/unsupported/PETtools/CE CENTER=/gpfs/cwfs/tmondrag LANGUAGE=en_US.UTF-8 SHLVL=2 ALSA_CONFIG_PATH=/etc/alsa-pulse.conf CPU=x86_64 PETSC_DIR=/p/home/tmondrag/WORK/moose/scripts/../petsc MODULESHOME=/usr/share/Modules/3.2.10 JAVA_BINDIR=/usr/lib64/jvm/java/bin INFOPATH=/p/home/apps/gnu_compiler/7.3.0/share/info DAAC_HOME=/app/DAAC PROJECTS_HOME=/app/unsupported PKG_CONFIG_PATH=/app/unsupported/COST/tcltk/8.6.4/gnu//lib/pkgconfig:/app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//lib/pkgconfig:/app/unsupported/COST/valgrind/3.12.0/gnu//lib/pkgconfig GPG_TTY=/dev/pts/4 XNLSPATH=/usr/share/X11/nls TMPDIR=/p/work2/tmondrag MODULEPATH=/app/unsupported/COST/modules:/p/home/apps/modulefiles/devel:/p/home/apps/modulefiles/apps:/p/home/apps/modulefiles/unsupported:/usr/share/modules:/usr/share/Modules/$MODULE_VERSION/modulefiles:/usr/share/modules/modulefiles:/p/home/tmondrag/my_modules BC_HOST=jim MACHTYPE=x86_64-suse-linux XDG_CONFIG_DIRS=/etc/xdg I_MPI_CXX=g++ WINDOWMANAGER=env GNOME_SHELL_SESSION_MODE=classic SLE_CLASSIC_MODE=1 gnome-session --session gnome-classic CMAKE_LIBRARY_PATH=/app/unsupported/COST/git/2.4.4/gnu//lib:/app/unsupported/COST/tcltk/8.6.4/gnu//lib:/app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//lib:/app/unsupported/COST/valgrind/3.12.0/gnu//lib COST_MODULES_DIR=/app/unsupported/COST/modules MPSCP_PORTS=tcp[9000-9999] COLORTERM=1 PETSC_HOME=/app/unsupported/COST/petsc-cxx-real/3.6.3/gnu/ QEMU_AUDIO_DRV=pa _LMFILES_=/p/home/apps/modulefiles/devel/compiler/gcc/7.3.0:/p/home/apps/modulefiles/devel/mpi/sgimpt/2.19:/p/home/apps/modulefiles/unsupported/costinit:/app/unsupported/COST/modules/valgrind/gnu/3.12.0:/app/unsupported/COST/modules/petsc-cxx-real/gnu/3.6.3:/app/unsupported/COST/modules/tcltk/gnu/8.6.4:/app/unsupported/COST/modules/git/gnu/2.4.4 PAGER=less ACCOUNT=ERDCV9100CDAG MODULE_VERSION=3.2.10 LIBGL_DEBUG=quiet QT_SYSTEM_DIR=/usr/share/desktop-data I_MPI_F90=gfortran HOME=/p/home/tmondrag LD_LIBRARY_PATH=/app/unsupported/COST/dependencies/openssl/1.0.2n/gnu/lib:/app/unsupported/COST/dependencies/curl/7.43.0/gnu/lib:/app/unsupported/COST/git/2.4.4/gnu//lib:/app/unsupported/COST/tcltk/8.6.4/gnu//lib:/app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//lib:/app/unsupported/COST/valgrind/3.12.0/gnu//lib:/p/home/apps/hpe/mpt-2.19/lib:/p/home/apps/gnu_compiler/7.3.0/lib64 LANG=en_US.UTF-8 LIBRARY_PATH=/p/home/apps/hpe/mpt-2.19/lib KRB5_HOME=/usr/local/krb5 LS_OPTIONS=-N --color=auto -T 0 G_BROKEN_FILENAMES=1 SAMPLES_HOME=/usr/local/cac/Example_Codes F90=gfortran _=./configure OSTYPE=linux C3_RSH=ssh -oConnectTimeout=10 -oForwardX11=no BC_CORES_PER_NODE=36 CC=gcc NNTPSERVER=news G_FILENAME_ENCODING=@locale,UTF-8,ISO-8859-15,CP1252 HOST=jim07.erdc.hpc.mil MPT_VERSION=2.19 GIT_HOME=/app/unsupported/COST/git/2.4.4/gnu/ F77=gfortran FROM_HEADER= LESSCLOSE=lessclose.sh %s %s SSH_TTY=/dev/pts/4 MPSCP_CONFIG_FILENAME=/app/unsupported/local/etc/mpscp_config.jim07 MPICXX_CXX=g++ JRE_HOME=/usr/lib64/jvm/java/jre MORE=-sl WORKDIR2=/p/work1/tmondrag HOSTTYPE=x86_64 SSH_CLIENT=134.164.188.51 49744 22 LOGNAME=tmondrag PATH=/app/unsupported/COST/git/2.4.4/gnu//bin:/app/unsupported/COST/tcltk/8.6.4/gnu//bin:/app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin:/app/unsupported/COST/valgrind/3.12.0/gnu//bin:/usr/local/krb5/bin:/p/home/apps/hpe/mpt-2.19/bin:/p/home/apps/gnu_compiler/7.3.0/bin:/opt/clmgr/sbin:/opt/clmgr/bin:/opt/sgi/sbin:/opt/sgi/bin:/usr/local/krb5/bin:/usr/local/krb5/libexec:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/opt/c3/bin:/opt/pbs/default/bin:/sbin:/bin:/pbs/SLB:/app/unsupported/local/bin:/app/mpiutil PETTT_HOME=/app/unsupported/PETtools/CE TERM=xterm-256color CMAKE_INCLUDE_PATH=/app/unsupported/COST/tcltk/8.6.4/gnu//include:/app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//include:/app/unsupported/COST/valgrind/3.12.0/gnu//include SDL_AUDIODRIVER=pulse KRB5_CONFIG=/usr/local/krb5/etc/krb5.conf LDFLAGS=-L/app/unsupported/COST/git/2.4.4/gnu//lib -L/app/unsupported/COST/tcltk/8.6.4/gnu//lib -L/app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//lib -L/app/unsupported/COST/valgrind/3.12.0/gnu//lib MPICC_CC=gcc COST_HOME=/app/unsupported/COST MODULE_VERSION_STACK=3.2.10 I_MPI_FC=gfortran MPI_ROOT=/p/home/apps/hpe/mpt-2.19 USE_PCM_DB=2 KRB5CCNAME=PIPE:4095 LESSKEY=/etc/lesskey.bin JDK_HOME=/usr/lib64/jvm/java WORKDIR=/p/work2/tmondrag DISPLAY=localhost:13.0 AUDIODRIVER=pulseaudio PYTHONSTARTUP=/etc/pythonstart OLDPWD=/p/home/tmondrag/WORK/moose LOADEDMODULES=compiler/gcc/7.3.0:mpi/sgimpt/2.19:costinit:valgrind/gnu/3.12.0:petsc-cxx-real/gnu/3.6.3:tcltk/gnu/8.6.4:git/gnu/2.4.4 PWD=/p/home/tmondrag/WORK/moose/petsc ================================================================================ TEST resetEnvCompilers from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1722) TESTING: resetEnvCompilers from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1722) =============================================================================== ***** WARNING: CC (set to gcc) found in environment variables - ignoring use ./configure CC=$CC if you really want to use that value ****** =============================================================================== =============================================================================== ***** WARNING: CXX (set to g++) found in environment variables - ignoring use ./configure CXX=$CXX if you really want to use that value ****** =============================================================================== =============================================================================== ***** WARNING: F77 (set to gfortran) found in environment variables - ignoring use ./configure F77=$F77 if you really want to use that value ****** =============================================================================== =============================================================================== ***** WARNING: F90 (set to gfortran) found in environment variables - ignoring use ./configure F90=$F90 if you really want to use that value ****** =============================================================================== =============================================================================== ***** WARNING: CPPFLAGS (set to -I/app/unsupported/COST/tcltk/8.6.4/gnu//include -I/app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//include -I/app/unsupported/COST/valgrind/3.12.0/gnu//include) found in environment variables - ignoring use ./configure CPPFLAGS=$CPPFLAGS if you really want to use that value ****** =============================================================================== =============================================================================== ***** WARNING: LDFLAGS (set to -L/app/unsupported/COST/git/2.4.4/gnu//lib -L/app/unsupported/COST/tcltk/8.6.4/gnu//lib -L/app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//lib -L/app/unsupported/COST/valgrind/3.12.0/gnu//lib) found in environment variables - ignoring use ./configure LDFLAGS=$LDFLAGS if you really want to use that value ****** =============================================================================== ================================================================================ TEST checkEnvCompilers from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1752) TESTING: checkEnvCompilers from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1752) ================================================================================ TEST checkMPICompilerOverride from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1685) TESTING: checkMPICompilerOverride from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1685) Check if --with-mpi-dir is used along with CC CXX or FC compiler options. This usually prevents mpi compilers from being used - so issue a warning ================================================================================ TEST requireMpiLdPath from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1706) TESTING: requireMpiLdPath from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1706) OpenMPI wrappers require LD_LIBRARY_PATH set ================================================================================ TEST checkInitialFlags from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:450) TESTING: checkInitialFlags from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:450) Initialize the compiler and linker flags Initialized CFLAGS to Initialized CFLAGS to Initialized LDFLAGS to Initialized CUDAFLAGS to Initialized CUDAFLAGS to Initialized LDFLAGS to Initialized CXXFLAGS to Initialized CXX_CXXFLAGS to Initialized LDFLAGS to Initialized FFLAGS to Initialized FFLAGS to Initialized LDFLAGS to Initialized CPPFLAGS to Initialized FPPFLAGS to Initialized CUDAPPFLAGS to -Wno-deprecated-gpu-targets Initialized CXXPPFLAGS to Initialized CC_LINKER_FLAGS to [] Initialized CXX_LINKER_FLAGS to [] Initialized FC_LINKER_FLAGS to [] Initialized CUDAC_LINKER_FLAGS to [] Initialized sharedLibraryFlags to [] Initialized dynamicLibraryFlags to [] ================================================================================ TEST checkCCompiler from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:620) TESTING: checkCCompiler from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:620) Locate a functional C compiler Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/mpicc...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/mpicc...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/mpicc...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/mpicc...not found Checking for program /usr/local/krb5/bin/mpicc...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/mpicc...found Defined make macro "CC" to "mpicc" All intermediate test results are stored in /p/work2/tmondrag/petsc-0UdWsO All intermediate test results are stored in /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o Testing executable /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest to see if it can be run Executing: /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest Executing: /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest Executing: mpicc --version stdout: gcc (GCC) 7.3.0 Copyright (C) 2017 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. ================================================================================ TEST checkCPreprocessor from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:657) TESTING: checkCPreprocessor from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:657) Locate a functional C preprocessor Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/mpicc...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/mpicc...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/mpicc...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/mpicc...not found Checking for program /usr/local/krb5/bin/mpicc...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/mpicc...found Defined make macro "CPP" to "mpicc -E" Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: ================================================================================ TEST checkCUDACompiler from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:695) TESTING: checkCUDACompiler from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:695) Locate a functional CUDA compiler Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/nvcc...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/nvcc...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/nvcc...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/nvcc...not found Checking for program /usr/local/krb5/bin/nvcc...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/nvcc...not found Checking for program /p/home/apps/gnu_compiler/7.3.0/bin/nvcc...not found Checking for program /opt/clmgr/sbin/nvcc...not found Checking for program /opt/clmgr/bin/nvcc...not found Checking for program /opt/sgi/sbin/nvcc...not found Checking for program /opt/sgi/bin/nvcc...not found Checking for program /usr/local/krb5/bin/nvcc...not found Checking for program /usr/local/krb5/libexec/nvcc...not found Checking for program /usr/local/bin/nvcc...not found Checking for program /usr/bin/nvcc...not found Checking for program /bin/nvcc...not found Checking for program /usr/bin/X11/nvcc...not found Checking for program /usr/games/nvcc...not found Checking for program /opt/c3/bin/nvcc...not found Checking for program /opt/pbs/default/bin/nvcc...not found Checking for program /sbin/nvcc...not found Checking for program /bin/nvcc...not found Checking for program /pbs/SLB/nvcc...not found Checking for program /app/unsupported/local/bin/nvcc...not found Checking for program /app/mpiutil/nvcc...not found Checking for program /p/home/tmondrag/WORK/moose/scripts/../petsc/lib/petsc/bin/win32fe/nvcc...not found Checking for program /Developer/NVIDIA/CUDA-6.5/bin/nvcc...not found Checking for program /p/home/tmondrag/WORK/moose/scripts/../petsc/lib/petsc/bin/win32fe/nvcc...not found Checking for program /usr/local/cuda/bin/nvcc...not found Checking for program /p/home/tmondrag/WORK/moose/scripts/../petsc/lib/petsc/bin/win32fe/nvcc...not found ================================================================================ TEST checkCUDAPreprocessor from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:735) TESTING: checkCUDAPreprocessor from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:735) Locate a functional CUDA preprocessor ================================================================================ TEST checkCxxCompiler from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:835) TESTING: checkCxxCompiler from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:835) Locate a functional Cxx compiler Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/mpicxx...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/mpicxx...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/mpicxx...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/mpicxx...not found Checking for program /usr/local/krb5/bin/mpicxx...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/mpicxx...found Defined make macro "CXX" to "mpicxx" Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o Testing executable /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest to see if it can be run Executing: /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest Executing: /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest Executing: mpicxx --version stdout: g++ (GCC) 7.3.0 Copyright (C) 2017 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. ================================================================================ TEST checkCxxPreprocessor from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:877) TESTING: checkCxxPreprocessor from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:877) Locate a functional Cxx preprocessor Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/mpicxx...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/mpicxx...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/mpicxx...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/mpicxx...not found Checking for program /usr/local/krb5/bin/mpicxx...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/mpicxx...found Defined make macro "CXXPP" to "mpicxx -E" Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicxx -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Preprocess stderr before filtering:: Preprocess stderr after filtering:: ================================================================================ TEST checkFortranCompiler from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:980) TESTING: checkFortranCompiler from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:980) Locate a functional Fortran compiler Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/mpif90...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/mpif90...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/mpif90...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/mpif90...not found Checking for program /usr/local/krb5/bin/mpif90...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/mpif90...found Defined make macro "FC" to "mpif90" Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: mpif90 -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: mpif90 -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: mpif90 -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o Testing executable /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest to see if it can be run Executing: /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest Executing: /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest Executing: mpif90 --version stdout: GNU Fortran (GCC) 7.3.0 Copyright (C) 2017 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. ================================================================================ TEST checkFortranPreprocessor from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1017) TESTING: checkFortranPreprocessor from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1017) Locate a functional Fortran preprocessor Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/mpif90...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/mpif90...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/mpif90...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/mpif90...not found Checking for program /usr/local/krb5/bin/mpif90...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/mpif90...found Defined make macro "FPP" to "mpif90 -E" Deleting "FPP" Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/mpif90...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/mpif90...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/mpif90...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/mpif90...not found Checking for program /usr/local/krb5/bin/mpif90...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/mpif90...found Defined make macro "FPP" to "mpif90 --use cpp32" Deleting "FPP" ================================================================================ TEST checkFortranComments from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1040) TESTING: checkFortranComments from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1040) Make sure fortran comment "!" works Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.F90 Successful compile: Source: program main ! comment end Fortran comments can use ! in column 1 ================================================================================ TEST checkLargeFileIO from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1171) TESTING: checkLargeFileIO from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1171) ================================================================================ TEST checkArchiver from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1270) TESTING: checkArchiver from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1270) Check that the archiver exists and can make a library usable by the compiler Executing: ar -V stdout: GNU ar (GNU Binutils; SUSE Linux Enterprise 12) 2.32.0.20190909-9.36 Copyright (C) 2019 Free Software Foundation, Inc. This program is free software; you may redistribute it under the terms of the GNU General Public License version 3 or (at your option) any later version. This program has absolutely no warranty. Executing: ar -V stdout: GNU ar (GNU Binutils; SUSE Linux Enterprise 12) 2.32.0.20190909-9.36 Copyright (C) 2019 Free Software Foundation, Inc. This program is free software; you may redistribute it under the terms of the GNU General Public License version 3 or (at your option) any later version. This program has absolutely no warranty. Defined make macro "FAST_AR_FLAGS" to "Scq" Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int foo(int a) { return a+1; } Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/ar...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/ar...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/ar...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/ar...not found Checking for program /usr/local/krb5/bin/ar...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/ar...not found Checking for program /p/home/apps/gnu_compiler/7.3.0/bin/ar...not found Checking for program /opt/clmgr/sbin/ar...not found Checking for program /opt/clmgr/bin/ar...not found Checking for program /opt/sgi/sbin/ar...not found Checking for program /opt/sgi/bin/ar...not found Checking for program /usr/local/krb5/bin/ar...not found Checking for program /usr/local/krb5/libexec/ar...not found Checking for program /usr/local/bin/ar...not found Checking for program /usr/bin/ar...found Defined make macro "AR" to "/usr/bin/ar" Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/ranlib...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/ranlib...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/ranlib...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/ranlib...not found Checking for program /usr/local/krb5/bin/ranlib...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/ranlib...not found Checking for program /p/home/apps/gnu_compiler/7.3.0/bin/ranlib...not found Checking for program /opt/clmgr/sbin/ranlib...not found Checking for program /opt/clmgr/bin/ranlib...not found Checking for program /opt/sgi/sbin/ranlib...not found Checking for program /opt/sgi/bin/ranlib...not found Checking for program /usr/local/krb5/bin/ranlib...not found Checking for program /usr/local/krb5/libexec/ranlib...not found Checking for program /usr/local/bin/ranlib...not found Checking for program /usr/bin/ranlib...found Defined make macro "RANLIB" to "/usr/bin/ranlib -c" Executing: /usr/bin/ar cr /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/libconf1.a /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conf1.o Executing: /usr/bin/ranlib -c /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/libconf1.a Possible ERROR while running ranlib: stderr: /usr/bin/ranlib: invalid option -- 'c' Ranlib is not functional with your archiver. Try --with-ranlib=true if ranlib is unnecessary. Executing: ar -V stdout: GNU ar (GNU Binutils; SUSE Linux Enterprise 12) 2.32.0.20190909-9.36 Copyright (C) 2019 Free Software Foundation, Inc. This program is free software; you may redistribute it under the terms of the GNU General Public License version 3 or (at your option) any later version. This program has absolutely no warranty. Executing: ar -V stdout: GNU ar (GNU Binutils; SUSE Linux Enterprise 12) 2.32.0.20190909-9.36 Copyright (C) 2019 Free Software Foundation, Inc. This program is free software; you may redistribute it under the terms of the GNU General Public License version 3 or (at your option) any later version. This program has absolutely no warranty. Defined make macro "FAST_AR_FLAGS" to "Scq" Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int foo(int a) { return a+1; } Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/ar...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/ar...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/ar...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/ar...not found Checking for program /usr/local/krb5/bin/ar...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/ar...not found Checking for program /p/home/apps/gnu_compiler/7.3.0/bin/ar...not found Checking for program /opt/clmgr/sbin/ar...not found Checking for program /opt/clmgr/bin/ar...not found Checking for program /opt/sgi/sbin/ar...not found Checking for program /opt/sgi/bin/ar...not found Checking for program /usr/local/krb5/bin/ar...not found Checking for program /usr/local/krb5/libexec/ar...not found Checking for program /usr/local/bin/ar...not found Checking for program /usr/bin/ar...found Defined make macro "AR" to "/usr/bin/ar" Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/ranlib...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/ranlib...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/ranlib...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/ranlib...not found Checking for program /usr/local/krb5/bin/ranlib...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/ranlib...not found Checking for program /p/home/apps/gnu_compiler/7.3.0/bin/ranlib...not found Checking for program /opt/clmgr/sbin/ranlib...not found Checking for program /opt/clmgr/bin/ranlib...not found Checking for program /opt/sgi/sbin/ranlib...not found Checking for program /opt/sgi/bin/ranlib...not found Checking for program /usr/local/krb5/bin/ranlib...not found Checking for program /usr/local/krb5/libexec/ranlib...not found Checking for program /usr/local/bin/ranlib...not found Checking for program /usr/bin/ranlib...found Defined make macro "RANLIB" to "/usr/bin/ranlib" Executing: /usr/bin/ar cr /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/libconf1.a /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conf1.o Executing: /usr/bin/ranlib /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/libconf1.a Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" extern int foo(int); int main() { int b = foo(1); if (b); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -L/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -lconf1 Defined make macro "AR_FLAGS" to "cr" Defined make macro "AR_LIB_SUFFIX" to "a" ================================================================================ TEST checkSharedLinker from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1384) TESTING: checkSharedLinker from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1384) Check that the linker can produce shared libraries Executing: uname -s stdout: Linux Checking shared linker mpicc using flags ['-shared'] Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/mpicc...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/mpicc...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/mpicc...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/mpicc...not found Checking for program /usr/local/krb5/bin/mpicc...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/mpicc...found Defined make macro "LD_SHARED" to "mpicc" Trying C compiler flag Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest -shared /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o Valid C linker flag -shared Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/libconftest.so -shared /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o: relocation R_X86_64_PC32 against symbol `fprintf_ptr' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: final link failed: nonrepresentable section on output collect2: error: ld returned 1 exit status Rejected C compiler flag because it was not compatible with shared linker mpicc using flags ['-shared'] Executing: mpicc --help | head -n 20 stdout: Usage: gcc [options] file... Options: -pass-exit-codes Exit with highest error code from a phase. --help Display this information. --target-help Display target specific command line options. --help={common|optimizers|params|target|warnings|[^]{joined|separate|undocumented}}[,...]. Display specific types of command line options. (Use '-v --help' to display command line options of sub-processes). --version Display compiler version information. -dumpspecs Display all of the built in spec strings. -dumpversion Display the version of the compiler. -dumpmachine Display the compiler's target processor. -print-search-dirs Display the directories in the compiler's search path. -print-libgcc-file-name Display the name of the compiler's companion library. -print-file-name= Display the full path to library . -print-prog-name= Display the full path to compiler component . -print-multiarch Display the target's normalized GNU triplet, used as a component in the library path. -print-multi-directory Display the root directory for versions of libgcc. -print-multi-lib Display the mapping between command line options and Trying C compiler flag -fPIC Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -fPIC Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest -shared -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o Valid C linker flag -shared Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/libconftest.so -shared -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int foo(void); int main() { int ret = foo(); if (ret) {} ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -L/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -lconftest Using shared linker mpicc with flags ['-shared'] and library extension so Executing: uname -s stdout: Linux Executing: uname -s stdout: Linux ================================================================================ TEST checkPIC from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1118) TESTING: checkPIC from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1118) Determine the PIC option for each compiler Trying Cxx for PIC code without any compiler flag Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/libconftest.so -shared -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o: relocation R_X86_64_PC32 against symbol `fprintf_ptr' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: final link failed: nonrepresentable section on output collect2: error: ld returned 1 exit status Rejected Cxx compiler flag because shared linker cannot handle it Executing: mpicxx --help | head -n 20 stdout: Usage: g++ [options] file... Options: -pass-exit-codes Exit with highest error code from a phase. --help Display this information. --target-help Display target specific command line options. --help={common|optimizers|params|target|warnings|[^]{joined|separate|undocumented}}[,...]. Display specific types of command line options. (Use '-v --help' to display command line options of sub-processes). --version Display compiler version information. -dumpspecs Display all of the built in spec strings. -dumpversion Display the version of the compiler. -dumpmachine Display the compiler's target processor. -print-search-dirs Display the directories in the compiler's search path. -print-libgcc-file-name Display the name of the compiler's companion library. -print-file-name= Display the full path to library . -print-prog-name= Display the full path to compiler component . -print-multiarch Display the target's normalized GNU triplet, used as a component in the library path. -print-multi-directory Display the root directory for versions of libgcc. -print-multi-lib Display the mapping between command line options and Trying Cxx compiler flag -fPIC for PIC code Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -fPIC Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/libconftest.so -shared -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o Accepted Cxx compiler flag -fPIC for PIC code Trying FC for PIC code without any compiler flag Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.F90 Successful compile: Source: function foo(a) real:: a,x,bar common /xx/ x x=a foo = bar(x) end Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/libconftest.so -shared -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o: relocation R_X86_64_PC32 against symbol `xx_' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: final link failed: nonrepresentable section on output collect2: error: ld returned 1 exit status Rejected FC compiler flag because shared linker cannot handle it Executing: mpif90 --help | head -n 20 stdout: Usage: gfortran [options] file... Options: -pass-exit-codes Exit with highest error code from a phase. --help Display this information. --target-help Display target specific command line options. --help={common|optimizers|params|target|warnings|[^]{joined|separate|undocumented}}[,...]. Display specific types of command line options. (Use '-v --help' to display command line options of sub-processes). --version Display compiler version information. -dumpspecs Display all of the built in spec strings. -dumpversion Display the version of the compiler. -dumpmachine Display the compiler's target processor. -print-search-dirs Display the directories in the compiler's search path. -print-libgcc-file-name Display the name of the compiler's companion library. -print-file-name= Display the full path to library . -print-prog-name= Display the full path to compiler component . -print-multiarch Display the target's normalized GNU triplet, used as a component in the library path. -print-multi-directory Display the root directory for versions of libgcc. -print-multi-lib Display the mapping between command line options and Trying FC compiler flag -fPIC for PIC code Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -fPIC Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.F90 Successful compile: Source: function foo(a) real:: a,x,bar common /xx/ x x=a foo = bar(x) end Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/libconftest.so -shared -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o Accepted FC compiler flag -fPIC for PIC code ================================================================================ TEST checkSharedLinkerPaths from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1496) TESTING: checkSharedLinkerPaths from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1496) Determine the shared linker path options - IRIX: -rpath - Linux, OSF: -Wl,-rpath, - Solaris: -R - FreeBSD: -Wl,-R, Executing: uname -s stdout: Linux Executing: mpicc -V Trying C linker flag -Wl,-rpath, Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest -Wl,-rpath,/p/work2/tmondrag/moose/petsc -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o Valid C linker flag -Wl,-rpath,/p/work2/tmondrag/moose/petsc Executing: uname -s stdout: Linux Executing: mpicc -V Trying Cxx linker flag -Wl,-rpath, Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest -Wl,-rpath,/p/work2/tmondrag/moose/petsc /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o Valid Cxx linker flag -Wl,-rpath,/p/work2/tmondrag/moose/petsc Executing: uname -s stdout: Linux Executing: mpicc -V Trying FC linker flag -Wl,-rpath, Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: mpif90 -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest -Wl,-rpath,/p/work2/tmondrag/moose/petsc -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o Valid FC linker flag -Wl,-rpath,/p/work2/tmondrag/moose/petsc ================================================================================ TEST checkLibC from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1531) TESTING: checkLibC from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1531) Test whether we need to explicitly include libc in shared linking - Mac OSX requires an explicit reference to libc for shared linking Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int foo(void) {void *chunk = malloc(31); free(chunk); return 0;} Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/libconftest.so -shared -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o Shared linking does not require an explicit libc reference ================================================================================ TEST checkDynamicLinker from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1577) TESTING: checkDynamicLinker from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1577) Check that the linker can dynamicaly load shared libraries Checking for header: dlfcn.h All intermediate test results are stored in /p/work2/tmondrag/petsc-0UdWsO/config.headers Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_DLFCN_H" to "1" Checking for functions [dlopen dlsym dlclose] in library ['dl'] [] All intermediate test results are stored in /p/work2/tmondrag/petsc-0UdWsO/config.libraries Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char dlopen(); static void _check_dlopen() { dlopen(); } char dlsym(); static void _check_dlsym() { dlsym(); } char dlclose(); static void _check_dlclose() { dlclose(); } int main() { _check_dlopen(); _check_dlsym(); _check_dlclose();; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -ldl Defined "HAVE_LIBDL" to "1" Adding ['dl'] to LIBS Executing: uname -s stdout: Linux Checking dynamic linker mpicc using flags ['-shared'] Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/mpicc...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/mpicc...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/mpicc...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/mpicc...not found Checking for program /usr/local/krb5/bin/mpicc...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/mpicc...found Defined make macro "DYNAMICLINKER" to "mpicc" Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest -shared -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -ldl Valid C linker flag -shared Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int foo(void) {printf("test");return 0;} Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/libconftest.so -shared -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -ldl Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { void *handle = dlopen("/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/libconftest.so", 0); int (*foo)(void) = (int (*)(void)) dlsym(handle, "foo"); if (!foo) { printf("Could not load symbol\n"); return -1; } if ((*foo)()) { printf("Invalid return from foo()\n"); return -1; } if (dlclose(handle)) { printf("Could not close library\n"); return -1; } ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -ldl Using dynamic linker mpicc with flags ['-shared'] and library extension so ================================================================================ TEST output from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1626) TESTING: output from config.setCompilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1626) Output module data as defines and substitutions Substituting "CC" with "mpicc" Substituting "CFLAGS" with " -fPIC" Defined make macro "CC_LINKER_SLFLAG" to "-Wl,-rpath," Substituting "CPP" with "mpicc -E" Substituting "CPPFLAGS" with "" Substituting "CXX" with "mpicxx" Substituting "CXX_CXXFLAGS" with " -fPIC" Substituting "CXXFLAGS" with "" Substituting "CXX_LINKER_SLFLAG" with "-Wl,-rpath," Substituting "CXXPP" with "mpicxx -E" Substituting "CXXPPFLAGS" with "" Substituting "FC" with "mpif90" Substituting "FFLAGS" with " -fPIC" Defined make macro "FC_LINKER_SLFLAG" to "-Wl,-rpath," Substituting "LDFLAGS" with "" Substituting "LIBS" with "-ldl " Substituting "SHARED_LIBRARY_FLAG" with "-shared" child config.setCompilers 6.372900 ================================================================================ TEST checkSharedDynamicPicOptions from PETSc.options.sharedLibraries(/p/work2/tmondrag/moose/petsc/config/PETSc/options/sharedLibraries.py:36) TESTING: checkSharedDynamicPicOptions from PETSc.options.sharedLibraries(/p/work2/tmondrag/moose/petsc/config/PETSc/options/sharedLibraries.py:36) ================================================================================ TEST configureSharedLibraries from PETSc.options.sharedLibraries(/p/work2/tmondrag/moose/petsc/config/PETSc/options/sharedLibraries.py:52) TESTING: configureSharedLibraries from PETSc.options.sharedLibraries(/p/work2/tmondrag/moose/petsc/config/PETSc/options/sharedLibraries.py:52) Checks whether shared libraries should be used, for which you must - Specify --with-shared-libraries - Have found a working shared linker Defines PETSC_USE_SHARED_LIBRARIES if they are used Executing: uname -s stdout: Linux Defined make rule "shared_arch" with dependencies "shared_linux" and code [] Defined make macro "SONAME_FUNCTION" to "$(1).so.$(2)" Defined make macro "SL_LINKER_FUNCTION" to "-shared -Wl,-soname,$(call SONAME_FUNCTION,$(notdir $(1)),$(2))" Defined make macro "BUILDSHAREDLIB" to "yes" Defined "USE_SHARED_LIBRARIES" to "1" ================================================================================ TEST configureDynamicLibraries from PETSc.options.sharedLibraries(/p/work2/tmondrag/moose/petsc/config/PETSc/options/sharedLibraries.py:94) TESTING: configureDynamicLibraries from PETSc.options.sharedLibraries(/p/work2/tmondrag/moose/petsc/config/PETSc/options/sharedLibraries.py:94) Checks whether dynamic loading is available (with dlfcn.h and libdl) Defined "HAVE_DYNAMIC_LIBRARIES" to "1" ================================================================================ TEST configureSerializedFunctions from PETSc.options.sharedLibraries(/p/work2/tmondrag/moose/petsc/config/PETSc/options/sharedLibraries.py:100) TESTING: configureSerializedFunctions from PETSc.options.sharedLibraries(/p/work2/tmondrag/moose/petsc/config/PETSc/options/sharedLibraries.py:100) Defines PETSC_SERIALIZE_FUNCTIONS if they are used Requires shared libraries child PETSc.options.sharedLibraries 0.010910 ================================================================================ TEST configureIndexSize from PETSc.options.indexTypes(/p/work2/tmondrag/moose/petsc/config/PETSc/options/indexTypes.py:30) TESTING: configureIndexSize from PETSc.options.indexTypes(/p/work2/tmondrag/moose/petsc/config/PETSc/options/indexTypes.py:30) Defined make macro "PETSC_INDEX_SIZE" to "32" child PETSc.options.indexTypes 0.001569 ================================================================================ TEST configureCompilerFlags from config.compilerFlags(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilerFlags.py:72) TESTING: configureCompilerFlags from config.compilerFlags(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilerFlags.py:72) Get the default compiler flags Defined make macro "C_VERSION" to "gcc (GCC) 7.3.0" Defined make macro "MPICC_SHOW" to "gcc -I/p/home/apps/hpe/mpt-2.19/include -lpthread /usr/lib64/libcpuset.so.1 /usr/lib64/libbitmask.so.1 -L/p/home/apps/hpe/mpt-2.19/lib -lmpi" Trying C compiler flag -Wall Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -Wall Trying C compiler flag -Wwrite-strings Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -Wwrite-strings /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -Wwrite-strings Trying C compiler flag -Wno-strict-aliasing Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -Wno-strict-aliasing Trying C compiler flag -Wno-unknown-pragmas Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -Wno-unknown-pragmas Trying C compiler flag -fstack-protector Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -fstack-protector Trying C compiler flag -mfp16-format=ieee Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -mfp16-format=ieee /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Possible ERROR while running compiler: exit code 1 stderr: gcc: error: unrecognized command line option ???-mfp16-format=ieee??? Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Rejecting compiler flag -mfp16-format=ieee due to nonzero status from link Rejecting compiler flag -mfp16-format=ieee due to gcc: error: unrecognized command line option ???-mfp16-format=ieee??? PETSc Error: No output file produced Rejected C compiler flag -mfp16-format=ieee Trying C compiler flag -fvisibility=hidden Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -fvisibility=hidden Defined make macro "MPICC_SHOW" to "gcc -I/p/home/apps/hpe/mpt-2.19/include -lpthread /usr/lib64/libcpuset.so.1 /usr/lib64/libbitmask.so.1 -L/p/home/apps/hpe/mpt-2.19/lib -lmpi" Trying C compiler flag -g Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -g Trying C compiler flag -O Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -O Defined make macro "Cxx_VERSION" to "g++ (GCC) 7.3.0" Defined make macro "MPICXX_SHOW" to "g++ -I/p/home/apps/hpe/mpt-2.19/include -lpthread /usr/lib64/libcpuset.so.1 /usr/lib64/libbitmask.so.1 -L/p/home/apps/hpe/mpt-2.19/lib -lmpi++ -lmpi" Trying Cxx compiler flag -Wall Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -Wall Trying Cxx compiler flag -Wwrite-strings Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -Wwrite-strings Trying Cxx compiler flag -Wno-strict-aliasing Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -Wno-strict-aliasing Trying Cxx compiler flag -Wno-unknown-pragmas Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -Wno-unknown-pragmas Trying Cxx compiler flag -fstack-protector Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -fstack-protector Trying Cxx compiler flag -fvisibility=hidden Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -fvisibility=hidden Defined make macro "MPICXX_SHOW" to "g++ -I/p/home/apps/hpe/mpt-2.19/include -lpthread /usr/lib64/libcpuset.so.1 /usr/lib64/libbitmask.so.1 -L/p/home/apps/hpe/mpt-2.19/lib -lmpi++ -lmpi" Trying Cxx compiler flag -g Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -g Trying Cxx compiler flag -O Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -O Defined make macro "FC_VERSION" to "GNU Fortran (GCC) 7.3.0" Defined make macro "MPIFC_SHOW" to "gfortran -I/p/home/apps/hpe/mpt-2.19/include -I/p/home/apps/gnu_compiler/7.3.0/include -I/p/home/apps/hpe/mpt-2.19/include -lpthread /usr/lib64/libcpuset.so.1 /usr/lib64/libbitmask.so.1 -L/p/home/apps/hpe/mpt-2.19/lib -lmpi" Trying FC compiler flag -Wall Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -Wall Trying FC compiler flag -ffree-line-length-0 Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -ffree-line-length-0 /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -ffree-line-length-0 Trying FC compiler flag -Wno-unused-dummy-argument Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -Wno-unused-dummy-argument Defined make macro "MPIFC_SHOW" to "gfortran -I/p/home/apps/hpe/mpt-2.19/include -I/p/home/apps/gnu_compiler/7.3.0/include -I/p/home/apps/hpe/mpt-2.19/include -lpthread /usr/lib64/libcpuset.so.1 /usr/lib64/libbitmask.so.1 -L/p/home/apps/hpe/mpt-2.19/lib -lmpi" Trying FC compiler flag -g Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -g Trying FC compiler flag -O Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -O child config.compilerFlags 2.869541 ================================================================================ TEST checkRestrict from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:138) TESTING: checkRestrict from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:138) Check for the C/CXX restrict keyword Executing: mpicc -V All intermediate test results are stored in /p/work2/tmondrag/petsc-0UdWsO/config.compilers Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.c: In function ???main???: /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.c:5:20: warning: unused variable ???x??? [-Wunused-variable] float * __restrict x;; ^ Source: #include "confdefs.h" #include "conffix.h" int main() { float * __restrict x;; return 0; } compilers: Set C restrict keyword to __restrict Defined "C_RESTRICT" to "__restrict" ================================================================================ TEST checkCFormatting from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:391) TESTING: checkCFormatting from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:391) Activate format string checking if using the GNU compilers ================================================================================ TEST checkCInline from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:108) TESTING: checkCInline from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:108) Check for C inline keyword Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" static inline int foo(int a) {return a;} int main() { foo(1);; return 0; } compilers: Set C Inline keyword to inline Defined "C_INLINE" to "inline" ================================================================================ TEST checkDynamicLoadFlag from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:402) TESTING: checkDynamicLoadFlag from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:402) Checks that dlopen() takes RTLD_XXX, and defines PETSC_HAVE_RTLD_XXX if it does Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include char *libname; int main() { dlopen(libname, RTLD_LAZY);dlopen(libname, RTLD_NOW);dlopen(libname, RTLD_LOCAL);dlopen(libname, RTLD_GLOBAL); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -ldl Defined "HAVE_RTLD_LAZY" to "1" Defined "HAVE_RTLD_NOW" to "1" Defined "HAVE_RTLD_LOCAL" to "1" Defined "HAVE_RTLD_GLOBAL" to "1" ================================================================================ TEST checkCLibraries from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:202) TESTING: checkCLibraries from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:202) Determines the libraries needed to link with C compiled code Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include void asub(void) {char s[16];printf("testing %s",s);} Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.F90 Successful compile: Source: program main print*,'testing' stop end Executing: mpif90 -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/confc.o -ldl C libraries are not needed when using Fortran linker Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include void asub(void) {char s[16];printf("testing %s",s);} Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main(int argc,char **args) {return 0;} Executing: mpicxx -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/confc.o -ldl C libraries are not needed when using C++ linker ================================================================================ TEST checkDependencyGenerationFlag from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:1343) TESTING: checkDependencyGenerationFlag from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:1343) Check if -MMD works for dependency generation, and add it if it does Trying C compiler flag -MMD -MP Defined make macro "C_DEPFLAGS" to "-MMD -MP" Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -MMD -MP /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Trying Cxx compiler flag -MMD -MP Defined make macro "CXX_DEPFLAGS" to "-MMD -MP" Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC -MMD -MP /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } ================================================================================ TEST checkC99Flag from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:1388) TESTING: checkC99Flag from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:1388) Check for -std=c99 or equivalent flag Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c: In function ???main???: /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c:7:11: warning: variable ???x??? set but not used [-Wunused-but-set-variable] float x[2],y; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { float x[2],y; y = FLT_ROUNDS; // c++ comment int j = 2; for (int i=0; i<2; i++){ x[i] = i*j*y; } ; return 0; } Accepted C99 compile flag: Defined "HAVE_C99" to "1" ================================================================================ TEST checkRestrict from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:138) TESTING: checkRestrict from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:138) Check for the C/CXX restrict keyword Executing: mpicc -V Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.cc Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.cc: In function ???int main()???: /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.cc:5:20: warning: unused variable ???x??? [-Wunused-variable] float * __restrict x;; ^ Source: #include "confdefs.h" #include "conffix.h" int main() { float * __restrict x;; return 0; } compilers: Set Cxx restrict keyword to __restrict Defined "CXX_RESTRICT" to "__restrict" ================================================================================ TEST checkCxxOptionalExtensions from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:421) TESTING: checkCxxOptionalExtensions from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:421) Check whether the C++ compiler (IBM xlC, OSF5) need special flag for .c files which contain C++ Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { class somename { int i; };; return 0; } ================================================================================ TEST checkCxxInline from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:123) TESTING: checkCxxInline from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:123) Check for C++ inline keyword Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" static inline int foo(int a) {return a;} int main() { foo(1);; return 0; } compilers: Set Cxx Inline keyword to inline Defined "CXX_INLINE" to "inline" ================================================================================ TEST checkCxxLibraries from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:531) TESTING: checkCxxLibraries from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:531) Determines the libraries needed to link with C++ from C and Fortran Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include void asub(void) {std::vector v; try { throw 20; } catch (int e) { std::cout << "An exception occurred"; }} Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main(int argc,char **args) {return 0;} Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/confc.o -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.compilers/confc.o: in function `asub()': /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.cc:7: undefined reference to `__cxa_allocate_exception' /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.cc:7: undefined reference to `typeinfo for int' /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.cc:7: undefined reference to `__cxa_throw' /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.cc:7: undefined reference to `__cxa_begin_catch' /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.cc:7: undefined reference to `std::cout' /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.cc:7: undefined reference to `std::basic_ostream >& std::operator<< >(std::basic_ostream >&, char const*)' /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.cc:7: undefined reference to `__cxa_end_catch' /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.cc:7: undefined reference to `__cxa_end_catch' /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.compilers/confc.o: in function `__static_initialization_and_destruction_0': /p/home/apps/gnu_compiler/7.3.0/include/c++/7.3.0/iostream:74: undefined reference to `std::ios_base::Init::Init()' /usr/bin/ld: /p/home/apps/gnu_compiler/7.3.0/include/c++/7.3.0/iostream:74: undefined reference to `std::ios_base::Init::~Init()' /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.compilers/confc.o:(.data.DW.ref._ZTIi[DW.ref._ZTIi]+0x0): undefined reference to `typeinfo for int' /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.compilers/confc.o:(.data.DW.ref.__gxx_personality_v0[DW.ref.__gxx_personality_v0]+0x0): undefined reference to `__gxx_personality_v0' collect2: error: ld returned 1 exit status Executing: uname -s stdout: Linux Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include void asub(void) {std::vector v; try { throw 20; } catch (int e) { std::cout << "An exception occurred"; }} Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main(int argc,char **args) {return 0;} Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/confc.o -lstdc++ -ldl compilers: C++ requires -lstdc++ to link with C compiler Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include void asub(void) {std::vector v; try { throw 20; } catch (int e) { std::cout << "An exception occurred"; }} Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.F90 Successful compile: Source: program main print*,'testing' stop end Executing: mpif90 -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/confc.o -lstdc++ -ldl C++ libraries are not needed when using FC linker ================================================================================ TEST checkCxxDialect from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:449) TESTING: checkCxxDialect from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:449) Determine the Cxx dialect supported by the compiler [and correspoding compiler option - if any]. -with-cxx-dialect can take options: auto: use highest dialect configure can determine cxx17: [future?] cxx14: gnu++14 or c++14 cxx11: gnu++11 or c++11 0: disable CxxDialect check and use compiler default checkCxxDialect: checking CXX11 with flag: Defined "HAVE_CXX_DIALECT_CXX11" to "1" Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include template constexpr T Cubed( T x ) { return x*x*x; } int main() { std::random_device rd; std::mt19937 mt(rd()); std::normal_distribution dist(0,1); const double x = dist(mt); std::cout << x; ; return 0; } Executing: mpicxx -V ================================================================================ TEST checkFortranNameMangling from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:836) TESTING: checkFortranNameMangling from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:836) Checks Fortran name mangling, and defines HAVE_FORTRAN_UNDERSCORE, HAVE_FORTRAN_NOUNDERSCORE, HAVE_FORTRAN_CAPS, or HAVE_FORTRAN_STDCALL Testing Fortran mangling type underscore with code void d1chk_(void){return;} Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" void d1chk_(void){return;} Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.F90 Successful compile: Source: program main call d1chk() end Executing: mpif90 -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/confc.o -lstdc++ -ldl compilers: Fortran name mangling is underscore Defined "HAVE_FORTRAN_UNDERSCORE" to "1" Executing: mpif90 --version stdout: GNU Fortran (GCC) 7.3.0 Copyright (C) 2017 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Defined "FORTRAN_CHARLEN_T" to "int" ================================================================================ TEST checkFortranNameManglingDouble from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:877) TESTING: checkFortranNameManglingDouble from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:877) Checks if symbols containing an underscore append an extra underscore, and defines HAVE_FORTRAN_UNDERSCORE_UNDERSCORE if necessary Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" void d1_chk__(void){return;} Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.F90 Successful compile: Source: program main call d1_chk() end Executing: mpif90 -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/confc.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o: in function `MAIN__': /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.F90:2: undefined reference to `d1_chk_' collect2: error: ld returned 1 exit status ================================================================================ TEST checkFortranLibraries from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:887) TESTING: checkFortranLibraries from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:887) Substitutes for FLIBS the libraries needed to link with Fortran This macro is intended to be used in those situations when it is necessary to mix, e.g. C++ and Fortran 77, source code into a single program or shared library. For example, if object files from a C++ and Fortran 77 compiler must be linked together, then the C++ compiler/linker must be used for linking (since special C++-ish things need to happen at link time like calling global constructors, instantiating templates, enabling exception support, etc.). However, the Fortran 77 intrinsic and run-time libraries must be linked in as well, but the C++ compiler/linker does not know how to add these Fortran 77 libraries. This code was translated from the autoconf macro which was packaged in its current form by Matthew D. Langston . However, nearly all of this macro came from the OCTAVE_FLIBS macro in octave-2.0.13/aclocal.m4, and full credit should go to John W. Eaton for writing this extremely useful macro. Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.F90 Possible ERROR while running compiler: stderr: /p/home/apps/hpe/mpt-2.19/include/mpif.h:561:54: integer MPI_STATUSES_IGNORE(MPI_STATUS_SIZE,1) 1 Warning: Unused variable ???mpi_statuses_ignore??? declared at (1) [-Wunused-variable] Source: program main #include call MPI_Allreduce() end Executing: mpif90 -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -lstdc++ -ldl Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.F90 Successful compile: Source: subroutine asub() print*,'testing' call MPI_Allreduce() return end Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main(int argc,char **args) {return 0;} Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/confc.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.compilers/confc.o: in function `asub_': /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.F90:2: undefined reference to `_gfortran_st_write' /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.F90:2: undefined reference to `_gfortran_transfer_character_write' /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.F90:2: undefined reference to `_gfortran_st_write_done' collect2: error: ld returned 1 exit status Fortran code cannot directly be linked with C linker, therefore will determine needed Fortran libraries Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.F90 Successful compile: Source: program main end Executing: mpif90 -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest -v -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -lstdc++ -ldl Possible ERROR while running linker: stderr: Driving: gfortran -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest -v -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -lstdc++ -ldl -I/p/home/apps/hpe/mpt-2.19/include -I/p/home/apps/gnu_compiler/7.3.0/include -I/p/home/apps/hpe/mpt-2.19/include -lpthread /usr/lib64/libcpuset.so.1 /usr/lib64/libbitmask.so.1 -L/p/home/apps/hpe/mpt-2.19/lib -lmpi -l gfortran -l m -shared-libgcc Using built-in specs. COLLECT_GCC=gfortran COLLECT_LTO_WRAPPER=/p/home/apps/gnu_compiler/7.3.0/libexec/gcc/x86_64-pc-linux-gnu/7.3.0/lto-wrapper Target: x86_64-pc-linux-gnu Configured with: /p/home/u4immtww/g730/objdir/../gcc-7.3.0/configure --prefix=/p/home/apps/gnu_compiler/7.3.0 --enable-languages=c,c++,fortran,go --enable-multilib Thread model: posix gcc version 7.3.0 (GCC) Reading specs from /p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../../lib64/libgfortran.spec rename spec lib to liborig COLLECT_GCC_OPTIONS='-o' '/p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest' '-v' '-fPIC' '-Wall' '-ffree-line-length-0' '-Wno-unused-dummy-argument' '-g' '-O' '-I' '/p/home/apps/hpe/mpt-2.19/include' '-I' '/p/home/apps/gnu_compiler/7.3.0/include' '-I' '/p/home/apps/hpe/mpt-2.19/include' '-L/p/home/apps/hpe/mpt-2.19/lib' '-shared-libgcc' '-mtune=generic' '-march=x86-64' COMPILER_PATH=/p/home/apps/gnu_compiler/7.3.0/libexec/gcc/x86_64-pc-linux-gnu/7.3.0/:/p/home/apps/gnu_compiler/7.3.0/libexec/gcc/x86_64-pc-linux-gnu/7.3.0/:/p/home/apps/gnu_compiler/7.3.0/libexec/gcc/x86_64-pc-linux-gnu/:/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/:/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/ LIBRARY_PATH=/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/:/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../../lib64/:/lib/../lib64/:/usr/lib/../lib64/:/p/home/apps/hpe/mpt-2.19/lib/:/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-o' '/p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest' '-v' '-fPIC' '-Wall' '-ffree-line-length-0' '-Wno-unused-dummy-argument' '-g' '-O' '-I' '/p/home/apps/hpe/mpt-2.19/include' '-I' '/p/home/apps/gnu_compiler/7.3.0/include' '-I' '/p/home/apps/hpe/mpt-2.19/include' '-L/p/home/apps/hpe/mpt-2.19/lib' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /p/home/apps/gnu_compiler/7.3.0/libexec/gcc/x86_64-pc-linux-gnu/7.3.0/collect2 -plugin /p/home/apps/gnu_compiler/7.3.0/libexec/gcc/x86_64-pc-linux-gnu/7.3.0/liblto_plugin.so -plugin-opt=/p/home/apps/gnu_compiler/7.3.0/libexec/gcc/x86_64-pc-linux-gnu/7.3.0/lto-wrapper -plugin-opt=-fresolution=/p/work2/tmondrag/ccWK5GXE.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lquadmath -plugin-opt=-pass-through=-lm -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --eh-frame-hdr -m elf_x86_64 -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest /usr/lib/../lib64/crt1.o /usr/lib/../lib64/crti.o /p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/crtbegin.o -L/p/home/apps/hpe/mpt-2.19/lib -L/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0 -L/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/p/home/apps/hpe/mpt-2.19/lib -L/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../.. /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -lstdc++ -ldl -lpthread /usr/lib64/libcpuset.so.1 /usr/lib64/libbitmask.so.1 -lmpi -lgfortran -lm -lgcc_s -lgcc -lquadmath -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/crtend.o /usr/lib/../lib64/crtn.o COLLECT_GCC_OPTIONS='-o' '/p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest' '-v' '-fPIC' '-Wall' '-ffree-line-length-0' '-Wno-unused-dummy-argument' '-g' '-O' '-I' '/p/home/apps/hpe/mpt-2.19/include' '-I' '/p/home/apps/gnu_compiler/7.3.0/include' '-I' '/p/home/apps/hpe/mpt-2.19/include' '-L/p/home/apps/hpe/mpt-2.19/lib' '-shared-libgcc' '-mtune=generic' '-march=x86-64' compilers: Checking arg Driving: compilers: Unknown arg Driving: compilers: Checking arg gfortran compilers: Unknown arg gfortran compilers: Checking arg -o compilers: Unknown arg -o compilers: Checking arg /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest compilers: Unknown arg /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest compilers: Checking arg -v compilers: Unknown arg -v compilers: Checking arg -fPIC compilers: Unknown arg -fPIC compilers: Checking arg -Wall compilers: Unknown arg -Wall compilers: Checking arg -ffree-line-length-0 compilers: Unknown arg -ffree-line-length-0 compilers: Checking arg -Wno-unused-dummy-argument compilers: Unknown arg -Wno-unused-dummy-argument compilers: Checking arg -g compilers: Unknown arg -g compilers: Checking arg -O compilers: Unknown arg -O compilers: Checking arg /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o compilers: Unknown arg /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o compilers: Checking arg -lstdc++ compilers: Found library: -lstdc++ compilers: Checking arg -ldl compilers: Found library: -ldl compilers: Checking arg -I/p/home/apps/hpe/mpt-2.19/include compilers: Found include directory: /p/home/apps/hpe/mpt-2.19/include compilers: Checking arg -I/p/home/apps/gnu_compiler/7.3.0/include compilers: Found include directory: /p/home/apps/gnu_compiler/7.3.0/include compilers: Checking arg -I/p/home/apps/hpe/mpt-2.19/include compilers: Found include directory: /p/home/apps/hpe/mpt-2.19/include compilers: Checking arg -lpthread compilers: Found library: -lpthread compilers: Checking arg /usr/lib64/libcpuset.so.1 compilers: Unknown arg /usr/lib64/libcpuset.so.1 compilers: Checking arg /usr/lib64/libbitmask.so.1 compilers: Unknown arg /usr/lib64/libbitmask.so.1 compilers: Checking arg -L/p/home/apps/hpe/mpt-2.19/lib compilers: Found library directory: -L/p/home/apps/hpe/mpt-2.19/lib compilers: Checking arg -lmpi compilers: Found library: -lmpi compilers: Checking arg -l compilers: Found canonical library: -lgfortran compilers: Checking arg -l compilers: Found canonical library: -lm compilers: Checking arg -shared-libgcc compilers: Unknown arg -shared-libgcc compilers: Checking arg Using compilers: Unknown arg Using compilers: Checking arg built-in compilers: Unknown arg built-in compilers: Checking arg specs. compilers: Unknown arg specs. compilers: Checking arg COLLECT_GCC=gfortran compilers: Unknown arg COLLECT_GCC=gfortran compilers: Checking arg COLLECT_LTO_WRAPPER=/p/home/apps/gnu_compiler/7.3.0/libexec/gcc/x86_64-pc-linux-gnu/7.3.0/lto-wrapper compilers: Unknown arg COLLECT_LTO_WRAPPER=/p/home/apps/gnu_compiler/7.3.0/libexec/gcc/x86_64-pc-linux-gnu/7.3.0/lto-wrapper compilers: Checking arg Target: compilers: Unknown arg Target: compilers: Checking arg x86_64-pc-linux-gnu compilers: Unknown arg x86_64-pc-linux-gnu compilers: Checking arg Configured compilers: Unknown arg Configured compilers: Checking arg with: compilers: Unknown arg with: compilers: Checking arg /p/home/u4immtww/g730/objdir/../gcc-7.3.0/configure compilers: Unknown arg /p/home/u4immtww/g730/objdir/../gcc-7.3.0/configure compilers: Checking arg --prefix=/p/home/apps/gnu_compiler/7.3.0 compilers: Unknown arg --prefix=/p/home/apps/gnu_compiler/7.3.0 compilers: Checking arg --enable-languages=c,c++,fortran,go compilers: Unknown arg --enable-languages=c,c++,fortran,go compilers: Checking arg --enable-multilib compilers: Unknown arg --enable-multilib compilers: Checking arg Thread compilers: Unknown arg Thread compilers: Checking arg model: compilers: Unknown arg model: compilers: Checking arg posix compilers: Unknown arg posix compilers: Checking arg gcc compilers: Unknown arg gcc compilers: Checking arg version compilers: Unknown arg version compilers: Checking arg 7.3.0 compilers: Unknown arg 7.3.0 compilers: Checking arg (GCC) compilers: Unknown arg (GCC) compilers: Checking arg Reading compilers: Unknown arg Reading compilers: Checking arg specs compilers: Unknown arg specs compilers: Checking arg from compilers: Unknown arg from compilers: Checking arg /p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../../lib64/libgfortran.spec compilers: Unknown arg /p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../../lib64/libgfortran.spec compilers: Checking arg rename compilers: Unknown arg rename compilers: Checking arg spec compilers: Unknown arg spec compilers: Checking arg lib compilers: Unknown arg lib compilers: Checking arg to compilers: Unknown arg to compilers: Checking arg liborig compilers: Unknown arg liborig compilers: Checking arg COLLECT_GCC_OPTIONS= compilers: Unknown arg COLLECT_GCC_OPTIONS= compilers: Checking arg COMPILER_PATH=/p/home/apps/gnu_compiler/7.3.0/libexec/gcc/x86_64-pc-linux-gnu/7.3.0/:/p/home/apps/gnu_compiler/7.3.0/libexec/gcc/x86_64-pc-linux-gnu/7.3.0/:/p/home/apps/gnu_compiler/7.3.0/libexec/gcc/x86_64-pc-linux-gnu/:/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/:/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/ compilers: Skipping arg COMPILER_PATH=/p/home/apps/gnu_compiler/7.3.0/libexec/gcc/x86_64-pc-linux-gnu/7.3.0/:/p/home/apps/gnu_compiler/7.3.0/libexec/gcc/x86_64-pc-linux-gnu/7.3.0/:/p/home/apps/gnu_compiler/7.3.0/libexec/gcc/x86_64-pc-linux-gnu/:/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/:/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/ compilers: Checking arg LIBRARY_PATH=/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/:/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../../lib64/:/lib/../lib64/:/usr/lib/../lib64/:/p/home/apps/hpe/mpt-2.19/lib/:/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../:/lib/:/usr/lib/ compilers: Skipping arg LIBRARY_PATH=/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/:/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../../lib64/:/lib/../lib64/:/usr/lib/../lib64/:/p/home/apps/hpe/mpt-2.19/lib/:/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../:/lib/:/usr/lib/ compilers: Checking arg COLLECT_GCC_OPTIONS= compilers: Unknown arg COLLECT_GCC_OPTIONS= compilers: Checking arg /p/home/apps/gnu_compiler/7.3.0/libexec/gcc/x86_64-pc-linux-gnu/7.3.0/collect2 compilers: Unknown arg /p/home/apps/gnu_compiler/7.3.0/libexec/gcc/x86_64-pc-linux-gnu/7.3.0/collect2 compilers: Checking arg -plugin compilers: Unknown arg -plugin compilers: Checking arg /p/home/apps/gnu_compiler/7.3.0/libexec/gcc/x86_64-pc-linux-gnu/7.3.0/liblto_plugin.so compilers: Unknown arg /p/home/apps/gnu_compiler/7.3.0/libexec/gcc/x86_64-pc-linux-gnu/7.3.0/liblto_plugin.so compilers: Checking arg -plugin-opt=/p/home/apps/gnu_compiler/7.3.0/libexec/gcc/x86_64-pc-linux-gnu/7.3.0/lto-wrapper compilers: Unknown arg -plugin-opt=/p/home/apps/gnu_compiler/7.3.0/libexec/gcc/x86_64-pc-linux-gnu/7.3.0/lto-wrapper compilers: Checking arg -plugin-opt=-fresolution=/p/work2/tmondrag/ccWK5GXE.res compilers: Unknown arg -plugin-opt=-fresolution=/p/work2/tmondrag/ccWK5GXE.res compilers: Checking arg -plugin-opt=-pass-through=-lgcc_s compilers: Unknown arg -plugin-opt=-pass-through=-lgcc_s compilers: Checking arg -plugin-opt=-pass-through=-lgcc compilers: Unknown arg -plugin-opt=-pass-through=-lgcc compilers: Checking arg -plugin-opt=-pass-through=-lquadmath compilers: Unknown arg -plugin-opt=-pass-through=-lquadmath compilers: Checking arg -plugin-opt=-pass-through=-lm compilers: Unknown arg -plugin-opt=-pass-through=-lm compilers: Checking arg -plugin-opt=-pass-through=-lgcc_s compilers: Unknown arg -plugin-opt=-pass-through=-lgcc_s compilers: Checking arg -plugin-opt=-pass-through=-lgcc compilers: Unknown arg -plugin-opt=-pass-through=-lgcc compilers: Checking arg -plugin-opt=-pass-through=-lc compilers: Unknown arg -plugin-opt=-pass-through=-lc compilers: Checking arg -plugin-opt=-pass-through=-lgcc_s compilers: Unknown arg -plugin-opt=-pass-through=-lgcc_s compilers: Checking arg -plugin-opt=-pass-through=-lgcc compilers: Unknown arg -plugin-opt=-pass-through=-lgcc compilers: Checking arg --eh-frame-hdr compilers: Unknown arg --eh-frame-hdr compilers: Checking arg -m compilers: Unknown arg -m compilers: Checking arg elf_x86_64 compilers: Unknown arg elf_x86_64 compilers: Checking arg -dynamic-linker compilers: Unknown arg -dynamic-linker compilers: Checking arg /lib64/ld-linux-x86-64.so.2 compilers: Unknown arg /lib64/ld-linux-x86-64.so.2 compilers: Checking arg -o compilers: Unknown arg -o compilers: Checking arg /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest compilers: Unknown arg /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest compilers: Checking arg /usr/lib/../lib64/crt1.o compilers: Unknown arg /usr/lib/../lib64/crt1.o compilers: Checking arg /usr/lib/../lib64/crti.o compilers: Unknown arg /usr/lib/../lib64/crti.o compilers: Checking arg /p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/crtbegin.o compilers: Unknown arg /p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/crtbegin.o compilers: Checking arg -L/p/home/apps/hpe/mpt-2.19/lib compilers: Already in lflags so skipping: -L/p/home/apps/hpe/mpt-2.19/lib compilers: Checking arg -L/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0 compilers: Found library directory: -L/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0 compilers: Checking arg -L/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../../lib64 compilers: Found library directory: -L/p/home/apps/gnu_compiler/7.3.0/lib64 compilers: Checking arg -L/lib/../lib64 compilers: Checking arg -L/usr/lib/../lib64 compilers: Checking arg -L/p/home/apps/hpe/mpt-2.19/lib compilers: Already in lflags so skipping: -L/p/home/apps/hpe/mpt-2.19/lib compilers: Checking arg -L/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../.. compilers: Found library directory: -L/p/home/apps/gnu_compiler/7.3.0/lib compilers: Checking arg /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o compilers: Unknown arg /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o compilers: Checking arg -lstdc++ compilers: Already in lflags: -lstdc++ compilers: Checking arg -ldl compilers: Already in lflags: -ldl compilers: Checking arg -lpthread compilers: Already in lflags: -lpthread compilers: Checking arg /usr/lib64/libcpuset.so.1 compilers: Unknown arg /usr/lib64/libcpuset.so.1 compilers: Checking arg /usr/lib64/libbitmask.so.1 compilers: Unknown arg /usr/lib64/libbitmask.so.1 compilers: Checking arg -lmpi compilers: Already in lflags: -lmpi compilers: Checking arg -lgfortran compilers: Found library: -lgfortran compilers: Checking arg -lm compilers: Found library: -lm compilers: Checking arg -lgcc_s compilers: Found library: -lgcc_s compilers: Checking arg -lgcc compilers: Found system library therefore skipping: -lgcc compilers: Checking arg -lquadmath compilers: Found library: -lquadmath compilers: Checking arg -lm compilers: Already in lflags: -lm compilers: Checking arg -lgcc_s compilers: Already in lflags: -lgcc_s compilers: Checking arg -lgcc compilers: Found system library therefore skipping: -lgcc compilers: Checking arg -lc compilers: Found system library therefore skipping: -lc compilers: Checking arg -lgcc_s compilers: Already in lflags: -lgcc_s compilers: Checking arg -lgcc compilers: Found system library therefore skipping: -lgcc compilers: Checking arg /p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/crtend.o compilers: Unknown arg /p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0/crtend.o compilers: Checking arg /usr/lib/../lib64/crtn.o compilers: Unknown arg /usr/lib/../lib64/crtn.o compilers: Checking arg COLLECT_GCC_OPTIONS= compilers: Unknown arg COLLECT_GCC_OPTIONS= compilers: Libraries needed to link Fortran code with the C linker: ['-lstdc++', '-ldl', '-lpthread', '-Wl,-rpath,/p/home/apps/hpe/mpt-2.19/lib', '-L/p/home/apps/hpe/mpt-2.19/lib', '-lmpi', '-lgfortran', '-lm', '-Wl,-rpath,/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0', '-L/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0', '-Wl,-rpath,/p/home/apps/gnu_compiler/7.3.0/lib64', '-L/p/home/apps/gnu_compiler/7.3.0/lib64', '-Wl,-rpath,/p/home/apps/gnu_compiler/7.3.0/lib', '-L/p/home/apps/gnu_compiler/7.3.0/lib', '-lgfortran', '-lm', '-lgcc_s', '-lquadmath'] compilers: Libraries needed to link Fortran main with the C linker: [] compilers: Check that Fortran libraries can be used with C as the linker Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -lstdc++ -ldl -lpthread -Wl,-rpath,/p/home/apps/hpe/mpt-2.19/lib -L/p/home/apps/hpe/mpt-2.19/lib -lmpi -lgfortran -lm -Wl,-rpath,/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0 -L/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0 -Wl,-rpath,/p/home/apps/gnu_compiler/7.3.0/lib64 -L/p/home/apps/gnu_compiler/7.3.0/lib64 -Wl,-rpath,/p/home/apps/gnu_compiler/7.3.0/lib -L/p/home/apps/gnu_compiler/7.3.0/lib -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -lstdc++ -ldl -lpthread -Wl,-rpath,/p/home/apps/hpe/mpt-2.19/lib -L/p/home/apps/hpe/mpt-2.19/lib -lmpi -lgfortran -lm -Wl,-rpath,/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0 -L/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0 -Wl,-rpath,/p/home/apps/gnu_compiler/7.3.0/lib64 -L/p/home/apps/gnu_compiler/7.3.0/lib64 -Wl,-rpath,/p/home/apps/gnu_compiler/7.3.0/lib -L/p/home/apps/gnu_compiler/7.3.0/lib -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -lstdc++ -ldl -lpthread -Wl,-rpath,/p/home/apps/hpe/mpt-2.19/lib -L/p/home/apps/hpe/mpt-2.19/lib -lmpi -lgfortran -lm -Wl,-rpath,/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0 -L/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0 -Wl,-rpath,/p/home/apps/gnu_compiler/7.3.0/lib64 -L/p/home/apps/gnu_compiler/7.3.0/lib64 -Wl,-rpath,/p/home/apps/gnu_compiler/7.3.0/lib -L/p/home/apps/gnu_compiler/7.3.0/lib -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl Testing executable /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest to see if it can be run Executing: /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest Executing: /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest compilers: Check that Fortran libraries can be used with C++ as linker compilers: Fortran libraries can be used from C++ Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -lstdc++ -ldl -lpthread -Wl,-rpath,/p/home/apps/hpe/mpt-2.19/lib -L/p/home/apps/hpe/mpt-2.19/lib -lmpi -lgfortran -lm -Wl,-rpath,/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0 -L/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0 -Wl,-rpath,/p/home/apps/gnu_compiler/7.3.0/lib64 -L/p/home/apps/gnu_compiler/7.3.0/lib64 -Wl,-rpath,/p/home/apps/gnu_compiler/7.3.0/lib -L/p/home/apps/gnu_compiler/7.3.0/lib -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -lstdc++ -ldl -lpthread -Wl,-rpath,/p/home/apps/hpe/mpt-2.19/lib -L/p/home/apps/hpe/mpt-2.19/lib -lmpi -lgfortran -lm -Wl,-rpath,/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0 -L/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0 -Wl,-rpath,/p/home/apps/gnu_compiler/7.3.0/lib64 -L/p/home/apps/gnu_compiler/7.3.0/lib64 -Wl,-rpath,/p/home/apps/gnu_compiler/7.3.0/lib -L/p/home/apps/gnu_compiler/7.3.0/lib -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -lstdc++ -ldl -lpthread -Wl,-rpath,/p/home/apps/hpe/mpt-2.19/lib -L/p/home/apps/hpe/mpt-2.19/lib -lmpi -lgfortran -lm -Wl,-rpath,/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0 -L/p/home/apps/gnu_compiler/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0 -Wl,-rpath,/p/home/apps/gnu_compiler/7.3.0/lib64 -L/p/home/apps/gnu_compiler/7.3.0/lib64 -Wl,-rpath,/p/home/apps/gnu_compiler/7.3.0/lib -L/p/home/apps/gnu_compiler/7.3.0/lib -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl Testing executable /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest to see if it can be run Executing: /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest Executing: /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest ================================================================================ TEST checkFortranLinkingCxx from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:1308) TESTING: checkFortranLinkingCxx from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:1308) Check that Fortran can link C++ libraries Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" extern "C" void d1chk_(void); void foo(void){d1chk_();} Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" extern "C" void d1chk_(void); void d1chk_(void){return;} Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.F90 Successful compile: Source: program main call d1chk() end Executing: mpif90 -o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilers/conftest.o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/cxxobj.o /p/work2/tmondrag/petsc-0UdWsO/config.compilers/confc.o -lstdc++ -ldl compilers: Fortran can link C++ functions ================================================================================ TEST setupFrameworkCompilers from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:1453) TESTING: setupFrameworkCompilers from config.compilers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:1453) child config.compilers 6.047090 ================================================================================ TEST configureClosure from config.utilities.closure(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/closure.py:17) TESTING: configureClosure from config.utilities.closure(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/closure.py:17) Determine if Apple ^close syntax is supported in C All intermediate test results are stored in /p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure/conftest.c: In function ???main???: /p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure/conftest.c:6:6: error: expected identifier or ???(??? before ???^??? token int (^closure)(int);; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int (^closure)(int);; return 0; } Compile failed inside link child config.utilities.closure 0.045664 ================================================================================ TEST checkFortranTypeSizes from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:56) TESTING: checkFortranTypeSizes from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:56) Check whether real*8 is supported and suggest flags which will allow support All intermediate test results are stored in /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.F90:2:21: real*8 variable 1 Warning: Unused variable ???variable??? declared at (1) [-Wunused-variable] Source: program main real*8 variable end ================================================================================ TEST checkFortranPreprocessor from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:73) TESTING: checkFortranPreprocessor from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:73) Determine if Fortran handles preprocessing properly Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.F90 Successful compile: Source: program main #define dummy dummy #ifndef dummy fooey #endif end compilers: Fortran uses preprocessor ================================================================================ TEST checkFortranDefineCompilerOption from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:96) TESTING: checkFortranDefineCompilerOption from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:96) Check if -WF,-Dfoobar or -Dfoobar is the compiler option to define a macro Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O -DTesting /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.F90 Successful compile: Source: program main #define dummy dummy #ifndef Testing fooey #endif end Defined make macro "FC_DEFINE_FLAG" to "-D" compilers: Fortran uses -D for defining macro ================================================================================ TEST checkFortran90 from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:146) TESTING: checkFortran90 from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:146) Determine whether the Fortran compiler handles F90 Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.F90 Successful compile: Source: program main INTEGER, PARAMETER :: int = SELECTED_INT_KIND(8) INTEGER (KIND=int) :: ierr ierr = 1 end Executing: mpif90 -o /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.o -lstdc++ -ldl Defined "USING_F90" to "1" Fortran compiler supports F90 ================================================================================ TEST checkFortran90FreeForm from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:159) TESTING: checkFortran90FreeForm from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:159) Determine whether the Fortran compiler handles F90FreeForm We also require that the compiler handles lines longer than 132 characters Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.F90 Successful compile: Source: program main INTEGER, PARAMETER :: int = SELECTED_INT_KIND(8); INTEGER (KIND=int) :: ierr; ierr = 1 end Executing: mpif90 -o /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.o -lstdc++ -ldl Defined "USING_F90FREEFORM" to "1" Fortran compiler supports F90FreeForm ================================================================================ TEST checkFortran2003 from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:173) TESTING: checkFortran2003 from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:173) Determine whether the Fortran compiler handles F2003 Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.F90 Successful compile: Source: module Base_module type, public :: base_type integer :: A contains procedure, public :: Print => BasePrint end type base_type contains subroutine BasePrint(this) class(base_type) :: this end subroutine BasePrint end module Base_module program main use,intrinsic :: iso_c_binding Type(C_Ptr),Dimension(:),Pointer :: CArray character(kind=c_char),pointer :: nullc => null() character(kind=c_char,len=5),dimension(:),pointer::list1 allocate(list1(5)) CArray = (/(c_loc(list1(i)),i=1,5),c_loc(nullc)/) end Executing: mpif90 -o /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.o -lstdc++ -ldl Defined "USING_F2003" to "1" Fortran compiler supports F2003 ================================================================================ TEST checkFortran90Array from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:208) TESTING: checkFortran90Array from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:208) Check for F90 array interfaces Executing: uname -s stdout: Linux Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include void f90arraytest_(void* a1, void* a2,void* a3, void* i) { printf("arrays [%p %p %p]\n",a1,a2,a3); fflush(stdout); return; } void f90ptrtest_(void* a1, void* a2,void* a3, void* i, void* p1 ,void* p2, void* p3) { printf("arrays [%p %p %p]\n",a1,a2,a3); if ((p1 == p3) && (p1 != p2)) { printf("pointers match! [%p %p] [%p]\n",p1,p3,p2); fflush(stdout); } else { printf("pointers do not match! [%p %p] [%p]\n",p1,p3,p2); fflush(stdout); exit(111); } return; } Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.F90 Successful compile: Source: program main Interface Subroutine f90ptrtest(p1,p2,p3,i) integer, pointer :: p1(:,:) integer, pointer :: p2(:,:) integer, pointer :: p3(:,:) integer i End Subroutine End Interface integer, pointer :: ptr1(:,:),ptr2(:,:) integer, target :: array(6:8,9:21) integer in in = 25 ptr1 => array ptr2 => array call f90arraytest(ptr1,ptr2,ptr1,in) call f90ptrtest(ptr1,ptr2,ptr1,in) end Executing: mpif90 -o /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.o /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/fooobj.o -lstdc++ -ldl Testing executable /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest to see if it can be run Executing: /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest Executing: /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest stdout: arrays [0x7fffffffce70 0x7fffffffce70 0x7fffffffce70] arrays [0x7fffffffce20 0x7fffffffcdd0 0x7fffffffce20] pointers do not match! [0x2aaaaaaf9400 0x7fffffffce70] [(nil)] ERROR while running executable: Could not execute "['/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest']": arrays [0x7fffffffce70 0x7fffffffce70 0x7fffffffce70] arrays [0x7fffffffce20 0x7fffffffcdd0 0x7fffffffce20] pointers do not match! [0x2aaaaaaf9400 0x7fffffffce70] [(nil)] compilers: F90 uses a single argument for array pointers ================================================================================ TEST checkFortranModuleInclude from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:295) TESTING: checkFortranModuleInclude from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:295) Figures out what flag is used to specify the include path for Fortran modules Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.F90 Successful compile: Source: module configtest integer testint parameter (testint = 42) end module configtest Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.F90 Successful compile: Source: program main use configtest write(*,*) testint end Executing: mpif90 -o /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.o /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/configtest.o -lstdc++ -ldl compilers: Fortran module include flag -I found ================================================================================ TEST checkFortranModuleOutput from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:361) TESTING: checkFortranModuleOutput from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:361) Figures out what flag is used to specify the include path for Fortran modules Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -module /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: exit code 1 stderr: gfortran: error: unrecognized command line option ???-module???; did you mean ???-mhle???? Source: module configtest integer testint parameter (testint = 42) end module configtest compilers: Fortran module output flag -module compile failed Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -module:/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: exit code 1 stderr: gfortran: error: unrecognized command line option ???-module:/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/confdir??? Source: module configtest integer testint parameter (testint = 42) end module configtest compilers: Fortran module output flag -module: compile failed Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fmod=/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: exit code 1 stderr: gfortran: error: unrecognized command line option ???-fmod=/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/confdir??? Source: module configtest integer testint parameter (testint = 42) end module configtest compilers: Fortran module output flag -fmod= compile failed Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -J/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.F90 Successful compile: Source: module configtest integer testint parameter (testint = 42) end module configtest compilers: Fortran module output flag -J found ================================================================================ TEST checkFortranTypeStar from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:135) TESTING: checkFortranTypeStar from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:135) Determine whether the Fortran compiler handles type(*) Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.F90 Successful compile: Source: program main interface subroutine a(b) type(*) :: b(:) end subroutine end interface end Defined "HAVE_FORTRAN_TYPE_STAR" to "1" Fortran compiler supports type(*) ================================================================================ TEST checkFortranTypeInitialize from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:125) TESTING: checkFortranTypeInitialize from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:125) Determines if PETSc objects in Fortran are initialized by default (doesn't work with common blocks) Defined "FORTRAN_TYPE_INITIALIZE" to " = -2" Initializing Fortran objects ================================================================================ TEST configureFortranFlush from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:116) TESTING: configureFortranFlush from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:116) Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.F90 Successful compile: Source: program main call flush(6) end Executing: mpif90 -o /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran/conftest.o -lstdc++ -ldl Defined "HAVE_FORTRAN_FLUSH" to "1" ================================================================================ TEST checkDependencyGenerationFlag from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:406) TESTING: checkDependencyGenerationFlag from config.compilersFortran(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:406) Check if -MMD works for dependency generation, and add it if it does Trying FC compiler flag -MMD -MP Defined make macro "FC_DEPFLAGS" to "-MMD -MP" Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O -MMD -MP /p/work2/tmondrag/petsc-0UdWsO/config.setCompilers/conftest.F90 Successful compile: Source: program main end child config.compilersFortran 2.200979 ================================================================================ TEST checkStdC from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:105) TESTING: checkStdC from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:105) Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include int main() { ; return 0; } Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #define ISLOWER(c) ('a' <= (c) && (c) <= 'z') #define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) #define XOR(e, f) (((e) && !(f)) || (!(e) && (f))) int main() { int i; for(i = 0; i < 256; i++) if (XOR(islower(i), ISLOWER(i)) || toupper(i) != TOUPPER(i)) exit(2); exit(0); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.o -lstdc++ -ldl Testing executable /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest to see if it can be run Executing: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest Executing: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest ================================================================================ TEST checkStat from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:138) TESTING: checkStat from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:138) Checks whether stat file-mode macros are broken, and defines STAT_MACROS_BROKEN if they are Preprocessing source: #include "confdefs.h" #include "conffix.h" #include #include #if defined(S_ISBLK) && defined(S_IFDIR) # if S_ISBLK (S_IFDIR) You lose. # endif #endif #if defined(S_ISBLK) && defined(S_IFCHR) # if S_ISBLK (S_IFCHR) You lose. # endif #endif #if defined(S_ISLNK) && defined(S_IFREG) # if S_ISLNK (S_IFREG) You lose. # endif #endif #if defined(S_ISSOCK) && defined(S_IFREG) # if S_ISSOCK (S_IFREG) You lose. # endif #endif Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c ================================================================================ TEST checkSysWait from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:173) TESTING: checkSysWait from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:173) Check for POSIX.1 compatible sys/wait.h, and defines HAVE_SYS_WAIT_H if found Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #ifndef WEXITSTATUS #define WEXITSTATUS(stat_val) ((unsigned)(stat_val) >> 8) #endif #ifndef WIFEXITED #define WIFEXITED(stat_val) (((stat_val) & 255) == 0) #endif int main() { int s; wait (&s); s = WIFEXITED (s) ? WEXITSTATUS (s) : 1; ; return 0; } Defined "HAVE_SYS_WAIT_H" to "1" ================================================================================ TEST checkTime from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:195) TESTING: checkTime from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:195) Checks if you can safely include both and , and if so defines TIME_WITH_SYS_TIME Checking for header: time.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_TIME_H" to "1" Checking for header: sys/time.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_TIME_H" to "1" ================================================================================ TEST checkMath from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:201) TESTING: checkMath from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:201) Checks for the math headers and defines Checking for header: math.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { double pi = M_PI; if (pi); ; return 0; } Found math #defines, like M_PI ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: setjmp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SETJMP_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: dos.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/confdefs.h" 1 # 2 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conffix.h" 1 # 3 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory #include ^~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory #include ^~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory #include ^~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: fcntl.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FCNTL_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: float.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FLOAT_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: io.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/confdefs.h" 1 # 2 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conffix.h" 1 # 3 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory #include ^~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory #include ^~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory #include ^~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: malloc.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_MALLOC_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: pwd.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_PWD_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: strings.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_STRINGS_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: unistd.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_UNISTD_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/sysinfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_SYSINFO_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: machine/endian.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/confdefs.h" 1 # 2 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conffix.h" 1 # 3 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/param.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_PARAM_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/procfs.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_PROCFS_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/resource.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_RESOURCE_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/systeminfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/confdefs.h" 1 # 2 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conffix.h" 1 # 3 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/times.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_TIMES_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/utsname.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_UTSNAME_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/socket.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_SOCKET_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/wait.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_WAIT_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: netinet/in.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_NETINET_IN_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: netdb.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_NETDB_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: Direct.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/confdefs.h" 1 # 2 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conffix.h" 1 # 3 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory #include ^~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: time.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_TIME_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: Ws2tcpip.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/confdefs.h" 1 # 2 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conffix.h" 1 # 3 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory #include ^~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/types.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_TYPES_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: WindowsX.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/confdefs.h" 1 # 2 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conffix.h" 1 # 3 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory #include ^~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: float.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FLOAT_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: ieeefp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/confdefs.h" 1 # 2 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conffix.h" 1 # 3 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory #include ^~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: stdint.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_STDINT_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: pthread.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_PTHREAD_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: inttypes.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_INTTYPES_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: immintrin.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_IMMINTRIN_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: zmmintrin.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/confdefs.h" 1 # 2 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conffix.h" 1 # 3 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory #include ^~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory #include ^~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory #include ^~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: setjmp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SETJMP_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: dos.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/confdefs.h" 1 # 2 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conffix.h" 1 # 3 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory #include ^~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory #include ^~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory #include ^~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: fcntl.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FCNTL_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: float.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FLOAT_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: io.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/confdefs.h" 1 # 2 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conffix.h" 1 # 3 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory #include ^~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory #include ^~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory #include ^~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: malloc.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_MALLOC_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: pwd.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_PWD_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: strings.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_STRINGS_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: unistd.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_UNISTD_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/sysinfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_SYSINFO_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: machine/endian.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/confdefs.h" 1 # 2 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conffix.h" 1 # 3 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/param.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_PARAM_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/procfs.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_PROCFS_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/resource.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_RESOURCE_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/systeminfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/confdefs.h" 1 # 2 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conffix.h" 1 # 3 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/times.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_TIMES_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/utsname.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_UTSNAME_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/socket.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_SOCKET_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/wait.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_WAIT_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: netinet/in.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_NETINET_IN_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: netdb.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_NETDB_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: Direct.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/confdefs.h" 1 # 2 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conffix.h" 1 # 3 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory #include ^~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: time.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_TIME_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: Ws2tcpip.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/confdefs.h" 1 # 2 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conffix.h" 1 # 3 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory #include ^~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/types.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_TYPES_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: WindowsX.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/confdefs.h" 1 # 2 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conffix.h" 1 # 3 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory #include ^~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: float.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FLOAT_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: ieeefp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/confdefs.h" 1 # 2 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conffix.h" 1 # 3 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory #include ^~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: stdint.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_STDINT_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: pthread.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_PTHREAD_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: inttypes.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_INTTYPES_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: immintrin.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_IMMINTRIN_H" to "1" ================================================================================ TEST check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: zmmintrin.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/confdefs.h" 1 # 2 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conffix.h" 1 # 3 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory #include ^~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory #include ^~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory #include ^~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST checkRecursiveMacros from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:216) TESTING: checkRecursiveMacros from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:216) Checks that the preprocessor allows recursive macros, and if not defines HAVE_BROKEN_RECURSIVE_MACRO Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" void a(int i, int j) {} #define a(b) a(b,__LINE__) int main() { a(0); ; return 0; } child config.headers 3.854072 ================================================================================ TEST configureCacheDetails from config.utilities.cacheDetails(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/cacheDetails.py:78) TESTING: configureCacheDetails from config.utilities.cacheDetails(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/cacheDetails.py:78) Try to determine the size and associativity of the cache. All intermediate test results are stored in /p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include long getconf_LEVEL1_DCACHE_LINESIZE() { long val = sysconf(_SC_LEVEL1_DCACHE_LINESIZE); return (16 <= val && val <= 2147483647) ? val : 32; } int main() { ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include long getconf_LEVEL1_DCACHE_LINESIZE() { long val = sysconf(_SC_LEVEL1_DCACHE_LINESIZE); return (16 <= val && val <= 2147483647) ? val : 32; } int main() { FILE *output = fopen("conftestval","w"); if (!output) return 1; fprintf(output,"%ld",getconf_LEVEL1_DCACHE_LINESIZE()); fclose(output);; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails/conftest.o -lstdc++ -ldl Testing executable /p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails/conftest to see if it can be run Executing: /p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails/conftest Executing: /p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails/conftest Defined "LEVEL1_DCACHE_LINESIZE" to "64" child config.utilities.cacheDetails 0.270939 ================================================================================ TEST check_struct_sigaction from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:43) TESTING: check_struct_sigaction from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:43) Checks if "struct sigaction" exists in signal.h. This check is for C89 check. Checking for type: struct sigaction All intermediate test results are stored in /p/work2/tmondrag/petsc-0UdWsO/config.types Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c: In function ???main???: /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c:11:18: warning: unused variable ???a??? [-Wunused-variable] struct sigaction a;; ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include int main() { struct sigaction a;; return 0; } struct sigaction found Defined "HAVE_STRUCT_SIGACTION" to "1" ================================================================================ TEST check__int64 from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:49) TESTING: check__int64 from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:49) Checks if __int64 exists. This is primarily for windows. Checking for type: __int64 Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c: In function ???main???: /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c:11:1: error: unknown type name ???__int64???; did you mean ???__int64_t???? __int64 a;; ^~~~~~~ __int64_t /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c:11:9: warning: unused variable ???a??? [-Wunused-variable] __int64 a;; ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { __int64 a;; return 0; } __int64 found ================================================================================ TEST checkSizeTypes from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:55) TESTING: checkSizeTypes from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:55) Checks for types associated with sizes, such as size_t. Checking for type: size_t Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c: In function ???main???: /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c:11:8: warning: unused variable ???a??? [-Wunused-variable] size_t a;; ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { size_t a;; return 0; } size_t found ================================================================================ TEST checkFileTypes from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:65) TESTING: checkFileTypes from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:65) Checks for types associated with files, such as mode_t, off_t, etc. Checking for type: mode_t Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c: In function ???main???: /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c:11:8: warning: unused variable ???a??? [-Wunused-variable] mode_t a;; ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { mode_t a;; return 0; } mode_t found Checking for type: off_t Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c: In function ???main???: /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c:11:7: warning: unused variable ???a??? [-Wunused-variable] off_t a;; ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { off_t a;; return 0; } off_t found ================================================================================ TEST checkIntegerTypes from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:60) TESTING: checkIntegerTypes from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:60) Checks for types associated with integers, such as int32_t. Checking for type: int32_t Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c: In function ???main???: /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c:11:9: warning: unused variable ???a??? [-Wunused-variable] int32_t a;; ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { int32_t a;; return 0; } int32_t found ================================================================================ TEST checkPID from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:71) TESTING: checkPID from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:71) Checks for pid_t, and defines it if necessary Checking for type: pid_t Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c: In function ???main???: /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c:11:7: warning: unused variable ???a??? [-Wunused-variable] pid_t a;; ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { pid_t a;; return 0; } pid_t found ================================================================================ TEST checkUID from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:75) TESTING: checkUID from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:75) Checks for uid_t and gid_t, and defines them if necessary Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.types /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c ================================================================================ TEST checkC99Complex from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:82) TESTING: checkC99Complex from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:82) Check for complex numbers in in C99 std Note that since PETSc source code uses _Complex we test specifically for that, not complex Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c: In function ???main???: /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c:6:17: warning: variable ???x??? set but not used [-Wunused-but-set-variable] double _Complex x; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { double _Complex x; x = I; ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c: In function ???main???: /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c:6:17: warning: variable ???x??? set but not used [-Wunused-but-set-variable] double _Complex x; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { double _Complex x; x = I; ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.o -lstdc++ -ldl Defined "HAVE_C99_COMPLEX" to "1" ================================================================================ TEST checkCxxComplex from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:93) TESTING: checkCxxComplex from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:93) Check for complex numbers in namespace std Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { std::complex x; ; return 0; } Executing: mpicxx -o /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.o -lstdc++ -ldl Defined "HAVE_CXX_COMPLEX" to "1" ================================================================================ TEST checkFortranKind from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:114) TESTING: checkFortranKind from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:114) Checks whether selected_int_kind etc work USE_FORTRANKIND Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.F90 Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.F90:4:43: real(kind=selected_real_kind(10)) d 1 Warning: Unused variable ???d??? declared at (1) [-Wunused-variable] /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.F90:3:45: integer(kind=selected_int_kind(10)) i 1 Warning: Unused variable ???i??? declared at (1) [-Wunused-variable] Source: program main integer(kind=selected_int_kind(10)) i real(kind=selected_real_kind(10)) d end Defined "USE_FORTRANKIND" to "1" ================================================================================ TEST checkConst from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:126) TESTING: checkConst from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:126) Checks for working const, and if not found defines it to empty string Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c: In function ???main???: /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c:25:5: warning: this ???if??? clause does not guard... [-Wmisleading-indentation] if (x[0]); ^~ /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c:26:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ???if??? { /* SCO 3.2v4 cc rejects this. */ ^ /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c:25:10: warning: ???x[0]??? is used uninitialized in this function [-Wuninitialized] if (x[0]); ~^~~ /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c:30:9: warning: ???t??? is used uninitialized in this function [-Wuninitialized] *t++ = 0; ~^~ /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c:46:25: warning: ???b??? is used uninitialized in this function [-Wuninitialized] struct s *b; b->j = 5; ~~~~~^~~ Source: #include "confdefs.h" #include "conffix.h" int main() { /* Ultrix mips cc rejects this. */ typedef int charset[2]; const charset x; /* SunOS 4.1.1 cc rejects this. */ char const *const *ccp; char **p; /* NEC SVR4.0.2 mips cc rejects this. */ struct point {int x, y;}; static struct point const zero = {0,0}; /* AIX XL C 1.02.0.0 rejects this. It does not let you subtract one const X* pointer from another in an arm of an if-expression whose if-part is not a constant expression */ const char *g = "string"; ccp = &g + (g ? g-g : 0); /* HPUX 7.0 cc rejects these. */ ++ccp; p = (char**) ccp; ccp = (char const *const *) p; /* This section avoids unused variable warnings */ if (zero.x); if (x[0]); { /* SCO 3.2v4 cc rejects this. */ char *t; char const *s = 0 ? (char *) 0 : (char const *) 0; *t++ = 0; if (*s); } { /* Someone thinks the Sun supposedly-ANSI compiler will reject this. */ int x[] = {25, 17}; const int *foo = &x[0]; ++foo; } { /* Sun SC1.0 ANSI compiler rejects this -- but not the above. */ typedef const int *iptr; iptr p = 0; ++p; } { /* AIX XL C 1.02.0.0 rejects this saying "k.c", line 2.27: 1506-025 (S) Operand must be a modifiable lvalue. */ struct s { int j; const int *ap[3]; }; struct s *b; b->j = 5; } { /* ULTRIX-32 V3.1 (Rev 9) vcc rejects this */ const int foo = 10; /* Get rid of unused variable warning */ if (foo); } ; return 0; } ================================================================================ TEST checkSizeof from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:182) TESTING: checkSizeof from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:182) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: short Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(short)==2)*2-1]; Defined "SIZEOF_SHORT" to "2" ================================================================================ TEST checkSizeof from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:182) TESTING: checkSizeof from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:182) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: int Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(int)==4)*2-1]; Defined "SIZEOF_INT" to "4" ================================================================================ TEST checkSizeof from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:182) TESTING: checkSizeof from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:182) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: long Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(long)==8)*2-1]; Defined "SIZEOF_LONG" to "8" ================================================================================ TEST checkSizeof from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:182) TESTING: checkSizeof from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:182) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: void * Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(void *)==8)*2-1]; Defined "SIZEOF_VOID_P" to "8" ================================================================================ TEST checkSizeof from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:182) TESTING: checkSizeof from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:182) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: long long Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(long long)==8)*2-1]; Defined "SIZEOF_LONG_LONG" to "8" ================================================================================ TEST checkSizeof from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:182) TESTING: checkSizeof from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:182) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: size_t Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(size_t)==8)*2-1]; Defined "SIZEOF_SIZE_T" to "8" ================================================================================ TEST checkVisibility from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:213) TESTING: checkVisibility from config.types(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/types.py:213) Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { __attribute__((visibility ("default"))) int foo(void);; return 0; } Defined "USE_VISIBILITY_C" to "1" Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.types -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.types/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { __attribute__((visibility ("default"))) int foo(void);; return 0; } Defined "USE_VISIBILITY_CXX" to "1" child config.types 1.728776 ================================================================================ TEST configureMemAlign from PETSc.options.memAlign(/p/work2/tmondrag/moose/petsc/config/PETSc/options/memAlign.py:29) TESTING: configureMemAlign from PETSc.options.memAlign(/p/work2/tmondrag/moose/petsc/config/PETSc/options/memAlign.py:29) Choose alignment Defined "MEMALIGN" to "16" Memory alignment is 16 child PETSc.options.memAlign 0.004819 ================================================================================ TEST check from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [handle_sigfpes] in library ['fpe'] [] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char handle_sigfpes(); static void _check_handle_sigfpes() { handle_sigfpes(); } int main() { _check_handle_sigfpes();; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -lfpe -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lfpe collect2: error: ld returned 1 exit status ================================================================================ TEST check from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [socket] in library ['socket', 'nsl'] [] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char socket(); static void _check_socket() { socket(); } int main() { _check_socket();; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -lsocket -lnsl -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lsocket collect2: error: ld returned 1 exit status ================================================================================ TEST check from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [handle_sigfpes] in library ['fpe'] [] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char handle_sigfpes(); static void _check_handle_sigfpes() { handle_sigfpes(); } int main() { _check_handle_sigfpes();; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -lfpe -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lfpe collect2: error: ld returned 1 exit status ================================================================================ TEST check from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [socket] in library ['socket', 'nsl'] [] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char socket(); static void _check_socket() { socket(); } int main() { _check_socket();; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -lsocket -lnsl -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lsocket collect2: error: ld returned 1 exit status ================================================================================ TEST checkMath from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:264) TESTING: checkMath from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:264) Check for sin() in libm, the math library Checking for functions [sin floor log10 pow] in library [''] [] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include double sin(double); static void _check_sin() { double x,y; scanf("%lf",&x); y = sin(x); printf("%f",y); ; } #include double floor(double); static void _check_floor() { double x,y; scanf("%lf",&x); y = floor(x); printf("%f",y); ; } #include double log10(double); static void _check_log10() { double x,y; scanf("%lf",&x); y = log10(x); printf("%f",y); ; } #include double pow(double, double); static void _check_pow() { double x,y; scanf("%lf",&x); y = pow(x,x); printf("%f",y); ; } int main() { _check_sin(); _check_floor(); _check_log10(); _check_pow();; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o: undefined reference to symbol 'log10@@GLIBC_2.2.5' /usr/bin/ld: /lib64/libm.so.6: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status Checking for functions [sin floor log10 pow] in library ['m'] [] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include double sin(double); static void _check_sin() { double x,y; scanf("%lf",&x); y = sin(x); printf("%f",y); ; } #include double floor(double); static void _check_floor() { double x,y; scanf("%lf",&x); y = floor(x); printf("%f",y); ; } #include double log10(double); static void _check_log10() { double x,y; scanf("%lf",&x); y = log10(x); printf("%f",y); ; } #include double pow(double, double); static void _check_pow() { double x,y; scanf("%lf",&x); y = pow(x,x); printf("%f",y); ; } int main() { _check_sin(); _check_floor(); _check_log10(); _check_pow();; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -lm -lstdc++ -ldl Defined "HAVE_LIBM" to "1" CheckMath: using math library ['libm.a'] ================================================================================ TEST checkMathErf from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:283) TESTING: checkMathErf from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:283) Check for erf() in libm, the math library Checking for functions [erf] in library ['libm.a'] [] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c: In function ???_check_erf???: /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c:5:74: warning: variable ???y??? set but not used [-Wunused-but-set-variable] static void _check_erf() { double (*checkErf)(double) = erf;double x = 0,y; y = (*checkErf)(x); } ^ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_erf() { double (*checkErf)(double) = erf;double x = 0,y; y = (*checkErf)(x); } int main() { _check_erf();; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -lm -lstdc++ -ldl Defined "HAVE_LIBM" to "1" erf() found Defined "HAVE_ERF" to "1" ================================================================================ TEST checkMathTgamma from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:292) TESTING: checkMathTgamma from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:292) Check for tgamma() in libm, the math library Checking for functions [tgamma] in library ['libm.a'] [] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c: In function ???_check_tgamma???: /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c:5:83: warning: variable ???y??? set but not used [-Wunused-but-set-variable] static void _check_tgamma() { double (*checkTgamma)(double) = tgamma;double x = 0,y; y = (*checkTgamma)(x); } ^ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_tgamma() { double (*checkTgamma)(double) = tgamma;double x = 0,y; y = (*checkTgamma)(x); } int main() { _check_tgamma();; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -lm -lstdc++ -ldl Defined "HAVE_LIBM" to "1" tgamma() found Defined "HAVE_TGAMMA" to "1" ================================================================================ TEST checkMathFenv from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:301) TESTING: checkMathFenv from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:301) Checks if can be used with FE_DFL_ENV Checking for functions [fesetenv] in library ['libm.a'] [] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_fesetenv() { fesetenv(FE_DFL_ENV);; } int main() { _check_fesetenv();; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -lm -lstdc++ -ldl Defined "HAVE_LIBM" to "1" Defined "HAVE_FENV_H" to "1" ================================================================================ TEST checkMathLog2 from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:309) TESTING: checkMathLog2 from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:309) Check for log2() in libm, the math library Checking for functions [log2] in library ['libm.a'] [] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c: In function ???_check_log2???: /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c:5:81: warning: unused variable ???y??? [-Wunused-variable] static void _check_log2() { double (*checkLog2)(double) = log2; double x = 2.5, y = (*checkLog2)(x); } ^ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_log2() { double (*checkLog2)(double) = log2; double x = 2.5, y = (*checkLog2)(x); } int main() { _check_log2();; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -lm -lstdc++ -ldl Defined "HAVE_LIBM" to "1" log2() found Defined "HAVE_LOG2" to "1" ================================================================================ TEST checkRealtime from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:318) TESTING: checkRealtime from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:318) Check for presence of clock_gettime() in realtime library (POSIX Realtime extensions) Checking for functions [clock_gettime] in library [''] [] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_clock_gettime() { struct timespec tp; clock_gettime(CLOCK_REALTIME,&tp);; } int main() { _check_clock_gettime();; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -lstdc++ -ldl realtime functions are linked in by default ================================================================================ TEST checkDynamic from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:334) TESTING: checkDynamic from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:334) Check for the header and libraries necessary for dynamic library manipulation Checking for functions [dlopen] in library ['dl'] [] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char dlopen(); static void _check_dlopen() { dlopen(); } int main() { _check_dlopen();; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -ldl -lstdc++ -ldl Defined "HAVE_LIBDL" to "1" Checking for header: dlfcn.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_DLFCN_H" to "1" child config.libraries 1.604511 ================================================================================ TEST configureLibraryOptions from PETSc.options.libraryOptions(/p/work2/tmondrag/moose/petsc/config/PETSc/options/libraryOptions.py:37) TESTING: configureLibraryOptions from PETSc.options.libraryOptions(/p/work2/tmondrag/moose/petsc/config/PETSc/options/libraryOptions.py:37) Sets PETSC_USE_DEBUG, PETSC_USE_INFO, PETSC_USE_LOG, PETSC_USE_CTABLE, PETSC_USE_FORTRAN_KERNELS, and PETSC_USE_AVX512_KERNELS Defined "USE_LOG" to "1" Executing: mpicc -qversion Defined "USE_MALLOC_COALESCED" to "1" Defined "USE_INFO" to "1" Defined "USE_CTABLE" to "1" Defined "USE_BACKWARD_LOOP" to "1" **********Checking if running on BGL/IBM detected Checking for functions [bgl_perfctr_void] in library [''] [] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char bgl_perfctr_void(); static void _check_bgl_perfctr_void() { bgl_perfctr_void(); } int main() { _check_bgl_perfctr_void();; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o: in function `_check_bgl_perfctr_void': /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c:5: undefined reference to `bgl_perfctr_void' collect2: error: ld returned 1 exit status Checking for functions [ADIOI_BGL_Open] in library [''] [] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char ADIOI_BGL_Open(); static void _check_ADIOI_BGL_Open() { ADIOI_BGL_Open(); } int main() { _check_ADIOI_BGL_Open();; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o: in function `_check_ADIOI_BGL_Open': /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c:5: undefined reference to `ADIOI_BGL_Open' collect2: error: ld returned 1 exit status *********BGL/IBM test failure Defined "USE_AVX512_KERNELS" to "1" Defined "Alignx(a,b)" to " " ================================================================================ TEST configureISColorValueType from PETSc.options.libraryOptions(/p/work2/tmondrag/moose/petsc/config/PETSc/options/libraryOptions.py:95) TESTING: configureISColorValueType from PETSc.options.libraryOptions(/p/work2/tmondrag/moose/petsc/config/PETSc/options/libraryOptions.py:95) Sets PETSC_IS_COLOR_VALUE_TYPE, MPIU_COLORING_VALUE, IS_COLORING_MAX required by ISColor Defined "MPIU_COLORING_VALUE" to "MPI_UNSIGNED_SHORT" Defined "IS_COLORING_MAX" to "USHRT_MAX" Defined "IS_COLOR_VALUE_TYPE" to "short" Defined "IS_COLOR_VALUE_TYPE_F" to "integer2" child PETSc.options.libraryOptions 0.297258 child config.atomics 0.000012 ================================================================================ TEST checkSysinfo from config.functions(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:106) TESTING: checkSysinfo from config.functions(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:106) Check whether sysinfo takes three arguments, and if it does define HAVE_SYSINFO_3ARG Checking for functions [sysinfo] All intermediate test results are stored in /p/work2/tmondrag/petsc-0UdWsO/config.functions Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char sysinfo(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_sysinfo) || defined (__stub___sysinfo) sysinfo_will_always_fail_with_ENOSYS(); #else sysinfo(); #endif ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_SYSINFO" to "1" Checking for header: sys/sysinfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_SYSINFO_H" to "1" Checking for header: sys/systeminfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/confdefs.h" 1 # 2 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conffix.h" 1 # 3 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~compilation terminated.: Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:9:4: error: #error "Cannot check sysinfo without special headers" # error "Cannot check sysinfo without special headers" ^~~~~ /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c: In function ???main???: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:13:30: warning: implicit declaration of function ???sysinfo??? [-Wimplicit-function-declaration] char buf[10]; long count=10; sysinfo(1, buf, count); ^~~~~~~ Source: #include "confdefs.h" #include "conffix.h" #ifdef HAVE_SYS_SYSINFO_H # include #elif defined(HAVE_SYS_SYSTEMINFO_H) # include #else # error "Cannot check sysinfo without special headers" #endif int main() { char buf[10]; long count=10; sysinfo(1, buf, count); ; return 0; } Compile failed inside link ================================================================================ TEST checkVPrintf from config.functions(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:125) TESTING: checkVPrintf from config.functions(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:125) Checks whether vprintf requires a char * last argument, and if it does defines HAVE_VPRINTF_CHAR Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { va_list Argp; vprintf( "%d", Argp ); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl ================================================================================ TEST checkVFPrintf from config.functions(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:131) TESTING: checkVFPrintf from config.functions(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:131) Checks whether vfprintf requires a char * last argument, and if it does defines HAVE_VFPRINTF_CHAR Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { va_list Argp; vfprintf(stdout, "%d", Argp ); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl ================================================================================ TEST checkVSNPrintf from config.functions(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:137) TESTING: checkVSNPrintf from config.functions(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:137) Checks whether vsnprintf requires a char * last argument, and if it does defines HAVE_VSNPRINTF_CHAR Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { va_list Argp;char str[6]; vsnprintf(str,5, "%d", Argp ); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_VSNPRINTF" to "1" ================================================================================ TEST checkNanosleep from config.functions(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:167) TESTING: checkNanosleep from config.functions(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:167) Check for functional nanosleep() - as time.h behaves differently for different compiler flags - like -std=c89 Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { struct timespec tp; tp.tv_sec = 0; tp.tv_nsec = (long)(1e9); nanosleep(&tp,0); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_NANOSLEEP" to "1" ================================================================================ TEST checkMemmove from config.functions(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:173) TESTING: checkMemmove from config.functions(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:173) Check for functional memmove() - as MS VC requires correct includes to for this test Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { char c1[1], c2[1] = "c"; size_t n=1; memmove(c1,c2,n); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_MEMMOVE" to "1" ================================================================================ TEST checkSignalHandlerType from config.functions(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:143) TESTING: checkSignalHandlerType from config.functions(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:143) Checks the type of C++ signals handlers, and defines SIGNAL_CAST to the correct value Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.types -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include static void myhandler(int sig) {} int main() { signal(SIGFPE,myhandler); ; return 0; } Executing: mpicxx -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Defined "SIGNAL_CAST" to " " ================================================================================ TEST checkFreeReturnType from config.functions(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:153) TESTING: checkFreeReturnType from config.functions(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:153) Checks whether free returns void or int, and defines HAVE_FREE_RETURN_INT Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c: In function ???main???: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:6:25: error: void value not ignored as it ought to be int ierr; void *p; ierr = free(p); return 0; ^ /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:6:5: warning: variable ???ierr??? set but not used [-Wunused-but-set-variable] int ierr; void *p; ierr = free(p); return 0; ^~~~ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int ierr; void *p; ierr = free(p); return 0; ; return 0; } Compile failed inside link ================================================================================ TEST checkVariableArgumentLists from config.functions(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:159) TESTING: checkVariableArgumentLists from config.functions(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:159) Checks whether the variable argument list functionality is working Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { va_list l1, l2; va_copy(l1, l2); return 0; ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_VA_COPY" to "1" ================================================================================ TEST checkClassify from config.functions(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:85) TESTING: checkClassify from config.functions(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:85) Recursive decompose to rapidly classify functions as found or missing To confirm that a function is missing, we require a compile/link failure with only that function in a compilation unit. In contrast, we can confirm that many functions are present by compiling them all together in a large compilation unit. We optimistically compile everything together, then trim all functions that were named in the error message and bisect the result. The trimming is only an optimization to increase the likelihood of a big-batch compile succeeding; we do not rely on the compiler naming missing functions. Checking for functions [rand getdomainname _access snprintf realpath dlsym bzero _getcwd getwd uname _lseek sleep _sleep lseek usleep dlclose gethostname clock access _snprintf dlerror fork getpagesize sbreak memalign getcwd gethostbyname readlink _set_output_format PXFGETARG strcasecmp dlopen drand48 socket popen getrusage _mkdir time stricmp] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:16:6: warning: conflicting types for built-in function ???snprintf??? [-Wbuiltin-declaration-mismatch] char snprintf(); ^~~~~~~~ /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:19:6: warning: conflicting types for built-in function ???bzero??? [-Wbuiltin-declaration-mismatch] char bzero(); ^~~~~ /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:34:6: warning: conflicting types for built-in function ???fork??? [-Wbuiltin-declaration-mismatch] char fork(); ^~~~ /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:43:6: warning: conflicting types for built-in function ???strcasecmp??? [-Wbuiltin-declaration-mismatch] char strcasecmp(); ^~~~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char rand(); char getdomainname(); char _access(); char snprintf(); char realpath(); char dlsym(); char bzero(); char _getcwd(); char getwd(); char uname(); char _lseek(); char sleep(); char _sleep(); char lseek(); char usleep(); char dlclose(); char gethostname(); char clock(); char access(); char _snprintf(); char dlerror(); char fork(); char getpagesize(); char sbreak(); char memalign(); char getcwd(); char gethostbyname(); char readlink(); char _set_output_format(); char PXFGETARG(); char strcasecmp(); char dlopen(); char drand48(); char socket(); char popen(); char getrusage(); char _mkdir(); char time(); char stricmp(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_rand) || defined (__stub___rand) rand_will_always_fail_with_ENOSYS(); #else rand(); #endif #if defined (__stub_getdomainname) || defined (__stub___getdomainname) getdomainname_will_always_fail_with_ENOSYS(); #else getdomainname(); #endif #if defined (__stub__access) || defined (__stub____access) _access_will_always_fail_with_ENOSYS(); #else _access(); #endif #if defined (__stub_snprintf) || defined (__stub___snprintf) snprintf_will_always_fail_with_ENOSYS(); #else snprintf(); #endif #if defined (__stub_realpath) || defined (__stub___realpath) realpath_will_always_fail_with_ENOSYS(); #else realpath(); #endif #if defined (__stub_dlsym) || defined (__stub___dlsym) dlsym_will_always_fail_with_ENOSYS(); #else dlsym(); #endif #if defined (__stub_bzero) || defined (__stub___bzero) bzero_will_always_fail_with_ENOSYS(); #else bzero(); #endif #if defined (__stub__getcwd) || defined (__stub____getcwd) _getcwd_will_always_fail_with_ENOSYS(); #else _getcwd(); #endif #if defined (__stub_getwd) || defined (__stub___getwd) getwd_will_always_fail_with_ENOSYS(); #else getwd(); #endif #if defined (__stub_uname) || defined (__stub___uname) uname_will_always_fail_with_ENOSYS(); #else uname(); #endif #if defined (__stub__lseek) || defined (__stub____lseek) _lseek_will_always_fail_with_ENOSYS(); #else _lseek(); #endif #if defined (__stub_sleep) || defined (__stub___sleep) sleep_will_always_fail_with_ENOSYS(); #else sleep(); #endif #if defined (__stub__sleep) || defined (__stub____sleep) _sleep_will_always_fail_with_ENOSYS(); #else _sleep(); #endif #if defined (__stub_lseek) || defined (__stub___lseek) lseek_will_always_fail_with_ENOSYS(); #else lseek(); #endif #if defined (__stub_usleep) || defined (__stub___usleep) usleep_will_always_fail_with_ENOSYS(); #else usleep(); #endif #if defined (__stub_dlclose) || defined (__stub___dlclose) dlclose_will_always_fail_with_ENOSYS(); #else dlclose(); #endif #if defined (__stub_gethostname) || defined (__stub___gethostname) gethostname_will_always_fail_with_ENOSYS(); #else gethostname(); #endif #if defined (__stub_clock) || defined (__stub___clock) clock_will_always_fail_with_ENOSYS(); #else clock(); #endif #if defined (__stub_access) || defined (__stub___access) access_will_always_fail_with_ENOSYS(); #else access(); #endif #if defined (__stub__snprintf) || defined (__stub____snprintf) _snprintf_will_always_fail_with_ENOSYS(); #else _snprintf(); #endif #if defined (__stub_dlerror) || defined (__stub___dlerror) dlerror_will_always_fail_with_ENOSYS(); #else dlerror(); #endif #if defined (__stub_fork) || defined (__stub___fork) fork_will_always_fail_with_ENOSYS(); #else fork(); #endif #if defined (__stub_getpagesize) || defined (__stub___getpagesize) getpagesize_will_always_fail_with_ENOSYS(); #else getpagesize(); #endif #if defined (__stub_sbreak) || defined (__stub___sbreak) sbreak_will_always_fail_with_ENOSYS(); #else sbreak(); #endif #if defined (__stub_memalign) || defined (__stub___memalign) memalign_will_always_fail_with_ENOSYS(); #else memalign(); #endif #if defined (__stub_getcwd) || defined (__stub___getcwd) getcwd_will_always_fail_with_ENOSYS(); #else getcwd(); #endif #if defined (__stub_gethostbyname) || defined (__stub___gethostbyname) gethostbyname_will_always_fail_with_ENOSYS(); #else gethostbyname(); #endif #if defined (__stub_readlink) || defined (__stub___readlink) readlink_will_always_fail_with_ENOSYS(); #else readlink(); #endif #if defined (__stub__set_output_format) || defined (__stub____set_output_format) _set_output_format_will_always_fail_with_ENOSYS(); #else _set_output_format(); #endif #if defined (__stub_PXFGETARG) || defined (__stub___PXFGETARG) PXFGETARG_will_always_fail_with_ENOSYS(); #else PXFGETARG(); #endif #if defined (__stub_strcasecmp) || defined (__stub___strcasecmp) strcasecmp_will_always_fail_with_ENOSYS(); #else strcasecmp(); #endif #if defined (__stub_dlopen) || defined (__stub___dlopen) dlopen_will_always_fail_with_ENOSYS(); #else dlopen(); #endif #if defined (__stub_drand48) || defined (__stub___drand48) drand48_will_always_fail_with_ENOSYS(); #else drand48(); #endif #if defined (__stub_socket) || defined (__stub___socket) socket_will_always_fail_with_ENOSYS(); #else socket(); #endif #if defined (__stub_popen) || defined (__stub___popen) popen_will_always_fail_with_ENOSYS(); #else popen(); #endif #if defined (__stub_getrusage) || defined (__stub___getrusage) getrusage_will_always_fail_with_ENOSYS(); #else getrusage(); #endif #if defined (__stub__mkdir) || defined (__stub____mkdir) _mkdir_will_always_fail_with_ENOSYS(); #else _mkdir(); #endif #if defined (__stub_time) || defined (__stub___time) time_will_always_fail_with_ENOSYS(); #else time(); #endif #if defined (__stub_stricmp) || defined (__stub___stricmp) stricmp_will_always_fail_with_ENOSYS(); #else stricmp(); #endif ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o: in function `main': /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:110: warning: the `getwd' function is dangerous and should not be used. /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:74: undefined reference to `_access' /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:104: undefined reference to `_getcwd' /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:122: undefined reference to `_lseek' /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:134: undefined reference to `_sleep' /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:176: undefined reference to `_snprintf' /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:200: undefined reference to `sbreak' /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:230: undefined reference to `_set_output_format' /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:236: undefined reference to `PXFGETARG' /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:278: undefined reference to `_mkdir' /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:290: undefined reference to `stricmp' collect2: error: ld returned 1 exit status Checking for functions [rand getdomainname realpath dlsym bzero uname usleep dlclose gethostname clock dlerror] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:17:6: warning: conflicting types for built-in function ???bzero??? [-Wbuiltin-declaration-mismatch] char bzero(); ^~~~~ Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char rand(); char getdomainname(); char realpath(); char dlsym(); char bzero(); char uname(); char usleep(); char dlclose(); char gethostname(); char clock(); char dlerror(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_rand) || defined (__stub___rand) rand_will_always_fail_with_ENOSYS(); #else rand(); #endif #if defined (__stub_getdomainname) || defined (__stub___getdomainname) getdomainname_will_always_fail_with_ENOSYS(); #else getdomainname(); #endif #if defined (__stub_realpath) || defined (__stub___realpath) realpath_will_always_fail_with_ENOSYS(); #else realpath(); #endif #if defined (__stub_dlsym) || defined (__stub___dlsym) dlsym_will_always_fail_with_ENOSYS(); #else dlsym(); #endif #if defined (__stub_bzero) || defined (__stub___bzero) bzero_will_always_fail_with_ENOSYS(); #else bzero(); #endif #if defined (__stub_uname) || defined (__stub___uname) uname_will_always_fail_with_ENOSYS(); #else uname(); #endif #if defined (__stub_usleep) || defined (__stub___usleep) usleep_will_always_fail_with_ENOSYS(); #else usleep(); #endif #if defined (__stub_dlclose) || defined (__stub___dlclose) dlclose_will_always_fail_with_ENOSYS(); #else dlclose(); #endif #if defined (__stub_gethostname) || defined (__stub___gethostname) gethostname_will_always_fail_with_ENOSYS(); #else gethostname(); #endif #if defined (__stub_clock) || defined (__stub___clock) clock_will_always_fail_with_ENOSYS(); #else clock(); #endif #if defined (__stub_dlerror) || defined (__stub___dlerror) dlerror_will_always_fail_with_ENOSYS(); #else dlerror(); #endif ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_RAND" to "1" Defined "HAVE_GETDOMAINNAME" to "1" Defined "HAVE_REALPATH" to "1" Defined "HAVE_DLSYM" to "1" Defined "HAVE_BZERO" to "1" Defined "HAVE_UNAME" to "1" Defined "HAVE_USLEEP" to "1" Defined "HAVE_DLCLOSE" to "1" Defined "HAVE_GETHOSTNAME" to "1" Defined "HAVE_CLOCK" to "1" Defined "HAVE_DLERROR" to "1" Checking for functions [fork getpagesize memalign gethostbyname readlink strcasecmp dlopen drand48 socket popen getrusage time] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:13:6: warning: conflicting types for built-in function ???fork??? [-Wbuiltin-declaration-mismatch] char fork(); ^~~~ /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:18:6: warning: conflicting types for built-in function ???strcasecmp??? [-Wbuiltin-declaration-mismatch] char strcasecmp(); ^~~~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char fork(); char getpagesize(); char memalign(); char gethostbyname(); char readlink(); char strcasecmp(); char dlopen(); char drand48(); char socket(); char popen(); char getrusage(); char time(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_fork) || defined (__stub___fork) fork_will_always_fail_with_ENOSYS(); #else fork(); #endif #if defined (__stub_getpagesize) || defined (__stub___getpagesize) getpagesize_will_always_fail_with_ENOSYS(); #else getpagesize(); #endif #if defined (__stub_memalign) || defined (__stub___memalign) memalign_will_always_fail_with_ENOSYS(); #else memalign(); #endif #if defined (__stub_gethostbyname) || defined (__stub___gethostbyname) gethostbyname_will_always_fail_with_ENOSYS(); #else gethostbyname(); #endif #if defined (__stub_readlink) || defined (__stub___readlink) readlink_will_always_fail_with_ENOSYS(); #else readlink(); #endif #if defined (__stub_strcasecmp) || defined (__stub___strcasecmp) strcasecmp_will_always_fail_with_ENOSYS(); #else strcasecmp(); #endif #if defined (__stub_dlopen) || defined (__stub___dlopen) dlopen_will_always_fail_with_ENOSYS(); #else dlopen(); #endif #if defined (__stub_drand48) || defined (__stub___drand48) drand48_will_always_fail_with_ENOSYS(); #else drand48(); #endif #if defined (__stub_socket) || defined (__stub___socket) socket_will_always_fail_with_ENOSYS(); #else socket(); #endif #if defined (__stub_popen) || defined (__stub___popen) popen_will_always_fail_with_ENOSYS(); #else popen(); #endif #if defined (__stub_getrusage) || defined (__stub___getrusage) getrusage_will_always_fail_with_ENOSYS(); #else getrusage(); #endif #if defined (__stub_time) || defined (__stub___time) time_will_always_fail_with_ENOSYS(); #else time(); #endif ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_FORK" to "1" Defined "HAVE_GETPAGESIZE" to "1" Defined "HAVE_MEMALIGN" to "1" Defined "HAVE_GETHOSTBYNAME" to "1" Defined "HAVE_READLINK" to "1" Defined "HAVE_STRCASECMP" to "1" Defined "HAVE_DLOPEN" to "1" Defined "HAVE_DRAND48" to "1" Defined "HAVE_SOCKET" to "1" Defined "HAVE_POPEN" to "1" Defined "HAVE_GETRUSAGE" to "1" Defined "HAVE_TIME" to "1" Checking for functions [_access] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _access(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__access) || defined (__stub____access) _access_will_always_fail_with_ENOSYS(); #else _access(); #endif ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o: in function `main': /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:24: undefined reference to `_access' collect2: error: ld returned 1 exit status Checking for functions [snprintf] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:13:6: warning: conflicting types for built-in function ???snprintf??? [-Wbuiltin-declaration-mismatch] char snprintf(); ^~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char snprintf(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_snprintf) || defined (__stub___snprintf) snprintf_will_always_fail_with_ENOSYS(); #else snprintf(); #endif ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_SNPRINTF" to "1" Checking for functions [_getcwd] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _getcwd(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__getcwd) || defined (__stub____getcwd) _getcwd_will_always_fail_with_ENOSYS(); #else _getcwd(); #endif ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o: in function `main': /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:24: undefined reference to `_getcwd' collect2: error: ld returned 1 exit status Checking for functions [getwd] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char getwd(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_getwd) || defined (__stub___getwd) getwd_will_always_fail_with_ENOSYS(); #else getwd(); #endif ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: stderr: /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o: in function `main': /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:24: warning: the `getwd' function is dangerous and should not be used. Defined "HAVE_GETWD" to "1" Checking for functions [_lseek] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _lseek(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__lseek) || defined (__stub____lseek) _lseek_will_always_fail_with_ENOSYS(); #else _lseek(); #endif ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o: in function `main': /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:24: undefined reference to `_lseek' collect2: error: ld returned 1 exit status Checking for functions [sleep] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char sleep(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_sleep) || defined (__stub___sleep) sleep_will_always_fail_with_ENOSYS(); #else sleep(); #endif ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_SLEEP" to "1" Checking for functions [_sleep] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _sleep(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__sleep) || defined (__stub____sleep) _sleep_will_always_fail_with_ENOSYS(); #else _sleep(); #endif ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o: in function `main': /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:24: undefined reference to `_sleep' collect2: error: ld returned 1 exit status Checking for functions [lseek] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char lseek(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_lseek) || defined (__stub___lseek) lseek_will_always_fail_with_ENOSYS(); #else lseek(); #endif ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_LSEEK" to "1" Checking for functions [access] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char access(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_access) || defined (__stub___access) access_will_always_fail_with_ENOSYS(); #else access(); #endif ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_ACCESS" to "1" Checking for functions [_snprintf] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _snprintf(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__snprintf) || defined (__stub____snprintf) _snprintf_will_always_fail_with_ENOSYS(); #else _snprintf(); #endif ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o: in function `main': /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:24: undefined reference to `_snprintf' collect2: error: ld returned 1 exit status Checking for functions [sbreak] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char sbreak(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_sbreak) || defined (__stub___sbreak) sbreak_will_always_fail_with_ENOSYS(); #else sbreak(); #endif ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o: in function `main': /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:24: undefined reference to `sbreak' collect2: error: ld returned 1 exit status Checking for functions [getcwd] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char getcwd(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_getcwd) || defined (__stub___getcwd) getcwd_will_always_fail_with_ENOSYS(); #else getcwd(); #endif ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_GETCWD" to "1" Checking for functions [_set_output_format] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _set_output_format(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__set_output_format) || defined (__stub____set_output_format) _set_output_format_will_always_fail_with_ENOSYS(); #else _set_output_format(); #endif ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o: in function `main': /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:24: undefined reference to `_set_output_format' collect2: error: ld returned 1 exit status Checking for functions [PXFGETARG] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char PXFGETARG(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_PXFGETARG) || defined (__stub___PXFGETARG) PXFGETARG_will_always_fail_with_ENOSYS(); #else PXFGETARG(); #endif ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o: in function `main': /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:24: undefined reference to `PXFGETARG' collect2: error: ld returned 1 exit status Checking for functions [_mkdir] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _mkdir(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__mkdir) || defined (__stub____mkdir) _mkdir_will_always_fail_with_ENOSYS(); #else _mkdir(); #endif ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o: in function `main': /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:24: undefined reference to `_mkdir' collect2: error: ld returned 1 exit status Checking for functions [stricmp] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char stricmp(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_stricmp) || defined (__stub___stricmp) stricmp_will_always_fail_with_ENOSYS(); #else stricmp(); #endif ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o: in function `main': /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c:24: undefined reference to `stricmp' collect2: error: ld returned 1 exit status ================================================================================ TEST checkMmap from config.functions(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:179) TESTING: checkMmap from config.functions(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:179) Check for functional mmap() to allocate shared memory and define HAVE_MMAP Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include int main() { int fd; fd=open("/tmp/file",O_RDWR); mmap((void*)0,100,PROT_READ|PROT_WRITE,MAP_SHARED,fd,0); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_MMAP" to "1" child config.functions 7.452227 ================================================================================ TEST configureMemorySize from config.utilities.getResidentSetSize(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/getResidentSetSize.py:31) TESTING: configureMemorySize from config.utilities.getResidentSetSize(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/getResidentSetSize.py:31) Try to determine how to measure the memory usage Defined "USE_PROC_FOR_SIZE" to "1" Using /proc for PetscMemoryGetCurrentUsage() child config.utilities.getResidentSetSize 0.004022 ================================================================================ TEST configureFortranCommandLine from config.utilities.fortranCommandLine(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/fortranCommandLine.py:27) TESTING: configureFortranCommandLine from config.utilities.fortranCommandLine(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/fortranCommandLine.py:27) Check for the mechanism to retrieve command line arguments in Fortran Checking for functions [] in library [''] [] Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.F90 Successful compile: Source: program main integer i character*(80) arg i = command_argument_count() call get_command_argument(i,arg) end Executing: mpif90 -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -lstdc++ -ldl Defined "HAVE_FORTRAN_GET_COMMAND_ARGUMENT" to "1" child config.utilities.fortranCommandLine 0.177800 ================================================================================ TEST configureFeatureTestMacros from config.utilities.featureTestMacros(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/featureTestMacros.py:13) TESTING: configureFeatureTestMacros from config.utilities.featureTestMacros(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/featureTestMacros.py:13) Checks if certain feature test macros are support All intermediate test results are stored in /p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros/conftest.c:4:10: fatal error: sysctl.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #define _POSIX_C_SOURCE 200112L #include int main() { ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #define _BSD_SOURCE #include int main() { ; return 0; } Defined "_BSD_SOURCE" to "1" Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #define _DEFAULT_SOURCE #include int main() { ; return 0; } Defined "_DEFAULT_SOURCE" to "1" Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #define _GNU_SOURCE #include int main() { cpu_set_t mset; CPU_ZERO(&mset);; return 0; } Defined "_GNU_SOURCE" to "1" child config.utilities.featureTestMacros 0.516560 ================================================================================ TEST configureMissingUtypeTypedefs from config.utilities.missing(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/missing.py:55) TESTING: configureMissingUtypeTypedefs from config.utilities.missing(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/missing.py:55) Checks if u_short is undefined All intermediate test results are stored in /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c: In function ???main???: /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c:6:9: warning: unused variable ???foo??? [-Wunused-variable] u_short foo; ^~~ Source: #include "confdefs.h" #include "conffix.h" #include int main() { u_short foo; ; return 0; } ================================================================================ TEST configureMissingFunctions from config.utilities.missing(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/missing.py:61) TESTING: configureMissingFunctions from config.utilities.missing(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/missing.py:61) Checks for SOCKETS ================================================================================ TEST configureMissingSignals from config.utilities.missing(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/missing.py:79) TESTING: configureMissingSignals from config.utilities.missing(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/missing.py:79) Check for missing signals, and define MISSING_ if necessary Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGABRT; if (i); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGALRM; if (i); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGBUS; if (i); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGCHLD; if (i); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGCONT; if (i); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGFPE; if (i); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGHUP; if (i); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGILL; if (i); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGINT; if (i); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGKILL; if (i); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGPIPE; if (i); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGQUIT; if (i); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGSEGV; if (i); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGSTOP; if (i); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGSYS; if (i); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGTERM; if (i); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGTRAP; if (i); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGTSTP; if (i); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGURG; if (i); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGUSR1; if (i); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGUSR2; if (i); ; return 0; } ================================================================================ TEST configureMissingGetdomainnamePrototype from config.utilities.missing(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/missing.py:96) TESTING: configureMissingGetdomainnamePrototype from config.utilities.missing(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/missing.py:96) Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #if !defined(_BSD_SOURCE) #define _BSD_SOURCE #endif #if !defined(_DEFAULT_SOURCE) #define _DEFAULT_SOURCE #endif #if !defined(_GNU_SOURCE) #define _GNU_SOURCE #endif #ifdef PETSC_HAVE_UNISTD_H #include #endif #ifdef PETSC_HAVE_NETDB_H #include #endif int main() { int (*getdomainname_ptr)(char*,size_t) = getdomainname; char test[10]; if (getdomainname_ptr(test,10)) return 1; ; return 0; } Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #if !defined(_BSD_SOURCE) #define _BSD_SOURCE #endif #if !defined(_DEFAULT_SOURCE) #define _DEFAULT_SOURCE #endif #if !defined(_GNU_SOURCE) #define _GNU_SOURCE #endif #ifdef PETSC_HAVE_UNISTD_H #include #endif #ifdef PETSC_HAVE_NETDB_H #include #endif int main() { int (*getdomainname_ptr)(char*,size_t) = getdomainname; char test[10]; if (getdomainname_ptr(test,10)) return 1; ; return 0; } Executing: mpicxx -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -lstdc++ -ldl ================================================================================ TEST configureMissingSrandPrototype from config.utilities.missing(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/missing.py:121) TESTING: configureMissingSrandPrototype from config.utilities.missing(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/missing.py:121) Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #if !defined(_BSD_SOURCE) #define _BSD_SOURCE #endif #if !defined(_DEFAULT_SOURCE) #define _DEFAULT_SOURCE #endif #if !defined(_GNU_SOURCE) #define _GNU_SOURCE #endif #include int main() { double (*drand48_ptr)(void) = drand48; void (*srand48_ptr)(long int) = srand48; long int seed=10; srand48_ptr(seed); if (drand48_ptr() > 0.5) return 1; ; return 0; } Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #if !defined(_BSD_SOURCE) #define _BSD_SOURCE #endif #if !defined(_DEFAULT_SOURCE) #define _DEFAULT_SOURCE #endif #if !defined(_GNU_SOURCE) #define _GNU_SOURCE #endif #include int main() { double (*drand48_ptr)(void) = drand48; void (*srand48_ptr)(long int) = srand48; long int seed=10; srand48_ptr(seed); if (drand48_ptr() > 0.5) return 1; ; return 0; } Executing: mpicxx -o /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing/conftest.o -lstdc++ -ldl child config.utilities.missing 1.995077 ================================================================================ TEST configureFPTrap from config.utilities.FPTrap(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/FPTrap.py:27) TESTING: configureFPTrap from config.utilities.FPTrap(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/utilities/FPTrap.py:27) Checking the handling of floating point traps Checking for header: sigfpe.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/confdefs.h" 1 # 2 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conffix.h" 1 # 3 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: sigfpe.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: sigfpe.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: sigfpe.h: No such file or directory #include ^~~~~~~~~~compilation terminated.: Checking for header: fpxcp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/confdefs.h" 1 # 2 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conffix.h" 1 # 3 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: fpxcp.h: No such file or directory #include ^~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: fpxcp.h: No such file or directory #include ^~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: fpxcp.h: No such file or directory #include ^~~~~~~~~compilation terminated.: Checking for header: floatingpoint.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.headers /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/confdefs.h" 1 # 2 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 # 1 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conffix.h" 1 # 3 "/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c" 2 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: floatingpoint.h: No such file or directory #include ^~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: floatingpoint.h: No such file or directory #include ^~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c:3:10: fatal error: floatingpoint.h: No such file or directory #include ^~~~~~~~~~~~~~~~~compilation terminated.: child config.utilities.FPTrap 0.073553 ================================================================================ TEST configureScalarType from PETSc.options.scalarTypes(/p/work2/tmondrag/moose/petsc/config/PETSc/options/scalarTypes.py:40) TESTING: configureScalarType from PETSc.options.scalarTypes(/p/work2/tmondrag/moose/petsc/config/PETSc/options/scalarTypes.py:40) Choose between real and complex numbers Scalar type is real All intermediate test results are stored in /p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes/conftest.c: In function ???main???: /p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes/conftest.c:6:21: warning: unused variable ???a??? [-Wunused-variable] double b = 2.0; int a = isnormal(b); ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { double b = 2.0; int a = isnormal(b); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes/conftest.o -lstdc++ -ldl Defined "HAVE_ISNORMAL" to "1" Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes/conftest.c: In function ???main???: /p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes/conftest.c:6:21: warning: unused variable ???a??? [-Wunused-variable] double b = 2.0; int a = isnan(b); ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { double b = 2.0; int a = isnan(b); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes/conftest.o -lstdc++ -ldl Defined "HAVE_ISNAN" to "1" Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes/conftest.c: In function ???main???: /p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes/conftest.c:6:21: warning: unused variable ???a??? [-Wunused-variable] double b = 2.0; int a = isinf(b); ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { double b = 2.0; int a = isinf(b); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes/conftest.o -lstdc++ -ldl Defined "HAVE_ISINF" to "1" ================================================================================ TEST configurePrecision from PETSc.options.scalarTypes(/p/work2/tmondrag/moose/petsc/config/PETSc/options/scalarTypes.py:81) TESTING: configurePrecision from PETSc.options.scalarTypes(/p/work2/tmondrag/moose/petsc/config/PETSc/options/scalarTypes.py:81) Set the default real number precision for PETSc objects Checking C compiler works with __float128 Checking for functions [logq] in library ['quadmath'] [] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c: In function ???_check_logq???: /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c:5:43: warning: ???f??? is used uninitialized in this function [-Wuninitialized] static void _check_logq() { __float128 f; logq(f);; } ^~~~~~~ /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c:5:40: note: ???f??? was declared here static void _check_logq() { __float128 f; logq(f);; } ^ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_logq() { __float128 f; logq(f);; } int main() { _check_logq();; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_LIBQUADMATH" to "1" C compiler with quadmath library Checking Fortran works with quadmath library Checking for functions [ ] in library ['quadmath'] [] Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.F90 Successful compile: Source: program main real*16 s,w; w = 2.0 ;s = cos(w) end Executing: mpif90 -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_LIBQUADMATH" to "1" Fortran works with quadmath library Checking for functions [logq] in library ['quadmath'] [] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c: In function ???_check_logq???: /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c:5:43: warning: ???f??? is used uninitialized in this function [-Wuninitialized] static void _check_logq() { __float128 f; logq(f);; } ^~~~~~~ /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c:5:40: note: ???f??? was declared here static void _check_logq() { __float128 f; logq(f);; } ^ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_logq() { __float128 f; logq(f);; } int main() { _check_logq();; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_LIBQUADMATH" to "1" Adding ['quadmath'] to LIBS Defined "HAVE_REAL___FLOAT128" to "1" Defined "USE_REAL_DOUBLE" to "1" Defined make macro "PETSC_SCALAR_SIZE" to "64" Precision is double child PETSc.options.scalarTypes 0.993041 ================================================================================ TEST configureMkdir from config.programs(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/programs.py:22) TESTING: configureMkdir from config.programs(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/programs.py:22) Make sure we can have mkdir automatically make intermediate directories Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/mkdir...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/mkdir...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/mkdir...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/mkdir...not found Checking for program /usr/local/krb5/bin/mkdir...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/mkdir...not found Checking for program /p/home/apps/gnu_compiler/7.3.0/bin/mkdir...not found Checking for program /opt/clmgr/sbin/mkdir...not found Checking for program /opt/clmgr/bin/mkdir...not found Checking for program /opt/sgi/sbin/mkdir...not found Checking for program /opt/sgi/bin/mkdir...not found Checking for program /usr/local/krb5/bin/mkdir...not found Checking for program /usr/local/krb5/libexec/mkdir...not found Checking for program /usr/local/bin/mkdir...not found Checking for program /usr/bin/mkdir...found Executing: /usr/bin/mkdir -p .conftest/tmp Adding -p flag to /usr/bin/mkdir -p to automatically create directories Defined make macro "MKDIR" to "/usr/bin/mkdir -p" ================================================================================ TEST configureAutoreconf from config.programs(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/programs.py:44) TESTING: configureAutoreconf from config.programs(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/programs.py:44) Check for autoreconf Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/autoreconf...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/autoreconf...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/autoreconf...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/autoreconf...not found Checking for program /usr/local/krb5/bin/autoreconf...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/autoreconf...not found Checking for program /p/home/apps/gnu_compiler/7.3.0/bin/autoreconf...not found Checking for program /opt/clmgr/sbin/autoreconf...not found Checking for program /opt/clmgr/bin/autoreconf...not found Checking for program /opt/sgi/sbin/autoreconf...not found Checking for program /opt/sgi/bin/autoreconf...not found Checking for program /usr/local/krb5/bin/autoreconf...not found Checking for program /usr/local/krb5/libexec/autoreconf...not found Checking for program /usr/local/bin/autoreconf...not found Checking for program /usr/bin/autoreconf...found All intermediate test results are stored in /p/work2/tmondrag/petsc-0UdWsO/config.programs Executing: ['/usr/bin/autoreconf'] autoreconf test successful! Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/libtoolize...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/libtoolize...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/libtoolize...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/libtoolize...not found Checking for program /usr/local/krb5/bin/libtoolize...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/libtoolize...not found Checking for program /p/home/apps/gnu_compiler/7.3.0/bin/libtoolize...not found Checking for program /opt/clmgr/sbin/libtoolize...not found Checking for program /opt/clmgr/bin/libtoolize...not found Checking for program /opt/sgi/sbin/libtoolize...not found Checking for program /opt/sgi/bin/libtoolize...not found Checking for program /usr/local/krb5/bin/libtoolize...not found Checking for program /usr/local/krb5/libexec/libtoolize...not found Checking for program /usr/local/bin/libtoolize...not found Checking for program /usr/bin/libtoolize...found ================================================================================ TEST configurePrograms from config.programs(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/programs.py:71) TESTING: configurePrograms from config.programs(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/programs.py:71) Check for the programs needed to build and run PETSc Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/sh...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/sh...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/sh...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/sh...not found Checking for program /usr/local/krb5/bin/sh...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/sh...not found Checking for program /p/home/apps/gnu_compiler/7.3.0/bin/sh...not found Checking for program /opt/clmgr/sbin/sh...not found Checking for program /opt/clmgr/bin/sh...not found Checking for program /opt/sgi/sbin/sh...not found Checking for program /opt/sgi/bin/sh...not found Checking for program /usr/local/krb5/bin/sh...not found Checking for program /usr/local/krb5/libexec/sh...not found Checking for program /usr/local/bin/sh...not found Checking for program /usr/bin/sh...found Defined make macro "SHELL" to "/usr/bin/sh" Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/sed...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/sed...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/sed...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/sed...not found Checking for program /usr/local/krb5/bin/sed...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/sed...not found Checking for program /p/home/apps/gnu_compiler/7.3.0/bin/sed...not found Checking for program /opt/clmgr/sbin/sed...not found Checking for program /opt/clmgr/bin/sed...not found Checking for program /opt/sgi/sbin/sed...not found Checking for program /opt/sgi/bin/sed...not found Checking for program /usr/local/krb5/bin/sed...not found Checking for program /usr/local/krb5/libexec/sed...not found Checking for program /usr/local/bin/sed...not found Checking for program /usr/bin/sed...found Defined make macro "SED" to "/usr/bin/sed" Executing: /usr/bin/sed -i s/sed/sd/g "/p/work2/tmondrag/petsc-0UdWsO/config.programs/sed1" Adding SEDINPLACE cmd: /usr/bin/sed -i Defined make macro "SEDINPLACE" to "/usr/bin/sed -i" Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/mv...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/mv...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/mv...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/mv...not found Checking for program /usr/local/krb5/bin/mv...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/mv...not found Checking for program /p/home/apps/gnu_compiler/7.3.0/bin/mv...not found Checking for program /opt/clmgr/sbin/mv...not found Checking for program /opt/clmgr/bin/mv...not found Checking for program /opt/sgi/sbin/mv...not found Checking for program /opt/sgi/bin/mv...not found Checking for program /usr/local/krb5/bin/mv...not found Checking for program /usr/local/krb5/libexec/mv...not found Checking for program /usr/local/bin/mv...not found Checking for program /usr/bin/mv...found Defined make macro "MV" to "/usr/bin/mv" Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/cp...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/cp...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/cp...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/cp...not found Checking for program /usr/local/krb5/bin/cp...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/cp...not found Checking for program /p/home/apps/gnu_compiler/7.3.0/bin/cp...not found Checking for program /opt/clmgr/sbin/cp...not found Checking for program /opt/clmgr/bin/cp...not found Checking for program /opt/sgi/sbin/cp...not found Checking for program /opt/sgi/bin/cp...not found Checking for program /usr/local/krb5/bin/cp...not found Checking for program /usr/local/krb5/libexec/cp...not found Checking for program /usr/local/bin/cp...not found Checking for program /usr/bin/cp...found Defined make macro "CP" to "/usr/bin/cp" Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/grep...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/grep...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/grep...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/grep...not found Checking for program /usr/local/krb5/bin/grep...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/grep...not found Checking for program /p/home/apps/gnu_compiler/7.3.0/bin/grep...not found Checking for program /opt/clmgr/sbin/grep...not found Checking for program /opt/clmgr/bin/grep...not found Checking for program /opt/sgi/sbin/grep...not found Checking for program /opt/sgi/bin/grep...not found Checking for program /usr/local/krb5/bin/grep...not found Checking for program /usr/local/krb5/libexec/grep...not found Checking for program /usr/local/bin/grep...not found Checking for program /usr/bin/grep...found Defined make macro "GREP" to "/usr/bin/grep" Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/rm...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/rm...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/rm...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/rm...not found Checking for program /usr/local/krb5/bin/rm...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/rm...not found Checking for program /p/home/apps/gnu_compiler/7.3.0/bin/rm...not found Checking for program /opt/clmgr/sbin/rm...not found Checking for program /opt/clmgr/bin/rm...not found Checking for program /opt/sgi/sbin/rm...not found Checking for program /opt/sgi/bin/rm...not found Checking for program /usr/local/krb5/bin/rm...not found Checking for program /usr/local/krb5/libexec/rm...not found Checking for program /usr/local/bin/rm...not found Checking for program /usr/bin/rm...found Defined make macro "RM" to "/usr/bin/rm -f" Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/diff...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/diff...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/diff...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/diff...not found Checking for program /usr/local/krb5/bin/diff...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/diff...not found Checking for program /p/home/apps/gnu_compiler/7.3.0/bin/diff...not found Checking for program /opt/clmgr/sbin/diff...not found Checking for program /opt/clmgr/bin/diff...not found Checking for program /opt/sgi/sbin/diff...not found Checking for program /opt/sgi/bin/diff...not found Checking for program /usr/local/krb5/bin/diff...not found Checking for program /usr/local/krb5/libexec/diff...not found Checking for program /usr/local/bin/diff...not found Checking for program /usr/bin/diff...found Executing: "/usr/bin/diff" -w "/p/work2/tmondrag/petsc-0UdWsO/config.programs/diff1" "/p/work2/tmondrag/petsc-0UdWsO/config.programs/diff2" Defined make macro "DIFF" to "/usr/bin/diff -w" Checking for program /usr/ucb/ps...not found Checking for program /usr/usb/ps...not found Checking for program /p/home/tmondrag/WORK/moose/scripts/../petsc/lib/petsc/bin/win32fe/ps...not found Defined make macro "PYTHON" to "/usr/bin/python" Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/m4...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/m4...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/m4...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/m4...not found Checking for program /usr/local/krb5/bin/m4...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/m4...not found Checking for program /p/home/apps/gnu_compiler/7.3.0/bin/m4...not found Checking for program /opt/clmgr/sbin/m4...not found Checking for program /opt/clmgr/bin/m4...not found Checking for program /opt/sgi/sbin/m4...not found Checking for program /opt/sgi/bin/m4...not found Checking for program /usr/local/krb5/bin/m4...not found Checking for program /usr/local/krb5/libexec/m4...not found Checking for program /usr/local/bin/m4...not found Checking for program /usr/bin/m4...found Defined make macro "M4" to "/usr/bin/m4" child config.programs 1.760389 ================================================================================ TEST configureMake from config.packages.make(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/make.py:87) TESTING: configureMake from config.packages.make(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/make.py:87) Check Guesses for GNU make Executing: gmake --version stdout: GNU Make 4.0 Built for x86_64-unknown-linux-gnu Copyright (C) 1988-2013 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/gmake...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/gmake...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/gmake...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/gmake...not found Checking for program /usr/local/krb5/bin/gmake...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/gmake...not found Checking for program /p/home/apps/gnu_compiler/7.3.0/bin/gmake...not found Checking for program /opt/clmgr/sbin/gmake...not found Checking for program /opt/clmgr/bin/gmake...not found Checking for program /opt/sgi/sbin/gmake...not found Checking for program /opt/sgi/bin/gmake...not found Checking for program /usr/local/krb5/bin/gmake...not found Checking for program /usr/local/krb5/libexec/gmake...not found Checking for program /usr/local/bin/gmake...not found Checking for program /usr/bin/gmake...found Defined make macro "MAKE" to "/usr/bin/gmake" ================================================================================ TEST setupGNUMake from config.packages.make(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/make.py:121) TESTING: setupGNUMake from config.packages.make(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/make.py:121) Setup other GNU make stuff Executing: uname -s stdout: Linux Executing: uname -s stdout: Linux Defined make rule "libc" with dependencies "${LIBNAME}(${OBJSC})" and code [] Defined make rule "libcxx" with dependencies "${LIBNAME}(${OBJSCXX})" and code [] Defined make rule "libcu" with dependencies "${LIBNAME}(${OBJSCU})" and code [] Defined make rule "libf" with dependencies "${OBJSF}" and code -${AR} ${AR_FLAGS} ${LIBNAME} ${OBJSF} Defined make macro "OMAKE_PRINTDIR " to "/usr/bin/gmake --print-directory" Defined make macro "OMAKE" to "/usr/bin/gmake --no-print-directory" Defined make macro "MAKE_PAR_OUT_FLG" to "--output-sync=recurse" ================================================================================ TEST configureMakeNP from config.packages.make(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/make.py:168) TESTING: configureMakeNP from config.packages.make(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/make.py:168) check no of cores on the build machine [perhaps to do make '-j ncores'] module multiprocessing found 56 cores: using make_np = 36 Defined make macro "MAKE_NP" to "36" Defined make macro "MAKE_TEST_NP" to "24" Defined make macro "MAKE_LOAD" to "84.0" Defined make macro "NPMAX" to "56" child config.packages.make 0.032604 ================================================================================ TEST alternateConfigureLibrary from config.packages.OpenMPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/package.py:913) TESTING: alternateConfigureLibrary from config.packages.OpenMPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/package.py:913) Called if --with-packagename=0; does nothing by default child config.packages.OpenMPI 0.001335 Executing: uname -s stdout: Linux ================================================================================ TEST alternateConfigureLibrary from config.packages.MPICH(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/package.py:913) TESTING: alternateConfigureLibrary from config.packages.MPICH(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/package.py:913) Called if --with-packagename=0; does nothing by default child config.packages.MPICH 0.007196 ================================================================================ TEST checkDependencies from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/package.py:830) TESTING: checkDependencies from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/package.py:830) ================================================================================ TEST configureLibrary from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:581) TESTING: configureLibrary from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:581) ================================================================================== Checking for a functional MPI Checking for library in Compiler specific search MPI: [] ================================================================================ TEST check from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names ================================================================================ TEST check from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [MPI_Init MPI_Comm_create] in library [] [] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char MPI_Init(); static void _check_MPI_Init() { MPI_Init(); } char MPI_Comm_create(); static void _check_MPI_Comm_create() { MPI_Comm_create(); } int main() { _check_MPI_Init(); _check_MPI_Comm_create();; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -lquadmath -lstdc++ -ldl No functions to check for in library [] [] Checking for headers Compiler specific search MPI: ['/p/home/apps/hpe/mpt-2.19/include', '/p/home/apps/gnu_compiler/7.3.0/include'] ================================================================================ TEST checkInclude from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:86) TESTING: checkInclude from config.headers(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files ['mpi.h'] in ['/p/home/apps/hpe/mpt-2.19/include', '/p/home/apps/gnu_compiler/7.3.0/include'] Checking include with compiler flags var CPPFLAGS ['/p/home/apps/hpe/mpt-2.19/include', '/p/home/apps/gnu_compiler/7.3.0/include'] Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/home/apps/hpe/mpt-2.19/include -I/p/home/apps/gnu_compiler/7.3.0/include /p/work2/tmondrag/petsc-0UdWsO/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Found header files ['mpi.h'] in ['/p/home/apps/hpe/mpt-2.19/include', '/p/home/apps/gnu_compiler/7.3.0/include'] ================================================================================ TEST checkMPICHorOpenMPI from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:468) TESTING: checkMPICHorOpenMPI from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:468) Determine if MPICH_NUMVERSION or OMPI_MAJOR_VERSION exist in mpi.h Used for consistency checking of MPI installation at compile time All intermediate test results are stored in /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c:4:25: error: ???I_MPI_VERSION??? undeclared here (not in a function); did you mean ???MPI_VERSION???? const char *mpich_ver = I_MPI_VERSION; ^~~~~~~~~~~~~ MPI_VERSION Source: #include "confdefs.h" #include "conffix.h" #include const char *mpich_ver = I_MPI_VERSION; int main() { ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c:4:17: error: ???I_MPI_NUMVERSION??? undeclared here (not in a function); did you mean ???MPI_SUBVERSION???? int mpich_ver = I_MPI_NUMVERSION; ^~~~~~~~~~~~~~~~ MPI_SUBVERSION Source: #include "confdefs.h" #include "conffix.h" #include int mpich_ver = I_MPI_NUMVERSION; int main() { ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c:4:17: error: ???MVAPICH2_NUMVERSION??? undeclared here (not in a function); did you mean ???MPI_SUBVERSION???? int mpich_ver = MVAPICH2_NUMVERSION; ^~~~~~~~~~~~~~~~~~~ MPI_SUBVERSION Source: #include "confdefs.h" #include "conffix.h" #include int mpich_ver = MVAPICH2_NUMVERSION; int main() { ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c:4:17: error: ???MPICH_NUMVERSION??? undeclared here (not in a function); did you mean ???MPI_SUBVERSION???? int mpich_ver = MPICH_NUMVERSION; ^~~~~~~~~~~~~~~~ MPI_SUBVERSION Source: #include "confdefs.h" #include "conffix.h" #include int mpich_ver = MPICH_NUMVERSION; int main() { ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c:4:18: error: ???OMPI_MAJOR_VERSION??? undeclared here (not in a function); did you mean ???MPI_SUBVERSION???? int ompi_major = OMPI_MAJOR_VERSION; ^~~~~~~~~~~~~~~~~~ MPI_SUBVERSION /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c:5:18: error: ???OMPI_MINOR_VERSION??? undeclared here (not in a function); did you mean ???OMPI_MAJOR_VERSION???? int ompi_minor = OMPI_MINOR_VERSION; ^~~~~~~~~~~~~~~~~~ OMPI_MAJOR_VERSION /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c:6:20: error: ???OMPI_RELEASE_VERSION??? undeclared here (not in a function); did you mean ???OMPI_MINOR_VERSION???? int ompi_release = OMPI_RELEASE_VERSION; ^~~~~~~~~~~~~~~~~~~~ OMPI_MINOR_VERSION Source: #include "confdefs.h" #include "conffix.h" #include int ompi_major = OMPI_MAJOR_VERSION; int ompi_minor = OMPI_MINOR_VERSION; int ompi_release = OMPI_RELEASE_VERSION; int main() { ; return 0; } Executing: uname -s stdout: Linux ================================================================================ TEST configureMPI2 from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:250) TESTING: configureMPI2 from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:250) Check for functions added to the interface in MPI-2 Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int flag;if (MPI_Finalized(&flag)); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_FINALIZED" to "1" Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { if (MPI_Allreduce(MPI_IN_PLACE,0, 1, MPI_INT, MPI_SUM, MPI_COMM_SELF)); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_IN_PLACE" to "1" Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int count=2; int blocklens[2]={0,1}; MPI_Aint indices[2]={0,1}; MPI_Datatype old_types[2]={0,1}; MPI_Datatype *newtype = 0; if (MPI_Type_create_struct(count, blocklens, indices, old_types, newtype)); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Comm_errhandler_fn * p_err_fun = 0; MPI_Errhandler * p_errhandler = 0; if (MPI_Comm_create_errhandler(p_err_fun,p_errhandler)); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { if (MPI_Comm_set_errhandler(MPI_COMM_WORLD,MPI_ERRORS_RETURN)); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { if (MPI_Reduce_local(0, 0, 0, MPI_INT, MPI_SUM));; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_REDUCE_LOCAL" to "1" Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { char version[MPI_MAX_LIBRARY_VERSION_STRING];int verlen;if (MPI_Get_library_version(version,&verlen)); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_GET_LIBRARY_VERSION" to "1" Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int base[100]; MPI_Win win; if (MPI_Win_create(base,100,4,MPI_INFO_NULL,MPI_COMM_WORLD,&win)); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_WIN_CREATE" to "1" ================================================================================ TEST configureMPI3 from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:292) TESTING: configureMPI3 from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:292) Check for functions added to the interface in MPI-3 Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Comm scomm; MPI_Aint size=128; int disp_unit=8,*baseptr; MPI_Win win; if (MPI_Comm_split_type(MPI_COMM_WORLD, MPI_COMM_TYPE_SHARED, 0, MPI_INFO_NULL, &scomm)); if (MPI_Win_allocate_shared(size,disp_unit,MPI_INFO_NULL,MPI_COMM_WORLD,&baseptr,&win)); if (MPI_Win_shared_query(win,0,&size,&disp_unit,&baseptr)); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_PROCESS_SHARED_MEMORY" to "1" Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c: In function ???main???: /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c:7:24: warning: this ???if??? clause does not guard... [-Wmisleading-indentation] if (MPI_Iscatter(&send,1,MPI_INT,&recv,1,MPI_INT,0,MPI_COMM_WORLD,&req)); ^~ /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c:8:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ???if??? if (MPI_Iscatterv(&send,counts,displs,MPI_INT,&recv,1,MPI_INT,0,MPI_COMM_WORLD,&req)); ^~ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int send=0,recv,counts[2]={1,1},displs[2]={1,2}; MPI_Request req; if (MPI_Iscatter(&send,1,MPI_INT,&recv,1,MPI_INT,0,MPI_COMM_WORLD,&req)); if (MPI_Iscatterv(&send,counts,displs,MPI_INT,&recv,1,MPI_INT,0,MPI_COMM_WORLD,&req)); if (MPI_Igather(&send,1,MPI_INT,&recv,1,MPI_INT,0,MPI_COMM_WORLD,&req)); if (MPI_Igatherv(&send,1,MPI_INT,&recv,counts,displs,MPI_INT,0,MPI_COMM_WORLD,&req)); if (MPI_Iallgather(&send,1,MPI_INT,&recv,1,MPI_INT,MPI_COMM_WORLD,&req)); if (MPI_Iallgatherv(&send,1,MPI_INT,&recv,counts,displs,MPI_INT,MPI_COMM_WORLD,&req)); if (MPI_Ialltoall(&send,1,MPI_INT,&recv,1,MPI_INT,MPI_COMM_WORLD,&req)); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_NONBLOCKING_COLLECTIVES" to "1" Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Comm distcomm; MPI_Request req; if (MPI_Dist_graph_create_adjacent(MPI_COMM_WORLD,0,0,MPI_WEIGHTS_EMPTY,0,0,MPI_WEIGHTS_EMPTY,MPI_INFO_NULL,0,&distcomm)); if (MPI_Neighbor_alltoallv(0,0,0,MPI_INT,0,0,0,MPI_INT,distcomm)); if (MPI_Ineighbor_alltoallv(0,0,0,MPI_INT,0,0,0,MPI_INT,distcomm,&req)); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_NEIGHBORHOOD_COLLECTIVES" to "1" ================================================================================ TEST configureMPITypes from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:335) TESTING: configureMPITypes from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:335) Checking for MPI Datatype handles Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_LONG_DOUBLE, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_LONG_DOUBLE, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Testing executable /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest to see if it can be run Executing: /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest Executing: /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest ERROR while running executable: Could not execute "['/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest']": Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_INT64_T, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_INT64_T, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Testing executable /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest to see if it can be run Executing: /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest Executing: /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest ERROR while running executable: Could not execute "['/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest']": Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_C_DOUBLE_COMPLEX, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_C_DOUBLE_COMPLEX, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Testing executable /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest to see if it can be run Executing: /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest Executing: /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest ERROR while running executable: Could not execute "['/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest']": ================================================================================ TEST SGIMPICheck from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:396) TESTING: SGIMPICheck from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:396) Returns true if SGI MPI is used Checking for functions [MPI_SGI_barrier] in library [] [] Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char MPI_SGI_barrier(); static void _check_MPI_SGI_barrier() { MPI_SGI_barrier(); } int main() { _check_MPI_SGI_barrier();; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -lquadmath -lstdc++ -ldl SGI MPI detected - defining MISSING_SIGTERM Defined "MISSING_SIGTERM" to "1" ================================================================================ TEST CxxMPICheck from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:406) TESTING: CxxMPICheck from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:406) Make sure C++ can compile and link Checking for header mpi.h Checking for C++ MPI_Finalize() Checking for functions [MPI_Finalize] in library [] [] Executing: mpicxx -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O -fPIC /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.cc Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.cc: In function ???void _check_MPI_Finalize()???: /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.cc:5:41: warning: variable ???ierr??? set but not used [-Wunused-but-set-variable] static void _check_MPI_Finalize() { int ierr; ^~~~ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_MPI_Finalize() { int ierr; ierr = MPI_Finalize();; } int main() { _check_MPI_Finalize();; return 0; } Executing: mpicxx -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -lquadmath -lstdc++ -ldl ================================================================================ TEST FortranMPICheck from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:422) TESTING: FortranMPICheck from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:422) Make sure fortran include [mpif.h] and library symbols are found Checking for fortran mpi_init() Checking for functions [] in library [] [] Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.F90 Possible ERROR while running compiler: stderr: /p/home/apps/hpe/mpt-2.19/include/mpif.h:561:54: integer MPI_STATUSES_IGNORE(MPI_STATUS_SIZE,1) 1 Warning: Unused variable ???mpi_statuses_ignore??? declared at (1) [-Wunused-variable] Source: program main #include "mpif.h" integer ierr call mpi_init(ierr) end Executing: mpif90 -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Checking for mpi.mod Checking for functions [] in library [] [] Executing: mpif90 -c -o /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g -O /p/work2/tmondrag/petsc-0UdWsO/config.libraries/conftest.F90 Possible ERROR while running compiler: exit code 1 stderr: f951: Fatal Error: Reading module ???mpi??? at line 1 column 2: Unexpected EOF compilation terminated. Source: program main use mpi integer ierr,rank call mpi_init(ierr) call mpi_comm_rank(MPI_COMM_WORLD,rank,ierr) end Compile failed inside link ================================================================================ TEST configureIO from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:444) TESTING: configureIO from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:444) Check for the functions in MPI/IO - Define HAVE_MPIIO if they are present - Some older MPI 1 implementations are missing these Executing: mpicc -c -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.closure -I/p/work2/tmondrag/petsc-0UdWsO/config.compilers -I/p/work2/tmondrag/petsc-0UdWsO/config.setCompilers -I/p/work2/tmondrag/petsc-0UdWsO/config.compilersFortran -I/p/work2/tmondrag/petsc-0UdWsO/config.headers -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.cacheDetails -I/p/work2/tmondrag/petsc-0UdWsO/config.types -I/p/work2/tmondrag/petsc-0UdWsO/config.functions -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.featureTestMacros -I/p/work2/tmondrag/petsc-0UdWsO/config.utilities.missing -I/p/work2/tmondrag/petsc-0UdWsO/PETSc.options.scalarTypes -I/p/work2/tmondrag/petsc-0UdWsO/config.libraries -I/p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c: In function ???main???: /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c:7:1: warning: this ???if??? clause does not guard... [-Wmisleading-indentation] if (MPI_Type_get_extent(MPI_INT, &lb, &extent)); ^~ /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c:9:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ???if??? MPI_File fh; ^~~~~~~~ /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c:12:1: warning: this ???if??? clause does not guard... [-Wmisleading-indentation] if (MPI_File_write_all(fh, buf, 1, MPI_INT, &status)); ^~ /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c:14:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ???if??? if (MPI_File_read_all(fh, buf, 1, MPI_INT, &status)); ^~ /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c:18:1: warning: this ???if??? clause does not guard... [-Wmisleading-indentation] if (MPI_File_set_view(fh, disp, MPI_INT, MPI_INT, "", info)); ^~ /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c:20:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ???if??? if (MPI_File_open(MPI_COMM_SELF, "", 0, info, &fh)); ^~ /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c:12:5: warning: ???buf??? is used uninitialized in this function [-Wuninitialized] if (MPI_File_write_all(fh, buf, 1, MPI_INT, &status)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c:18:5: warning: ???disp??? is used uninitialized in this function [-Wuninitialized] if (MPI_File_set_view(fh, disp, MPI_INT, MPI_INT, "", info)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.c:18:5: warning: ???info??? is used uninitialized in this function [-Wuninitialized] Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Aint lb, extent; if (MPI_Type_get_extent(MPI_INT, &lb, &extent)); MPI_File fh; void *buf; MPI_Status status; if (MPI_File_write_all(fh, buf, 1, MPI_INT, &status)); if (MPI_File_read_all(fh, buf, 1, MPI_INT, &status)); MPI_Offset disp; MPI_Info info; if (MPI_File_set_view(fh, disp, MPI_INT, MPI_INT, "", info)); if (MPI_File_open(MPI_COMM_SELF, "", 0, info, &fh)); if (MPI_File_close(&fh)); ; return 0; } Executing: mpicc -o /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O /p/work2/tmondrag/petsc-0UdWsO/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPIIO" to "1" ================================================================================ TEST findMPIInc from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:522) TESTING: findMPIInc from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:522) Find MPI include paths from "mpicc -show" and use with CUDAC_FLAGS ================================================================================ TEST PetscArchMPICheck from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:556) TESTING: PetscArchMPICheck from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:556) ================================================================================ TEST configureMPIEXEC from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:174) TESTING: configureMPIEXEC from config.packages.MPI(/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:174) Checking for location of mpiexec Checking for program /app/unsupported/COST/git/2.4.4/gnu//bin/mpiexec_mpt...not found Checking for program /app/unsupported/COST/tcltk/8.6.4/gnu//bin/mpiexec_mpt...not found Checking for program /app/unsupported/COST/petsc-cxx-real/3.6.3/gnu//bin/mpiexec_mpt...not found Checking for program /app/unsupported/COST/valgrind/3.12.0/gnu//bin/mpiexec_mpt...not found Checking for program /usr/local/krb5/bin/mpiexec_mpt...not found Checking for program /p/home/apps/hpe/mpt-2.19/bin/mpiexec_mpt...found Defined make macro "MPIEXEC" to "mpiexec_mpt" Executing: mpiexec_mpt -n 1 printenv **** Configure header /p/work2/tmondrag/petsc-0UdWsO/confdefs.h **** #if !defined(INCLUDED_UNKNOWN) #define INCLUDED_UNKNOWN #define IS_COLORING_MAX USHRT_MAX #define MPIU_COLORING_VALUE MPI_UNSIGNED_SHORT #define PETSC_CLANGUAGE_C 1 #define PETSC_HAVE_ERF 1 #define PETSC_HAVE_FENV_H 1 #define PETSC_HAVE_LOG2 1 #define PETSC_HAVE_TGAMMA 1 #define PETSC_CXX_INLINE inline #define PETSC_CXX_RESTRICT __restrict #define PETSC_C_INLINE inline #define PETSC_C_RESTRICT __restrict #define PETSC_FORTRAN_CHARLEN_T int #define PETSC_HAVE_C99 1 #define PETSC_HAVE_CXX_DIALECT_CXX11 1 #define PETSC_HAVE_FORTRAN_UNDERSCORE 1 #define PETSC_HAVE_RTLD_GLOBAL 1 #define PETSC_HAVE_RTLD_LAZY 1 #define PETSC_HAVE_RTLD_LOCAL 1 #define PETSC_HAVE_RTLD_NOW 1 #define PETSC_HAVE_DLFCN_H 1 #define PETSC_HAVE_FCNTL_H 1 #define PETSC_HAVE_FLOAT_H 1 #define PETSC_HAVE_IMMINTRIN_H 1 #define PETSC_HAVE_INTTYPES_H 1 #define PETSC_HAVE_MALLOC_H 1 #define PETSC_HAVE_NETDB_H 1 #define PETSC_HAVE_NETINET_IN_H 1 #define PETSC_HAVE_PTHREAD_H 1 #define PETSC_HAVE_PWD_H 1 #define PETSC_HAVE_SETJMP_H 1 #define PETSC_HAVE_STDINT_H 1 #define PETSC_HAVE_STRINGS_H 1 #define PETSC_HAVE_SYS_PARAM_H 1 #define PETSC_HAVE_SYS_PROCFS_H 1 #define PETSC_HAVE_SYS_RESOURCE_H 1 #define PETSC_HAVE_SYS_SOCKET_H 1 #define PETSC_HAVE_SYS_SYSINFO_H 1 #define PETSC_HAVE_SYS_TIMES_H 1 #define PETSC_HAVE_SYS_TIME_H 1 #define PETSC_HAVE_SYS_TYPES_H 1 #define PETSC_HAVE_SYS_UTSNAME_H 1 #define PETSC_HAVE_SYS_WAIT_H 1 #define PETSC_HAVE_TIME_H 1 #define PETSC_HAVE_UNISTD_H 1 #define PETSC_HAVE_ISINF 1 #define PETSC_HAVE_ISNAN 1 #define PETSC_HAVE_ISNORMAL 1 #define PETSC_HAVE_REAL___FLOAT128 1 #define PETSC_USE_REAL_DOUBLE 1 #define PETSC_HAVE_C99_COMPLEX 1 #define PETSC_HAVE_CXX_COMPLEX 1 #define PETSC_HAVE_STRUCT_SIGACTION 1 #define PETSC_SIZEOF_INT 4 #define PETSC_SIZEOF_LONG 8 #define PETSC_SIZEOF_LONG_LONG 8 #define PETSC_SIZEOF_SHORT 2 #define PETSC_SIZEOF_SIZE_T 8 #define PETSC_SIZEOF_VOID_P 8 #define PETSC_USE_FORTRANKIND 1 #define PETSC_USE_VISIBILITY_C 1 #define PETSC_USE_VISIBILITY_CXX 1 #define PETSC_HAVE_ACCESS 1 #define PETSC_HAVE_BZERO 1 #define PETSC_HAVE_CLOCK 1 #define PETSC_HAVE_DLCLOSE 1 #define PETSC_HAVE_DLERROR 1 #define PETSC_HAVE_DLOPEN 1 #define PETSC_HAVE_DLSYM 1 #define PETSC_HAVE_DRAND48 1 #define PETSC_HAVE_FORK 1 #define PETSC_HAVE_GETCWD 1 #define PETSC_HAVE_GETDOMAINNAME 1 #define PETSC_HAVE_GETHOSTBYNAME 1 #define PETSC_HAVE_GETHOSTNAME 1 #define PETSC_HAVE_GETPAGESIZE 1 #define PETSC_HAVE_GETRUSAGE 1 #define PETSC_HAVE_GETWD 1 #define PETSC_HAVE_LSEEK 1 #define PETSC_HAVE_MEMALIGN 1 #define PETSC_HAVE_MEMMOVE 1 #define PETSC_HAVE_MMAP 1 #define PETSC_HAVE_NANOSLEEP 1 #define PETSC_HAVE_POPEN 1 #define PETSC_HAVE_RAND 1 #define PETSC_HAVE_READLINK 1 #define PETSC_HAVE_REALPATH 1 #define PETSC_HAVE_SLEEP 1 #define PETSC_HAVE_SNPRINTF 1 #define PETSC_HAVE_SOCKET 1 #define PETSC_HAVE_STRCASECMP 1 #define PETSC_HAVE_SYSINFO 1 #define PETSC_HAVE_TIME 1 #define PETSC_HAVE_UNAME 1 #define PETSC_HAVE_USLEEP 1 #define PETSC_HAVE_VA_COPY 1 #define PETSC_HAVE_VSNPRINTF 1 #define PETSC_SIGNAL_CAST #define PETSC_FORTRAN_TYPE_INITIALIZE = -2 #define PETSC_HAVE_FORTRAN_FLUSH 1 #define PETSC_HAVE_FORTRAN_TYPE_STAR 1 #define PETSC_USING_F2003 1 #define PETSC_USING_F90 1 #define PETSC_USING_F90FREEFORM 1 #define PETSC_HAVE_DYNAMIC_LIBRARIES 1 #define PETSC_USE_SHARED_LIBRARIES 1 #define PETSC_USE_DEBUGGER "gdb" #define PETSC_VERSION_BRANCH_GIT "(HEAD detached at 5ea3abf)" #define PETSC_VERSION_DATE_GIT "2019-10-29 13:35:52 +0000" #define PETSC_VERSION_GIT "v3.12.1-23-g5ea3abf" #define PETSC_HAVE_MPIIO 1 #define PETSC_HAVE_MPI_FINALIZED 1 #define PETSC_HAVE_MPI_GET_LIBRARY_VERSION 1 #define PETSC_HAVE_MPI_IN_PLACE 1 #define PETSC_HAVE_MPI_NEIGHBORHOOD_COLLECTIVES 1 #define PETSC_HAVE_MPI_NONBLOCKING_COLLECTIVES 1 #define PETSC_HAVE_MPI_PROCESS_SHARED_MEMORY 1 #define PETSC_HAVE_MPI_REDUCE_LOCAL 1 #define PETSC_HAVE_MPI_WIN_CREATE 1 #define PETSC_MISSING_SIGTERM 1 #define PETSC_Alignx(a,b) #define PETSC_IS_COLOR_VALUE_TYPE short #define PETSC_IS_COLOR_VALUE_TYPE_F integer2 #define PETSC_USE_AVX512_KERNELS 1 #define PETSC_USE_BACKWARD_LOOP 1 #define PETSC_USE_CTABLE 1 #define PETSC_USE_INFO 1 #define PETSC_USE_LOG 1 #define PETSC_USE_MALLOC_COALESCED 1 #define PETSC_MEMALIGN 16 #define PETSC_LEVEL1_DCACHE_LINESIZE 64 #define PETSC__BSD_SOURCE 1 #define PETSC__DEFAULT_SOURCE 1 #define PETSC__GNU_SOURCE 1 #define PETSC_HAVE_FORTRAN_GET_COMMAND_ARGUMENT 1 #define PETSC_USE_PROC_FOR_SIZE 1 #endif **** C specific Configure header /p/work2/tmondrag/petsc-0UdWsO/conffix.h **** #if !defined(INCLUDED_UNKNOWN) #define INCLUDED_UNKNOWN #if defined(__cplusplus) extern "C" { } #else #endif #endif ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Unable to run mpiexec_mpt with option "-n 1" asallocash failed: array services not available mpiexec_mpt: all_launch.c:715: newash: Assertion `new_ash != old_ash' failed. ******************************************************************************* File "/p/work2/tmondrag/moose/petsc/config/configure.py", line 443, in petsc_configure framework.configure(out = sys.stdout) File "/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/framework.py", line 1190, in configure self.processChildren() File "/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/framework.py", line 1179, in processChildren self.serialEvaluation(self.childGraph) File "/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/framework.py", line 1154, in serialEvaluation child.configure() File "/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/package.py", line 1083, in configure self.executeTest(self.configureLibrary) File "/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/base.py", line 139, in executeTest ret = test(*args,**kargs) File "/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py", line 604, in configureLibrary self.executeTest(self.configureMPIEXEC) File "/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/base.py", line 139, in executeTest ret = test(*args,**kargs) File "/p/work2/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py", line 222, in configureMPIEXEC if ret: raise RuntimeError('Unable to run '+self.mpiexec+' with option "-n 1"\n'+err) ================================================================================ Finishing configure run at Mon, 16 Dec 2019 16:06:45 -0600 ================================================================================ -------------- next part -------------- ================================================================================ ================================================================================ Starting configure run at Mon, 16 Dec 2019 16:36:17 -0600 Configure Options: --configModules=PETSc.Configure --optionsModule=config.compilerOptions LDFLAGS=-dynamic --download-hypre=1 --with-debugging=no --with-shared-libraries=1 --download-fblaslapack=1 --download-metis=1 --download-ptscotch=1 --download-parmetis=1 --download-superlu_dist=1 --download-mumps=1 --download-scalapack=1 --download-slepc --with-mpi=1 --with-cxx-dialect=C++11 --with-fortran-bindings=0 --with-sowing=0 Working directory: /p/work/tmondrag/moose/petsc Machine platform: ('Linux', 'onyx05.erdc.hpc.mil', '4.4.178-94.91-default', '#1 SMP Thu May 2 20:14:31 UTC 2019 (d683ca1)', 'x86_64', 'x86_64') Python version: 2.7.13 (default, Jan 11 2017, 10:56:06) [GCC] ================================================================================ ================================================================================ TEST configureExternalPackagesDir from config.framework(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/framework.py:911) TESTING: configureExternalPackagesDir from config.framework(config/BuildSystem/config/framework.py:911) ================================================================================ TEST configureDebuggers from config.utilities.debuggers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/utilities/debuggers.py:21) TESTING: configureDebuggers from config.utilities.debuggers(config/BuildSystem/config/utilities/debuggers.py:21) Find a default debugger and determine its arguments Executing: uname -s stdout: Linux Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/gdb...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/gdb...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/gdb...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/gdb...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/gdb...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/gdb...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/gdb...not found Checking for program /opt/gcc/7.2.0/bin/gdb...not found Checking for program /usr/local/krb5/bin/gdb...not found Checking for program /usr/local/krb5/openssl/bin/gdb...not found Checking for program /usr/local/krb5/bin/gdb...not found Checking for program /usr/local/krb5/openssl/bin/gdb...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/gdb...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/gdb...not found Checking for program /opt/pbs/default/bin/gdb...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/gdb...not found Checking for program /opt/java/jdk1.8.0_152/bin/gdb...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/gdb...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/gdb...not found Checking for program /opt/cray/pe/modules/3.2.10.6/bin/gdb...not found Checking for program /usr/local/bin/gdb...not found Checking for program /usr/bin/gdb...found Defined make macro "GDB" to "/usr/bin/gdb" Defined "USE_DEBUGGER" to ""gdb"" Executing: uname -s stdout: Linux Defined make macro "DSYMUTIL" to "true" child config.utilities.debuggers 0.049731 ================================================================================ TEST configureDirectories from PETSc.options.petscdir(/p/work/tmondrag/moose/petsc/config/PETSc/options/petscdir.py:23) TESTING: configureDirectories from PETSc.options.petscdir(config/PETSc/options/petscdir.py:23) Checks PETSC_DIR and sets if not set Version Information: #define PETSC_VERSION_RELEASE 1 #define PETSC_VERSION_MAJOR 3 #define PETSC_VERSION_MINOR 12 #define PETSC_VERSION_SUBMINOR 1 #define PETSC_VERSION_PATCH 0 #define PETSC_VERSION_DATE "unknown" #define PETSC_VERSION_GIT "unknown" #define PETSC_VERSION_DATE_GIT "unknown" #define PETSC_VERSION_EQ(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_ PETSC_VERSION_EQ #define PETSC_VERSION_LT(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_LE(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_GT(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_GE(MAJOR,MINOR,SUBMINOR) \ child PETSc.options.petscdir 0.017563 ================================================================================ TEST getDatafilespath from PETSc.options.dataFilesPath(/p/work/tmondrag/moose/petsc/config/PETSc/options/dataFilesPath.py:29) TESTING: getDatafilespath from PETSc.options.dataFilesPath(config/PETSc/options/dataFilesPath.py:29) Checks what DATAFILESPATH should be child PETSc.options.dataFilesPath 0.000819 ================================================================================ TEST configureGit from config.sourceControl(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/sourceControl.py:24) TESTING: configureGit from config.sourceControl(config/BuildSystem/config/sourceControl.py:24) Find the Git executable Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/git...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/git...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/git...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/git...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/git...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/git...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/git...not found Checking for program /opt/gcc/7.2.0/bin/git...not found Checking for program /usr/local/krb5/bin/git...not found Checking for program /usr/local/krb5/openssl/bin/git...not found Checking for program /usr/local/krb5/bin/git...not found Checking for program /usr/local/krb5/openssl/bin/git...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/git...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/git...not found Checking for program /opt/pbs/default/bin/git...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/git...not found Checking for program /opt/java/jdk1.8.0_152/bin/git...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/git...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/git...not found Checking for program /opt/cray/pe/modules/3.2.10.6/bin/git...not found Checking for program /usr/local/bin/git...not found Checking for program /usr/bin/git...found Defined make macro "GIT" to "git" Executing: git --version stdout: git version 2.12.3 child config.sourceControl 0.019483 ================================================================================ TEST configureInstallationMethod from PETSc.options.petscclone(/p/work/tmondrag/moose/petsc/config/PETSc/options/petscclone.py:20) TESTING: configureInstallationMethod from PETSc.options.petscclone(config/PETSc/options/petscclone.py:20) lib/petsc/bin/maint exists. This appears to be a repository clone .git directory exists Executing: ['git', 'describe', '--match=v*'] stdout: v3.12.1-23-g5ea3abfa7f Executing: ['git', 'log', '-1', '--pretty=format:%H'] stdout: 5ea3abfa7fe8791a5f316416921daa28f47703d9 Executing: ['git', 'log', '-1', '--pretty=format:%ci'] stdout: 2019-10-29 13:35:52 +0000 Executing: ['git', 'branch'] stdout: * (HEAD detached at 5ea3abfa7f) master Defined "VERSION_GIT" to ""v3.12.1-23-g5ea3abfa7f"" Defined "VERSION_DATE_GIT" to ""2019-10-29 13:35:52 +0000"" Defined "VERSION_BRANCH_GIT" to ""(HEAD detached at 5ea3abfa7f)"" child PETSc.options.petscclone 0.694917 ================================================================================ TEST setNativeArchitecture from PETSc.options.arch(/p/work/tmondrag/moose/petsc/config/PETSc/options/arch.py:31) TESTING: setNativeArchitecture from PETSc.options.arch(config/PETSc/options/arch.py:31) ================================================================================ TEST configureArchitecture from PETSc.options.arch(/p/work/tmondrag/moose/petsc/config/PETSc/options/arch.py:43) TESTING: configureArchitecture from PETSc.options.arch(config/PETSc/options/arch.py:43) Checks PETSC_ARCH and sets if not set No previous hashfile found Setting hashfile: arch-moose/lib/petsc/conf/configure-hash Deleting configure hash file: arch-moose/lib/petsc/conf/configure-hash Unable to delete configure hash file: arch-moose/lib/petsc/conf/configure-hash child PETSc.options.arch 2.905922 ================================================================================ TEST setInstallDir from PETSc.options.installDir(/p/work/tmondrag/moose/petsc/config/PETSc/options/installDir.py:35) TESTING: setInstallDir from PETSc.options.installDir(config/PETSc/options/installDir.py:35) setup installDir to either prefix or if that is not set to PETSC_DIR/PETSC_ARCH Defined make macro "PREFIXDIR" to "/p/home/tmondrag/WORK/moose/petsc/arch-moose" ================================================================================ TEST saveReconfigure from PETSc.options.installDir(/p/work/tmondrag/moose/petsc/config/PETSc/options/installDir.py:79) TESTING: saveReconfigure from PETSc.options.installDir(config/PETSc/options/installDir.py:79) ================================================================================ TEST cleanConfDir from PETSc.options.installDir(/p/work/tmondrag/moose/petsc/config/PETSc/options/installDir.py:72) TESTING: cleanConfDir from PETSc.options.installDir(config/PETSc/options/installDir.py:72) ================================================================================ TEST configureInstallDir from PETSc.options.installDir(/p/work/tmondrag/moose/petsc/config/PETSc/options/installDir.py:56) TESTING: configureInstallDir from PETSc.options.installDir(config/PETSc/options/installDir.py:56) Makes installDir subdirectories if it does not exist for both prefix install location and PETSc work install location Changed persistence directory to /p/home/tmondrag/WORK/moose/petsc/arch-moose/lib/petsc/conf ================================================================================ TEST restoreReconfigure from PETSc.options.installDir(/p/work/tmondrag/moose/petsc/config/PETSc/options/installDir.py:92) TESTING: restoreReconfigure from PETSc.options.installDir(config/PETSc/options/installDir.py:92) child PETSc.options.installDir 0.004222 ================================================================================ TEST setExternalPackagesDir from PETSc.options.externalpackagesdir(/p/work/tmondrag/moose/petsc/config/PETSc/options/externalpackagesdir.py:15) TESTING: setExternalPackagesDir from PETSc.options.externalpackagesdir(config/PETSc/options/externalpackagesdir.py:15) ================================================================================ TEST cleanExternalpackagesDir from PETSc.options.externalpackagesdir(/p/work/tmondrag/moose/petsc/config/PETSc/options/externalpackagesdir.py:22) TESTING: cleanExternalpackagesDir from PETSc.options.externalpackagesdir(config/PETSc/options/externalpackagesdir.py:22) child PETSc.options.externalpackagesdir 0.000357 ================================================================================ TEST configureCLanguage from PETSc.options.languages(/p/work/tmondrag/moose/petsc/config/PETSc/options/languages.py:27) TESTING: configureCLanguage from PETSc.options.languages(config/PETSc/options/languages.py:27) Choose whether to compile the PETSc library using a C or C++ compiler C language is C Defined "CLANGUAGE_C" to "1" child PETSc.options.languages 0.001061 ================================================================================ TEST printEnvVariables from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1715) TESTING: printEnvVariables from config.setCompilers(config/BuildSystem/config/setCompilers.py:1715) **** printenv **** CRAY_MPICH_BASEDIR=/opt/cray/pe/mpt/7.6.3/gni CRAY_LIBSCI_BASE_DIR=/opt/cray/pe/libsci/17.11.1 CPU=x86_64 PE_PETSC_DEFAULT_VOLATILE_PKGCONFIG_PATH=/opt/cray/pe/petsc/3.7.6.0/complex/@PRGENV@/@PE_PETSC_DEFAULT_GENCOMPS@/@PE_PETSC_DEFAULT_TARGET@/lib/pkgconfig INFOPATH=/opt/gcc/7.2.0/snos/share/info PE_LIBSCI_GENCOMPILERS_CRAY_x86_64=8.6 PE_FFTW_DEFAULT_TARGET_share=share HISTSIZE=1000 PE_TPSL_64_DEFAULT_GENCOMPS_INTEL_x86_64=160 CSI_HOME=/usr/local/applic CRAY_LIBSCI_VERSION=17.11.1 JAVA_HOME=/opt/java/jdk1.8.0_152 craype_already_loaded=0 PE_LIBSCI_VOLATILE_PKGCONFIG_PATH=/opt/cray/pe/libsci/17.11.1/@PRGENV@/@PE_LIBSCI_GENCOMPS@/@PE_LIBSCI_TARGET@/lib/pkgconfig FPATH=:/opt/cray/pe/modules/3.2.10.6/init/sh_funcs/no_redirect:/opt/cray/pe/modules/3.2.10.6/init/sh_funcs/no_redirect PE_NETCDF_HDF5PARALLEL_DEFAULT_VOLATILE_PKGCONFIG_PATH=/opt/cray/pe/netcdf-hdf5parallel/4.4.1.1.3/@PRGENV@/@PE_NETCDF_HDF5PARALLEL_DEFAULT_GENCOMPS@/lib/pkgconfig PE_HDF5_DEFAULT_VOLATILE_PKGCONFIG_PATH=/opt/cray/pe/hdf5/1.10.0.3/@PRGENV@/@PE_HDF5_DEFAULT_GENCOMPS@/lib/pkgconfig PE_TPSL_DEFAULT_GENCOMPILERS_GNU_x86_skylake=6.1 XDG_SESSION_ID=c63897 PE_TRILINOS_DEFAULT_VOLATILE_PKGCONFIG_PATH=/opt/cray/pe/trilinos/12.10.1.1/@PRGENV@/@PE_TRILINOS_DEFAULT_GENCOMPS@/@PE_TRILINOS_DEFAULT_TARGET@/lib/pkgconfig PE_FFTW_DEFAULT_TARGET_x86_skylake=x86_skylake PE_SMA_DEFAULT_DIR_PGI_DEFAULT64=64 KSH_AUTOLOAD=1 PE_PETSC_DEFAULT_GENCOMPILERS_GNU_haswell=5.3 4.9 CSHEDIT=emacs PE_TRILINOS_DEFAULT_GENCOMPILERS_INTEL_x86_64=16.0 CRAY_UDREG_INCLUDE_OPTS=-I/opt/cray/udreg/2.3.2-6.0.7.1_5.13__g5196236.ari/include USER=tmondrag PE_LIBSCI_DEFAULT_GENCOMPS_INTEL_x86_64=160 PET_HOME=/p/app/unsupported/PETtools/CE PE_TPSL_64_DEFAULT_GENCOMPILERS_GNU_x86_64=5.1 4.9 JDK_HOME=/usr/lib64/jvm/java PE_HDF5_DEFAULT_GENCOMPS_GNU=51 49 PE_TPSL_DEFAULT_GENCOMPILERS_INTEL_x86_64=16.0 CRAY_LIBSCI_DIR=/opt/cray/pe/libsci/17.11.1 PE_TPSL_64_DEFAULT_GENCOMPILERS_INTEL_x86_64=16.0 PE_HDF5_PARALLEL_DEFAULT_GENCOMPILERS_GNU=5.1 4.9 APP2_STATE=6.5.2 JAVA_BINDIR=/opt/java/jdk1.8.0_152/bin PE_TPSL_DEFAULT_GENCOMPS_INTEL_x86_skylake=160 PE_LIBSCI_DEFAULT_OMP_REQUIRES= PE_NETCDF_DEFAULT_VOLATILE_PKGCONFIG_PATH=/opt/cray/pe/netcdf/4.4.1.1.3/@PRGENV@/@PE_NETCDF_DEFAULT_GENCOMPS@/lib/pkgconfig PE_PETSC_DEFAULT_GENCOMPILERS_GNU_mic_knl=5.3 PE_PETSC_DEFAULT_GENCOMPS_GNU_skylake=61 PETSCCXXREALMPI_HOME=/p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt PE_TPSL_DEFAULT_GENCOMPS_CRAY_x86_64=86 PE_MPICH_DEFAULT_FIXED_PRGENV=INTEL PE_HDF5_PARALLEL_DEFAULT_FIXED_PRGENV=CRAY INTEL PE_TPSL_64_DEFAULT_GENCOMPS_CRAY_sandybridge=86 TMPDIR=/p/work/tmondrag TGHOME=/usr/local/applic/truegrid/default LSTC_SECURITY_DIR=/usr/local/applic/ls-dyna/NETsecurity PE_LIBSCI_DEFAULT_OMP_REQUIRES_openmp=_mp PE_HDF5_PARALLEL_DEFAULT_GENCOMPS_GNU=51 49 _LMFILES_=/opt/cray/pe/modulefiles/modules/3.2.10.6:/opt/cray/pe/craype/2.5.13/modulefiles/craype-broadwell:/opt/cray/pe/craype/2.5.13/modulefiles/craype-hugepages2M:/opt/cray/pe/craype/2.5.13/modulefiles/craype-network-aries:/opt/cray/pe/modulefiles/craype/2.5.13:/opt/cray/pe/modulefiles/cray-mpich/7.6.3:/opt/modulefiles/java/jdk1.8.0_152:/opt/modulefiles/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari:/opt/modulefiles/pbs:/opt/cray/ari/modulefiles/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari:/opt/modulefiles/gcc/7.2.0:/usr/local/modulefiles/unsupported/costinit:/opt/cray/pe/modulefiles/cray-libsci/17.11.1:/opt/cray/ari/modulefiles/udreg/2.3.2-6.0.7.1_5.13__g5196236.ari:/opt/cray/ari/modulefiles/ugni/6.0.14.0-6.0.7.1_3.13__gea11d3d.ari:/opt/cray/pe/modulefiles/pmi/5.0.12:/opt/cray/ari/modulefiles/dmapp/7.1.1-6.0.7.1_6.2__g45d1b37.ari:/opt/cray/ari/modulefiles/gni-headers/5.0.12.0-6.0.7.1_3.11__g3b1768f.ari:/opt/cray/ari/modulefiles/xpmem/2.2.15-6.0.7.1_5.11__g7549d06.ari:/opt/cray/ari/modulefiles/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari:/opt/cray/ari/modulefiles/dvs/2.7_2.2.120-6.0.7.1_12.1__g74cb2cc4:/opt/cray/ari/modulefiles/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari:/opt/cray/ari/modulefiles/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari:/opt/cray/pe/modulefiles/atp/2.1.1:/opt/cray/pe/modulefiles/perftools-base/6.5.2:/opt/cray/pe/modulefiles/PrgEnv-gnu/6.0.4:/p/app/unsupported/COST/modules/valgrind-mpi/gnu/craympt/3.12.0:/p/app/unsupported/COST/modules/petsc-cxx-real-mpi/gnu/craympt/3.7.4 MODULE_VERSION=3.2.10.6 LIBSCI_VERSION=17.11.1 CRAYPAT_LD_LIBRARY_PATH=/opt/cray/pe/gcc-libs:/opt/cray/gcc-libs:/opt/cray/pe/perftools/6.5.2/lib64 CRAY_XPMEM_INCLUDE_OPTS=-I/opt/cray/xpmem/2.2.15-6.0.7.1_5.11__g7549d06.ari/include FC=ftn PE_MPICH_DEFAULT_GENCOMPS_GNU=51 49 HOME=/p/home/tmondrag PE_LIBSCI_GENCOMPS_INTEL_x86_64=160 PE_GA_DEFAULT_FIXED_PRGENV=CRAY PGI INTEL SAMPLES_HOME=/p/app/unsupported/Example_Codes PE_GA_DEFAULT_GENCOMPILERS_GNU=5.1 4.9 PE_FORTRAN_PKGCONFIG_LIBS=mpichf90 PAT_REPORT_PRUNE_NAME=_cray$mt_start_,__cray_hwpc_,f_cray_hwpc_,cstart,__pat_,pat_region_,PAT_,OMP.slave_loop,slave_entry,_new_slave_entry,THREAD_POOL_join,__libc_start_main,_start,__start,start_thread,__wrap_,UPC_ADIO_,_upc_,upc_,__caf_,__pgas_,syscall,__device_stub LSTC_LICENSE_SERVER=10.128.0.95 PE_PAPI_DEFAULT_ACCEL_LIBS_nvidia35=,-lcupti,-lcudart,-lcuda NNTPSERVER=news ATP_IGNORE_SIGTERM=1 HOST=onyx05.erdc.hpc.mil PE_NETCDF_HDF5PARALLEL_DEFAULT_VOLATILE_PRGENV=GNU HUGETLB_MORECORE_HEAPBASE=10000000000 PE_PGI_DEFAULT_FIXED_PKGCONFIG_PATH=/opt/cray/pe/ga/5.3.0.7/PGI/15.3/lib/pkgconfig PE_MPICH_DEFAULT_GENCOMPILERS_GNU=5.1 4.9 PE_MPICH_MODULE_NAME=cray-mpich PE_LIBSCI_ACC_DEFAULT_VOLATILE_PRGENV=CRAY GNU PE_TPSL_64_DEFAULT_GENCOMPS_CRAY_x86_skylake=86 PE_FFTW_DEFAULT_VOLATILE_PKGCONFIG_PATH=/opt/cray/pe/fftw/3.3.6.2/@PE_FFTW_DEFAULT_TARGET@/lib/pkgconfig PE_PETSC_DEFAULT_GENCOMPS_INTEL_haswell=160 PE_PARALLEL_NETCDF_DEFAULT_VOLATILE_PKGCONFIG_PATH=/opt/cray/pe/parallel-netcdf/1.8.1.3/@PRGENV@/@PE_PARALLEL_NETCDF_DEFAULT_GENCOMPS@/lib/pkgconfig JRE_HOME=/opt/java/jdk1.8.0_152/jre PE_TPSL_DEFAULT_VOLATILE_PKGCONFIG_PATH=/opt/cray/pe/tpsl/17.06.1/@PRGENV@/@PE_TPSL_DEFAULT_GENCOMPS@/@PE_TPSL_DEFAULT_TARGET@/lib/pkgconfig PE_LIBSCI_DEFAULT_GENCOMPS_GNU_x86_64=61 51 49 PE_LIBSCI_REQUIRED_PRODUCTS=PE_MPICH PE_HDF5_DEFAULT_FIXED_PRGENV=CRAY INTEL PE_SMA_DEFAULT_VOLATILE_PKGCONFIG_PATH=/opt/cray/pe/mpt/7.6.3/gni/sma at PE_SMA_DEFAULT_DIR_DEFAULT64@/lib64/pkgconfig PE_TPSL_DEFAULT_VOLATILE_PRGENV=CRAY CRAY64 GNU GNU64 INTEL INTEL64 PAT_BUILD_PAPI_BASEDIR=/opt/cray/pe/papi/5.5.1.3 BC_STANDARD_NODE_CORES=44 PE_MPICH_PKGCONFIG_VARIABLES=PE_MPICH_NV_LIBS_ at accelerator@:PE_MPICH_ALTERNATE_LIBS_ at multithreaded@:PE_MPICH_ALTERNATE_LIBS_ at dpm@ LIBSCI_BASE_DIR=/opt/cray/pe/libsci/17.11.1 PE_TPSL_64_DEFAULT_GENCOMPS_GNU_x86_skylake=61 ATP_POST_LINK_OPTS=-Wl,-L/opt/cray/pe/atp/2.1.1/libApp/ COLORTERM=1 PE_TPSL_64_DEFAULT_GENCOMPS_GNU_sandybridge=51 49 KRB5CCNAME=PIPE:1023 PE_HDF5_PARALLEL_DEFAULT_VOLATILE_PKGCONFIG_PATH=/opt/cray/pe/hdf5-parallel/1.10.0.3/@PRGENV@/@PE_HDF5_PARALLEL_DEFAULT_GENCOMPS@/lib/pkgconfig BC_PHI_NODE_CORES=64 PE_GA_DEFAULT_VOLATILE_PRGENV=GNU OLDPWD=/p/home/tmondrag/WORK/moose LOADEDMODULES=modules/3.2.10.6:craype-broadwell:craype-hugepages2M:craype-network-aries:craype/2.5.13:cray-mpich/7.6.3:java/jdk1.8.0_152:eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari:pbs:ccm/2.5.4-6.0.7.1_5.27__g394754f.ari:gcc/7.2.0:costinit:cray-libsci/17.11.1:udreg/2.3.2-6.0.7.1_5.13__g5196236.ari:ugni/6.0.14.0-6.0.7.1_3.13__gea11d3d.ari:pmi/5.0.12:dmapp/7.1.1-6.0.7.1_6.2__g45d1b37.ari:gni-headers/5.0.12.0-6.0.7.1_3.11__g3b1768f.ari:xpmem/2.2.15-6.0.7.1_5.11__g7549d06.ari:job/2.2.3-6.0.7.1_5.44__g6c4e934.ari:dvs/2.7_2.2.120-6.0.7.1_12.1__g74cb2cc4:alps/6.6.43-6.0.7.1_5.46__ga796da32.ari:rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari:atp/2.1.1:perftools-base/6.5.2:PrgEnv-gnu/6.0.4:valgrind-mpi/gnu/craympt/3.12.0:petsc-cxx-real-mpi/gnu/craympt/3.7.4 PE_PETSC_DEFAULT_GENCOMPILERS_CRAY_x86_64=8.6 AEROSOFT_HOME=/usr/local/applic/gasp/default/aerosoft PE_PETSC_DEFAULT_GENCOMPS_INTEL_sandybridge=160 PE_PAPI_DEFAULT_PKGCONFIG_VARIABLES=PE_PAPI_ACCEL_LIBS_ at accelerator@ PE_MPICH_ALTERNATE_LIBS_multithreaded=_mt CRAY_LD_LIBRARY_PATH=/opt/cray/pe/perftools/6.5.2/lib64:/opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/lib64:/opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/lib64:/opt/cray/xpmem/2.2.15-6.0.7.1_5.11__g7549d06.ari/lib64:/opt/cray/dmapp/7.1.1-6.0.7.1_6.2__g45d1b37.ari/lib64:/opt/cray/pe/pmi/5.0.12/lib64:/opt/cray/ugni/6.0.14.0-6.0.7.1_3.13__gea11d3d.ari/lib64:/opt/cray/udreg/2.3.2-6.0.7.1_5.13__g5196236.ari/lib64:/opt/cray/pe/libsci/17.11.1/GNU/6.1/x86_64/lib:/opt/cray/pe/mpt/7.6.3/gni/mpich-gnu/5.1/lib PE_TRILINOS_DEFAULT_VOLATILE_PRGENV=CRAY GNU INTEL PE_LIBSCI_DEFAULT_VOLATILE_PRGENV=CRAY GNU INTEL PE_PAPI_DEFAULT_ACCEL_LIBS= LESS=-M -I -R PE_LIBSCI_GENCOMPILERS_GNU_x86_64=6.1 5.1 4.9 PE_TPSL_64_DEFAULT_GENCOMPILERS_INTEL_sandybridge=16.0 PE_TPSL_64_DEFAULT_GENCOMPILERS_CRAY_x86_64=8.6 PE_LIBSCI_ACC_DEFAULT_GENCOMPS_CRAY_x86_64=85 PE_HUGEPAGES_PAGE_SIZE=0x20000000 CRAYPE_NETWORK_TARGET=aries USERMODULES=PrgEnv-cray:PrgEnv-gnu:PrgEnv-intel:PrgEnv-pathscale:PrgEnv-pgi:acml:alps:apprentice:apprentice2:atp:blcr:cce:chapel:cray-ccdb:cray-fftw:cray-ga:cray-hdf5:cray-hdf5-parallel:cray-lgdb:cray-libsci:cray-libsci_acc:cray-mpich:cray-mpich-compat:cray-mpich2:cray-netcdf:cray-netcdf-hdf5parallel:cray-parallel-netcdf:cray-petsc:cray-petsc-complex:cray-shmem:cray-snplauncher:cray-tpsl:cray-trilinos:craypat:craype:craypkg-gen:cudatoolkit:ddt:fftw:ga:gcc:hdf5:hdf5-parallel:intel:iobuf:java:lgdb:libfast:libsci_acc:mpich1:netcdf:netcdf-hdf5parallel:netcdf-nofsync:netcdf-nofsync-hdf5parallel:ntk:onesided:papi:parallel-netcdf:pathscale:perftools:perftools-lite:petsc:petsc-complex:pgi:pmi:stat:totalview:tpsl:trilinos:xt-asyncpe:xt-craypat:xt-lgdb:xt-libsci:xt-mpich2:xt-mpt:xt-papi:xt-shmem:xt-totalview GCC_PATH=/opt/gcc/7.2.0 XKEYSYMDB=/usr/X11R6/lib/X11/XKeysymDB PE_TPSL_64_DEFAULT_GENCOMPS_INTEL_x86_skylake=160 CRAY_CPU_TARGET=broadwell CHPL_CG_CPP_LINES=1 PE_PKGCONFIG_PRODUCTS=PE_LIBSCI:PE_HUGEPAGES:PE_MPICH LDFLAGS=-L/p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/lib -L/p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/lib PE_LIBSCI_MODULE_NAME=cray-libsci/17.11.1 PE_FFTW_DEFAULT_REQUIRED_PRODUCTS=PE_MPICH PELOCAL_PRGENV=true PE_PETSC_DEFAULT_GENCOMPS_INTEL_skylake=160 PE_TPSL_DEFAULT_GENCOMPS_INTEL_x86_64=160 TARGETMODULES=craype-abudhabi:craype-abudhabi-cu:craype-accel-host:craype-accel-nvidia20:craype-accel-nvidia30:craype-accel-nvidia35:craype-barcelona:craype-broadwell:craype-haswell:craype-hugepages128K:craype-hugepages128M:craype-hugepages16M:craype-hugepages256M:craype-hugepages2M:craype-hugepages32M:craype-hugepages4M:craype-hugepages512K:craype-hugepages512M:craype-hugepages64M:craype-hugepages8M:craype-intel-knc:craype-interlagos:craype-interlagos-cu:craype-istanbul:craype-ivybridge:craype-mc12:craype-mc8:craype-mic-knl:craype-network-aries:craype-network-gemini:craype-network-infiniband:craype-network-none:craype-network-seastar:craype-sandybridge:craype-shanghai:craype-target-compute_node:craype-target-local_host:craype-target-native:craype-xeon:xtpe-barcelona:xtpe-interlagos:xtpe-interlagos-cu:xtpe-istanbul:xtpe-mc12:xtpe-mc8:xtpe-network-gemini:xtpe-network-seastar:xtpe-shanghai:xtpe-target-native:xtpe-xeon PE_TPSL_64_DEFAULT_GENCOMPS_CRAY_mic_knl=86 PE_PAPI_DEFAULT_ACCEL_FAMILY_LIBS_nvidia=,-lcupti,-lcudart,-lcuda CRAY_DMAPP_POST_LINK_OPTS=-L/opt/cray/dmapp/7.1.1-6.0.7.1_6.2__g45d1b37.ari/lib64 LSTC_LICENSE=network LS_COLORS=no=00:fi=00:di=01;34:ln=00;36:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=41;33;01:ex=00;32:*.cmd=00;32:*.exe=01;32:*.com=01;32:*.bat=01;32:*.btm=01;32:*.dll=01;32:*.tar=00;31:*.tbz=00;31:*.tgz=00;31:*.rpm=00;31:*.deb=00;31:*.arj=00;31:*.taz=00;31:*.lzh=00;31:*.lzma=00;31:*.zip=00;31:*.zoo=00;31:*.z=00;31:*.Z=00;31:*.gz=00;31:*.bz2=00;31:*.tb2=00;31:*.tz2=00;31:*.tbz2=00;31:*.xz=00;31:*.avi=01;35:*.bmp=01;35:*.fli=01;35:*.gif=01;35:*.jpg=01;35:*.jpeg=01;35:*.mng=01;35:*.mov=01;35:*.mpg=01;35:*.pcx=01;35:*.pbm=01;35:*.pgm=01;35:*.png=01;35:*.ppm=01;35:*.tga=01;35:*.tif=01;35:*.xbm=01;35:*.xpm=01;35:*.dl=01;35:*.gl=01;35:*.wmv=01;35:*.aiff=00;32:*.au=00;32:*.mid=00;32:*.mp3=00;32:*.ogg=00;32:*.voc=00;32:*.wav=00;32: HUGETLB_ELFMAP=W PE_SMA_DEFAULT_COMPFLAG= PE_PETSC_DEFAULT_GENCOMPS_GNU_x86_64=53 49 JAVA_ROOT=/opt/java/jdk1.8.0_152 TGPORT=50028 50029 50030 50031 50032 50033 50034 50035 50036 50037 PE_TPSL_DEFAULT_GENCOMPS_CRAY_sandybridge=86 MODULE_VERSION_STACK=3.2.10.6 PE_MPICH_PKGCONFIG_LIBS=mpich SHLVL=2 CRAY_ALPS_INCLUDE_OPTS=-I/opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/include PE_MPICH_DEFAULT_DIR_CRAY_DEFAULT64=64 PE_LIBSCI_PKGCONFIG_VARIABLES=PE_LIBSCI_OMP_REQUIRES_ at openmp@:PE_SCI_EXT_LIBPATH:PE_SCI_EXT_LIBNAME CRAY_XPMEM_POST_LINK_OPTS=-L/opt/cray/xpmem/2.2.15-6.0.7.1_5.11__g7549d06.ari/lib64 PETSC_DIR=/p/home/tmondrag/WORK/moose/scripts/../petsc PE_PETSC_DEFAULT_GENCOMPILERS_CRAY_sandybridge=8.6 PERFTOOLS_VERSION=6.5.2 PE_TPSL_DEFAULT_GENCOMPS_CRAY_mic_knl=86 PE_LIBSCI_ACC_DEFAULT_NV_SUFFIX_nvidia35=nv35 PE_PETSC_DEFAULT_REQUIRED_PRODUCTS=PE_MPICH:PE_LIBSCI:PE_HDF5_PARALLEL:PE_TPSL XTPE_NETWORK_TARGET=aries PE_TPSL_DEFAULT_GENCOMPS_INTEL_mic_knl=160 PE_TPSL_64_DEFAULT_GENCOMPS_INTEL_mic_knl=160 PE_PETSC_DEFAULT_GENCOMPS_INTEL_x86_64=160 LS_OPTIONS=-N --color=auto -T 0 MODULEPATH=/opt/cray/pe/perftools/6.5.2/modulefiles:/opt/cray/pe/craype/2.5.13/modulefiles:/opt/cray/pe/modulefiles:/opt/cray/modulefiles:/opt/modulefiles:/usr/local/modulefiles/apps:/usr/local/modulefiles/unsupported:/p/home/tmondrag/modulefiles:/p/app/unsupported/COST/modules:/opt/cray/ari/modulefiles:/opt/cray/pe/ari/modulefiles PE_HDF5_DEFAULT_GENCOMPILERS_GNU=5.1 4.9 PE_PETSC_DEFAULT_GENCOMPS_CRAY_skylake=86 CMAKE_LIBRARY_PATH=/p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/lib:/p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/lib COST_MODULES_DIR=/p/app/unsupported/COST/modules MPSCP_PORTS=tcp[9000-9999] PE_TPSL_64_DEFAULT_GENCOMPS_INTEL_sandybridge=160 PE_TPSL_64_DEFAULT_GENCOMPS_CRAY_x86_64=86 HUGETLB_DEFAULT_PAGE_SIZE=2M PE_TRILINOS_DEFAULT_GENCOMPILERS_GNU_x86_64=5.1 4.9 PE_MPICH_DEFAULT_GENCOMPS_CRAY=86 PE_PETSC_DEFAULT_GENCOMPS_CRAY_sandybridge=86 KRB5_HOME=/usr/local/krb5 WORK=/p/work PE_FFTW_DEFAULT_TARGET_ivybridge=ivybridge PE_TPSL_DEFAULT_GENCOMPILERS_INTEL_haswell=16.0 PE_TPSL_64_DEFAULT_GENCOMPILERS_INTEL_mic_knl=16.0 ATP_HOME=/opt/cray/pe/atp/2.1.1 DVS_INCLUDE_OPTS=-I/opt/cray/dvs/2.7_2.2.120-6.0.7.1_12.1__g74cb2cc4/include CRAY_UGNI_POST_LINK_OPTS=-L/opt/cray/ugni/6.0.14.0-6.0.7.1_3.13__gea11d3d.ari/lib64 PE_PETSC_DEFAULT_GENCOMPILERS_GNU_skylake=6.1 SHMEM_ABORT_ON_ERROR=1 PKG_CONFIG_PATH_DEFAULT=/opt/cray/pe/papi/5.5.1.3/lib64/pkgconfig LESSOPEN=lessopen.sh %s PE_TPSL_64_DEFAULT_GENCOMPILERS_GNU_x86_skylake=6.1 PE_PARALLEL_NETCDF_DEFAULT_VOLATILE_PRGENV=GNU PE_CXX_PKGCONFIG_LIBS=mpichcxx PE_TPSL_DEFAULT_GENCOMPILERS_CRAY_x86_skylake=8.6 SSH_TTY=/dev/pts/7 PE_TPSL_DEFAULT_GENCOMPILERS_GNU_sandybridge=5.1 4.9 PE_TPSL_64_DEFAULT_GENCOMPILERS_INTEL_haswell=16.0 PE_TPSL_DEFAULT_GENCOMPILERS_CRAY_x86_64=8.6 MPSCP_CONFIG_FILENAME=/p/app/unsupported/local/etc/mpscp_config.onyx05 CVS_RSH=ssh PE_PARALLEL_NETCDF_DEFAULT_FIXED_PRGENV=CRAY INTEL PE_FFTW_DEFAULT_TARGET_broadwell=broadwell PE_MPICH_GENCOMPILERS_GNU=5.1 4.9 PE_TPSL_DEFAULT_GENCOMPS_GNU_x86_64=51 49 SSH_CLIENT=134.164.188.51 58340 22 LOGNAME=tmondrag PE_MPICH_DEFAULT_VOLATILE_PKGCONFIG_PATH=/opt/cray/pe/mpt/7.6.3/gni/mpich- at PRGENV@@PE_MPICH_DEFAULT_DIR_DEFAULT64@/@PE_MPICH_DEFAULT_GENCOMPS@/lib/pkgconfig PATH=/p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin:/p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin:/opt/cray/pe/perftools/6.5.2/bin:/opt/cray/pe/papi/5.5.1.3/bin:/opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin:/opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin:/opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin:/opt/gcc/7.2.0/bin:/usr/local/krb5/bin:/usr/local/krb5/openssl/bin:/usr/local/krb5/bin:/usr/local/krb5/openssl/bin:/opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin:/opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin:/opt/pbs/default/bin:/opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin:/opt/java/jdk1.8.0_152/bin:/opt/cray/pe/mpt/7.6.3/gni/bin:/opt/cray/pe/craype/2.5.13/bin:/opt/cray/pe/modules/3.2.10.6/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/usr/lib/mit/bin:/usr/lib/mit/sbin:/opt/pbs/bin:/opt/cray/pe/bin:/pbs/SLB:/usr/local/man:/p/app/unsupported/local/bin:/usr/local/applic/COTS:/app/mpiutil:/pbs/SLB:/usr/local/man:/p/app/unsupported/local/bin:/usr/local/applic/COTS:/app/mpiutil PE_TPSL_64_DEFAULT_GENCOMPS_INTEL_haswell=160 PE_HDF5_PARALLEL_DEFAULT_REQUIRED_PRODUCTS=PE_MPICH CMAKE_INCLUDE_PATH=/p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/include:/p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/include CRAY_PRE_COMPILE_OPTS=-hnetwork=aries COST_HOME=/p/app/unsupported/COST PE_TPSL_DEFAULT_GENCOMPILERS_INTEL_x86_skylake=16.0 MPICH_DIR=/opt/cray/pe/mpt/7.6.3/gni/mpich-gnu/5.1 PE_PETSC_DEFAULT_GENCOMPILERS_CRAY_mic_knl=8.6 PE_LIBSCI_OMP_REQUIRES= PE_INTEL_DEFAULT_FIXED_PKGCONFIG_PATH=/opt/cray/pe/parallel-netcdf/1.8.1.3/INTEL/16.0/lib/pkgconfig:/opt/cray/pe/netcdf-hdf5parallel/4.4.1.1.3/INTEL/16.0/lib/pkgconfig:/opt/cray/pe/netcdf/4.4.1.1.3/INTEL/16.0/lib/pkgconfig:/opt/cray/pe/mpt/7.6.3/gni/mpich-intel/16.0/lib/pkgconfig:/opt/cray/pe/hdf5-parallel/1.10.0.3/INTEL/16.0/lib/pkgconfig:/opt/cray/pe/hdf5/1.10.0.3/INTEL/16.0/lib/pkgconfig:/opt/cray/pe/ga/5.3.0.7/INTEL/15.0/lib/pkgconfig PE_MPICH_FIXED_PRGENV=INTEL PE_PETSC_DEFAULT_GENCOMPILERS_INTEL_mic_knl=16.0 PE_LIBSCI_GENCOMPS_GNU_x86_64=61 51 49 PE_SMA_DEFAULT_PKGCONFIG_VARIABLES=PE_SMA_COMPFLAG_ at prgenv@ OFFLOAD_INIT=on_start PE_PAPI_DEFAULT_ACCELL_FAMILY_LIBS= PE_MPICH_NV_LIBS_nvidia60=-lcudart PE_PKGCONFIG_LIBS=AtpSigHandler:cray-rca:libsci_mpi:libsci:craype-hugepages:mpich ARCHIVE_HOST=gold.erdc.hpc.mil BC_NODE_TYPE=LOGIN PE_TRILINOS_DEFAULT_GENCOMPILERS_CRAY_x86_64=8.6 PE_NETCDF_HDF5PARALLEL_DEFAULT_GENCOMPILERS_GNU=5.1 4.9 PE_LIBSCI_DEFAULT_GENCOMPILERS_GNU_x86_64=6.1 5.1 4.9 PE_TPSL_64_DEFAULT_GENCOMPILERS_CRAY_x86_skylake=8.6 KRB5HOME=/usr/local/krb5 CRAYPE_DIR=/opt/cray/pe/craype/2.5.13 XDG_DATA_DIRS=/usr/share PE_TPSL_64_DEFAULT_GENCOMPILERS_CRAY_mic_knl=8.6 PE_MPICH_TARGET_VAR_nvidia35=-lcudart CRAY_PMI_INCLUDE_OPTS=-I/opt/cray/pe/pmi/5.0.12/include MANPATH=/opt/cray/pe/perftools/6.5.2/man:/opt/cray/pe/papi/5.5.1.3/share/pdoc/man:/opt/cray/pe/atp/2.1.1/man:/opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/man:/opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/man:/opt/cray/pe/pmi/5.0.12/man:/opt/cray/pe/libsci/17.11.1/man:/opt/cray/pe/man/csmlversion:/opt/gcc/7.2.0/snos/share/man:/usr/local/krb5/share/man:/usr/local/krb5/share/man:/opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/man:/opt/pbs/default/man:/opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/man:/opt/java/jdk1.8.0_152/man:/opt/cray/pe/mpt/7.6.3/gni/man/mpich:/opt/cray/pe/craype/2.5.13/man:/opt/cray/pe/modules/3.2.10.6/share/man:/usr/local/man:/usr/local/share/man:/usr/share/man:/opt/cray/share/man:/opt/pbs/share/man:/opt/cray/pe/man:/p/app/unsupported/local/man:/p/app/unsupported/local/man BC_BIGMEM_NODE_CORES=44 PE_TPSL_DEFAULT_GENCOMPILERS_GNU_x86_64=5.1 4.9 PROFILEREAD=true PE_PETSC_DEFAULT_GENCOMPS_GNU_sandybridge=53 49 PE_PETSC_DEFAULT_GENCOMPS_GNU_mic_knl=53 PE_LIBSCI_ACC_DEFAULT_VOLATILE_PKGCONFIG_PATH=/opt/cray/pe/libsci_acc/17.03.1/@PRGENV@/@PE_LIBSCI_ACC_DEFAULT_GENCOMPS@/@PE_LIBSCI_ACC_DEFAULT_TARGET@/lib/pkgconfig PE_NETCDF_HDF5PARALLEL_DEFAULT_REQUIRED_PRODUCTS=PE_HDF5_PARALLEL:PE_MPICH ARCHIVE_HOME=/erdc1/tmondrag PE_PETSC_DEFAULT_GENCOMPILERS_CRAY_haswell=8.6 HOSTNAME=onyx05.erdc.hpc.mil PE_FFTW_DEFAULT_TARGET_mic_knl=mic_knl PETSC_ARCH=arch-moose PE_LIBSCI_PKGCONFIG_LIBS=libsci_mpi:libsci PE_TPSL_DEFAULT_GENCOMPS_INTEL_sandybridge=160 MACHTYPE=x86_64-suse-linux PE_NETCDF_HDF5PARALLEL_DEFAULT_FIXED_PRGENV=CRAY INTEL BASH_FUNC_module%%=() { eval `/opt/cray/pe/modules/3.2.10.6/bin/modulecmd bash $*` } CRAY_MPICH_DIR=/opt/cray/pe/mpt/7.6.3/gni/mpich-gnu/5.1 MINICOM=-c on PE_TPSL_64_DEFAULT_REQUIRED_PRODUCTS=PE_MPICH:PE_LIBSCI PE_MPICH_NV_LIBS= PKGCONFIG_ENABLED=1 PE_PETSC_DEFAULT_GENCOMPILERS_CRAY_skylake=8.6 PE_TPSL_64_DEFAULT_GENCOMPS_GNU_haswell=51 49 PE_TPSL_DEFAULT_GENCOMPILERS_GNU_mic_knl=5.1 PE_SMA_DEFAULT_DIR_CRAY_DEFAULT64=64 PE_TRILINOS_DEFAULT_GENCOMPS_GNU_x86_64=51 49 DVS_VERSION=0.9.0 PE_TPSL_DEFAULT_GENCOMPILERS_CRAY_mic_knl=8.6 LIBRARYMODULES=acml:alps:cray-dwarf:cray-fftw:cray-ga:cray-hdf5:cray-hdf5-parallel:cray-libsci:cray-libsci_acc:cray-mpich:cray-mpich-abi:cray-mpich2:cray-netcdf:cray-netcdf-hdf5parallel:cray-parallel-netcdf:cray-petsc:cray-petsc-complex:cray-shmem:cray-tpsl:cray-trilinos:cudatoolkit:fftw:ga:hdf5:hdf5-parallel:iobuf:libfast:netcdf:netcdf-hdf5parallel:ntk:onesided:papi:petsc:petsc-complex:pmi:tpsl:trilinos:xt-libsci:xt-mpich2:xt-mpt:xt-papi MODULESHOME=/opt/cray/pe/modules/3.2.10.6 PE_HUGEPAGES_PKGCONFIG_VARIABLES=PE_HUGEPAGES_TEXT_SEGMENT:PE_HUGEPAGES_PAGE_SIZE PE_LIBSCI_DEFAULT_GENCOMPILERS_CRAY_x86_64=8.6 DAAC_HOME=/p/app/DAAC PE_TPSL_DEFAULT_GENCOMPS_CRAY_haswell=86 GCC_VERSION=7.2.0 PE_PETSC_DEFAULT_GENCOMPS_CRAY_haswell=86 PE_MPICH_NV_LIBS_nvidia35=-lcudart PE_LIBSCI_GENCOMPS_CRAY_x86_64=86 PE_MPICH_CXX_PKGCONFIG_LIBS=mpichcxx XDG_CONFIG_DIRS=/etc/xdg PE_TPSL_DEFAULT_GENCOMPILERS_CRAY_haswell=8.6 PE_LIBSCI_ACC_DEFAULT_GENCOMPILERS_CRAY_x86_64=8.5 PE_NETCDF_DEFAULT_GENCOMPS_GNU=51 49 PE_TPSL_64_DEFAULT_GENCOMPILERS_GNU_haswell=5.1 4.9 PE_LIBSCI_ACC_DEFAULT_NV_SUFFIX_nvidia20=nv20 PAGER=less PE_GA_DEFAULT_GENCOMPS_GNU=51 49 LIBGL_DEBUG=quiet CRAY_PMI_POST_LINK_OPTS=-L/opt/cray/pe/pmi/5.0.12/lib64 ATP_MRNET_COMM_PATH=/opt/cray/pe/atp/2.1.1/libexec/atp_mrnet_commnode_wrapper CRAY_MPICH2_VER=7.6.3 PE_LIBSCI_GENCOMPILERS_INTEL_x86_64=16.0 LD_LIBRARY_PATH=/p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/lib:/p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/lib:/opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/lib64:/opt/gcc/7.2.0/snos/lib64 CRAY_LIBSCI_PREFIX_DIR=/opt/cray/pe/libsci/17.11.1/GNU/6.1/x86_64 PE_HUGEPAGES_TEXT_SEGMENT=0x20000000 F90=ftn ALLINEA_QUEUE_DLL=/opt/cray/pe/mpt/7.6.3/gni/mpich-gnu/5.1/lib/libtvmpich.so.3.0.1 LSTC_LICENSE_SERVER_PORT=1747 PE_PKGCONFIG_PRODUCTS_DEFAULT=PE_PAPI CC=cc PE_TPSL_64_DEFAULT_GENCOMPILERS_GNU_sandybridge=5.1 4.9 PE_TPSL_DEFAULT_GENCOMPS_CRAY_x86_skylake=86 PE_TPSL_DEFAULT_GENCOMPS_GNU_sandybridge=51 49 PE_LIBSCI_VOLATILE_PRGENV=CRAY GNU INTEL GPG_TTY=/dev/pts/7 FROM_HEADER= LESSCLOSE=lessclose.sh %s %s PE_MPICH_VOLATILE_PKGCONFIG_PATH=/opt/cray/pe/mpt/7.6.3/gni/mpich- at PRGENV@@PE_MPICH_DIR_DEFAULT64@/@PE_MPICH_GENCOMPS@/lib/pkgconfig CRAY_ALPS_POST_LINK_OPTS=-L/opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/lib64 PE_MPICH_DEFAULT_GENCOMPILERS_CRAY=8.6 MORE=-sl PE_GA_DEFAULT_VOLATILE_PKGCONFIG_PATH=/opt/cray/pe/ga/5.3.0.7/@PRGENV@/@PE_GA_DEFAULT_GENCOMPS@/lib/pkgconfig PE_TPSL_DEFAULT_GENCOMPS_GNU_mic_knl=51 GNU_VERSION=7.2.0 HOSTTYPE=x86_64 CRAYPE_VERSION=2.5.13 CRAY_PRGENVGNU=loaded TERM=xterm-256color PE_PETSC_DEFAULT_GENCOMPILERS_INTEL_sandybridge=16.0 PE_LIBSCI_ACC_DEFAULT_REQUIRED_PRODUCTS=PE_MPICH:PE_LIBSCI CRAY_MPICH2_DIR=/opt/cray/pe/mpt/7.6.3/gni/mpich-gnu/5.1 PE_NETCDF_DEFAULT_VOLATILE_PRGENV=GNU CRAY_GNI_HEADERS_INCLUDE_OPTS=-I/opt/cray/gni-headers/5.0.12.0-6.0.7.1_3.11__g3b1768f.ari/include PE_PKG_CONFIG_PATH=/opt/cray/pe/cti/1.0.6/lib/pkgconfig:/opt/cray/pe/cti/1.0.4/lib/pkgconfig:/opt/cray/pe/cti/1.0.2/lib/pkgconfig PE_CRAY_DEFAULT_FIXED_PKGCONFIG_PATH=/opt/cray/pe/parallel-netcdf/1.8.1.3/CRAY/8.6/lib/pkgconfig:/opt/cray/pe/netcdf-hdf5parallel/4.4.1.1.3/CRAY/8.6/lib/pkgconfig:/opt/cray/pe/netcdf/4.4.1.1.3/CRAY/8.6/lib/pkgconfig:/opt/cray/pe/hdf5-parallel/1.10.0.3/CRAY/8.6/lib/pkgconfig:/opt/cray/pe/hdf5/1.10.0.3/CRAY/8.6/lib/pkgconfig:/opt/cray/pe/ga/5.3.0.7/CRAY/8.4/lib/pkgconfig CRAYPAT_OPTS_EXECUTABLE=sbin/pat-opts PE_FFTW_DEFAULT_TARGET_x86_64=x86_64 PE_PETSC_DEFAULT_GENCOMPILERS_INTEL_haswell=16.0 LESSKEY=/etc/lesskey.bin PE_TPSL_64_DEFAULT_GENCOMPS_GNU_mic_knl=51 HUGETLB_FORCE_ELFMAP=yes+ PYTHONSTARTUP=/etc/pythonstart PWD=/p/home/tmondrag/WORK/moose/petsc PE_LIBSCI_ACC_DEFAULT_NV_SUFFIX_nvidia60=nv60 PE_PETSC_DEFAULT_GENCOMPS_CRAY_mic_knl=86 PE_TPSL_64_DEFAULT_GENCOMPILERS_CRAY_haswell=8.6 PE_SMA_DEFAULT_COMPFLAG_GNU=-fcray-pointer CPPFLAGS=-I/p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/include -I/p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/include PE_LIBSCI_ACC_DEFAULT_GENCOMPILERS_GNU_x86_64=4.9 PE_LIBSCI_DEFAULT_VOLATILE_PKGCONFIG_PATH=/opt/cray/pe/libsci/17.11.1/@PRGENV@/@PE_LIBSCI_DEFAULT_GENCOMPS@/@PE_LIBSCI_DEFAULT_TARGET@/lib/pkgconfig PE_FFTW_DEFAULT_TARGET_haswell=haswell PE_FFTW_DEFAULT_TARGET_sandybridge=sandybridge BC_ACCELERATOR_NODE_CORES=22 SHELL=/bin/bash PE_HDF5_PARALLEL_DEFAULT_VOLATILE_PRGENV=GNU PE_PETSC_DEFAULT_VOLATILE_PRGENV=CRAY CRAY64 GNU GNU64 INTEL INTEL64 LESS_ADVANCED_PREPROCESSOR=no PE_HDF5_DEFAULT_VOLATILE_PRGENV=GNU PE_TPSL_DEFAULT_GENCOMPILERS_CRAY_sandybridge=8.6 PRGENVMODULES=PrgEnv-cray:PrgEnv-gnu:PrgEnv-intel:PrgEnv-pathscale:PrgEnv-pgi DMAPP_ABORT_ON_ERROR=1 XDG_RUNTIME_DIR=/run/user/905790 PE_TPSL_DEFAULT_REQUIRED_PRODUCTS=PE_MPICH:PE_LIBSCI PE_TPSL_64_DEFAULT_GENCOMPILERS_CRAY_sandybridge=8.6 PE_PETSC_DEFAULT_GENCOMPILERS_GNU_sandybridge=5.3 4.9 MPICH_ABORT_ON_ERROR=1 PE_ENV=GNU MPSCP_BLOCKED_FILE=/p/app/unsupported/local/etc/mpscp_blocked_ports PE_PRODUCT_LIST=CRAY_RCA:CRAY_ALPS:DVS:CRAY_XPMEM:CRAY_DMAPP:CRAY_PMI:CRAY_UGNI:CRAY_UDREG:CRAY_LIBSCI:CRAYPE:CRAYPE_BROADWELL:GNU:GCC:HUGETLB2M:PERFTOOLS:CRAYPAT PE_MPICH_VOLATILE_PRGENV=CRAY GNU PE_PETSC_DEFAULT_GENCOMPS_CRAY_x86_64=86 PE_PETSC_DEFAULT_GENCOMPS_GNU_haswell=53 49 SDK_HOME=/usr/lib64/jvm/java CXX=CC PE_MPICH_GENCOMPILERS_CRAY=8.6 PE_MPICH_GENCOMPS_CRAY=86 CRAY_RCA_POST_LINK_OPTS=-L/opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/lib64 -lrca PE_MPICH_TARGET_VAR_nvidia20=-lcudart MAIL=/var/mail/tmondrag SSH_CONNECTION=134.164.188.51 58340 140.31.13.105 22 TOOLMODULES=apprentice:apprentice2:atp:chapel:cray-lgdb:cray-snplauncher:craypat:craypkg-gen:ddt:gdb:iobuf:papi:perftools:perftools-lite:stat:totalview:xt-craypat:xt-lgdb:xt-papi:xt-totalview PE_MPICH_DIR_CRAY_DEFAULT64=64 PE_TPSL_DEFAULT_GENCOMPILERS_GNU_haswell=5.1 4.9 PE_LIBSCI_ACC_DEFAULT_PKGCONFIG_VARIABLES=PE_LIBSCI_ACC_DEFAULT_NV_SUFFIX_ at accelerator@ PE_LIBSCI_ACC_DEFAULT_GENCOMPS_GNU_x86_64=49 PE_LIBSCI_DEFAULT_GENCOMPS_CRAY_x86_64=86 CENTER=/gpfs/cwfs/tmondrag PE_PARALLEL_NETCDF_DEFAULT_GENCOMPS_GNU=51 49 CRAY_UGNI_INCLUDE_OPTS=-I/opt/cray/ugni/6.0.14.0-6.0.7.1_3.13__gea11d3d.ari/include PE_PKGCONFIG_DEFAULT_PRODUCTS=PE_TRILINOS:PE_TPSL_64:PE_TPSL:PE_PETSC:PE_PARALLEL_NETCDF:PE_NETCDF_HDF5PARALLEL:PE_NETCDF:PE_MPICH:PE_LIBSCI_ACC:PE_LIBSCI:PE_HDF5_PARALLEL:PE_HDF5:PE_GA:PE_FFTW CRAYPAT_ALPS_COMPONENT=/opt/cray/pe/perftools/6.5.2/sbin/pat_alps JAVA_PATH=/opt/java/jdk1.8.0_152 PKG_CONFIG_PATH=/p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/lib/pkgconfig:/p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/lib/pkgconfig:/opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/lib64/pkgconfig:/opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/lib64/pkgconfig:/opt/cray/xpmem/2.2.15-6.0.7.1_5.11__g7549d06.ari/lib64/pkgconfig:/opt/cray/gni-headers/5.0.12.0-6.0.7.1_3.11__g3b1768f.ari/lib64/pkgconfig:/opt/cray/dmapp/7.1.1-6.0.7.1_6.2__g45d1b37.ari/lib64/pkgconfig:/opt/cray/pe/pmi/5.0.12/lib64/pkgconfig:/opt/cray/ugni/6.0.14.0-6.0.7.1_3.13__gea11d3d.ari/lib64/pkgconfig:/opt/cray/udreg/2.3.2-6.0.7.1_5.13__g5196236.ari/lib64/pkgconfig:/opt/cray/pe/craype/2.5.13/pkg-config:/opt/cray/pe/iobuf/2.0.8/lib/pkgconfig:/opt/cray/pe/atp/2.1.1/lib/pkgconfig CRAY_MPICH_ROOTDIR=/opt/cray/pe/mpt/7.6.3 XNLSPATH=/usr/share/X11/nls _=./configure BC_HOST=onyx VALGRINDMPI_HOME=/p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt JAVA_VERSION=jdk1.8.0_152 WINDOWMANAGER= PE_TPSL_DEFAULT_GENCOMPS_GNU_haswell=51 49 PE_TRILINOS_DEFAULT_REQUIRED_PRODUCTS=PE_MPICH:PE_HDF5_PARALLEL:PE_NETCDF_HDF5PARALLEL:PE_LIBSCI:PE_TPSL CRAY_DMAPP_INCLUDE_OPTS=-I/opt/cray/dmapp/7.1.1-6.0.7.1_6.2__g45d1b37.ari/include -I/opt/cray/gni-headers/5.0.12.0-6.0.7.1_3.11__g3b1768f.ari/include ACCOUNT=ERDCV00898ERS CRAYPAT_ROOT=/opt/cray/pe/perftools/6.5.2 G_BROKEN_FILENAMES=1 PE_MPICH_ALTERNATE_LIBS_dpm=_dpm QT_SYSTEM_DIR=/usr/share/desktop-data PE_MPICH_NV_LIBS_nvidia20=-lcudart DISPLAY=140.31.13.105:10.0 PE_PETSC_DEFAULT_GENCOMPILERS_INTEL_skylake=16.0 PE_NETCDF_DEFAULT_FIXED_PRGENV=CRAY INTEL PE_INTEL_FIXED_PKGCONFIG_PATH=/opt/cray/pe/mpt/7.6.3/gni/mpich-intel/16.0/lib/pkgconfig PE_TPSL_DEFAULT_GENCOMPS_INTEL_haswell=160 PE_LIBSCI_DEFAULT_REQUIRED_PRODUCTS=PE_MPICH OSTYPE=linux PE_NETCDF_DEFAULT_REQUIRED_PRODUCTS=PE_HDF5 PE_NETCDF_HDF5PARALLEL_DEFAULT_GENCOMPS_GNU=51 49 BC_CORES_PER_NODE=44 PE_TRILINOS_DEFAULT_GENCOMPS_INTEL_x86_64=160 PE_TPSL_64_DEFAULT_GENCOMPILERS_INTEL_x86_skylake=16.0 PE_HDF5_DEFAULT_REQUIRED_PRODUCTS=PE_MPICH gcc_already_loaded=1 F77=ftn PE_MPICH_GENCOMPS_GNU=51 49 CRAY_RCA_INCLUDE_OPTS=-I/opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/include -I/opt/cray/krca/2.2.4-6.0.7.1_5.44__g8505b97.ari/include -I/opt/cray-hss-devel/8.0.0/include EPROXY_LOGIN=onet1 PE_PETSC_DEFAULT_GENCOMPILERS_INTEL_x86_64=16.0 PROJECTS_HOME=/p/app/unsupported PE_TRILINOS_DEFAULT_GENCOMPS_CRAY_x86_64=86 PE_TPSL_DEFAULT_GENCOMPS_GNU_x86_skylake=61 PE_TPSL_64_DEFAULT_GENCOMPS_CRAY_haswell=86 INPUTRC=/etc/inputrc HUGETLB_MORECORE=yes PE_TPSL_DEFAULT_GENCOMPILERS_INTEL_mic_knl=16.0 TZ=US/Central PE_PARALLEL_NETCDF_DEFAULT_GENCOMPILERS_GNU=5.1 4.9 PE_TPSL_64_DEFAULT_VOLATILE_PKGCONFIG_PATH=/opt/cray/pe/tpsl/17.06.1/@PRGENV at 64/@PE_TPSL_64_DEFAULT_GENCOMPS@/@PE_TPSL_64_DEFAULT_TARGET@/lib/pkgconfig PE_TPSL_DEFAULT_GENCOMPILERS_INTEL_sandybridge=16.0 PE_MPICH_DEFAULT_VOLATILE_PRGENV=CRAY GNU PE_TPSL_64_DEFAULT_VOLATILE_PRGENV=CRAY CRAY64 GNU GNU64 INTEL INTEL64 PE_LIBSCI_DEFAULT_GENCOMPILERS_INTEL_x86_64=16.0 PE_LIBSCI_OMP_REQUIRES_openmp=_mp PE_MPICH_FORTRAN_PKGCONFIG_LIBS=mpichf90 PE_NETCDF_DEFAULT_GENCOMPILERS_GNU=5.1 4.9 CRAY_SITE_LIST_DIR=/etc/opt/cray/pe/modules PE_TPSL_64_DEFAULT_GENCOMPILERS_GNU_mic_knl=5.1 RCLOCAL_PRGENV=true SPARK_EVENT_DIR=/p/home/tmondrag/.minerva/sparkHistory PE_PETSC_DEFAULT_GENCOMPILERS_GNU_x86_64=5.3 4.9 WORKDIR=/p/work/tmondrag PE_TPSL_64_DEFAULT_GENCOMPS_GNU_x86_64=51 49 PE_LIBSCI_DEFAULT_PKGCONFIG_VARIABLES=PE_LIBSCI_DEFAULT_OMP_REQUIRES_ at openmp@:PE_SCI_EXT_LIBPATH:PE_SCI_EXT_LIBNAME PE_PETSC_DEFAULT_GENCOMPS_INTEL_mic_knl=160 CRAY_UDREG_POST_LINK_OPTS=-L/opt/cray/udreg/2.3.2-6.0.7.1_5.13__g5196236.ari/lib64 ================================================================================ TEST resetEnvCompilers from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1722) TESTING: resetEnvCompilers from config.setCompilers(config/BuildSystem/config/setCompilers.py:1722) =============================================================================== ***** WARNING: CC (set to cc) found in environment variables - ignoring use ./configure CC=$CC if you really want to use that value ****** =============================================================================== =============================================================================== ***** WARNING: CXX (set to CC) found in environment variables - ignoring use ./configure CXX=$CXX if you really want to use that value ****** =============================================================================== =============================================================================== ***** WARNING: FC (set to ftn) found in environment variables - ignoring use ./configure FC=$FC if you really want to use that value ****** =============================================================================== =============================================================================== ***** WARNING: F77 (set to ftn) found in environment variables - ignoring use ./configure F77=$F77 if you really want to use that value ****** =============================================================================== =============================================================================== ***** WARNING: F90 (set to ftn) found in environment variables - ignoring use ./configure F90=$F90 if you really want to use that value ****** =============================================================================== =============================================================================== ***** WARNING: CPPFLAGS (set to -I/p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/include -I/p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/include) found in environment variables - ignoring use ./configure CPPFLAGS=$CPPFLAGS if you really want to use that value ****** =============================================================================== LDFLAGS (set to -L/p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/lib -L/p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/lib) found in environment variables - ignoring since also set on command line ================================================================================ TEST checkEnvCompilers from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1752) TESTING: checkEnvCompilers from config.setCompilers(config/BuildSystem/config/setCompilers.py:1752) ================================================================================ TEST checkMPICompilerOverride from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1685) TESTING: checkMPICompilerOverride from config.setCompilers(config/BuildSystem/config/setCompilers.py:1685) Check if --with-mpi-dir is used along with CC CXX or FC compiler options. This usually prevents mpi compilers from being used - so issue a warning ================================================================================ TEST requireMpiLdPath from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1706) TESTING: requireMpiLdPath from config.setCompilers(config/BuildSystem/config/setCompilers.py:1706) OpenMPI wrappers require LD_LIBRARY_PATH set ================================================================================ TEST checkInitialFlags from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:450) TESTING: checkInitialFlags from config.setCompilers(config/BuildSystem/config/setCompilers.py:450) Initialize the compiler and linker flags Initialized CFLAGS to Initialized CFLAGS to Initialized LDFLAGS to -dynamic Initialized CUDAFLAGS to Initialized CUDAFLAGS to Initialized LDFLAGS to -dynamic Initialized CXXFLAGS to Initialized CXX_CXXFLAGS to Initialized LDFLAGS to -dynamic Initialized FFLAGS to Initialized FFLAGS to Initialized LDFLAGS to -dynamic Initialized CPPFLAGS to Initialized FPPFLAGS to Initialized CUDAPPFLAGS to -Wno-deprecated-gpu-targets Initialized CXXPPFLAGS to Initialized CC_LINKER_FLAGS to [] Initialized CXX_LINKER_FLAGS to [] Initialized FC_LINKER_FLAGS to [] Initialized CUDAC_LINKER_FLAGS to [] Initialized sharedLibraryFlags to [] Initialized dynamicLibraryFlags to [] ================================================================================ TEST checkCCompiler from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:620) TESTING: checkCCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:620) Locate a functional C compiler Executing: cc -craype-verbose stdout: gcc -march=broadwell -static -D__CRAYXC -D__CRAY_BROADWELL -D__CRAYXT_COMPUTE_LINUX_TARGET -upthread_mutex_destroy -D__TARGET_LINUX__ -I/opt/cray/pe/libsci/17.11.1/GNU/6.1/x86_64/include -I/opt/cray/pe/mpt/7.6.3/gni/mpich-gnu/5.1/include -I/opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/include -I/opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/include -I/opt/cray/xpmem/2.2.15-6.0.7.1_5.11__g7549d06.ari/include -I/opt/cray/gni-headers/5.0.12.0-6.0.7.1_3.11__g3b1768f.ari/include -I/opt/cray/pe/pmi/5.0.12/include -I/opt/cray/ugni/6.0.14.0-6.0.7.1_3.13__gea11d3d.ari/include -I/opt/cray/udreg/2.3.2-6.0.7.1_5.13__g5196236.ari/include -I/opt/cray/wlm_detect/1.3.3-6.0.7.1_5.6__g7109084.ari/include -I/opt/cray/krca/2.2.4-6.0.7.1_5.44__g8505b97.ari/include -I/opt/cray-hss-devel/8.0.0/include -L/opt/cray/pe/libsci/17.11.1/GNU/6.1/x86_64/lib -L/opt/cray/dmapp/default/lib64 -L/opt/cray/pe/mpt/7.6.3/gni/mpich-gnu/5.1/lib -L/opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/lib64 -L/opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/lib64 -L/opt/cray/xpmem/2.2.15-6.0.7.1_5.11__g7549d06.ari/lib64 -L/opt/cray/pe/pmi/5.0.12/lib64 -L/opt/cray/ugni/6.0.14.0-6.0.7.1_3.13__gea11d3d.ari/lib64 -L/opt/cray/udreg/2.3.2-6.0.7.1_5.13__g5196236.ari/lib64 -L/opt/cray/pe/atp/2.1.1/libApp -L/opt/cray/wlm_detect/1.3.3-6.0.7.1_5.6__g7109084.ari/lib64 -Wl,--no-as-needed,-lAtpSigHandler,-lAtpSigHCommData -Wl,--undefined=_ATP_Data_Globals -Wl,--undefined=__atpHandlerInstall -lpthread -Wl,-Ttext-segment=0x20000000,-zmax-page-size=0x20000000 -Wl,--whole-archive,-lhugetlbfs,--no-whole-archive -lsci_gnu_61_mpi -lsci_gnu_61 -lpthread -lhugetlbfs -lmpich_gnu_51 -lrt -lugni -lpthread -lpmi -lpthread -lalpslli -lpthread -lwlm_detect -lalpsutil -lpthread -lrca -lxpmem -lugni -lpthread -ludreg -Wl,--as-needed,-lgfortran,-lquadmath,--no-as-needed -Wl,--as-needed,-lm,--no-as-needed -Wl,--as-needed,-lpthread,--no-as-needed Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/cc...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/cc...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/cc...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/cc...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/cc...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/cc...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/cc...not found Checking for program /opt/gcc/7.2.0/bin/cc...not found Checking for program /usr/local/krb5/bin/cc...not found Checking for program /usr/local/krb5/openssl/bin/cc...not found Checking for program /usr/local/krb5/bin/cc...not found Checking for program /usr/local/krb5/openssl/bin/cc...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/cc...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/cc...not found Checking for program /opt/pbs/default/bin/cc...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/cc...not found Checking for program /opt/java/jdk1.8.0_152/bin/cc...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/cc...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/cc...found Defined make macro "CC" to "cc" All intermediate test results are stored in /p/work/tmondrag/petsc-QqlF3n All intermediate test results are stored in /p/work/tmondrag/petsc-QqlF3n/config.setCompilers Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest -dynamic /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest -dynamic /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest -dynamic /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o Testing executable /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest to see if it can be run Executing: /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest Executing: /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest Executing: cc --version stdout: gcc (GCC) 7.2.0 20170814 (Cray Inc.) Copyright (C) 2017 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. ================================================================================ TEST checkCPreprocessor from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:657) TESTING: checkCPreprocessor from config.setCompilers(config/BuildSystem/config/setCompilers.py:657) Locate a functional C preprocessor Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/cc...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/cc...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/cc...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/cc...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/cc...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/cc...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/cc...not found Checking for program /opt/gcc/7.2.0/bin/cc...not found Checking for program /usr/local/krb5/bin/cc...not found Checking for program /usr/local/krb5/openssl/bin/cc...not found Checking for program /usr/local/krb5/bin/cc...not found Checking for program /usr/local/krb5/openssl/bin/cc...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/cc...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/cc...not found Checking for program /opt/pbs/default/bin/cc...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/cc...not found Checking for program /opt/java/jdk1.8.0_152/bin/cc...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/cc...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/cc...found Defined make macro "CPP" to "cc -E" Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: ================================================================================ TEST checkCUDACompiler from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:695) TESTING: checkCUDACompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:695) Locate a functional CUDA compiler Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/nvcc...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/nvcc...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/nvcc...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/nvcc...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/nvcc...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/nvcc...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/nvcc...not found Checking for program /opt/gcc/7.2.0/bin/nvcc...not found Checking for program /usr/local/krb5/bin/nvcc...not found Checking for program /usr/local/krb5/openssl/bin/nvcc...not found Checking for program /usr/local/krb5/bin/nvcc...not found Checking for program /usr/local/krb5/openssl/bin/nvcc...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/nvcc...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/nvcc...not found Checking for program /opt/pbs/default/bin/nvcc...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/nvcc...not found Checking for program /opt/java/jdk1.8.0_152/bin/nvcc...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/nvcc...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/nvcc...not found Checking for program /opt/cray/pe/modules/3.2.10.6/bin/nvcc...not found Checking for program /usr/local/bin/nvcc...not found Checking for program /usr/bin/nvcc...not found Checking for program /bin/nvcc...not found Checking for program /usr/bin/X11/nvcc...not found Checking for program /usr/games/nvcc...not found Checking for program /usr/lib/mit/bin/nvcc...not found Checking for program /usr/lib/mit/sbin/nvcc...not found Checking for program /opt/pbs/bin/nvcc...not found Checking for program /opt/cray/pe/bin/nvcc...not found Checking for program /pbs/SLB/nvcc...not found Checking for program /usr/local/man/nvcc...not found Checking for program /p/app/unsupported/local/bin/nvcc...not found Checking for program /usr/local/applic/COTS/nvcc...not found Checking for program /app/mpiutil/nvcc...not found Checking for program /pbs/SLB/nvcc...not found Checking for program /usr/local/man/nvcc...not found Checking for program /p/app/unsupported/local/bin/nvcc...not found Checking for program /usr/local/applic/COTS/nvcc...not found Checking for program /app/mpiutil/nvcc...not found Checking for program /p/home/tmondrag/WORK/moose/scripts/../petsc/lib/petsc/bin/win32fe/nvcc...not found Checking for program /Developer/NVIDIA/CUDA-6.5/bin/nvcc...not found Checking for program /p/home/tmondrag/WORK/moose/scripts/../petsc/lib/petsc/bin/win32fe/nvcc...not found Checking for program /usr/local/cuda/bin/nvcc...found Defined make macro "CUDAC" to "/usr/local/cuda/bin/nvcc" Executing: /usr/local/cuda/bin/nvcc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -Wno-deprecated-gpu-targets /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cu Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: /usr/local/cuda/bin/nvcc --version stdout: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2018 NVIDIA Corporation Built on Tue_Jun_12_23:07:04_CDT_2018 Cuda compilation tools, release 9.2, V9.2.148 ================================================================================ TEST checkCUDAPreprocessor from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:735) TESTING: checkCUDAPreprocessor from config.setCompilers(config/BuildSystem/config/setCompilers.py:735) Locate a functional CUDA preprocessor Checking for program /usr/local/cuda/bin/nvcc...found Defined make macro "CUDAPP" to "/usr/local/cuda/bin/nvcc -E" Preprocessing source: #include "confdefs.h" #include "conffix.h" #include __global__ void testFunction() {return;}; Executing: /usr/local/cuda/bin/nvcc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -Wno-deprecated-gpu-targets /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cu Preprocess stderr before filtering:: Preprocess stderr after filtering:: ================================================================================ TEST checkCxxCompiler from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:835) TESTING: checkCxxCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:835) Locate a functional Cxx compiler Executing: CC -craype-verbose stdout: g++ -march=broadwell -static -D__CRAYXC -D__CRAY_BROADWELL -D__CRAYXT_COMPUTE_LINUX_TARGET -upthread_mutex_destroy -D__TARGET_LINUX__ -I/opt/cray/pe/libsci/17.11.1/GNU/6.1/x86_64/include -I/opt/cray/pe/mpt/7.6.3/gni/mpich-gnu/5.1/include -I/opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/include -I/opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/include -I/opt/cray/xpmem/2.2.15-6.0.7.1_5.11__g7549d06.ari/include -I/opt/cray/gni-headers/5.0.12.0-6.0.7.1_3.11__g3b1768f.ari/include -I/opt/cray/pe/pmi/5.0.12/include -I/opt/cray/ugni/6.0.14.0-6.0.7.1_3.13__gea11d3d.ari/include -I/opt/cray/udreg/2.3.2-6.0.7.1_5.13__g5196236.ari/include -I/opt/cray/wlm_detect/1.3.3-6.0.7.1_5.6__g7109084.ari/include -I/opt/cray/krca/2.2.4-6.0.7.1_5.44__g8505b97.ari/include -I/opt/cray-hss-devel/8.0.0/include -L/opt/cray/pe/libsci/17.11.1/GNU/6.1/x86_64/lib -L/opt/cray/dmapp/default/lib64 -L/opt/cray/pe/mpt/7.6.3/gni/mpich-gnu/5.1/lib -L/opt/cray/dmapp/default/lib64 -L/opt/cray/pe/mpt/7.6.3/gni/mpich-gnu/5.1/lib -L/opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/lib64 -L/opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/lib64 -L/opt/cray/xpmem/2.2.15-6.0.7.1_5.11__g7549d06.ari/lib64 -L/opt/cray/pe/pmi/5.0.12/lib64 -L/opt/cray/ugni/6.0.14.0-6.0.7.1_3.13__gea11d3d.ari/lib64 -L/opt/cray/udreg/2.3.2-6.0.7.1_5.13__g5196236.ari/lib64 -L/opt/cray/pe/atp/2.1.1/libApp -L/opt/cray/wlm_detect/1.3.3-6.0.7.1_5.6__g7109084.ari/lib64 -Wl,--no-as-needed,-lAtpSigHandler,-lAtpSigHCommData -Wl,--undefined=_ATP_Data_Globals -Wl,--undefined=__atpHandlerInstall -lpthread -Wl,-Ttext-segment=0x20000000,-zmax-page-size=0x20000000 -Wl,--whole-archive,-lhugetlbfs,--no-whole-archive -lsci_gnu_61_mpi -lsci_gnu_61 -lpthread -lhugetlbfs -lmpichcxx_gnu_51 -lrt -lugni -lpthread -lpmi -lmpich_gnu_51 -lrt -lugni -lpthread -lpmi -lpthread -lalpslli -lpthread -lwlm_detect -lalpsutil -lpthread -lrca -lugni -lpthread -lxpmem -ludreg -Wl,--as-needed,-lgfortran,-lquadmath,--no-as-needed -Wl,--as-needed,-lm,--no-as-needed -Wl,--as-needed,-lpthread,--no-as-needed Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/CC...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/CC...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/CC...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/CC...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/CC...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/CC...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/CC...not found Checking for program /opt/gcc/7.2.0/bin/CC...not found Checking for program /usr/local/krb5/bin/CC...not found Checking for program /usr/local/krb5/openssl/bin/CC...not found Checking for program /usr/local/krb5/bin/CC...not found Checking for program /usr/local/krb5/openssl/bin/CC...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/CC...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/CC...not found Checking for program /opt/pbs/default/bin/CC...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/CC...not found Checking for program /opt/java/jdk1.8.0_152/bin/CC...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/CC...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/CC...found Defined make macro "CXX" to "CC" Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: CC -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest -dynamic /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: CC -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest -dynamic /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: CC -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest -dynamic /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o Testing executable /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest to see if it can be run Executing: /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest Executing: /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest Executing: CC --version stdout: g++ (GCC) 7.2.0 20170814 (Cray Inc.) Copyright (C) 2017 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. ================================================================================ TEST checkCxxPreprocessor from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:877) TESTING: checkCxxPreprocessor from config.setCompilers(config/BuildSystem/config/setCompilers.py:877) Locate a functional Cxx preprocessor Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/CC...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/CC...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/CC...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/CC...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/CC...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/CC...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/CC...not found Checking for program /opt/gcc/7.2.0/bin/CC...not found Checking for program /usr/local/krb5/bin/CC...not found Checking for program /usr/local/krb5/openssl/bin/CC...not found Checking for program /usr/local/krb5/bin/CC...not found Checking for program /usr/local/krb5/openssl/bin/CC...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/CC...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/CC...not found Checking for program /opt/pbs/default/bin/CC...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/CC...not found Checking for program /opt/java/jdk1.8.0_152/bin/CC...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/CC...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/CC...found Defined make macro "CXXPP" to "CC -E" Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: CC -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cc Preprocess stderr before filtering:: Preprocess stderr after filtering:: ================================================================================ TEST checkFortranCompiler from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:980) TESTING: checkFortranCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:980) Locate a functional Fortran compiler Executing: ftn -craype-verbose stdout: gfortran -march=broadwell -static -D__CRAYXC -D__CRAY_BROADWELL -D__CRAYXT_COMPUTE_LINUX_TARGET -upthread_mutex_destroy -D__TARGET_LINUX__ -I/opt/cray/pe/libsci/17.11.1/GNU/6.1/x86_64/include -I/opt/cray/pe/mpt/7.6.3/gni/mpich-gnu/5.1/include -I/opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/include -I/opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/include -I/opt/cray/xpmem/2.2.15-6.0.7.1_5.11__g7549d06.ari/include -I/opt/cray/gni-headers/5.0.12.0-6.0.7.1_3.11__g3b1768f.ari/include -I/opt/cray/pe/pmi/5.0.12/include -I/opt/cray/ugni/6.0.14.0-6.0.7.1_3.13__gea11d3d.ari/include -I/opt/cray/udreg/2.3.2-6.0.7.1_5.13__g5196236.ari/include -I/opt/cray/wlm_detect/1.3.3-6.0.7.1_5.6__g7109084.ari/include -I/opt/cray/krca/2.2.4-6.0.7.1_5.44__g8505b97.ari/include -I/opt/cray-hss-devel/8.0.0/include -L/opt/cray/pe/libsci/17.11.1/GNU/6.1/x86_64/lib -L/opt/cray/dmapp/default/lib64 -L/opt/cray/pe/mpt/7.6.3/gni/mpich-gnu/5.1/lib -L/opt/cray/dmapp/default/lib64 -L/opt/cray/pe/mpt/7.6.3/gni/mpich-gnu/5.1/lib -L/opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/lib64 -L/opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/lib64 -L/opt/cray/xpmem/2.2.15-6.0.7.1_5.11__g7549d06.ari/lib64 -L/opt/cray/pe/pmi/5.0.12/lib64 -L/opt/cray/ugni/6.0.14.0-6.0.7.1_3.13__gea11d3d.ari/lib64 -L/opt/cray/udreg/2.3.2-6.0.7.1_5.13__g5196236.ari/lib64 -L/opt/cray/pe/atp/2.1.1/libApp -L/opt/cray/wlm_detect/1.3.3-6.0.7.1_5.6__g7109084.ari/lib64 -Wl,--no-as-needed,-lAtpSigHandler,-lAtpSigHCommData -Wl,--undefined=_ATP_Data_Globals -Wl,--undefined=__atpHandlerInstall -lpthread -Wl,-Ttext-segment=0x20000000,-zmax-page-size=0x20000000 -Wl,--whole-archive,-lhugetlbfs,--no-whole-archive -lsci_gnu_61_mpi -lsci_gnu_61 -lpthread -lhugetlbfs -lmpichf90_gnu_51 -lrt -lugni -lpthread -lpmi -lmpich_gnu_51 -lrt -lugni -lpthread -lpmi -lpthread -lalpslli -lpthread -lwlm_detect -lalpsutil -lpthread -lrca -lugni -lpthread -lxpmem -ludreg -Wl,--as-needed,-lgfortran,-lquadmath,--no-as-needed -Wl,--as-needed,-lpthread,--no-as-needed Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/ftn...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/ftn...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/ftn...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/ftn...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/ftn...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/ftn...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/ftn...not found Checking for program /opt/gcc/7.2.0/bin/ftn...not found Checking for program /usr/local/krb5/bin/ftn...not found Checking for program /usr/local/krb5/openssl/bin/ftn...not found Checking for program /usr/local/krb5/bin/ftn...not found Checking for program /usr/local/krb5/openssl/bin/ftn...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/ftn...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/ftn...not found Checking for program /opt/pbs/default/bin/ftn...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/ftn...not found Checking for program /opt/java/jdk1.8.0_152/bin/ftn...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/ftn...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/ftn...found Defined make macro "FC" to "ftn" Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: ftn -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest -dynamic /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: ftn -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest -dynamic /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: ftn -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest -dynamic /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o Testing executable /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest to see if it can be run Executing: /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest Executing: /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest Executing: ftn --version stdout: GNU Fortran (GCC) 7.2.0 20170814 (Cray Inc.) Copyright (C) 2017 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. ================================================================================ TEST checkFortranPreprocessor from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1017) TESTING: checkFortranPreprocessor from config.setCompilers(config/BuildSystem/config/setCompilers.py:1017) Locate a functional Fortran preprocessor Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/ftn...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/ftn...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/ftn...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/ftn...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/ftn...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/ftn...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/ftn...not found Checking for program /opt/gcc/7.2.0/bin/ftn...not found Checking for program /usr/local/krb5/bin/ftn...not found Checking for program /usr/local/krb5/openssl/bin/ftn...not found Checking for program /usr/local/krb5/bin/ftn...not found Checking for program /usr/local/krb5/openssl/bin/ftn...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/ftn...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/ftn...not found Checking for program /opt/pbs/default/bin/ftn...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/ftn...not found Checking for program /opt/java/jdk1.8.0_152/bin/ftn...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/ftn...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/ftn...found Defined make macro "FPP" to "ftn -E" Deleting "FPP" Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/ftn...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/ftn...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/ftn...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/ftn...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/ftn...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/ftn...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/ftn...not found Checking for program /opt/gcc/7.2.0/bin/ftn...not found Checking for program /usr/local/krb5/bin/ftn...not found Checking for program /usr/local/krb5/openssl/bin/ftn...not found Checking for program /usr/local/krb5/bin/ftn...not found Checking for program /usr/local/krb5/openssl/bin/ftn...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/ftn...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/ftn...not found Checking for program /opt/pbs/default/bin/ftn...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/ftn...not found Checking for program /opt/java/jdk1.8.0_152/bin/ftn...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/ftn...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/ftn...found Defined make macro "FPP" to "ftn --use cpp32" Deleting "FPP" ================================================================================ TEST checkFortranComments from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1040) TESTING: checkFortranComments from config.setCompilers(config/BuildSystem/config/setCompilers.py:1040) Make sure fortran comment "!" works Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.F90 Successful compile: Source: program main ! comment end Fortran comments can use ! in column 1 ================================================================================ TEST checkLargeFileIO from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1171) TESTING: checkLargeFileIO from config.setCompilers(config/BuildSystem/config/setCompilers.py:1171) ================================================================================ TEST checkArchiver from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1270) TESTING: checkArchiver from config.setCompilers(config/BuildSystem/config/setCompilers.py:1270) Check that the archiver exists and can make a library usable by the compiler Executing: ar -V stdout: GNU ar (GNU Binutils; SUSE Linux Enterprise 12) 2.31.1.20180828-9.26 Copyright (C) 2018 Free Software Foundation, Inc. This program is free software; you may redistribute it under the terms of the GNU General Public License version 3 or (at your option) any later version. This program has absolutely no warranty. Executing: ar -V stdout: GNU ar (GNU Binutils; SUSE Linux Enterprise 12) 2.31.1.20180828-9.26 Copyright (C) 2018 Free Software Foundation, Inc. This program is free software; you may redistribute it under the terms of the GNU General Public License version 3 or (at your option) any later version. This program has absolutely no warranty. Defined make macro "FAST_AR_FLAGS" to "Scq" Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int foo(int a) { return a+1; } Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/ar...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/ar...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/ar...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/ar...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/ar...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/ar...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/ar...not found Checking for program /opt/gcc/7.2.0/bin/ar...not found Checking for program /usr/local/krb5/bin/ar...not found Checking for program /usr/local/krb5/openssl/bin/ar...not found Checking for program /usr/local/krb5/bin/ar...not found Checking for program /usr/local/krb5/openssl/bin/ar...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/ar...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/ar...not found Checking for program /opt/pbs/default/bin/ar...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/ar...not found Checking for program /opt/java/jdk1.8.0_152/bin/ar...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/ar...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/ar...not found Checking for program /opt/cray/pe/modules/3.2.10.6/bin/ar...not found Checking for program /usr/local/bin/ar...not found Checking for program /usr/bin/ar...found Defined make macro "AR" to "/usr/bin/ar" Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/ranlib...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/ranlib...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/ranlib...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/ranlib...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/ranlib...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/ranlib...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/ranlib...not found Checking for program /opt/gcc/7.2.0/bin/ranlib...not found Checking for program /usr/local/krb5/bin/ranlib...not found Checking for program /usr/local/krb5/openssl/bin/ranlib...not found Checking for program /usr/local/krb5/bin/ranlib...not found Checking for program /usr/local/krb5/openssl/bin/ranlib...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/ranlib...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/ranlib...not found Checking for program /opt/pbs/default/bin/ranlib...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/ranlib...not found Checking for program /opt/java/jdk1.8.0_152/bin/ranlib...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/ranlib...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/ranlib...not found Checking for program /opt/cray/pe/modules/3.2.10.6/bin/ranlib...not found Checking for program /usr/local/bin/ranlib...not found Checking for program /usr/bin/ranlib...found Defined make macro "RANLIB" to "/usr/bin/ranlib -c" Executing: /usr/bin/ar cr /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/libconf1.a /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conf1.o Executing: /usr/bin/ranlib -c /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/libconf1.a Possible ERROR while running ranlib: stderr: /usr/bin/ranlib: invalid option -- 'c' Ranlib is not functional with your archiver. Try --with-ranlib=true if ranlib is unnecessary. Executing: ar -V stdout: GNU ar (GNU Binutils; SUSE Linux Enterprise 12) 2.31.1.20180828-9.26 Copyright (C) 2018 Free Software Foundation, Inc. This program is free software; you may redistribute it under the terms of the GNU General Public License version 3 or (at your option) any later version. This program has absolutely no warranty. Executing: ar -V stdout: GNU ar (GNU Binutils; SUSE Linux Enterprise 12) 2.31.1.20180828-9.26 Copyright (C) 2018 Free Software Foundation, Inc. This program is free software; you may redistribute it under the terms of the GNU General Public License version 3 or (at your option) any later version. This program has absolutely no warranty. Defined make macro "FAST_AR_FLAGS" to "Scq" Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int foo(int a) { return a+1; } Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/ar...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/ar...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/ar...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/ar...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/ar...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/ar...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/ar...not found Checking for program /opt/gcc/7.2.0/bin/ar...not found Checking for program /usr/local/krb5/bin/ar...not found Checking for program /usr/local/krb5/openssl/bin/ar...not found Checking for program /usr/local/krb5/bin/ar...not found Checking for program /usr/local/krb5/openssl/bin/ar...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/ar...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/ar...not found Checking for program /opt/pbs/default/bin/ar...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/ar...not found Checking for program /opt/java/jdk1.8.0_152/bin/ar...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/ar...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/ar...not found Checking for program /opt/cray/pe/modules/3.2.10.6/bin/ar...not found Checking for program /usr/local/bin/ar...not found Checking for program /usr/bin/ar...found Defined make macro "AR" to "/usr/bin/ar" Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/ranlib...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/ranlib...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/ranlib...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/ranlib...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/ranlib...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/ranlib...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/ranlib...not found Checking for program /opt/gcc/7.2.0/bin/ranlib...not found Checking for program /usr/local/krb5/bin/ranlib...not found Checking for program /usr/local/krb5/openssl/bin/ranlib...not found Checking for program /usr/local/krb5/bin/ranlib...not found Checking for program /usr/local/krb5/openssl/bin/ranlib...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/ranlib...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/ranlib...not found Checking for program /opt/pbs/default/bin/ranlib...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/ranlib...not found Checking for program /opt/java/jdk1.8.0_152/bin/ranlib...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/ranlib...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/ranlib...not found Checking for program /opt/cray/pe/modules/3.2.10.6/bin/ranlib...not found Checking for program /usr/local/bin/ranlib...not found Checking for program /usr/bin/ranlib...found Defined make macro "RANLIB" to "/usr/bin/ranlib" Executing: /usr/bin/ar cr /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/libconf1.a /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conf1.o Executing: /usr/bin/ranlib /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/libconf1.a Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" extern int foo(int); int main() { int b = foo(1); if (b); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest -dynamic /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -L/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -lconf1 Defined make macro "AR_FLAGS" to "cr" Defined make macro "AR_LIB_SUFFIX" to "a" ================================================================================ TEST checkSharedLinker from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1384) TESTING: checkSharedLinker from config.setCompilers(config/BuildSystem/config/setCompilers.py:1384) Check that the linker can produce shared libraries Executing: uname -s stdout: Linux Checking shared linker cc using flags ['-shared'] Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/cc...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/cc...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/cc...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/cc...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/cc...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/cc...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/cc...not found Checking for program /opt/gcc/7.2.0/bin/cc...not found Checking for program /usr/local/krb5/bin/cc...not found Checking for program /usr/local/krb5/openssl/bin/cc...not found Checking for program /usr/local/krb5/bin/cc...not found Checking for program /usr/local/krb5/openssl/bin/cc...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/cc...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/cc...not found Checking for program /opt/pbs/default/bin/cc...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/cc...not found Checking for program /opt/java/jdk1.8.0_152/bin/cc...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/cc...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/cc...found Defined make macro "LD_SHARED" to "cc" Trying C compiler flag Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest -dynamic -shared /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o Possible ERROR while running linker: stderr: Warning: -dynamic was already seen on command line, overriding with -shared. Valid C linker flag -shared Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/libconftest.so -dynamic -shared /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o Possible ERROR while running linker: exit code 1 stderr: Warning: -dynamic was already seen on command line, overriding with -shared. /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o: relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: final link failed: nonrepresentable section on output collect2: error: ld returned 1 exit status Rejected C compiler flag because it was not compatible with shared linker cc using flags ['-shared'] Executing: cc --help | head -n 20 stdout: Usage: cc [options] file... Options: -[no]-add-rpath Controls whether or not '-Wl,-rpath' options are added for all pkg-config generated '-L' options. This can be useful to 'lock in' specific versions of libraries at runtime for dynamically linked applications. (Off by default.) -[no-]as-needed Controls whether or not '-l' options provided by the driver will be wrapped with '-Wl,--as-needed' and '-Wl,--no-as-needed' when possible to minimize unnecessary dependencies when linking dynamically. (On by default.) --[no-]custom-ld-script[=script] Controls whether or not CrayPE attempts to pass ld a custom linker script. If a script is provided, it will be used. Otherwise, a Trying C compiler flag -PIC Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -PIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Possible ERROR while running compiler: exit code 1 stderr: gcc: error: unrecognized command line option '-PIC'; did you mean '-fPIC'? Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Rejecting compiler flag -PIC due to nonzero status from link Rejecting compiler flag -PIC due to gcc: error: unrecognized command line option '-PIC'; did you mean '-fPIC'? PETSc Error: No output file produced Rejected C compiler flag -PIC because it was not compatible with shared linker cc using flags ['-shared'] Trying C compiler flag -fPIC Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -fPIC Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest -dynamic -shared -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o Possible ERROR while running linker: stderr: Warning: -dynamic was already seen on command line, overriding with -shared. Valid C linker flag -shared Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/libconftest.so -dynamic -shared -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o Possible ERROR while running linker: stderr: Warning: -dynamic was already seen on command line, overriding with -shared. Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int foo(void); int main() { int ret = foo(); if (ret) {} ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest -dynamic -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -L/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -lconftest Using shared linker cc with flags ['-shared'] and library extension so Executing: uname -s stdout: Linux Executing: uname -s stdout: Linux ================================================================================ TEST checkPIC from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1118) TESTING: checkPIC from config.setCompilers(config/BuildSystem/config/setCompilers.py:1118) Determine the PIC option for each compiler Trying Cxx for PIC code without any compiler flag Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/libconftest.so -dynamic -shared -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o Possible ERROR while running linker: exit code 1 stderr: Warning: -dynamic was already seen on command line, overriding with -shared. /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o: relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: final link failed: nonrepresentable section on output collect2: error: ld returned 1 exit status Rejected Cxx compiler flag because shared linker cannot handle it Executing: CC --help | head -n 20 stdout: Usage: CC [options] file... Options: -[no]-add-rpath Controls whether or not '-Wl,-rpath' options are added for all pkg-config generated '-L' options. This can be useful to 'lock in' specific versions of libraries at runtime for dynamically linked applications. (Off by default.) -[no-]as-needed Controls whether or not '-l' options provided by the driver will be wrapped with '-Wl,--as-needed' and '-Wl,--no-as-needed' when possible to minimize unnecessary dependencies when linking dynamically. (On by default.) --[no-]custom-ld-script[=script] Controls whether or not CrayPE attempts to pass ld a custom linker script. If a script is provided, it will be used. Otherwise, a Trying Cxx compiler flag -PIC for PIC code Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -PIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cc Possible ERROR while running compiler: exit code 1 stderr: g++: error: unrecognized command line option '-PIC'; did you mean '-fPIC'? Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Rejecting compiler flag -PIC due to nonzero status from link Rejecting compiler flag -PIC due to g++: error: unrecognized command line option '-PIC'; did you mean '-fPIC'? PETSc Error: No output file produced Rejected Cxx compiler flag -PIC because shared linker cannot handle it Trying Cxx compiler flag -fPIC for PIC code Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -fPIC Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/libconftest.so -dynamic -shared -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o Possible ERROR while running linker: stderr: Warning: -dynamic was already seen on command line, overriding with -shared. Accepted Cxx compiler flag -fPIC for PIC code Trying FC for PIC code without any compiler flag Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.F90 Successful compile: Source: function foo(a) real:: a,x,bar common /xx/ x x=a foo = bar(x) end Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/libconftest.so -dynamic -shared -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o Possible ERROR while running linker: exit code 1 stderr: Warning: -dynamic was already seen on command line, overriding with -shared. /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o: relocation R_X86_64_32 against undefined symbol `xx_' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: final link failed: nonrepresentable section on output collect2: error: ld returned 1 exit status Rejected FC compiler flag because shared linker cannot handle it Executing: ftn --help | head -n 20 stdout: Usage: ftn [options] file... Options: -[no]-add-rpath Controls whether or not '-Wl,-rpath' options are added for all pkg-config generated '-L' options. This can be useful to 'lock in' specific versions of libraries at runtime for dynamically linked applications. (Off by default.) -[no-]as-needed Controls whether or not '-l' options provided by the driver will be wrapped with '-Wl,--as-needed' and '-Wl,--no-as-needed' when possible to minimize unnecessary dependencies when linking dynamically. (On by default.) --[no-]custom-ld-script[=script] Controls whether or not CrayPE attempts to pass ld a custom linker script. If a script is provided, it will be used. Otherwise, a Trying FC compiler flag -PIC for PIC code Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -PIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.F90 Possible ERROR while running compiler: exit code 1 stderr: gfortran: error: unrecognized command line option '-PIC'; did you mean '-fPIC'? Source: program main end Rejecting compiler flag -PIC due to nonzero status from link Rejecting compiler flag -PIC due to gfortran: error: unrecognized command line option '-PIC'; did you mean '-fPIC'? PETSc Error: No output file produced Rejected FC compiler flag -PIC because shared linker cannot handle it Trying FC compiler flag -fPIC for PIC code Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -fPIC Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.F90 Successful compile: Source: function foo(a) real:: a,x,bar common /xx/ x x=a foo = bar(x) end Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/libconftest.so -dynamic -shared -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o Possible ERROR while running linker: stderr: Warning: -dynamic was already seen on command line, overriding with -shared. Accepted FC compiler flag -fPIC for PIC code Trying CUDA for PIC code without any compiler flag Executing: /usr/local/cuda/bin/nvcc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -Wno-deprecated-gpu-targets /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cu Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: /usr/local/cuda/bin/nvcc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -Wno-deprecated-gpu-targets /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cu Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/libconftest.so -dynamic -shared -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o Possible ERROR while running linker: exit code 1 stderr: Warning: -dynamic was already seen on command line, overriding with -shared. /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o: relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: final link failed: nonrepresentable section on output collect2: error: ld returned 1 exit status Rejected CUDA compiler flag because shared linker cannot handle it Trying CUDA compiler flag -Xcompiler -fPIC for PIC code Executing: /usr/local/cuda/bin/nvcc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -Xcompiler -fPIC -Wno-deprecated-gpu-targets /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cu Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added CUDA compiler flag -Xcompiler -fPIC Executing: /usr/local/cuda/bin/nvcc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -Xcompiler -fPIC -Wno-deprecated-gpu-targets /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cu Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/libconftest.so -dynamic -shared -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o Possible ERROR while running linker: stderr: Warning: -dynamic was already seen on command line, overriding with -shared. Accepted CUDA compiler flag -Xcompiler -fPIC for PIC code ================================================================================ TEST checkSharedLinkerPaths from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1496) TESTING: checkSharedLinkerPaths from config.setCompilers(config/BuildSystem/config/setCompilers.py:1496) Determine the shared linker path options - IRIX: -rpath - Linux, OSF: -Wl,-rpath, - Solaris: -R - FreeBSD: -Wl,-R, Executing: uname -s stdout: Linux Executing: cc -V Trying C linker flag -Wl,-rpath, Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest -dynamic -Wl,-rpath,/p/work/tmondrag/moose/petsc -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o Valid C linker flag -Wl,-rpath,/p/work/tmondrag/moose/petsc Executing: uname -s stdout: Linux Executing: cc -V Trying Cxx linker flag -Wl,-rpath, Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: CC -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest -dynamic -Wl,-rpath,/p/work/tmondrag/moose/petsc /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o Valid Cxx linker flag -Wl,-rpath,/p/work/tmondrag/moose/petsc Executing: uname -s stdout: Linux Executing: cc -V Trying FC linker flag -Wl,-rpath, Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: ftn -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest -dynamic -Wl,-rpath,/p/work/tmondrag/moose/petsc -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o Valid FC linker flag -Wl,-rpath,/p/work/tmondrag/moose/petsc Executing: uname -s stdout: Linux Executing: cc -V Trying CUDA linker flag -Wl,-rpath, Executing: /usr/local/cuda/bin/nvcc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -Xcompiler -fPIC -Wno-deprecated-gpu-targets /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cu Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: /usr/local/cuda/bin/nvcc -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest -Xcompiler -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o Valid CUDA linker flag -Wl,-rpath,/p/work/tmondrag/moose/petsc ================================================================================ TEST checkLibC from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1531) TESTING: checkLibC from config.setCompilers(config/BuildSystem/config/setCompilers.py:1531) Test whether we need to explicitly include libc in shared linking - Mac OSX requires an explicit reference to libc for shared linking Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int foo(void) {void *chunk = malloc(31); free(chunk); return 0;} Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/libconftest.so -dynamic -shared -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o Possible ERROR while running linker: stderr: Warning: -dynamic was already seen on command line, overriding with -shared. Shared linking does not require an explicit libc reference ================================================================================ TEST checkDynamicLinker from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1577) TESTING: checkDynamicLinker from config.setCompilers(config/BuildSystem/config/setCompilers.py:1577) Check that the linker can dynamicaly load shared libraries Checking for header: dlfcn.h All intermediate test results are stored in /p/work/tmondrag/petsc-QqlF3n/config.headers Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_DLFCN_H" to "1" Checking for functions [dlopen dlsym dlclose] in library ['dl'] [] All intermediate test results are stored in /p/work/tmondrag/petsc-QqlF3n/config.libraries Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -fPIC /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char dlopen(); static void _check_dlopen() { dlopen(); } char dlsym(); static void _check_dlsym() { dlsym(); } char dlclose(); static void _check_dlclose() { dlclose(); } int main() { _check_dlopen(); _check_dlsym(); _check_dlclose();; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -fPIC /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -ldl Defined "HAVE_LIBDL" to "1" Adding ['dl'] to LIBS Executing: uname -s stdout: Linux Checking dynamic linker cc using flags ['-shared'] Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/cc...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/cc...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/cc...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/cc...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/cc...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/cc...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/cc...not found Checking for program /opt/gcc/7.2.0/bin/cc...not found Checking for program /usr/local/krb5/bin/cc...not found Checking for program /usr/local/krb5/openssl/bin/cc...not found Checking for program /usr/local/krb5/bin/cc...not found Checking for program /usr/local/krb5/openssl/bin/cc...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/cc...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/cc...not found Checking for program /opt/pbs/default/bin/cc...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/cc...not found Checking for program /opt/java/jdk1.8.0_152/bin/cc...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/cc...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/cc...found Defined make macro "DYNAMICLINKER" to "cc" Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest -dynamic -shared -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -ldl Possible ERROR while running linker: stderr: Warning: -dynamic was already seen on command line, overriding with -shared. Valid C linker flag -shared Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int foo(void) {printf("test");return 0;} Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/libconftest.so -dynamic -shared -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -ldl Possible ERROR while running linker: stderr: Warning: -dynamic was already seen on command line, overriding with -shared. Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { void *handle = dlopen("/p/work/tmondrag/petsc-QqlF3n/config.setCompilers/libconftest.so", 0); int (*foo)(void) = (int (*)(void)) dlsym(handle, "foo"); if (!foo) { printf("Could not load symbol\n"); return -1; } if ((*foo)()) { printf("Invalid return from foo()\n"); return -1; } if (dlclose(handle)) { printf("Could not close library\n"); return -1; } ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest -dynamic -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -ldl Using dynamic linker cc with flags ['-shared'] and library extension so ================================================================================ TEST output from config.setCompilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/setCompilers.py:1626) TESTING: output from config.setCompilers(config/BuildSystem/config/setCompilers.py:1626) Output module data as defines and substitutions Substituting "CC" with "cc" Substituting "CFLAGS" with " -fPIC" Defined make macro "CC_LINKER_SLFLAG" to "-Wl,-rpath," Substituting "CPP" with "cc -E" Substituting "CPPFLAGS" with "" Substituting "CUDAC" with "/usr/local/cuda/bin/nvcc" Substituting "CUDAFLAGS" with " -Xcompiler -fPIC" Substituting "CUDAPP" with "/usr/local/cuda/bin/nvcc -E" Substituting "CUDAPPFLAGS" with "-Wno-deprecated-gpu-targets" Substituting "CXX" with "CC" Substituting "CXX_CXXFLAGS" with " -fPIC" Substituting "CXXFLAGS" with "" Substituting "CXX_LINKER_SLFLAG" with "-Wl,-rpath," Substituting "CXXPP" with "CC -E" Substituting "CXXPPFLAGS" with "" Substituting "FC" with "ftn" Substituting "FFLAGS" with " -fPIC" Defined make macro "FC_LINKER_SLFLAG" to "-Wl,-rpath," Substituting "LDFLAGS" with "-dynamic" Substituting "LIBS" with "-ldl " Substituting "SHARED_LIBRARY_FLAG" with "-shared" child config.setCompilers 23.911891 ================================================================================ TEST checkSharedDynamicPicOptions from PETSc.options.sharedLibraries(/p/work/tmondrag/moose/petsc/config/PETSc/options/sharedLibraries.py:36) TESTING: checkSharedDynamicPicOptions from PETSc.options.sharedLibraries(config/PETSc/options/sharedLibraries.py:36) ================================================================================ TEST configureSharedLibraries from PETSc.options.sharedLibraries(/p/work/tmondrag/moose/petsc/config/PETSc/options/sharedLibraries.py:52) TESTING: configureSharedLibraries from PETSc.options.sharedLibraries(config/PETSc/options/sharedLibraries.py:52) Checks whether shared libraries should be used, for which you must - Specify --with-shared-libraries - Have found a working shared linker Defines PETSC_USE_SHARED_LIBRARIES if they are used Executing: uname -s stdout: Linux Defined make rule "shared_arch" with dependencies "shared_linux" and code [] Defined make macro "SONAME_FUNCTION" to "$(1).so.$(2)" Defined make macro "SL_LINKER_FUNCTION" to "-shared -Wl,-soname,$(call SONAME_FUNCTION,$(notdir $(1)),$(2))" Defined make macro "BUILDSHAREDLIB" to "yes" Defined "USE_SHARED_LIBRARIES" to "1" ================================================================================ TEST configureDynamicLibraries from PETSc.options.sharedLibraries(/p/work/tmondrag/moose/petsc/config/PETSc/options/sharedLibraries.py:94) TESTING: configureDynamicLibraries from PETSc.options.sharedLibraries(config/PETSc/options/sharedLibraries.py:94) Checks whether dynamic loading is available (with dlfcn.h and libdl) Defined "HAVE_DYNAMIC_LIBRARIES" to "1" ================================================================================ TEST configureSerializedFunctions from PETSc.options.sharedLibraries(/p/work/tmondrag/moose/petsc/config/PETSc/options/sharedLibraries.py:100) TESTING: configureSerializedFunctions from PETSc.options.sharedLibraries(config/PETSc/options/sharedLibraries.py:100) Defines PETSC_SERIALIZE_FUNCTIONS if they are used Requires shared libraries child PETSc.options.sharedLibraries 0.007075 ================================================================================ TEST configureIndexSize from PETSc.options.indexTypes(/p/work/tmondrag/moose/petsc/config/PETSc/options/indexTypes.py:30) TESTING: configureIndexSize from PETSc.options.indexTypes(config/PETSc/options/indexTypes.py:30) Defined make macro "PETSC_INDEX_SIZE" to "32" child PETSc.options.indexTypes 0.001043 ================================================================================ TEST configureCompilerFlags from config.compilerFlags(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilerFlags.py:72) TESTING: configureCompilerFlags from config.compilerFlags(config/BuildSystem/config/compilerFlags.py:72) Get the default compiler flags Defined make macro "C_VERSION" to "gcc (GCC) 7.2.0 20170814 (Cray Inc.)" Defined make macro "MPICC_SHOW" to "Unavailable" Defined make macro "MPICC_SHOW" to "Unavailable" Trying C compiler flag -O Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -O Defined make macro "Cxx_VERSION" to "g++ (GCC) 7.2.0 20170814 (Cray Inc.)" Defined make macro "MPICXX_SHOW" to "Unavailable" Defined make macro "MPICXX_SHOW" to "Unavailable" Trying Cxx compiler flag -O Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -O -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -O Defined make macro "FC_VERSION" to "GNU Fortran (GCC) 7.2.0 20170814 (Cray Inc.)" Defined make macro "MPIFC_SHOW" to "Unavailable" Defined make macro "MPIFC_SHOW" to "Unavailable" Trying FC compiler flag -O Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -O Defined make macro "CUDA_VERSION" to "nvcc: NVIDIA (R) Cuda compiler driver" Defined make macro "MPICC_SHOW" to "Unavailable" Defined make macro "MPICC_SHOW" to "Unavailable" Trying CUDA compiler flag -O Executing: /usr/local/cuda/bin/nvcc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -Xcompiler -fPIC -O -Wno-deprecated-gpu-targets /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cu Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added CUDA compiler flag -O child config.compilerFlags 2.055695 ================================================================================ TEST checkRestrict from config.compilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:138) TESTING: checkRestrict from config.compilers(config/BuildSystem/config/compilers.py:138) Check for the C/CXX restrict keyword Executing: cc -V All intermediate test results are stored in /p/work/tmondrag/petsc-QqlF3n/config.compilers Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { float * __restrict x;; return 0; } compilers: Set C restrict keyword to __restrict Defined "C_RESTRICT" to "__restrict" ================================================================================ TEST checkCFormatting from config.compilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:391) TESTING: checkCFormatting from config.compilers(config/BuildSystem/config/compilers.py:391) Activate format string checking if using the GNU compilers ================================================================================ TEST checkCInline from config.compilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:108) TESTING: checkCInline from config.compilers(config/BuildSystem/config/compilers.py:108) Check for C inline keyword Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" static inline int foo(int a) {return a;} int main() { foo(1);; return 0; } compilers: Set C Inline keyword to inline Defined "C_INLINE" to "inline" ================================================================================ TEST checkDynamicLoadFlag from config.compilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:402) TESTING: checkDynamicLoadFlag from config.compilers(config/BuildSystem/config/compilers.py:402) Checks that dlopen() takes RTLD_XXX, and defines PETSC_HAVE_RTLD_XXX if it does Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include char *libname; int main() { dlopen(libname, RTLD_LAZY);dlopen(libname, RTLD_NOW);dlopen(libname, RTLD_LOCAL);dlopen(libname, RTLD_GLOBAL); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -ldl Defined "HAVE_RTLD_LAZY" to "1" Defined "HAVE_RTLD_NOW" to "1" Defined "HAVE_RTLD_LOCAL" to "1" Defined "HAVE_RTLD_GLOBAL" to "1" ================================================================================ TEST checkCLibraries from config.compilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:202) TESTING: checkCLibraries from config.compilers(config/BuildSystem/config/compilers.py:202) Determines the libraries needed to link with C compiled code Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include void asub(void) {char s[16];printf("testing %s",s);} Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.F90 Successful compile: Source: program main print*,'testing' stop end Executing: ftn -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o /p/work/tmondrag/petsc-QqlF3n/config.compilers/confc.o -ldl C libraries are not needed when using Fortran linker Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include void asub(void) {char s[16];printf("testing %s",s);} Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -O -fPIC /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main(int argc,char **args) {return 0;} Executing: CC -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest -dynamic -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o /p/work/tmondrag/petsc-QqlF3n/config.compilers/confc.o -ldl C libraries are not needed when using C++ linker ================================================================================ TEST checkDependencyGenerationFlag from config.compilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:1343) TESTING: checkDependencyGenerationFlag from config.compilers(config/BuildSystem/config/compilers.py:1343) Check if -MMD works for dependency generation, and add it if it does Trying C compiler flag -MMD -MP Defined make macro "C_DEPFLAGS" to "-MMD -MP" Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -fPIC -O -MMD -MP /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Trying Cxx compiler flag -MMD -MP Defined make macro "CXX_DEPFLAGS" to "-MMD -MP" Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -O -fPIC -MMD -MP /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Trying CUDA compiler flag -MMD -MP Rejected CUDA compiler flag -MMD -MP Trying CUDA compiler flag -MMD Rejected CUDA compiler flag -MMD Trying CUDA compiler flag -xMMD Rejected CUDA compiler flag -xMMD Trying CUDA compiler flag -qmakedep=gcc Rejected CUDA compiler flag -qmakedep=gcc Trying CUDA compiler flag -MD Rejected CUDA compiler flag -MD Executing: /usr/local/cuda/bin/nvcc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -Xcompiler -fPIC -O -MMD -MP -Wno-deprecated-gpu-targets /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cu Possible ERROR while running compiler: exit code 1 stderr: nvcc fatal : Unknown option 'MMD' Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Rejecting compiler flag -MMD -MP due to nonzero status from link Rejecting compiler flag -MMD -MP due to nvcc fatal : Unknown option 'MMD' PETSc Error: No output file produced Executing: /usr/local/cuda/bin/nvcc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -Xcompiler -fPIC -O -MMD -Wno-deprecated-gpu-targets /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cu Possible ERROR while running compiler: exit code 1 stderr: nvcc fatal : Unknown option 'MMD' Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Rejecting compiler flag -MMD due to nonzero status from link Rejecting compiler flag -MMD due to nvcc fatal : Unknown option 'MMD' PETSc Error: No output file produced Executing: /usr/local/cuda/bin/nvcc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -Xcompiler -fPIC -O -xMMD -Wno-deprecated-gpu-targets /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cu Possible ERROR while running compiler: exit code 1 stderr: nvcc fatal : Unknown option 'xMMD' Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Rejecting compiler flag -xMMD due to nonzero status from link Rejecting compiler flag -xMMD due to nvcc fatal : Unknown option 'xMMD' PETSc Error: No output file produced Executing: /usr/local/cuda/bin/nvcc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -Xcompiler -fPIC -O -qmakedep=gcc -Wno-deprecated-gpu-targets /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cu Possible ERROR while running compiler: exit code 1 stderr: nvcc fatal : Unknown option 'qmakedep' Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Rejecting compiler flag -qmakedep=gcc due to nonzero status from link Rejecting compiler flag -qmakedep=gcc due to nvcc fatal : Unknown option 'qmakedep' PETSc Error: No output file produced Executing: /usr/local/cuda/bin/nvcc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -Xcompiler -fPIC -O -MD -Wno-deprecated-gpu-targets /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cu Possible ERROR while running compiler: exit code 1 stderr: nvcc fatal : Unknown option 'MD' Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Rejecting compiler flag -MD due to nonzero status from link Rejecting compiler flag -MD due to nvcc fatal : Unknown option 'MD' PETSc Error: No output file produced ================================================================================ TEST checkC99Flag from config.compilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:1388) TESTING: checkC99Flag from config.compilers(config/BuildSystem/config/compilers.py:1388) Check for -std=c99 or equivalent flag Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { float x[2],y; y = FLT_ROUNDS; // c++ comment int j = 2; for (int i=0; i<2; i++){ x[i] = i*j*y; } ; return 0; } Accepted C99 compile flag: Defined "HAVE_C99" to "1" ================================================================================ TEST checkRestrict from config.compilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:138) TESTING: checkRestrict from config.compilers(config/BuildSystem/config/compilers.py:138) Check for the C/CXX restrict keyword Executing: cc -V Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -O -fPIC /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { float * __restrict x;; return 0; } compilers: Set Cxx restrict keyword to __restrict Defined "CXX_RESTRICT" to "__restrict" ================================================================================ TEST checkCxxOptionalExtensions from config.compilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:421) TESTING: checkCxxOptionalExtensions from config.compilers(config/BuildSystem/config/compilers.py:421) Check whether the C++ compiler (IBM xlC, OSF5) need special flag for .c files which contain C++ Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -O -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { class somename { int i; };; return 0; } ================================================================================ TEST checkCxxInline from config.compilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:123) TESTING: checkCxxInline from config.compilers(config/BuildSystem/config/compilers.py:123) Check for C++ inline keyword Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -O -fPIC /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" static inline int foo(int a) {return a;} int main() { foo(1);; return 0; } compilers: Set Cxx Inline keyword to inline Defined "CXX_INLINE" to "inline" ================================================================================ TEST checkCxxLibraries from config.compilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:531) TESTING: checkCxxLibraries from config.compilers(config/BuildSystem/config/compilers.py:531) Determines the libraries needed to link with C++ from C and Fortran Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -O -fPIC /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include void asub(void) {std::vector v; try { throw 20; } catch (int e) { std::cout << "An exception occurred"; }} Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main(int argc,char **args) {return 0;} Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o /p/work/tmondrag/petsc-QqlF3n/config.compilers/confc.o -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.compilers/confc.o: in function `asub()': conftest.cc:(.text+0x7): undefined reference to `__cxa_allocate_exception' /usr/bin/ld: conftest.cc:(.text+0x19): undefined reference to `typeinfo for int' /usr/bin/ld: conftest.cc:(.text+0x21): undefined reference to `__cxa_throw' /usr/bin/ld: conftest.cc:(.text+0x34): undefined reference to `__cxa_begin_catch' /usr/bin/ld: conftest.cc:(.text+0x42): undefined reference to `std::cout' /usr/bin/ld: conftest.cc:(.text+0x47): undefined reference to `std::basic_ostream >& std::operator<< >(std::basic_ostream >&, char const*)' /usr/bin/ld: conftest.cc:(.text+0x4c): undefined reference to `__cxa_end_catch' /usr/bin/ld: conftest.cc:(.text+0x56): undefined reference to `__cxa_end_catch' /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.compilers/confc.o: in function `_GLOBAL__sub_I_conftest.cc': conftest.cc:(.text+0x6e): undefined reference to `std::ios_base::Init::Init()' /usr/bin/ld: conftest.cc:(.text+0x83): undefined reference to `std::ios_base::Init::~Init()' /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.compilers/confc.o:(.data.DW.ref._ZTIi[DW.ref._ZTIi]+0x0): undefined reference to `typeinfo for int' /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.compilers/confc.o:(.data.DW.ref.__gxx_personality_v0[DW.ref.__gxx_personality_v0]+0x0): undefined reference to `__gxx_personality_v0' collect2: error: ld returned 1 exit status Executing: uname -s stdout: Linux Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -O -fPIC /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include void asub(void) {std::vector v; try { throw 20; } catch (int e) { std::cout << "An exception occurred"; }} Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main(int argc,char **args) {return 0;} Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o /p/work/tmondrag/petsc-QqlF3n/config.compilers/confc.o -lstdc++ -ldl compilers: C++ requires -lstdc++ to link with C compiler Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -O -fPIC /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include void asub(void) {std::vector v; try { throw 20; } catch (int e) { std::cout << "An exception occurred"; }} Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.F90 Successful compile: Source: program main print*,'testing' stop end Executing: ftn -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o /p/work/tmondrag/petsc-QqlF3n/config.compilers/confc.o -lstdc++ -ldl C++ libraries are not needed when using FC linker ================================================================================ TEST checkCxxDialect from config.compilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:449) TESTING: checkCxxDialect from config.compilers(config/BuildSystem/config/compilers.py:449) Determine the Cxx dialect supported by the compiler [and correspoding compiler option - if any]. -with-cxx-dialect can take options: auto: use highest dialect configure can determine cxx17: [future?] cxx14: gnu++14 or c++14 cxx11: gnu++11 or c++11 0: disable CxxDialect check and use compiler default checkCxxDialect: checking CXX11 with flag: Defined "HAVE_CXX_DIALECT_CXX11" to "1" Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -O -fPIC /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include template constexpr T Cubed( T x ) { return x*x*x; } int main() { std::random_device rd; std::mt19937 mt(rd()); std::normal_distribution dist(0,1); const double x = dist(mt); std::cout << x; ; return 0; } Executing: CC -V ================================================================================ TEST checkFortranNameMangling from config.compilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:836) TESTING: checkFortranNameMangling from config.compilers(config/BuildSystem/config/compilers.py:836) Checks Fortran name mangling, and defines HAVE_FORTRAN_UNDERSCORE, HAVE_FORTRAN_NOUNDERSCORE, HAVE_FORTRAN_CAPS, or HAVE_FORTRAN_STDCALL Testing Fortran mangling type underscore with code void d1chk_(void){return;} Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" void d1chk_(void){return;} Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.F90 Successful compile: Source: program main call d1chk() end Executing: ftn -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o /p/work/tmondrag/petsc-QqlF3n/config.compilers/confc.o -lstdc++ -ldl compilers: Fortran name mangling is underscore Defined "HAVE_FORTRAN_UNDERSCORE" to "1" Executing: ftn --version stdout: GNU Fortran (GCC) 7.2.0 20170814 (Cray Inc.) Copyright (C) 2017 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Defined "FORTRAN_CHARLEN_T" to "int" ================================================================================ TEST checkFortranNameManglingDouble from config.compilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:877) TESTING: checkFortranNameManglingDouble from config.compilers(config/BuildSystem/config/compilers.py:877) Checks if symbols containing an underscore append an extra underscore, and defines HAVE_FORTRAN_UNDERSCORE_UNDERSCORE if necessary Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" void d1_chk__(void){return;} Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.F90 Successful compile: Source: program main call d1_chk() end Executing: ftn -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o /p/work/tmondrag/petsc-QqlF3n/config.compilers/confc.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o: in function `main': conftest.F90:(.text+0x20): undefined reference to `d1_chk_' collect2: error: ld returned 1 exit status ================================================================================ TEST checkFortranLibraries from config.compilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:887) TESTING: checkFortranLibraries from config.compilers(config/BuildSystem/config/compilers.py:887) Substitutes for FLIBS the libraries needed to link with Fortran This macro is intended to be used in those situations when it is necessary to mix, e.g. C++ and Fortran 77, source code into a single program or shared library. For example, if object files from a C++ and Fortran 77 compiler must be linked together, then the C++ compiler/linker must be used for linking (since special C++-ish things need to happen at link time like calling global constructors, instantiating templates, enabling exception support, etc.). However, the Fortran 77 intrinsic and run-time libraries must be linked in as well, but the C++ compiler/linker does not know how to add these Fortran 77 libraries. This code was translated from the autoconf macro which was packaged in its current form by Matthew D. Langston . However, nearly all of this macro came from the OCTAVE_FLIBS macro in octave-2.0.13/aclocal.m4, and full credit should go to John W. Eaton for writing this extremely useful macro. Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.F90 Successful compile: Source: program main #include call MPI_Allreduce() end Executing: ftn -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -lstdc++ -ldl Possible ERROR while running linker: stderr: /usr/bin/ld: warning: libgfortran.so.3, needed by /opt/cray/pe/mpt/7.6.3/gni/mpich-gnu/5.1/lib/libmpich_gnu_51.so, may conflict with libgfortran.so.4 /usr/bin/ld: warning: libgfortran.so.3, needed by /opt/cray/pe/mpt/7.6.3/gni/mpich-gnu/5.1/lib/libmpich_gnu_51.so, may conflict with libgfortran.so.4 Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.F90 Successful compile: Source: subroutine asub() print*,'testing' call MPI_Allreduce() return end Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main(int argc,char **args) {return 0;} Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o /p/work/tmondrag/petsc-QqlF3n/config.compilers/confc.o -lstdc++ -ldl Possible ERROR while running linker: stderr: /usr/bin/ld: warning: libgfortran.so.3, needed by /opt/cray/pe/mpt/7.6.3/gni/mpich-gnu/5.1/lib/libmpich_gnu_51.so, may conflict with libgfortran.so.4 Fortran libraries are not needed when using C linker Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.F90 Successful compile: Source: subroutine asub() print*,'testing' call MPI_Allreduce() return end Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -O -fPIC /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main(int argc,char **args) {return 0;} Executing: CC -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest -dynamic -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o /p/work/tmondrag/petsc-QqlF3n/config.compilers/confc.o -lstdc++ -ldl Possible ERROR while running linker: stderr: /usr/bin/ld: warning: libgfortran.so.3, needed by /opt/cray/pe/mpt/7.6.3/gni/mpich-gnu/5.1/lib/libmpich_gnu_51.so, may conflict with libgfortran.so.4 Fortran libraries are not needed when using C++ linker ================================================================================ TEST checkFortranLinkingCxx from config.compilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:1308) TESTING: checkFortranLinkingCxx from config.compilers(config/BuildSystem/config/compilers.py:1308) Check that Fortran can link C++ libraries Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -O -fPIC /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" extern "C" void d1chk_(void); void foo(void){d1chk_();} Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -O -fPIC /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" extern "C" void d1chk_(void); void d1chk_(void){return;} Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.F90 Successful compile: Source: program main call d1chk() end Executing: ftn -o /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilers/conftest.o /p/work/tmondrag/petsc-QqlF3n/config.compilers/cxxobj.o /p/work/tmondrag/petsc-QqlF3n/config.compilers/confc.o -lstdc++ -ldl compilers: Fortran can link C++ functions ================================================================================ TEST setupFrameworkCompilers from config.compilers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilers.py:1453) TESTING: setupFrameworkCompilers from config.compilers(config/BuildSystem/config/compilers.py:1453) child config.compilers 7.629742 ================================================================================ TEST configureClosure from config.utilities.closure(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/utilities/closure.py:17) TESTING: configureClosure from config.utilities.closure(config/BuildSystem/config/utilities/closure.py:17) Determine if Apple ^close syntax is supported in C All intermediate test results are stored in /p/work/tmondrag/petsc-QqlF3n/config.utilities.closure Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.closure/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.closure/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /p/work/tmondrag/petsc-QqlF3n/config.utilities.closure/conftest.c: In function 'main': /p/work/tmondrag/petsc-QqlF3n/config.utilities.closure/conftest.c:6:6: error: expected identifier or '(' before '^' token int (^closure)(int);; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int (^closure)(int);; return 0; } Compile failed inside link child config.utilities.closure 0.094605 ================================================================================ TEST checkFortranTypeSizes from config.compilersFortran(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:56) TESTING: checkFortranTypeSizes from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:56) Check whether real*8 is supported and suggest flags which will allow support All intermediate test results are stored in /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.F90 Successful compile: Source: program main real*8 variable end ================================================================================ TEST checkFortranPreprocessor from config.compilersFortran(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:73) TESTING: checkFortranPreprocessor from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:73) Determine if Fortran handles preprocessing properly Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.F90 Successful compile: Source: program main #define dummy dummy #ifndef dummy fooey #endif end compilers: Fortran uses preprocessor ================================================================================ TEST checkFortranDefineCompilerOption from config.compilersFortran(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:96) TESTING: checkFortranDefineCompilerOption from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:96) Check if -WF,-Dfoobar or -Dfoobar is the compiler option to define a macro Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC -O -DTesting /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.F90 Successful compile: Source: program main #define dummy dummy #ifndef Testing fooey #endif end Defined make macro "FC_DEFINE_FLAG" to "-D" compilers: Fortran uses -D for defining macro ================================================================================ TEST checkFortran90 from config.compilersFortran(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:146) TESTING: checkFortran90 from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:146) Determine whether the Fortran compiler handles F90 Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.F90 Successful compile: Source: program main INTEGER, PARAMETER :: int = SELECTED_INT_KIND(8) INTEGER (KIND=int) :: ierr ierr = 1 end Executing: ftn -o /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.o -lstdc++ -ldl Defined "USING_F90" to "1" Fortran compiler supports F90 ================================================================================ TEST checkFortran90FreeForm from config.compilersFortran(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:159) TESTING: checkFortran90FreeForm from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:159) Determine whether the Fortran compiler handles F90FreeForm We also require that the compiler handles lines longer than 132 characters Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: exit code 1 stderr: /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.F90:2:132: INTEGER, PARAMETER :: int = SELECTED_INT_KIND(8); INTEGER (KIND=int) :: ierr; ierr = 1 1 Error: Line truncated at (1) [-Werror=line-truncation] /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.F90:2:110: INTEGER, PARAMETER :: int = SELECTED_INT_KIND(8); INTEGER (KIND=int) :: ierr; ierr = 1 1 Error: Unclassifiable statement at (1) f951: some warnings being treated as errors Source: program main INTEGER, PARAMETER :: int = SELECTED_INT_KIND(8); INTEGER (KIND=int) :: ierr; ierr = 1 end Compile failed inside link Fortran compiler does not support F90FreeForm ================================================================================ TEST checkFortran2003 from config.compilersFortran(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:173) TESTING: checkFortran2003 from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:173) Determine whether the Fortran compiler handles F2003 Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.F90 Successful compile: Source: module Base_module type, public :: base_type integer :: A contains procedure, public :: Print => BasePrint end type base_type contains subroutine BasePrint(this) class(base_type) :: this end subroutine BasePrint end module Base_module program main use,intrinsic :: iso_c_binding Type(C_Ptr),Dimension(:),Pointer :: CArray character(kind=c_char),pointer :: nullc => null() character(kind=c_char,len=5),dimension(:),pointer::list1 allocate(list1(5)) CArray = (/(c_loc(list1(i)),i=1,5),c_loc(nullc)/) end Executing: ftn -o /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.o -lstdc++ -ldl Defined "USING_F2003" to "1" Fortran compiler supports F2003 ================================================================================ TEST checkFortran90Array from config.compilersFortran(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:208) TESTING: checkFortran90Array from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:208) Check for F90 array interfaces Executing: uname -s stdout: Linux Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include void f90arraytest_(void* a1, void* a2,void* a3, void* i) { printf("arrays [%p %p %p]\n",a1,a2,a3); fflush(stdout); return; } void f90ptrtest_(void* a1, void* a2,void* a3, void* i, void* p1 ,void* p2, void* p3) { printf("arrays [%p %p %p]\n",a1,a2,a3); if ((p1 == p3) && (p1 != p2)) { printf("pointers match! [%p %p] [%p]\n",p1,p3,p2); fflush(stdout); } else { printf("pointers do not match! [%p %p] [%p]\n",p1,p3,p2); fflush(stdout); exit(111); } return; } Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.F90 Successful compile: Source: program main Interface Subroutine f90ptrtest(p1,p2,p3,i) integer, pointer :: p1(:,:) integer, pointer :: p2(:,:) integer, pointer :: p3(:,:) integer i End Subroutine End Interface integer, pointer :: ptr1(:,:),ptr2(:,:) integer, target :: array(6:8,9:21) integer in in = 25 ptr1 => array ptr2 => array call f90arraytest(ptr1,ptr2,ptr1,in) call f90ptrtest(ptr1,ptr2,ptr1,in) end Executing: ftn -o /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.o /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/fooobj.o -lstdc++ -ldl Testing executable /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest to see if it can be run Executing: /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest Executing: /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest stdout: arrays [0x7ffe24e18190 0x7ffe24e18190 0x7ffe24e18190] arrays [0x7ffe24e18140 0x7ffe24e180f0 0x7ffe24e18140] pointers do not match! [0x7efdad343740 0x7ffe24e18190] [(nil)] ERROR while running executable: Could not execute "['/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest']": arrays [0x7ffe24e18190 0x7ffe24e18190 0x7ffe24e18190] arrays [0x7ffe24e18140 0x7ffe24e180f0 0x7ffe24e18140] pointers do not match! [0x7efdad343740 0x7ffe24e18190] [(nil)]libhugetlbfs [onyx05.erdc.hpc.mil:31363]: WARNING: Hugepage size 2097152 unavailable compilers: F90 uses a single argument for array pointers ================================================================================ TEST checkFortranModuleInclude from config.compilersFortran(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:295) TESTING: checkFortranModuleInclude from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:295) Figures out what flag is used to specify the include path for Fortran modules Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.F90 Successful compile: Source: module configtest integer testint parameter (testint = 42) end module configtest Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/confdir -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.F90 Successful compile: Source: program main use configtest write(*,*) testint end Executing: ftn -o /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest -dynamic -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/confdir -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.o /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/configtest.o -lstdc++ -ldl compilers: Fortran module include flag -I found ================================================================================ TEST checkFortranModuleOutput from config.compilersFortran(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:361) TESTING: checkFortranModuleOutput from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:361) Figures out what flag is used to specify the include path for Fortran modules Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -module /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/confdir -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: exit code 1 stderr: gfortran: error: unrecognized command line option '-module'; did you mean '-mhle'? Source: module configtest integer testint parameter (testint = 42) end module configtest compilers: Fortran module output flag -module compile failed Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -module:/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/confdir -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: exit code 1 stderr: gfortran: error: unrecognized command line option '-module:/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/confdir' Source: module configtest integer testint parameter (testint = 42) end module configtest compilers: Fortran module output flag -module: compile failed Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fmod=/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/confdir -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: exit code 1 stderr: gfortran: error: unrecognized command line option '-fmod=/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/confdir' Source: module configtest integer testint parameter (testint = 42) end module configtest compilers: Fortran module output flag -fmod= compile failed Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -J/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/confdir -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.F90 Successful compile: Source: module configtest integer testint parameter (testint = 42) end module configtest compilers: Fortran module output flag -J found ================================================================================ TEST checkFortranTypeStar from config.compilersFortran(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:135) TESTING: checkFortranTypeStar from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:135) Determine whether the Fortran compiler handles type(*) Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.F90 Successful compile: Source: program main interface subroutine a(b) type(*) :: b(:) end subroutine end interface end Defined "HAVE_FORTRAN_TYPE_STAR" to "1" Fortran compiler supports type(*) ================================================================================ TEST checkFortranTypeInitialize from config.compilersFortran(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:125) TESTING: checkFortranTypeInitialize from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:125) Determines if PETSc objects in Fortran are initialized by default (doesn't work with common blocks) Defined "FORTRAN_TYPE_INITIALIZE" to " = -2" Initializing Fortran objects ================================================================================ TEST configureFortranFlush from config.compilersFortran(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:116) TESTING: configureFortranFlush from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:116) Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.F90 Successful compile: Source: program main call flush(6) end Executing: ftn -o /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.compilersFortran/conftest.o -lstdc++ -ldl Defined "HAVE_FORTRAN_FLUSH" to "1" ================================================================================ TEST checkDependencyGenerationFlag from config.compilersFortran(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/compilersFortran.py:406) TESTING: checkDependencyGenerationFlag from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:406) Check if -MMD works for dependency generation, and add it if it does Trying FC compiler flag -MMD -MP Defined make macro "FC_DEPFLAGS" to "-MMD -MP" Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -fPIC -O -MMD -MP /p/work/tmondrag/petsc-QqlF3n/config.setCompilers/conftest.F90 Successful compile: Source: program main end child config.compilersFortran 2.895631 ================================================================================ TEST checkStdC from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:105) TESTING: checkStdC from config.headers(config/BuildSystem/config/headers.py:105) Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include int main() { ; return 0; } Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #define ISLOWER(c) ('a' <= (c) && (c) <= 'z') #define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) #define XOR(e, f) (((e) && !(f)) || (!(e) && (f))) int main() { int i; for(i = 0; i < 256; i++) if (XOR(islower(i), ISLOWER(i)) || toupper(i) != TOUPPER(i)) exit(2); exit(0); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.o -lstdc++ -ldl Testing executable /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest to see if it can be run Executing: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest Executing: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest ================================================================================ TEST checkStat from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:138) TESTING: checkStat from config.headers(config/BuildSystem/config/headers.py:138) Checks whether stat file-mode macros are broken, and defines STAT_MACROS_BROKEN if they are Preprocessing source: #include "confdefs.h" #include "conffix.h" #include #include #if defined(S_ISBLK) && defined(S_IFDIR) # if S_ISBLK (S_IFDIR) You lose. # endif #endif #if defined(S_ISBLK) && defined(S_IFCHR) # if S_ISBLK (S_IFCHR) You lose. # endif #endif #if defined(S_ISLNK) && defined(S_IFREG) # if S_ISLNK (S_IFREG) You lose. # endif #endif #if defined(S_ISSOCK) && defined(S_IFREG) # if S_ISSOCK (S_IFREG) You lose. # endif #endif Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c ================================================================================ TEST checkSysWait from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:173) TESTING: checkSysWait from config.headers(config/BuildSystem/config/headers.py:173) Check for POSIX.1 compatible sys/wait.h, and defines HAVE_SYS_WAIT_H if found Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #ifndef WEXITSTATUS #define WEXITSTATUS(stat_val) ((unsigned)(stat_val) >> 8) #endif #ifndef WIFEXITED #define WIFEXITED(stat_val) (((stat_val) & 255) == 0) #endif int main() { int s; wait (&s); s = WIFEXITED (s) ? WEXITSTATUS (s) : 1; ; return 0; } Defined "HAVE_SYS_WAIT_H" to "1" ================================================================================ TEST checkTime from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:195) TESTING: checkTime from config.headers(config/BuildSystem/config/headers.py:195) Checks if you can safely include both and , and if so defines TIME_WITH_SYS_TIME Checking for header: time.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_TIME_H" to "1" Checking for header: sys/time.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_TIME_H" to "1" ================================================================================ TEST checkMath from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:201) TESTING: checkMath from config.headers(config/BuildSystem/config/headers.py:201) Checks for the math headers and defines Checking for header: math.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { double pi = M_PI; if (pi); ; return 0; } Found math #defines, like M_PI ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: setjmp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SETJMP_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: dos.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/confdefs.h" 1 # 2 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conffix.h" 1 # 3 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 stderr: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory #include ^~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory #include ^~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory #include ^~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: fcntl.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FCNTL_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: float.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FLOAT_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: io.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/confdefs.h" 1 # 2 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conffix.h" 1 # 3 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 stderr: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory #include ^~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory #include ^~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory #include ^~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: malloc.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_MALLOC_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: pwd.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_PWD_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: strings.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_STRINGS_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: unistd.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_UNISTD_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/sysinfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_SYSINFO_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: machine/endian.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/confdefs.h" 1 # 2 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conffix.h" 1 # 3 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 stderr: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/param.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_PARAM_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/procfs.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_PROCFS_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/resource.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_RESOURCE_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/systeminfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/confdefs.h" 1 # 2 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conffix.h" 1 # 3 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 stderr: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/times.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_TIMES_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/utsname.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_UTSNAME_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/socket.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_SOCKET_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/wait.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_WAIT_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: netinet/in.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_NETINET_IN_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: netdb.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_NETDB_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: Direct.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/confdefs.h" 1 # 2 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conffix.h" 1 # 3 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 stderr: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory #include ^~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: time.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_TIME_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: Ws2tcpip.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/confdefs.h" 1 # 2 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conffix.h" 1 # 3 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 stderr: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory #include ^~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/types.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_TYPES_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: WindowsX.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/confdefs.h" 1 # 2 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conffix.h" 1 # 3 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 stderr: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory #include ^~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: float.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FLOAT_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: ieeefp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/confdefs.h" 1 # 2 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conffix.h" 1 # 3 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 stderr: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory #include ^~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: stdint.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_STDINT_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: pthread.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_PTHREAD_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: inttypes.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_INTTYPES_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: immintrin.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_IMMINTRIN_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: zmmintrin.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/confdefs.h" 1 # 2 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conffix.h" 1 # 3 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 stderr: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory #include ^~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory #include ^~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory #include ^~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: setjmp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SETJMP_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: dos.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/confdefs.h" 1 # 2 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conffix.h" 1 # 3 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 stderr: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory #include ^~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory #include ^~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory #include ^~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: fcntl.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FCNTL_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: float.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FLOAT_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: io.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/confdefs.h" 1 # 2 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conffix.h" 1 # 3 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 stderr: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory #include ^~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory #include ^~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory #include ^~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: malloc.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_MALLOC_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: pwd.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_PWD_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: strings.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_STRINGS_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: unistd.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_UNISTD_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/sysinfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_SYSINFO_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: machine/endian.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/confdefs.h" 1 # 2 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conffix.h" 1 # 3 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 stderr: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/param.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_PARAM_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/procfs.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_PROCFS_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/resource.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_RESOURCE_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/systeminfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/confdefs.h" 1 # 2 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conffix.h" 1 # 3 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 stderr: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/times.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_TIMES_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/utsname.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_UTSNAME_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/socket.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_SOCKET_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/wait.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_WAIT_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: netinet/in.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_NETINET_IN_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: netdb.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_NETDB_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: Direct.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/confdefs.h" 1 # 2 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conffix.h" 1 # 3 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 stderr: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory #include ^~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: time.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_TIME_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: Ws2tcpip.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/confdefs.h" 1 # 2 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conffix.h" 1 # 3 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 stderr: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory #include ^~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/types.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_TYPES_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: WindowsX.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/confdefs.h" 1 # 2 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conffix.h" 1 # 3 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 stderr: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory #include ^~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory #include ^~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: float.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FLOAT_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: ieeefp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/confdefs.h" 1 # 2 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conffix.h" 1 # 3 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 stderr: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory #include ^~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: stdint.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_STDINT_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: pthread.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_PTHREAD_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: inttypes.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_INTTYPES_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: immintrin.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_IMMINTRIN_H" to "1" ================================================================================ TEST check from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: zmmintrin.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/confdefs.h" 1 # 2 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conffix.h" 1 # 3 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 stderr: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory #include ^~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory #include ^~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory #include ^~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST checkRecursiveMacros from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:216) TESTING: checkRecursiveMacros from config.headers(config/BuildSystem/config/headers.py:216) Checks that the preprocessor allows recursive macros, and if not defines HAVE_BROKEN_RECURSIVE_MACRO Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" void a(int i, int j) {} #define a(b) a(b,__LINE__) int main() { a(0); ; return 0; } child config.headers 9.269236 ================================================================================ TEST configureCacheDetails from config.utilities.cacheDetails(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/utilities/cacheDetails.py:78) TESTING: configureCacheDetails from config.utilities.cacheDetails(config/BuildSystem/config/utilities/cacheDetails.py:78) Try to determine the size and associativity of the cache. All intermediate test results are stored in /p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.headers -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include long getconf_LEVEL1_DCACHE_LINESIZE() { long val = sysconf(_SC_LEVEL1_DCACHE_LINESIZE); return (16 <= val && val <= 2147483647) ? val : 32; } int main() { ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include long getconf_LEVEL1_DCACHE_LINESIZE() { long val = sysconf(_SC_LEVEL1_DCACHE_LINESIZE); return (16 <= val && val <= 2147483647) ? val : 32; } int main() { FILE *output = fopen("conftestval","w"); if (!output) return 1; fprintf(output,"%ld",getconf_LEVEL1_DCACHE_LINESIZE()); fclose(output);; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails/conftest.o -lstdc++ -ldl Testing executable /p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails/conftest to see if it can be run Executing: /p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails/conftest Executing: /p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails/conftest Defined "LEVEL1_DCACHE_LINESIZE" to "64" child config.utilities.cacheDetails 0.428704 ================================================================================ TEST check_struct_sigaction from config.types(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/types.py:43) TESTING: check_struct_sigaction from config.types(config/BuildSystem/config/types.py:43) Checks if "struct sigaction" exists in signal.h. This check is for C89 check. Checking for type: struct sigaction All intermediate test results are stored in /p/work/tmondrag/petsc-QqlF3n/config.types Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include int main() { struct sigaction a;; return 0; } struct sigaction found Defined "HAVE_STRUCT_SIGACTION" to "1" ================================================================================ TEST check__int64 from config.types(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/types.py:49) TESTING: check__int64 from config.types(config/BuildSystem/config/types.py:49) Checks if __int64 exists. This is primarily for windows. Checking for type: __int64 Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.c: In function 'main': /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.c:11:1: error: unknown type name '__int64'; did you mean '__int64_t'? __int64 a;; ^~~~~~~ __int64_t Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { __int64 a;; return 0; } __int64 found ================================================================================ TEST checkSizeTypes from config.types(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/types.py:55) TESTING: checkSizeTypes from config.types(config/BuildSystem/config/types.py:55) Checks for types associated with sizes, such as size_t. Checking for type: size_t Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { size_t a;; return 0; } size_t found ================================================================================ TEST checkFileTypes from config.types(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/types.py:65) TESTING: checkFileTypes from config.types(config/BuildSystem/config/types.py:65) Checks for types associated with files, such as mode_t, off_t, etc. Checking for type: mode_t Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { mode_t a;; return 0; } mode_t found Checking for type: off_t Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { off_t a;; return 0; } off_t found ================================================================================ TEST checkIntegerTypes from config.types(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/types.py:60) TESTING: checkIntegerTypes from config.types(config/BuildSystem/config/types.py:60) Checks for types associated with integers, such as int32_t. Checking for type: int32_t Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { int32_t a;; return 0; } int32_t found ================================================================================ TEST checkPID from config.types(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/types.py:71) TESTING: checkPID from config.types(config/BuildSystem/config/types.py:71) Checks for pid_t, and defines it if necessary Checking for type: pid_t Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { pid_t a;; return 0; } pid_t found ================================================================================ TEST checkUID from config.types(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/types.py:75) TESTING: checkUID from config.types(config/BuildSystem/config/types.py:75) Checks for uid_t and gid_t, and defines them if necessary Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.types /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.c ================================================================================ TEST checkC99Complex from config.types(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/types.py:82) TESTING: checkC99Complex from config.types(config/BuildSystem/config/types.py:82) Check for complex numbers in in C99 std Note that since PETSc source code uses _Complex we test specifically for that, not complex Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { double _Complex x; x = I; ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { double _Complex x; x = I; ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.types/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.o -lstdc++ -ldl Defined "HAVE_C99_COMPLEX" to "1" ================================================================================ TEST checkCxxComplex from config.types(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/types.py:93) TESTING: checkCxxComplex from config.types(config/BuildSystem/config/types.py:93) Check for complex numbers in namespace std Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.types -O -fPIC /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { std::complex x; ; return 0; } Executing: CC -o /p/work/tmondrag/petsc-QqlF3n/config.types/conftest -dynamic -O /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.o -lstdc++ -ldl Defined "HAVE_CXX_COMPLEX" to "1" ================================================================================ TEST checkFortranKind from config.types(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/types.py:114) TESTING: checkFortranKind from config.types(config/BuildSystem/config/types.py:114) Checks whether selected_int_kind etc work USE_FORTRANKIND Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.F90 Successful compile: Source: program main integer(kind=selected_int_kind(10)) i real(kind=selected_real_kind(10)) d end Defined "USE_FORTRANKIND" to "1" ================================================================================ TEST checkConst from config.types(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/types.py:126) TESTING: checkConst from config.types(config/BuildSystem/config/types.py:126) Checks for working const, and if not found defines it to empty string Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { /* Ultrix mips cc rejects this. */ typedef int charset[2]; const charset x; /* SunOS 4.1.1 cc rejects this. */ char const *const *ccp; char **p; /* NEC SVR4.0.2 mips cc rejects this. */ struct point {int x, y;}; static struct point const zero = {0,0}; /* AIX XL C 1.02.0.0 rejects this. It does not let you subtract one const X* pointer from another in an arm of an if-expression whose if-part is not a constant expression */ const char *g = "string"; ccp = &g + (g ? g-g : 0); /* HPUX 7.0 cc rejects these. */ ++ccp; p = (char**) ccp; ccp = (char const *const *) p; /* This section avoids unused variable warnings */ if (zero.x); if (x[0]); { /* SCO 3.2v4 cc rejects this. */ char *t; char const *s = 0 ? (char *) 0 : (char const *) 0; *t++ = 0; if (*s); } { /* Someone thinks the Sun supposedly-ANSI compiler will reject this. */ int x[] = {25, 17}; const int *foo = &x[0]; ++foo; } { /* Sun SC1.0 ANSI compiler rejects this -- but not the above. */ typedef const int *iptr; iptr p = 0; ++p; } { /* AIX XL C 1.02.0.0 rejects this saying "k.c", line 2.27: 1506-025 (S) Operand must be a modifiable lvalue. */ struct s { int j; const int *ap[3]; }; struct s *b; b->j = 5; } { /* ULTRIX-32 V3.1 (Rev 9) vcc rejects this */ const int foo = 10; /* Get rid of unused variable warning */ if (foo); } ; return 0; } ================================================================================ TEST checkSizeof from config.types(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/types.py:182) TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:182) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: short Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(short)==2)*2-1]; Defined "SIZEOF_SHORT" to "2" ================================================================================ TEST checkSizeof from config.types(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/types.py:182) TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:182) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: int Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(int)==4)*2-1]; Defined "SIZEOF_INT" to "4" ================================================================================ TEST checkSizeof from config.types(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/types.py:182) TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:182) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: long Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(long)==8)*2-1]; Defined "SIZEOF_LONG" to "8" ================================================================================ TEST checkSizeof from config.types(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/types.py:182) TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:182) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: void * Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(void *)==8)*2-1]; Defined "SIZEOF_VOID_P" to "8" ================================================================================ TEST checkSizeof from config.types(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/types.py:182) TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:182) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: long long Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(long long)==8)*2-1]; Defined "SIZEOF_LONG_LONG" to "8" ================================================================================ TEST checkSizeof from config.types(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/types.py:182) TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:182) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: size_t Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(size_t)==8)*2-1]; Defined "SIZEOF_SIZE_T" to "8" ================================================================================ TEST checkVisibility from config.types(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/types.py:213) TESTING: checkVisibility from config.types(config/BuildSystem/config/types.py:213) Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { __attribute__((visibility ("default"))) int foo(void);; return 0; } Defined "USE_VISIBILITY_C" to "1" Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.types -O -fPIC /p/work/tmondrag/petsc-QqlF3n/config.types/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { __attribute__((visibility ("default"))) int foo(void);; return 0; } Defined "USE_VISIBILITY_CXX" to "1" child config.types 3.909058 ================================================================================ TEST configureMemAlign from PETSc.options.memAlign(/p/work/tmondrag/moose/petsc/config/PETSc/options/memAlign.py:29) TESTING: configureMemAlign from PETSc.options.memAlign(config/PETSc/options/memAlign.py:29) Choose alignment Defined "MEMALIGN" to "16" Memory alignment is 16 child PETSc.options.memAlign 0.000991 ================================================================================ TEST check from config.libraries(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [handle_sigfpes] in library ['fpe'] [] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char handle_sigfpes(); static void _check_handle_sigfpes() { handle_sigfpes(); } int main() { _check_handle_sigfpes();; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -lfpe -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lfpe collect2: error: ld returned 1 exit status ================================================================================ TEST check from config.libraries(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [socket] in library ['socket', 'nsl'] [] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char socket(); static void _check_socket() { socket(); } int main() { _check_socket();; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -lsocket -lnsl -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lsocket collect2: error: ld returned 1 exit status ================================================================================ TEST check from config.libraries(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [handle_sigfpes] in library ['fpe'] [] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char handle_sigfpes(); static void _check_handle_sigfpes() { handle_sigfpes(); } int main() { _check_handle_sigfpes();; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -lfpe -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lfpe collect2: error: ld returned 1 exit status ================================================================================ TEST check from config.libraries(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [socket] in library ['socket', 'nsl'] [] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char socket(); static void _check_socket() { socket(); } int main() { _check_socket();; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -lsocket -lnsl -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: cannot find -lsocket collect2: error: ld returned 1 exit status ================================================================================ TEST checkMath from config.libraries(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:264) TESTING: checkMath from config.libraries(config/BuildSystem/config/libraries.py:264) Check for sin() in libm, the math library Checking for functions [sin floor log10 pow] in library [''] [] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include double sin(double); static void _check_sin() { double x,y; scanf("%lf",&x); y = sin(x); printf("%f",y); ; } #include double floor(double); static void _check_floor() { double x,y; scanf("%lf",&x); y = floor(x); printf("%f",y); ; } #include double log10(double); static void _check_log10() { double x,y; scanf("%lf",&x); y = log10(x); printf("%f",y); ; } #include double pow(double, double); static void _check_pow() { double x,y; scanf("%lf",&x); y = pow(x,x); printf("%f",y); ; } int main() { _check_sin(); _check_floor(); _check_log10(); _check_pow();; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -lstdc++ -ldl CheckMath: using math library [] ================================================================================ TEST checkMathErf from config.libraries(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:283) TESTING: checkMathErf from config.libraries(config/BuildSystem/config/libraries.py:283) Check for erf() in libm, the math library Checking for functions [erf] in library [] [] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_erf() { double (*checkErf)(double) = erf;double x = 0,y; y = (*checkErf)(x); } int main() { _check_erf();; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -lstdc++ -ldl erf() found Defined "HAVE_ERF" to "1" ================================================================================ TEST checkMathTgamma from config.libraries(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:292) TESTING: checkMathTgamma from config.libraries(config/BuildSystem/config/libraries.py:292) Check for tgamma() in libm, the math library Checking for functions [tgamma] in library [] [] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_tgamma() { double (*checkTgamma)(double) = tgamma;double x = 0,y; y = (*checkTgamma)(x); } int main() { _check_tgamma();; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -lstdc++ -ldl tgamma() found Defined "HAVE_TGAMMA" to "1" ================================================================================ TEST checkMathFenv from config.libraries(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:301) TESTING: checkMathFenv from config.libraries(config/BuildSystem/config/libraries.py:301) Checks if can be used with FE_DFL_ENV Checking for functions [fesetenv] in library [] [] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_fesetenv() { fesetenv(FE_DFL_ENV);; } int main() { _check_fesetenv();; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -lstdc++ -ldl Defined "HAVE_FENV_H" to "1" ================================================================================ TEST checkMathLog2 from config.libraries(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:309) TESTING: checkMathLog2 from config.libraries(config/BuildSystem/config/libraries.py:309) Check for log2() in libm, the math library Checking for functions [log2] in library [] [] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_log2() { double (*checkLog2)(double) = log2; double x = 2.5, y = (*checkLog2)(x); } int main() { _check_log2();; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -lstdc++ -ldl log2() found Defined "HAVE_LOG2" to "1" ================================================================================ TEST checkRealtime from config.libraries(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:318) TESTING: checkRealtime from config.libraries(config/BuildSystem/config/libraries.py:318) Check for presence of clock_gettime() in realtime library (POSIX Realtime extensions) Checking for functions [clock_gettime] in library [''] [] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_clock_gettime() { struct timespec tp; clock_gettime(CLOCK_REALTIME,&tp);; } int main() { _check_clock_gettime();; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -lstdc++ -ldl realtime functions are linked in by default ================================================================================ TEST checkDynamic from config.libraries(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:334) TESTING: checkDynamic from config.libraries(config/BuildSystem/config/libraries.py:334) Check for the header and libraries necessary for dynamic library manipulation Checking for functions [dlopen] in library ['dl'] [] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char dlopen(); static void _check_dlopen() { dlopen(); } int main() { _check_dlopen();; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -ldl -lstdc++ -ldl Defined "HAVE_LIBDL" to "1" Checking for header: dlfcn.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_DLFCN_H" to "1" child config.libraries 2.351877 ================================================================================ TEST configureLibraryOptions from PETSc.options.libraryOptions(/p/work/tmondrag/moose/petsc/config/PETSc/options/libraryOptions.py:37) TESTING: configureLibraryOptions from PETSc.options.libraryOptions(config/PETSc/options/libraryOptions.py:37) Sets PETSC_USE_DEBUG, PETSC_USE_INFO, PETSC_USE_LOG, PETSC_USE_CTABLE, PETSC_USE_FORTRAN_KERNELS, and PETSC_USE_AVX512_KERNELS Defined "USE_LOG" to "1" Executing: cc -qversion Defined "USE_MALLOC_COALESCED" to "1" Defined "USE_INFO" to "1" Defined "USE_CTABLE" to "1" Defined "USE_BACKWARD_LOOP" to "1" **********Checking if running on BGL/IBM detected Checking for functions [bgl_perfctr_void] in library [''] [] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char bgl_perfctr_void(); static void _check_bgl_perfctr_void() { bgl_perfctr_void(); } int main() { _check_bgl_perfctr_void();; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o: in function `main': conftest.c:(.text+0xa): undefined reference to `bgl_perfctr_void' collect2: error: ld returned 1 exit status Checking for functions [ADIOI_BGL_Open] in library [''] [] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char ADIOI_BGL_Open(); static void _check_ADIOI_BGL_Open() { ADIOI_BGL_Open(); } int main() { _check_ADIOI_BGL_Open();; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o: in function `main': conftest.c:(.text+0xa): undefined reference to `ADIOI_BGL_Open' collect2: error: ld returned 1 exit status *********BGL/IBM test failure Defined "USE_AVX512_KERNELS" to "1" Defined "Alignx(a,b)" to " " ================================================================================ TEST configureISColorValueType from PETSc.options.libraryOptions(/p/work/tmondrag/moose/petsc/config/PETSc/options/libraryOptions.py:95) TESTING: configureISColorValueType from PETSc.options.libraryOptions(config/PETSc/options/libraryOptions.py:95) Sets PETSC_IS_COLOR_VALUE_TYPE, MPIU_COLORING_VALUE, IS_COLORING_MAX required by ISColor Defined "MPIU_COLORING_VALUE" to "MPI_UNSIGNED_SHORT" Defined "IS_COLORING_MAX" to "USHRT_MAX" Defined "IS_COLOR_VALUE_TYPE" to "short" Defined "IS_COLOR_VALUE_TYPE_F" to "integer2" child PETSc.options.libraryOptions 0.442056 child config.atomics 0.000010 ================================================================================ TEST checkSysinfo from config.functions(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:106) TESTING: checkSysinfo from config.functions(config/BuildSystem/config/functions.py:106) Check whether sysinfo takes three arguments, and if it does define HAVE_SYSINFO_3ARG Checking for functions [sysinfo] All intermediate test results are stored in /p/work/tmondrag/petsc-QqlF3n/config.functions Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char sysinfo(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_sysinfo) || defined (__stub___sysinfo) sysinfo_will_always_fail_with_ENOSYS(); #else sysinfo(); #endif ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_SYSINFO" to "1" Checking for header: sys/sysinfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_SYSINFO_H" to "1" Checking for header: sys/systeminfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/confdefs.h" 1 # 2 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conffix.h" 1 # 3 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 stderr: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~compilation terminated.: Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c:9:4: error: #error "Cannot check sysinfo without special headers" # error "Cannot check sysinfo without special headers" ^~~~~ /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c: In function 'main': /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c:13:30: warning: implicit declaration of function 'sysinfo' [-Wimplicit-function-declaration] char buf[10]; long count=10; sysinfo(1, buf, count); ^~~~~~~ Source: #include "confdefs.h" #include "conffix.h" #ifdef HAVE_SYS_SYSINFO_H # include #elif defined(HAVE_SYS_SYSTEMINFO_H) # include #else # error "Cannot check sysinfo without special headers" #endif int main() { char buf[10]; long count=10; sysinfo(1, buf, count); ; return 0; } Compile failed inside link ================================================================================ TEST checkVPrintf from config.functions(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:125) TESTING: checkVPrintf from config.functions(config/BuildSystem/config/functions.py:125) Checks whether vprintf requires a char * last argument, and if it does defines HAVE_VPRINTF_CHAR Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { va_list Argp; vprintf( "%d", Argp ); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl ================================================================================ TEST checkVFPrintf from config.functions(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:131) TESTING: checkVFPrintf from config.functions(config/BuildSystem/config/functions.py:131) Checks whether vfprintf requires a char * last argument, and if it does defines HAVE_VFPRINTF_CHAR Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { va_list Argp; vfprintf(stdout, "%d", Argp ); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl ================================================================================ TEST checkVSNPrintf from config.functions(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:137) TESTING: checkVSNPrintf from config.functions(config/BuildSystem/config/functions.py:137) Checks whether vsnprintf requires a char * last argument, and if it does defines HAVE_VSNPRINTF_CHAR Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { va_list Argp;char str[6]; vsnprintf(str,5, "%d", Argp ); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_VSNPRINTF" to "1" ================================================================================ TEST checkNanosleep from config.functions(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:167) TESTING: checkNanosleep from config.functions(config/BuildSystem/config/functions.py:167) Check for functional nanosleep() - as time.h behaves differently for different compiler flags - like -std=c89 Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { struct timespec tp; tp.tv_sec = 0; tp.tv_nsec = (long)(1e9); nanosleep(&tp,0); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_NANOSLEEP" to "1" ================================================================================ TEST checkMemmove from config.functions(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:173) TESTING: checkMemmove from config.functions(config/BuildSystem/config/functions.py:173) Check for functional memmove() - as MS VC requires correct includes to for this test Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { char c1[1], c2[1] = "c"; size_t n=1; memmove(c1,c2,n); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_MEMMOVE" to "1" ================================================================================ TEST checkSignalHandlerType from config.functions(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:143) TESTING: checkSignalHandlerType from config.functions(config/BuildSystem/config/functions.py:143) Checks the type of C++ signals handlers, and defines SIGNAL_CAST to the correct value Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -O -fPIC /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include static void myhandler(int sig) {} int main() { signal(SIGFPE,myhandler); ; return 0; } Executing: CC -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Defined "SIGNAL_CAST" to " " ================================================================================ TEST checkFreeReturnType from config.functions(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:153) TESTING: checkFreeReturnType from config.functions(config/BuildSystem/config/functions.py:153) Checks whether free returns void or int, and defines HAVE_FREE_RETURN_INT Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c: In function 'main': /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c:6:25: error: void value not ignored as it ought to be int ierr; void *p; ierr = free(p); return 0; ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int ierr; void *p; ierr = free(p); return 0; ; return 0; } Compile failed inside link ================================================================================ TEST checkVariableArgumentLists from config.functions(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:159) TESTING: checkVariableArgumentLists from config.functions(config/BuildSystem/config/functions.py:159) Checks whether the variable argument list functionality is working Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { va_list l1, l2; va_copy(l1, l2); return 0; ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_VA_COPY" to "1" ================================================================================ TEST checkClassify from config.functions(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:85) TESTING: checkClassify from config.functions(config/BuildSystem/config/functions.py:85) Recursive decompose to rapidly classify functions as found or missing To confirm that a function is missing, we require a compile/link failure with only that function in a compilation unit. In contrast, we can confirm that many functions are present by compiling them all together in a large compilation unit. We optimistically compile everything together, then trim all functions that were named in the error message and bisect the result. The trimming is only an optimization to increase the likelihood of a big-batch compile succeeding; we do not rely on the compiler naming missing functions. Checking for functions [rand getdomainname _access snprintf realpath dlsym bzero _getcwd getwd uname _lseek sleep _sleep lseek usleep dlclose gethostname clock access _snprintf dlerror fork getpagesize sbreak memalign getcwd gethostbyname readlink _set_output_format PXFGETARG strcasecmp dlopen drand48 socket popen getrusage _mkdir time stricmp] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Possible ERROR while running compiler: stderr: /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c:16:6: warning: conflicting types for built-in function 'snprintf' [-Wbuiltin-declaration-mismatch] char snprintf(); ^~~~~~~~ /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c:19:6: warning: conflicting types for built-in function 'bzero' [-Wbuiltin-declaration-mismatch] char bzero(); ^~~~~ /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c:34:6: warning: conflicting types for built-in function 'fork' [-Wbuiltin-declaration-mismatch] char fork(); ^~~~ /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c:43:6: warning: conflicting types for built-in function 'strcasecmp' [-Wbuiltin-declaration-mismatch] char strcasecmp(); ^~~~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char rand(); char getdomainname(); char _access(); char snprintf(); char realpath(); char dlsym(); char bzero(); char _getcwd(); char getwd(); char uname(); char _lseek(); char sleep(); char _sleep(); char lseek(); char usleep(); char dlclose(); char gethostname(); char clock(); char access(); char _snprintf(); char dlerror(); char fork(); char getpagesize(); char sbreak(); char memalign(); char getcwd(); char gethostbyname(); char readlink(); char _set_output_format(); char PXFGETARG(); char strcasecmp(); char dlopen(); char drand48(); char socket(); char popen(); char getrusage(); char _mkdir(); char time(); char stricmp(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_rand) || defined (__stub___rand) rand_will_always_fail_with_ENOSYS(); #else rand(); #endif #if defined (__stub_getdomainname) || defined (__stub___getdomainname) getdomainname_will_always_fail_with_ENOSYS(); #else getdomainname(); #endif #if defined (__stub__access) || defined (__stub____access) _access_will_always_fail_with_ENOSYS(); #else _access(); #endif #if defined (__stub_snprintf) || defined (__stub___snprintf) snprintf_will_always_fail_with_ENOSYS(); #else snprintf(); #endif #if defined (__stub_realpath) || defined (__stub___realpath) realpath_will_always_fail_with_ENOSYS(); #else realpath(); #endif #if defined (__stub_dlsym) || defined (__stub___dlsym) dlsym_will_always_fail_with_ENOSYS(); #else dlsym(); #endif #if defined (__stub_bzero) || defined (__stub___bzero) bzero_will_always_fail_with_ENOSYS(); #else bzero(); #endif #if defined (__stub__getcwd) || defined (__stub____getcwd) _getcwd_will_always_fail_with_ENOSYS(); #else _getcwd(); #endif #if defined (__stub_getwd) || defined (__stub___getwd) getwd_will_always_fail_with_ENOSYS(); #else getwd(); #endif #if defined (__stub_uname) || defined (__stub___uname) uname_will_always_fail_with_ENOSYS(); #else uname(); #endif #if defined (__stub__lseek) || defined (__stub____lseek) _lseek_will_always_fail_with_ENOSYS(); #else _lseek(); #endif #if defined (__stub_sleep) || defined (__stub___sleep) sleep_will_always_fail_with_ENOSYS(); #else sleep(); #endif #if defined (__stub__sleep) || defined (__stub____sleep) _sleep_will_always_fail_with_ENOSYS(); #else _sleep(); #endif #if defined (__stub_lseek) || defined (__stub___lseek) lseek_will_always_fail_with_ENOSYS(); #else lseek(); #endif #if defined (__stub_usleep) || defined (__stub___usleep) usleep_will_always_fail_with_ENOSYS(); #else usleep(); #endif #if defined (__stub_dlclose) || defined (__stub___dlclose) dlclose_will_always_fail_with_ENOSYS(); #else dlclose(); #endif #if defined (__stub_gethostname) || defined (__stub___gethostname) gethostname_will_always_fail_with_ENOSYS(); #else gethostname(); #endif #if defined (__stub_clock) || defined (__stub___clock) clock_will_always_fail_with_ENOSYS(); #else clock(); #endif #if defined (__stub_access) || defined (__stub___access) access_will_always_fail_with_ENOSYS(); #else access(); #endif #if defined (__stub__snprintf) || defined (__stub____snprintf) _snprintf_will_always_fail_with_ENOSYS(); #else _snprintf(); #endif #if defined (__stub_dlerror) || defined (__stub___dlerror) dlerror_will_always_fail_with_ENOSYS(); #else dlerror(); #endif #if defined (__stub_fork) || defined (__stub___fork) fork_will_always_fail_with_ENOSYS(); #else fork(); #endif #if defined (__stub_getpagesize) || defined (__stub___getpagesize) getpagesize_will_always_fail_with_ENOSYS(); #else getpagesize(); #endif #if defined (__stub_sbreak) || defined (__stub___sbreak) sbreak_will_always_fail_with_ENOSYS(); #else sbreak(); #endif #if defined (__stub_memalign) || defined (__stub___memalign) memalign_will_always_fail_with_ENOSYS(); #else memalign(); #endif #if defined (__stub_getcwd) || defined (__stub___getcwd) getcwd_will_always_fail_with_ENOSYS(); #else getcwd(); #endif #if defined (__stub_gethostbyname) || defined (__stub___gethostbyname) gethostbyname_will_always_fail_with_ENOSYS(); #else gethostbyname(); #endif #if defined (__stub_readlink) || defined (__stub___readlink) readlink_will_always_fail_with_ENOSYS(); #else readlink(); #endif #if defined (__stub__set_output_format) || defined (__stub____set_output_format) _set_output_format_will_always_fail_with_ENOSYS(); #else _set_output_format(); #endif #if defined (__stub_PXFGETARG) || defined (__stub___PXFGETARG) PXFGETARG_will_always_fail_with_ENOSYS(); #else PXFGETARG(); #endif #if defined (__stub_strcasecmp) || defined (__stub___strcasecmp) strcasecmp_will_always_fail_with_ENOSYS(); #else strcasecmp(); #endif #if defined (__stub_dlopen) || defined (__stub___dlopen) dlopen_will_always_fail_with_ENOSYS(); #else dlopen(); #endif #if defined (__stub_drand48) || defined (__stub___drand48) drand48_will_always_fail_with_ENOSYS(); #else drand48(); #endif #if defined (__stub_socket) || defined (__stub___socket) socket_will_always_fail_with_ENOSYS(); #else socket(); #endif #if defined (__stub_popen) || defined (__stub___popen) popen_will_always_fail_with_ENOSYS(); #else popen(); #endif #if defined (__stub_getrusage) || defined (__stub___getrusage) getrusage_will_always_fail_with_ENOSYS(); #else getrusage(); #endif #if defined (__stub__mkdir) || defined (__stub____mkdir) _mkdir_will_always_fail_with_ENOSYS(); #else _mkdir(); #endif #if defined (__stub_time) || defined (__stub___time) time_will_always_fail_with_ENOSYS(); #else time(); #endif #if defined (__stub_stricmp) || defined (__stub___stricmp) stricmp_will_always_fail_with_ENOSYS(); #else stricmp(); #endif ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o: in function `main': conftest.c:(.text+0x5a): warning: the `getwd' function is dangerous and should not be used. /usr/bin/ld: conftest.c:(.text+0x1e): undefined reference to `_access' /usr/bin/ld: conftest.c:(.text+0x50): undefined reference to `_getcwd' /usr/bin/ld: conftest.c:(.text+0x6e): undefined reference to `_lseek' /usr/bin/ld: conftest.c:(.text+0x82): undefined reference to `_sleep' /usr/bin/ld: conftest.c:(.text+0xc8): undefined reference to `_snprintf' /usr/bin/ld: conftest.c:(.text+0xf0): undefined reference to `sbreak' /usr/bin/ld: conftest.c:(.text+0x122): undefined reference to `_set_output_format' /usr/bin/ld: conftest.c:(.text+0x12c): undefined reference to `PXFGETARG' /usr/bin/ld: conftest.c:(.text+0x172): undefined reference to `_mkdir' /usr/bin/ld: conftest.c:(.text+0x186): undefined reference to `stricmp' collect2: error: ld returned 1 exit status Checking for functions [rand getdomainname realpath dlsym bzero uname usleep dlclose gethostname clock dlerror] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Possible ERROR while running compiler: stderr: /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c:17:6: warning: conflicting types for built-in function 'bzero' [-Wbuiltin-declaration-mismatch] char bzero(); ^~~~~ Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char rand(); char getdomainname(); char realpath(); char dlsym(); char bzero(); char uname(); char usleep(); char dlclose(); char gethostname(); char clock(); char dlerror(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_rand) || defined (__stub___rand) rand_will_always_fail_with_ENOSYS(); #else rand(); #endif #if defined (__stub_getdomainname) || defined (__stub___getdomainname) getdomainname_will_always_fail_with_ENOSYS(); #else getdomainname(); #endif #if defined (__stub_realpath) || defined (__stub___realpath) realpath_will_always_fail_with_ENOSYS(); #else realpath(); #endif #if defined (__stub_dlsym) || defined (__stub___dlsym) dlsym_will_always_fail_with_ENOSYS(); #else dlsym(); #endif #if defined (__stub_bzero) || defined (__stub___bzero) bzero_will_always_fail_with_ENOSYS(); #else bzero(); #endif #if defined (__stub_uname) || defined (__stub___uname) uname_will_always_fail_with_ENOSYS(); #else uname(); #endif #if defined (__stub_usleep) || defined (__stub___usleep) usleep_will_always_fail_with_ENOSYS(); #else usleep(); #endif #if defined (__stub_dlclose) || defined (__stub___dlclose) dlclose_will_always_fail_with_ENOSYS(); #else dlclose(); #endif #if defined (__stub_gethostname) || defined (__stub___gethostname) gethostname_will_always_fail_with_ENOSYS(); #else gethostname(); #endif #if defined (__stub_clock) || defined (__stub___clock) clock_will_always_fail_with_ENOSYS(); #else clock(); #endif #if defined (__stub_dlerror) || defined (__stub___dlerror) dlerror_will_always_fail_with_ENOSYS(); #else dlerror(); #endif ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_RAND" to "1" Defined "HAVE_GETDOMAINNAME" to "1" Defined "HAVE_REALPATH" to "1" Defined "HAVE_DLSYM" to "1" Defined "HAVE_BZERO" to "1" Defined "HAVE_UNAME" to "1" Defined "HAVE_USLEEP" to "1" Defined "HAVE_DLCLOSE" to "1" Defined "HAVE_GETHOSTNAME" to "1" Defined "HAVE_CLOCK" to "1" Defined "HAVE_DLERROR" to "1" Checking for functions [fork getpagesize memalign gethostbyname readlink strcasecmp dlopen drand48 socket popen getrusage time] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Possible ERROR while running compiler: stderr: /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c:13:6: warning: conflicting types for built-in function 'fork' [-Wbuiltin-declaration-mismatch] char fork(); ^~~~ /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c:18:6: warning: conflicting types for built-in function 'strcasecmp' [-Wbuiltin-declaration-mismatch] char strcasecmp(); ^~~~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char fork(); char getpagesize(); char memalign(); char gethostbyname(); char readlink(); char strcasecmp(); char dlopen(); char drand48(); char socket(); char popen(); char getrusage(); char time(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_fork) || defined (__stub___fork) fork_will_always_fail_with_ENOSYS(); #else fork(); #endif #if defined (__stub_getpagesize) || defined (__stub___getpagesize) getpagesize_will_always_fail_with_ENOSYS(); #else getpagesize(); #endif #if defined (__stub_memalign) || defined (__stub___memalign) memalign_will_always_fail_with_ENOSYS(); #else memalign(); #endif #if defined (__stub_gethostbyname) || defined (__stub___gethostbyname) gethostbyname_will_always_fail_with_ENOSYS(); #else gethostbyname(); #endif #if defined (__stub_readlink) || defined (__stub___readlink) readlink_will_always_fail_with_ENOSYS(); #else readlink(); #endif #if defined (__stub_strcasecmp) || defined (__stub___strcasecmp) strcasecmp_will_always_fail_with_ENOSYS(); #else strcasecmp(); #endif #if defined (__stub_dlopen) || defined (__stub___dlopen) dlopen_will_always_fail_with_ENOSYS(); #else dlopen(); #endif #if defined (__stub_drand48) || defined (__stub___drand48) drand48_will_always_fail_with_ENOSYS(); #else drand48(); #endif #if defined (__stub_socket) || defined (__stub___socket) socket_will_always_fail_with_ENOSYS(); #else socket(); #endif #if defined (__stub_popen) || defined (__stub___popen) popen_will_always_fail_with_ENOSYS(); #else popen(); #endif #if defined (__stub_getrusage) || defined (__stub___getrusage) getrusage_will_always_fail_with_ENOSYS(); #else getrusage(); #endif #if defined (__stub_time) || defined (__stub___time) time_will_always_fail_with_ENOSYS(); #else time(); #endif ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_FORK" to "1" Defined "HAVE_GETPAGESIZE" to "1" Defined "HAVE_MEMALIGN" to "1" Defined "HAVE_GETHOSTBYNAME" to "1" Defined "HAVE_READLINK" to "1" Defined "HAVE_STRCASECMP" to "1" Defined "HAVE_DLOPEN" to "1" Defined "HAVE_DRAND48" to "1" Defined "HAVE_SOCKET" to "1" Defined "HAVE_POPEN" to "1" Defined "HAVE_GETRUSAGE" to "1" Defined "HAVE_TIME" to "1" Checking for functions [_access] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _access(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__access) || defined (__stub____access) _access_will_always_fail_with_ENOSYS(); #else _access(); #endif ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o: in function `main': conftest.c:(.text+0xa): undefined reference to `_access' collect2: error: ld returned 1 exit status Checking for functions [snprintf] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Possible ERROR while running compiler: stderr: /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c:13:6: warning: conflicting types for built-in function 'snprintf' [-Wbuiltin-declaration-mismatch] char snprintf(); ^~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char snprintf(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_snprintf) || defined (__stub___snprintf) snprintf_will_always_fail_with_ENOSYS(); #else snprintf(); #endif ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_SNPRINTF" to "1" Checking for functions [_getcwd] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _getcwd(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__getcwd) || defined (__stub____getcwd) _getcwd_will_always_fail_with_ENOSYS(); #else _getcwd(); #endif ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o: in function `main': conftest.c:(.text+0xa): undefined reference to `_getcwd' collect2: error: ld returned 1 exit status Checking for functions [getwd] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char getwd(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_getwd) || defined (__stub___getwd) getwd_will_always_fail_with_ENOSYS(); #else getwd(); #endif ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: stderr: /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o: in function `main': conftest.c:(.text+0xa): warning: the `getwd' function is dangerous and should not be used. Defined "HAVE_GETWD" to "1" Checking for functions [_lseek] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _lseek(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__lseek) || defined (__stub____lseek) _lseek_will_always_fail_with_ENOSYS(); #else _lseek(); #endif ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o: in function `main': conftest.c:(.text+0xa): undefined reference to `_lseek' collect2: error: ld returned 1 exit status Checking for functions [sleep] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char sleep(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_sleep) || defined (__stub___sleep) sleep_will_always_fail_with_ENOSYS(); #else sleep(); #endif ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_SLEEP" to "1" Checking for functions [_sleep] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _sleep(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__sleep) || defined (__stub____sleep) _sleep_will_always_fail_with_ENOSYS(); #else _sleep(); #endif ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o: in function `main': conftest.c:(.text+0xa): undefined reference to `_sleep' collect2: error: ld returned 1 exit status Checking for functions [lseek] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char lseek(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_lseek) || defined (__stub___lseek) lseek_will_always_fail_with_ENOSYS(); #else lseek(); #endif ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_LSEEK" to "1" Checking for functions [access] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char access(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_access) || defined (__stub___access) access_will_always_fail_with_ENOSYS(); #else access(); #endif ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_ACCESS" to "1" Checking for functions [_snprintf] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _snprintf(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__snprintf) || defined (__stub____snprintf) _snprintf_will_always_fail_with_ENOSYS(); #else _snprintf(); #endif ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o: in function `main': conftest.c:(.text+0xa): undefined reference to `_snprintf' collect2: error: ld returned 1 exit status Checking for functions [sbreak] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char sbreak(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_sbreak) || defined (__stub___sbreak) sbreak_will_always_fail_with_ENOSYS(); #else sbreak(); #endif ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o: in function `main': conftest.c:(.text+0xa): undefined reference to `sbreak' collect2: error: ld returned 1 exit status Checking for functions [getcwd] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char getcwd(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_getcwd) || defined (__stub___getcwd) getcwd_will_always_fail_with_ENOSYS(); #else getcwd(); #endif ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_GETCWD" to "1" Checking for functions [_set_output_format] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _set_output_format(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__set_output_format) || defined (__stub____set_output_format) _set_output_format_will_always_fail_with_ENOSYS(); #else _set_output_format(); #endif ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o: in function `main': conftest.c:(.text+0xa): undefined reference to `_set_output_format' collect2: error: ld returned 1 exit status Checking for functions [PXFGETARG] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char PXFGETARG(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_PXFGETARG) || defined (__stub___PXFGETARG) PXFGETARG_will_always_fail_with_ENOSYS(); #else PXFGETARG(); #endif ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o: in function `main': conftest.c:(.text+0xa): undefined reference to `PXFGETARG' collect2: error: ld returned 1 exit status Checking for functions [_mkdir] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _mkdir(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__mkdir) || defined (__stub____mkdir) _mkdir_will_always_fail_with_ENOSYS(); #else _mkdir(); #endif ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o: in function `main': conftest.c:(.text+0xa): undefined reference to `_mkdir' collect2: error: ld returned 1 exit status Checking for functions [stricmp] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char stricmp(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_stricmp) || defined (__stub___stricmp) stricmp_will_always_fail_with_ENOSYS(); #else stricmp(); #endif ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o: in function `main': conftest.c:(.text+0xa): undefined reference to `stricmp' collect2: error: ld returned 1 exit status ================================================================================ TEST checkMmap from config.functions(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/functions.py:179) TESTING: checkMmap from config.functions(config/BuildSystem/config/functions.py:179) Check for functional mmap() to allocate shared memory and define HAVE_MMAP Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include int main() { int fd; fd=open("/tmp/file",O_RDWR); mmap((void*)0,100,PROT_READ|PROT_WRITE,MAP_SHARED,fd,0); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_MMAP" to "1" child config.functions 7.296978 ================================================================================ TEST configureMemorySize from config.utilities.getResidentSetSize(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/utilities/getResidentSetSize.py:31) TESTING: configureMemorySize from config.utilities.getResidentSetSize(config/BuildSystem/config/utilities/getResidentSetSize.py:31) Try to determine how to measure the memory usage Defined "USE_PROC_FOR_SIZE" to "1" Using /proc for PetscMemoryGetCurrentUsage() child config.utilities.getResidentSetSize 0.001112 ================================================================================ TEST configureFortranCommandLine from config.utilities.fortranCommandLine(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/utilities/fortranCommandLine.py:27) TESTING: configureFortranCommandLine from config.utilities.fortranCommandLine(config/BuildSystem/config/utilities/fortranCommandLine.py:27) Check for the mechanism to retrieve command line arguments in Fortran Checking for functions [] in library [''] [] Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.F90 Successful compile: Source: program main integer i character*(80) arg i = command_argument_count() call get_command_argument(i,arg) end Executing: ftn -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -lstdc++ -ldl Defined "HAVE_FORTRAN_GET_COMMAND_ARGUMENT" to "1" child config.utilities.fortranCommandLine 0.218043 ================================================================================ TEST configureFeatureTestMacros from config.utilities.featureTestMacros(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/utilities/featureTestMacros.py:13) TESTING: configureFeatureTestMacros from config.utilities.featureTestMacros(config/BuildSystem/config/utilities/featureTestMacros.py:13) Checks if certain feature test macros are support All intermediate test results are stored in /p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros/conftest.c:4:10: fatal error: sysctl.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #define _POSIX_C_SOURCE 200112L #include int main() { ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #define _BSD_SOURCE #include int main() { ; return 0; } Defined "_BSD_SOURCE" to "1" Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #define _DEFAULT_SOURCE #include int main() { ; return 0; } Defined "_DEFAULT_SOURCE" to "1" Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #define _GNU_SOURCE #include int main() { cpu_set_t mset; CPU_ZERO(&mset);; return 0; } Defined "_GNU_SOURCE" to "1" child config.utilities.featureTestMacros 0.653154 ================================================================================ TEST configureMissingUtypeTypedefs from config.utilities.missing(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/utilities/missing.py:55) TESTING: configureMissingUtypeTypedefs from config.utilities.missing(config/BuildSystem/config/utilities/missing.py:55) Checks if u_short is undefined All intermediate test results are stored in /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { u_short foo; ; return 0; } ================================================================================ TEST configureMissingFunctions from config.utilities.missing(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/utilities/missing.py:61) TESTING: configureMissingFunctions from config.utilities.missing(config/BuildSystem/config/utilities/missing.py:61) Checks for SOCKETS ================================================================================ TEST configureMissingSignals from config.utilities.missing(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/utilities/missing.py:79) TESTING: configureMissingSignals from config.utilities.missing(config/BuildSystem/config/utilities/missing.py:79) Check for missing signals, and define MISSING_ if necessary Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGABRT; if (i); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGALRM; if (i); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGBUS; if (i); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGCHLD; if (i); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGCONT; if (i); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGFPE; if (i); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGHUP; if (i); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGILL; if (i); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGINT; if (i); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGKILL; if (i); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGPIPE; if (i); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGQUIT; if (i); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGSEGV; if (i); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGSTOP; if (i); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGSYS; if (i); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGTERM; if (i); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGTRAP; if (i); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGTSTP; if (i); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGURG; if (i); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGUSR1; if (i); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGUSR2; if (i); ; return 0; } ================================================================================ TEST configureMissingGetdomainnamePrototype from config.utilities.missing(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/utilities/missing.py:96) TESTING: configureMissingGetdomainnamePrototype from config.utilities.missing(config/BuildSystem/config/utilities/missing.py:96) Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #if !defined(_BSD_SOURCE) #define _BSD_SOURCE #endif #if !defined(_DEFAULT_SOURCE) #define _DEFAULT_SOURCE #endif #if !defined(_GNU_SOURCE) #define _GNU_SOURCE #endif #ifdef PETSC_HAVE_UNISTD_H #include #endif #ifdef PETSC_HAVE_NETDB_H #include #endif int main() { int (*getdomainname_ptr)(char*,size_t) = getdomainname; char test[10]; if (getdomainname_ptr(test,10)) return 1; ; return 0; } Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -O -fPIC /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #if !defined(_BSD_SOURCE) #define _BSD_SOURCE #endif #if !defined(_DEFAULT_SOURCE) #define _DEFAULT_SOURCE #endif #if !defined(_GNU_SOURCE) #define _GNU_SOURCE #endif #ifdef PETSC_HAVE_UNISTD_H #include #endif #ifdef PETSC_HAVE_NETDB_H #include #endif int main() { int (*getdomainname_ptr)(char*,size_t) = getdomainname; char test[10]; if (getdomainname_ptr(test,10)) return 1; ; return 0; } Executing: CC -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest -dynamic -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -lstdc++ -ldl ================================================================================ TEST configureMissingSrandPrototype from config.utilities.missing(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/utilities/missing.py:121) TESTING: configureMissingSrandPrototype from config.utilities.missing(config/BuildSystem/config/utilities/missing.py:121) Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #if !defined(_BSD_SOURCE) #define _BSD_SOURCE #endif #if !defined(_DEFAULT_SOURCE) #define _DEFAULT_SOURCE #endif #if !defined(_GNU_SOURCE) #define _GNU_SOURCE #endif #include int main() { double (*drand48_ptr)(void) = drand48; void (*srand48_ptr)(long int) = srand48; long int seed=10; srand48_ptr(seed); if (drand48_ptr() > 0.5) return 1; ; return 0; } Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -O -fPIC /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #if !defined(_BSD_SOURCE) #define _BSD_SOURCE #endif #if !defined(_DEFAULT_SOURCE) #define _DEFAULT_SOURCE #endif #if !defined(_GNU_SOURCE) #define _GNU_SOURCE #endif #include int main() { double (*drand48_ptr)(void) = drand48; void (*srand48_ptr)(long int) = srand48; long int seed=10; srand48_ptr(seed); if (drand48_ptr() > 0.5) return 1; ; return 0; } Executing: CC -o /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest -dynamic -O /p/work/tmondrag/petsc-QqlF3n/config.utilities.missing/conftest.o -lstdc++ -ldl child config.utilities.missing 5.218988 ================================================================================ TEST configureFPTrap from config.utilities.FPTrap(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/utilities/FPTrap.py:27) TESTING: configureFPTrap from config.utilities.FPTrap(config/BuildSystem/config/utilities/FPTrap.py:27) Checking the handling of floating point traps Checking for header: sigfpe.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/confdefs.h" 1 # 2 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conffix.h" 1 # 3 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 stderr: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: sigfpe.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: sigfpe.h: No such file or directory #include ^~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: sigfpe.h: No such file or directory #include ^~~~~~~~~~compilation terminated.: Checking for header: fpxcp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/confdefs.h" 1 # 2 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conffix.h" 1 # 3 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 stderr: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: fpxcp.h: No such file or directory #include ^~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: fpxcp.h: No such file or directory #include ^~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: fpxcp.h: No such file or directory #include ^~~~~~~~~compilation terminated.: Checking for header: floatingpoint.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "" # 1 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 1 "" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/confdefs.h" 1 # 2 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 # 1 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conffix.h" 1 # 3 "/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c" 2 stderr: /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: floatingpoint.h: No such file or directory #include ^~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: floatingpoint.h: No such file or directory #include ^~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c:3:10: fatal error: floatingpoint.h: No such file or directory #include ^~~~~~~~~~~~~~~~~compilation terminated.: child config.utilities.FPTrap 0.326699 ================================================================================ TEST configureScalarType from PETSc.options.scalarTypes(/p/work/tmondrag/moose/petsc/config/PETSc/options/scalarTypes.py:40) TESTING: configureScalarType from PETSc.options.scalarTypes(config/PETSc/options/scalarTypes.py:40) Choose between real and complex numbers Scalar type is real All intermediate test results are stored in /p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -fPIC -O /p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { double b = 2.0; int a = isnormal(b); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes/conftest.o -lstdc++ -ldl Defined "HAVE_ISNORMAL" to "1" Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -fPIC -O /p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { double b = 2.0; int a = isnan(b); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes/conftest.o -lstdc++ -ldl Defined "HAVE_ISNAN" to "1" Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -fPIC -O /p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { double b = 2.0; int a = isinf(b); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes/conftest.o -lstdc++ -ldl Defined "HAVE_ISINF" to "1" ================================================================================ TEST configurePrecision from PETSc.options.scalarTypes(/p/work/tmondrag/moose/petsc/config/PETSc/options/scalarTypes.py:81) TESTING: configurePrecision from PETSc.options.scalarTypes(config/PETSc/options/scalarTypes.py:81) Set the default real number precision for PETSc objects Checking C compiler works with __float128 Checking for functions [logq] in library ['quadmath'] [] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_logq() { __float128 f; logq(f);; } int main() { _check_logq();; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_LIBQUADMATH" to "1" C compiler with quadmath library Checking Fortran works with quadmath library Checking for functions [ ] in library ['quadmath'] [] Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.F90 Successful compile: Source: program main real*16 s,w; w = 2.0 ;s = cos(w) end Executing: ftn -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_LIBQUADMATH" to "1" Fortran works with quadmath library Checking for functions [logq] in library ['quadmath'] [] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_logq() { __float128 f; logq(f);; } int main() { _check_logq();; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_LIBQUADMATH" to "1" Adding ['quadmath'] to LIBS Defined "HAVE_REAL___FLOAT128" to "1" Defined "USE_REAL_DOUBLE" to "1" Defined make macro "PETSC_SCALAR_SIZE" to "64" Precision is double child PETSc.options.scalarTypes 1.374887 ================================================================================ TEST configureMkdir from config.programs(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/programs.py:22) TESTING: configureMkdir from config.programs(config/BuildSystem/config/programs.py:22) Make sure we can have mkdir automatically make intermediate directories Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/mkdir...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/mkdir...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/mkdir...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/mkdir...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/mkdir...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/mkdir...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/mkdir...not found Checking for program /opt/gcc/7.2.0/bin/mkdir...not found Checking for program /usr/local/krb5/bin/mkdir...not found Checking for program /usr/local/krb5/openssl/bin/mkdir...not found Checking for program /usr/local/krb5/bin/mkdir...not found Checking for program /usr/local/krb5/openssl/bin/mkdir...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/mkdir...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/mkdir...not found Checking for program /opt/pbs/default/bin/mkdir...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/mkdir...not found Checking for program /opt/java/jdk1.8.0_152/bin/mkdir...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/mkdir...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/mkdir...not found Checking for program /opt/cray/pe/modules/3.2.10.6/bin/mkdir...not found Checking for program /usr/local/bin/mkdir...not found Checking for program /usr/bin/mkdir...found Executing: /usr/bin/mkdir -p .conftest/tmp Adding -p flag to /usr/bin/mkdir -p to automatically create directories Defined make macro "MKDIR" to "/usr/bin/mkdir -p" ================================================================================ TEST configureAutoreconf from config.programs(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/programs.py:44) TESTING: configureAutoreconf from config.programs(config/BuildSystem/config/programs.py:44) Check for autoreconf Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/autoreconf...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/autoreconf...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/autoreconf...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/autoreconf...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/autoreconf...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/autoreconf...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/autoreconf...not found Checking for program /opt/gcc/7.2.0/bin/autoreconf...not found Checking for program /usr/local/krb5/bin/autoreconf...not found Checking for program /usr/local/krb5/openssl/bin/autoreconf...not found Checking for program /usr/local/krb5/bin/autoreconf...not found Checking for program /usr/local/krb5/openssl/bin/autoreconf...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/autoreconf...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/autoreconf...not found Checking for program /opt/pbs/default/bin/autoreconf...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/autoreconf...not found Checking for program /opt/java/jdk1.8.0_152/bin/autoreconf...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/autoreconf...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/autoreconf...not found Checking for program /opt/cray/pe/modules/3.2.10.6/bin/autoreconf...not found Checking for program /usr/local/bin/autoreconf...not found Checking for program /usr/bin/autoreconf...found All intermediate test results are stored in /p/work/tmondrag/petsc-QqlF3n/config.programs Executing: ['/usr/bin/autoreconf'] autoreconf test successful! Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/libtoolize...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/libtoolize...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/libtoolize...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/libtoolize...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/libtoolize...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/libtoolize...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/libtoolize...not found Checking for program /opt/gcc/7.2.0/bin/libtoolize...not found Checking for program /usr/local/krb5/bin/libtoolize...not found Checking for program /usr/local/krb5/openssl/bin/libtoolize...not found Checking for program /usr/local/krb5/bin/libtoolize...not found Checking for program /usr/local/krb5/openssl/bin/libtoolize...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/libtoolize...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/libtoolize...not found Checking for program /opt/pbs/default/bin/libtoolize...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/libtoolize...not found Checking for program /opt/java/jdk1.8.0_152/bin/libtoolize...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/libtoolize...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/libtoolize...not found Checking for program /opt/cray/pe/modules/3.2.10.6/bin/libtoolize...not found Checking for program /usr/local/bin/libtoolize...not found Checking for program /usr/bin/libtoolize...found ================================================================================ TEST configurePrograms from config.programs(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/programs.py:71) TESTING: configurePrograms from config.programs(config/BuildSystem/config/programs.py:71) Check for the programs needed to build and run PETSc Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/sh...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/sh...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/sh...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/sh...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/sh...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/sh...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/sh...not found Checking for program /opt/gcc/7.2.0/bin/sh...not found Checking for program /usr/local/krb5/bin/sh...not found Checking for program /usr/local/krb5/openssl/bin/sh...not found Checking for program /usr/local/krb5/bin/sh...not found Checking for program /usr/local/krb5/openssl/bin/sh...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/sh...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/sh...not found Checking for program /opt/pbs/default/bin/sh...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/sh...not found Checking for program /opt/java/jdk1.8.0_152/bin/sh...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/sh...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/sh...not found Checking for program /opt/cray/pe/modules/3.2.10.6/bin/sh...not found Checking for program /usr/local/bin/sh...not found Checking for program /usr/bin/sh...found Defined make macro "SHELL" to "/usr/bin/sh" Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/sed...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/sed...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/sed...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/sed...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/sed...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/sed...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/sed...not found Checking for program /opt/gcc/7.2.0/bin/sed...not found Checking for program /usr/local/krb5/bin/sed...not found Checking for program /usr/local/krb5/openssl/bin/sed...not found Checking for program /usr/local/krb5/bin/sed...not found Checking for program /usr/local/krb5/openssl/bin/sed...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/sed...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/sed...not found Checking for program /opt/pbs/default/bin/sed...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/sed...not found Checking for program /opt/java/jdk1.8.0_152/bin/sed...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/sed...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/sed...not found Checking for program /opt/cray/pe/modules/3.2.10.6/bin/sed...not found Checking for program /usr/local/bin/sed...not found Checking for program /usr/bin/sed...found Defined make macro "SED" to "/usr/bin/sed" Executing: /usr/bin/sed -i s/sed/sd/g "/p/work/tmondrag/petsc-QqlF3n/config.programs/sed1" Adding SEDINPLACE cmd: /usr/bin/sed -i Defined make macro "SEDINPLACE" to "/usr/bin/sed -i" Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/mv...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/mv...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/mv...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/mv...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/mv...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/mv...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/mv...not found Checking for program /opt/gcc/7.2.0/bin/mv...not found Checking for program /usr/local/krb5/bin/mv...not found Checking for program /usr/local/krb5/openssl/bin/mv...not found Checking for program /usr/local/krb5/bin/mv...not found Checking for program /usr/local/krb5/openssl/bin/mv...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/mv...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/mv...not found Checking for program /opt/pbs/default/bin/mv...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/mv...not found Checking for program /opt/java/jdk1.8.0_152/bin/mv...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/mv...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/mv...not found Checking for program /opt/cray/pe/modules/3.2.10.6/bin/mv...not found Checking for program /usr/local/bin/mv...not found Checking for program /usr/bin/mv...found Defined make macro "MV" to "/usr/bin/mv" Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/cp...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/cp...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/cp...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/cp...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/cp...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/cp...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/cp...not found Checking for program /opt/gcc/7.2.0/bin/cp...not found Checking for program /usr/local/krb5/bin/cp...not found Checking for program /usr/local/krb5/openssl/bin/cp...not found Checking for program /usr/local/krb5/bin/cp...not found Checking for program /usr/local/krb5/openssl/bin/cp...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/cp...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/cp...not found Checking for program /opt/pbs/default/bin/cp...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/cp...not found Checking for program /opt/java/jdk1.8.0_152/bin/cp...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/cp...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/cp...not found Checking for program /opt/cray/pe/modules/3.2.10.6/bin/cp...not found Checking for program /usr/local/bin/cp...not found Checking for program /usr/bin/cp...found Defined make macro "CP" to "/usr/bin/cp" Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/grep...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/grep...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/grep...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/grep...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/grep...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/grep...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/grep...not found Checking for program /opt/gcc/7.2.0/bin/grep...not found Checking for program /usr/local/krb5/bin/grep...not found Checking for program /usr/local/krb5/openssl/bin/grep...not found Checking for program /usr/local/krb5/bin/grep...not found Checking for program /usr/local/krb5/openssl/bin/grep...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/grep...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/grep...not found Checking for program /opt/pbs/default/bin/grep...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/grep...not found Checking for program /opt/java/jdk1.8.0_152/bin/grep...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/grep...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/grep...not found Checking for program /opt/cray/pe/modules/3.2.10.6/bin/grep...not found Checking for program /usr/local/bin/grep...not found Checking for program /usr/bin/grep...found Defined make macro "GREP" to "/usr/bin/grep" Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/rm...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/rm...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/rm...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/rm...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/rm...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/rm...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/rm...not found Checking for program /opt/gcc/7.2.0/bin/rm...not found Checking for program /usr/local/krb5/bin/rm...not found Checking for program /usr/local/krb5/openssl/bin/rm...not found Checking for program /usr/local/krb5/bin/rm...not found Checking for program /usr/local/krb5/openssl/bin/rm...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/rm...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/rm...not found Checking for program /opt/pbs/default/bin/rm...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/rm...not found Checking for program /opt/java/jdk1.8.0_152/bin/rm...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/rm...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/rm...not found Checking for program /opt/cray/pe/modules/3.2.10.6/bin/rm...not found Checking for program /usr/local/bin/rm...not found Checking for program /usr/bin/rm...found Defined make macro "RM" to "/usr/bin/rm -f" Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/diff...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/diff...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/diff...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/diff...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/diff...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/diff...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/diff...not found Checking for program /opt/gcc/7.2.0/bin/diff...not found Checking for program /usr/local/krb5/bin/diff...not found Checking for program /usr/local/krb5/openssl/bin/diff...not found Checking for program /usr/local/krb5/bin/diff...not found Checking for program /usr/local/krb5/openssl/bin/diff...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/diff...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/diff...not found Checking for program /opt/pbs/default/bin/diff...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/diff...not found Checking for program /opt/java/jdk1.8.0_152/bin/diff...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/diff...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/diff...not found Checking for program /opt/cray/pe/modules/3.2.10.6/bin/diff...not found Checking for program /usr/local/bin/diff...not found Checking for program /usr/bin/diff...found Executing: "/usr/bin/diff" -w "/p/work/tmondrag/petsc-QqlF3n/config.programs/diff1" "/p/work/tmondrag/petsc-QqlF3n/config.programs/diff2" Defined make macro "DIFF" to "/usr/bin/diff -w" Checking for program /usr/ucb/ps...not found Checking for program /usr/usb/ps...not found Checking for program /p/home/tmondrag/WORK/moose/scripts/../petsc/lib/petsc/bin/win32fe/ps...not found Defined make macro "PYTHON" to "/usr/bin/python" Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/m4...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/m4...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/m4...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/m4...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/m4...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/m4...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/m4...not found Checking for program /opt/gcc/7.2.0/bin/m4...not found Checking for program /usr/local/krb5/bin/m4...not found Checking for program /usr/local/krb5/openssl/bin/m4...not found Checking for program /usr/local/krb5/bin/m4...not found Checking for program /usr/local/krb5/openssl/bin/m4...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/m4...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/m4...not found Checking for program /opt/pbs/default/bin/m4...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/m4...not found Checking for program /opt/java/jdk1.8.0_152/bin/m4...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/m4...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/m4...not found Checking for program /opt/cray/pe/modules/3.2.10.6/bin/m4...not found Checking for program /usr/local/bin/m4...not found Checking for program /usr/bin/m4...found Defined make macro "M4" to "/usr/bin/m4" child config.programs 2.065866 ================================================================================ TEST configureMake from config.packages.make(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/packages/make.py:87) TESTING: configureMake from config.packages.make(config/BuildSystem/config/packages/make.py:87) Check Guesses for GNU make Executing: gmake --version stdout: GNU Make 4.0 Built for x86_64-unknown-linux-gnu Copyright (C) 1988-2013 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/gmake...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/gmake...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/gmake...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/gmake...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/gmake...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/gmake...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/gmake...not found Checking for program /opt/gcc/7.2.0/bin/gmake...not found Checking for program /usr/local/krb5/bin/gmake...not found Checking for program /usr/local/krb5/openssl/bin/gmake...not found Checking for program /usr/local/krb5/bin/gmake...not found Checking for program /usr/local/krb5/openssl/bin/gmake...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/gmake...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/gmake...not found Checking for program /opt/pbs/default/bin/gmake...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/gmake...not found Checking for program /opt/java/jdk1.8.0_152/bin/gmake...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/gmake...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/gmake...not found Checking for program /opt/cray/pe/modules/3.2.10.6/bin/gmake...not found Checking for program /usr/local/bin/gmake...not found Checking for program /usr/bin/gmake...found Defined make macro "MAKE" to "/usr/bin/gmake" ================================================================================ TEST setupGNUMake from config.packages.make(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/packages/make.py:121) TESTING: setupGNUMake from config.packages.make(config/BuildSystem/config/packages/make.py:121) Setup other GNU make stuff Executing: uname -s stdout: Linux Executing: uname -s stdout: Linux Defined make rule "libc" with dependencies "${LIBNAME}(${OBJSC})" and code [] Defined make rule "libcxx" with dependencies "${LIBNAME}(${OBJSCXX})" and code [] Defined make rule "libcu" with dependencies "${LIBNAME}(${OBJSCU})" and code [] Defined make rule "libf" with dependencies "${OBJSF}" and code -${AR} ${AR_FLAGS} ${LIBNAME} ${OBJSF} Defined make macro "OMAKE_PRINTDIR " to "/usr/bin/gmake --print-directory" Defined make macro "OMAKE" to "/usr/bin/gmake --no-print-directory" Defined make macro "MAKE_PAR_OUT_FLG" to "--output-sync=recurse" ================================================================================ TEST configureMakeNP from config.packages.make(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/packages/make.py:168) TESTING: configureMakeNP from config.packages.make(config/BuildSystem/config/packages/make.py:168) check no of cores on the build machine [perhaps to do make '-j ncores'] module multiprocessing found 44 cores: using make_np = 30 Defined make macro "MAKE_NP" to "30" Defined make macro "MAKE_TEST_NP" to "20" Defined make macro "MAKE_LOAD" to "66.0" Defined make macro "NPMAX" to "44" child config.packages.make 0.028170 ================================================================================ TEST alternateConfigureLibrary from config.packages.OpenMPI(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/package.py:913) TESTING: alternateConfigureLibrary from config.packages.OpenMPI(config/BuildSystem/config/package.py:913) Called if --with-packagename=0; does nothing by default child config.packages.OpenMPI 0.000644 Executing: uname -s stdout: Linux ================================================================================ TEST alternateConfigureLibrary from config.packages.MPICH(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/package.py:913) TESTING: alternateConfigureLibrary from config.packages.MPICH(config/BuildSystem/config/package.py:913) Called if --with-packagename=0; does nothing by default child config.packages.MPICH 0.004902 ================================================================================ TEST checkDependencies from config.packages.MPI(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/package.py:830) TESTING: checkDependencies from config.packages.MPI(config/BuildSystem/config/package.py:830) ================================================================================ TEST configureLibrary from config.packages.MPI(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:581) TESTING: configureLibrary from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:581) ================================================================================== Checking for a functional MPI Checking for library in Compiler specific search MPI: [] ================================================================================ TEST check from config.libraries(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names ================================================================================ TEST check from config.libraries(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [MPI_Init MPI_Comm_create] in library [] [] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char MPI_Init(); static void _check_MPI_Init() { MPI_Init(); } char MPI_Comm_create(); static void _check_MPI_Comm_create() { MPI_Comm_create(); } int main() { _check_MPI_Init(); _check_MPI_Comm_create();; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -lquadmath -lstdc++ -ldl No functions to check for in library [] [] Checking for headers Compiler specific search MPI: [] ================================================================================ TEST checkInclude from config.headers(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/headers.py:86) TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files ['mpi.h'] in [] Checking include with compiler flags var CPPFLAGS [] Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.headers /p/work/tmondrag/petsc-QqlF3n/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Found header files ['mpi.h'] in [] ================================================================================ TEST checkMPICHorOpenMPI from config.packages.MPI(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:468) TESTING: checkMPICHorOpenMPI from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:468) Determine if MPICH_NUMVERSION or OMPI_MAJOR_VERSION exist in mpi.h Used for consistency checking of MPI installation at compile time All intermediate test results are stored in /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c:4:25: error: 'I_MPI_VERSION' undeclared here (not in a function); did you mean 'MPI_VERSION'? const char *mpich_ver = I_MPI_VERSION; ^~~~~~~~~~~~~ MPI_VERSION Source: #include "confdefs.h" #include "conffix.h" #include const char *mpich_ver = I_MPI_VERSION; int main() { ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c:4:17: error: 'I_MPI_NUMVERSION' undeclared here (not in a function); did you mean 'MPI_SUBVERSION'? int mpich_ver = I_MPI_NUMVERSION; ^~~~~~~~~~~~~~~~ MPI_SUBVERSION Source: #include "confdefs.h" #include "conffix.h" #include int mpich_ver = I_MPI_NUMVERSION; int main() { ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c:4:17: error: 'MVAPICH2_NUMVERSION' undeclared here (not in a function); did you mean 'MPICH_NUMVERSION'? int mpich_ver = MVAPICH2_NUMVERSION; ^~~~~~~~~~~~~~~~~~~ MPICH_NUMVERSION Source: #include "confdefs.h" #include "conffix.h" #include int mpich_ver = MVAPICH2_NUMVERSION; int main() { ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int mpich_ver = MPICH_NUMVERSION; int main() { ; return 0; } Preprocessing source: #include "confdefs.h" #include "conffix.h" #include int mpich_ver = MPICH_NUMVERSION; Executing: cc -E -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Defined "HAVE_MPICH_NUMVERSION" to "30200300" Executing: uname -s stdout: Linux ================================================================================ TEST configureMPI2 from config.packages.MPI(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:250) TESTING: configureMPI2 from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:250) Check for functions added to the interface in MPI-2 Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int flag;if (MPI_Finalized(&flag)); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_FINALIZED" to "1" Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { if (MPI_Allreduce(MPI_IN_PLACE,0, 1, MPI_INT, MPI_SUM, MPI_COMM_SELF)); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_IN_PLACE" to "1" Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int count=2; int blocklens[2]={0,1}; MPI_Aint indices[2]={0,1}; MPI_Datatype old_types[2]={0,1}; MPI_Datatype *newtype = 0; if (MPI_Type_create_struct(count, blocklens, indices, old_types, newtype)); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Comm_errhandler_fn * p_err_fun = 0; MPI_Errhandler * p_errhandler = 0; if (MPI_Comm_create_errhandler(p_err_fun,p_errhandler)); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { if (MPI_Comm_set_errhandler(MPI_COMM_WORLD,MPI_ERRORS_RETURN)); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { if (MPI_Reduce_local(0, 0, 0, MPI_INT, MPI_SUM));; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_REDUCE_LOCAL" to "1" Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { char version[MPI_MAX_LIBRARY_VERSION_STRING];int verlen;if (MPI_Get_library_version(version,&verlen)); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_GET_LIBRARY_VERSION" to "1" Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int base[100]; MPI_Win win; if (MPI_Win_create(base,100,4,MPI_INFO_NULL,MPI_COMM_WORLD,&win)); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_WIN_CREATE" to "1" ================================================================================ TEST configureMPI3 from config.packages.MPI(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:292) TESTING: configureMPI3 from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:292) Check for functions added to the interface in MPI-3 Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Comm scomm; MPI_Aint size=128; int disp_unit=8,*baseptr; MPI_Win win; if (MPI_Comm_split_type(MPI_COMM_WORLD, MPI_COMM_TYPE_SHARED, 0, MPI_INFO_NULL, &scomm)); if (MPI_Win_allocate_shared(size,disp_unit,MPI_INFO_NULL,MPI_COMM_WORLD,&baseptr,&win)); if (MPI_Win_shared_query(win,0,&size,&disp_unit,&baseptr)); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_PROCESS_SHARED_MEMORY" to "1" Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int send=0,recv,counts[2]={1,1},displs[2]={1,2}; MPI_Request req; if (MPI_Iscatter(&send,1,MPI_INT,&recv,1,MPI_INT,0,MPI_COMM_WORLD,&req)); if (MPI_Iscatterv(&send,counts,displs,MPI_INT,&recv,1,MPI_INT,0,MPI_COMM_WORLD,&req)); if (MPI_Igather(&send,1,MPI_INT,&recv,1,MPI_INT,0,MPI_COMM_WORLD,&req)); if (MPI_Igatherv(&send,1,MPI_INT,&recv,counts,displs,MPI_INT,0,MPI_COMM_WORLD,&req)); if (MPI_Iallgather(&send,1,MPI_INT,&recv,1,MPI_INT,MPI_COMM_WORLD,&req)); if (MPI_Iallgatherv(&send,1,MPI_INT,&recv,counts,displs,MPI_INT,MPI_COMM_WORLD,&req)); if (MPI_Ialltoall(&send,1,MPI_INT,&recv,1,MPI_INT,MPI_COMM_WORLD,&req)); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_NONBLOCKING_COLLECTIVES" to "1" Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Comm distcomm; MPI_Request req; if (MPI_Dist_graph_create_adjacent(MPI_COMM_WORLD,0,0,MPI_WEIGHTS_EMPTY,0,0,MPI_WEIGHTS_EMPTY,MPI_INFO_NULL,0,&distcomm)); if (MPI_Neighbor_alltoallv(0,0,0,MPI_INT,0,0,0,MPI_INT,distcomm)); if (MPI_Ineighbor_alltoallv(0,0,0,MPI_INT,0,0,0,MPI_INT,distcomm,&req)); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_NEIGHBORHOOD_COLLECTIVES" to "1" ================================================================================ TEST configureMPITypes from config.packages.MPI(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:335) TESTING: configureMPITypes from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:335) Checking for MPI Datatype handles Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_LONG_DOUBLE, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_LONG_DOUBLE, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Testing executable /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest to see if it can be run Executing: /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest Executing: /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest ERROR while running executable: Could not execute "['/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest']": libhugetlbfs [onyx05.erdc.hpc.mil:35617]: WARNING: Hugepage size 2097152 unavailablelibhugetlbfs [onyx05.erdc.hpc.mil:35617]: WARNING: New heap segment map at 0x10000000000 failed: Cannot allocate memory [Mon Dec 16 16:37:35 2019] [unknown] Fatal error in MPI_Init: Other MPI error, error stack: MPIR_Init_thread(537): MPID_Init(249).......: channel initialization failed MPID_Init(638).......: PMI2 init failed: 1 Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_INT64_T, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_INT64_T, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Testing executable /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest to see if it can be run Executing: /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest Executing: /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest ERROR while running executable: Could not execute "['/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest']": libhugetlbfs [onyx05.erdc.hpc.mil:35661]: WARNING: Hugepage size 2097152 unavailablelibhugetlbfs [onyx05.erdc.hpc.mil:35661]: WARNING: New heap segment map at 0x10000000000 failed: Cannot allocate memory [Mon Dec 16 16:37:35 2019] [unknown] Fatal error in MPI_Init: Other MPI error, error stack: MPIR_Init_thread(537): MPID_Init(249).......: channel initialization failed MPID_Init(638).......: PMI2 init failed: 1 Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_C_DOUBLE_COMPLEX, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_C_DOUBLE_COMPLEX, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Testing executable /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest to see if it can be run Executing: /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest Executing: /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest ERROR while running executable: Could not execute "['/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest']": libhugetlbfs [onyx05.erdc.hpc.mil:35705]: WARNING: Hugepage size 2097152 unavailablelibhugetlbfs [onyx05.erdc.hpc.mil:35705]: WARNING: New heap segment map at 0x10000000000 failed: Cannot allocate memory [Mon Dec 16 16:37:36 2019] [unknown] Fatal error in MPI_Init: Other MPI error, error stack: MPIR_Init_thread(537): MPID_Init(249).......: channel initialization failed MPID_Init(638).......: PMI2 init failed: 1 ================================================================================ TEST SGIMPICheck from config.packages.MPI(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:396) TESTING: SGIMPICheck from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:396) Returns true if SGI MPI is used Checking for functions [MPI_SGI_barrier] in library [] [] Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char MPI_SGI_barrier(); static void _check_MPI_SGI_barrier() { MPI_SGI_barrier(); } int main() { _check_MPI_SGI_barrier();; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /usr/bin/ld: /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o: in function `main': conftest.c:(.text+0xa): undefined reference to `MPI_SGI_barrier' collect2: error: ld returned 1 exit status SGI MPI test failure ================================================================================ TEST CxxMPICheck from config.packages.MPI(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:406) TESTING: CxxMPICheck from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:406) Make sure C++ can compile and link Checking for header mpi.h Checking for C++ MPI_Finalize() Checking for functions [MPI_Finalize] in library [] [] Executing: CC -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -O -fPIC /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_MPI_Finalize() { int ierr; ierr = MPI_Finalize();; } int main() { _check_MPI_Finalize();; return 0; } Executing: CC -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -lquadmath -lstdc++ -ldl ================================================================================ TEST FortranMPICheck from config.packages.MPI(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:422) TESTING: FortranMPICheck from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:422) Make sure fortran include [mpif.h] and library symbols are found Checking for fortran mpi_init() Checking for functions [] in library [] [] Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.F90 Successful compile: Source: program main #include "mpif.h" integer ierr call mpi_init(ierr) end Executing: ftn -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Possible ERROR while running linker: stderr: /usr/bin/ld: warning: libgfortran.so.3, needed by /opt/cray/pe/mpt/7.6.3/gni/mpich-gnu/5.1/lib/libmpich_gnu_51.so, may conflict with libgfortran.so.4 /usr/bin/ld: warning: libgfortran.so.3, needed by /opt/cray/pe/mpt/7.6.3/gni/mpich-gnu/5.1/lib/libmpich_gnu_51.so, may conflict with libgfortran.so.4 Checking for mpi.mod Checking for functions [] in library [] [] Executing: ftn -c -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.F90 Successful compile: Source: program main use mpi integer ierr,rank call mpi_init(ierr) call mpi_comm_rank(MPI_COMM_WORLD,rank,ierr) end Executing: ftn -o /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Possible ERROR while running linker: stderr: /usr/bin/ld: warning: libgfortran.so.3, needed by /opt/cray/pe/mpt/7.6.3/gni/mpich-gnu/5.1/lib/libmpich_gnu_51.so, may conflict with libgfortran.so.4 /usr/bin/ld: warning: libgfortran.so.3, needed by /opt/cray/pe/mpt/7.6.3/gni/mpich-gnu/5.1/lib/libmpich_gnu_51.so, may conflict with libgfortran.so.4 Defined "HAVE_MPI_F90MODULE" to "1" ================================================================================ TEST configureIO from config.packages.MPI(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:444) TESTING: configureIO from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:444) Check for the functions in MPI/IO - Define HAVE_MPIIO if they are present - Some older MPI 1 implementations are missing these Executing: cc -c -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -I/p/work/tmondrag/petsc-QqlF3n/config.setCompilers -I/p/work/tmondrag/petsc-QqlF3n/config.compilers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.closure -I/p/work/tmondrag/petsc-QqlF3n/config.compilersFortran -I/p/work/tmondrag/petsc-QqlF3n/config.headers -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.cacheDetails -I/p/work/tmondrag/petsc-QqlF3n/config.types -I/p/work/tmondrag/petsc-QqlF3n/config.functions -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.featureTestMacros -I/p/work/tmondrag/petsc-QqlF3n/config.utilities.missing -I/p/work/tmondrag/petsc-QqlF3n/PETSc.options.scalarTypes -I/p/work/tmondrag/petsc-QqlF3n/config.libraries -I/p/work/tmondrag/petsc-QqlF3n/config.packages.MPI -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Aint lb, extent; if (MPI_Type_get_extent(MPI_INT, &lb, &extent)); MPI_File fh; void *buf; MPI_Status status; if (MPI_File_write_all(fh, buf, 1, MPI_INT, &status)); if (MPI_File_read_all(fh, buf, 1, MPI_INT, &status)); MPI_Offset disp; MPI_Info info; if (MPI_File_set_view(fh, disp, MPI_INT, MPI_INT, "", info)); if (MPI_File_open(MPI_COMM_SELF, "", 0, info, &fh)); if (MPI_File_close(&fh)); ; return 0; } Executing: cc -o /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest -dynamic -fPIC -O /p/work/tmondrag/petsc-QqlF3n/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPIIO" to "1" ================================================================================ TEST findMPIInc from config.packages.MPI(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:522) TESTING: findMPIInc from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:522) Find MPI include paths from "mpicc -show" and use with CUDAC_FLAGS Executing: cc -show ================================================================================ TEST PetscArchMPICheck from config.packages.MPI(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:556) TESTING: PetscArchMPICheck from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:556) ================================================================================ TEST configureMPIEXEC from config.packages.MPI(/p/work/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py:174) TESTING: configureMPIEXEC from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:174) Checking for location of mpiexec Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/mpiexec...not found Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/mpirun...not found Checking for program /p/app/unsupported/COST/valgrind-mpi/3.12.0/gnu/craympt/bin/mprun...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/mpiexec...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/mpirun...not found Checking for program /p/app/unsupported/COST/petsc-cxx-real-mpi/3.7.4/gnu/craympt/bin/mprun...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/mpiexec...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/mpirun...not found Checking for program /opt/cray/pe/perftools/6.5.2/bin/mprun...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/mpiexec...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/mpirun...not found Checking for program /opt/cray/pe/papi/5.5.1.3/bin/mprun...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/mpiexec...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/mpirun...not found Checking for program /opt/cray/rca/2.2.18-6.0.7.1_5.48__g2aa4f39.ari/bin/mprun...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/mpiexec...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/mpirun...not found Checking for program /opt/cray/alps/6.6.43-6.0.7.1_5.46__ga796da32.ari/sbin/mprun...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/mpiexec...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/mpirun...not found Checking for program /opt/cray/job/2.2.3-6.0.7.1_5.44__g6c4e934.ari/bin/mprun...not found Checking for program /opt/gcc/7.2.0/bin/mpiexec...not found Checking for program /opt/gcc/7.2.0/bin/mpirun...not found Checking for program /opt/gcc/7.2.0/bin/mprun...not found Checking for program /usr/local/krb5/bin/mpiexec...not found Checking for program /usr/local/krb5/bin/mpirun...not found Checking for program /usr/local/krb5/bin/mprun...not found Checking for program /usr/local/krb5/openssl/bin/mpiexec...not found Checking for program /usr/local/krb5/openssl/bin/mpirun...not found Checking for program /usr/local/krb5/openssl/bin/mprun...not found Checking for program /usr/local/krb5/bin/mpiexec...not found Checking for program /usr/local/krb5/bin/mpirun...not found Checking for program /usr/local/krb5/bin/mprun...not found Checking for program /usr/local/krb5/openssl/bin/mpiexec...not found Checking for program /usr/local/krb5/openssl/bin/mpirun...not found Checking for program /usr/local/krb5/openssl/bin/mprun...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/mpiexec...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/mpirun...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/sbin/mprun...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/mpiexec...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/mpirun...not found Checking for program /opt/cray/ccm/2.5.4-6.0.7.1_5.27__g394754f.ari/bin/mprun...not found Checking for program /opt/pbs/default/bin/mpiexec...not found Checking for program /opt/pbs/default/bin/mpirun...not found Checking for program /opt/pbs/default/bin/mprun...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/mpiexec...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/mpirun...not found Checking for program /opt/cray/elogin/eproxy/2.0.22-6.0.7.1_7.5__g1ebe45c.ari/bin/mprun...not found Checking for program /opt/java/jdk1.8.0_152/bin/mpiexec...not found Checking for program /opt/java/jdk1.8.0_152/bin/mpirun...not found Checking for program /opt/java/jdk1.8.0_152/bin/mprun...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/mpiexec...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/mpirun...not found Checking for program /opt/cray/pe/mpt/7.6.3/gni/bin/mprun...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/mpiexec...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/mpirun...not found Checking for program /opt/cray/pe/craype/2.5.13/bin/mprun...not found Checking for program /opt/cray/pe/modules/3.2.10.6/bin/mpiexec...not found Checking for program /opt/cray/pe/modules/3.2.10.6/bin/mpirun...not found Checking for program /opt/cray/pe/modules/3.2.10.6/bin/mprun...not found Checking for program /usr/local/bin/mpiexec...not found Checking for program /usr/local/bin/mpirun...not found Checking for program /usr/local/bin/mprun...not found Checking for program /usr/bin/mpiexec...not found Checking for program /usr/bin/mpirun...not found Checking for program /usr/bin/mprun...not found Checking for program /bin/mpiexec...not found Checking for program /bin/mpirun...not found Checking for program /bin/mprun...not found Checking for program /usr/bin/X11/mpiexec...not found Checking for program /usr/bin/X11/mpirun...not found Checking for program /usr/bin/X11/mprun...not found Checking for program /usr/games/mpiexec...not found Checking for program /usr/games/mpirun...not found Checking for program /usr/games/mprun...not found Checking for program /usr/lib/mit/bin/mpiexec...not found Checking for program /usr/lib/mit/bin/mpirun...not found Checking for program /usr/lib/mit/bin/mprun...not found Checking for program /usr/lib/mit/sbin/mpiexec...not found Checking for program /usr/lib/mit/sbin/mpirun...not found Checking for program /usr/lib/mit/sbin/mprun...not found Checking for program /opt/pbs/bin/mpiexec...not found Checking for program /opt/pbs/bin/mpirun...not found Checking for program /opt/pbs/bin/mprun...not found Checking for program /opt/cray/pe/bin/mpiexec...not found Checking for program /opt/cray/pe/bin/mpirun...not found Checking for program /opt/cray/pe/bin/mprun...not found Checking for program /pbs/SLB/mpiexec...not found Checking for program /pbs/SLB/mpirun...not found Checking for program /pbs/SLB/mprun...not found Checking for program /usr/local/man/mpiexec...not found Checking for program /usr/local/man/mpirun...not found Checking for program /usr/local/man/mprun...not found Checking for program /p/app/unsupported/local/bin/mpiexec...not found Checking for program /p/app/unsupported/local/bin/mpirun...not found Checking for program /p/app/unsupported/local/bin/mprun...not found Checking for program /usr/local/applic/COTS/mpiexec...not found Checking for program /usr/local/applic/COTS/mpirun...not found Checking for program /usr/local/applic/COTS/mprun...not found Checking for program /app/mpiutil/mpiexec...not found Checking for program /app/mpiutil/mpirun...not found Checking for program /app/mpiutil/mprun...not found Checking for program /pbs/SLB/mpiexec...not found Checking for program /pbs/SLB/mpirun...not found Checking for program /pbs/SLB/mprun...not found Checking for program /usr/local/man/mpiexec...not found Checking for program /usr/local/man/mpirun...not found Checking for program /usr/local/man/mprun...not found Checking for program /p/app/unsupported/local/bin/mpiexec...not found Checking for program /p/app/unsupported/local/bin/mpirun...not found Checking for program /p/app/unsupported/local/bin/mprun...not found Checking for program /usr/local/applic/COTS/mpiexec...not found Checking for program /usr/local/applic/COTS/mpirun...not found Checking for program /usr/local/applic/COTS/mprun...not found Checking for program /app/mpiutil/mpiexec...not found Checking for program /app/mpiutil/mpirun...not found Checking for program /app/mpiutil/mprun...not found Checking for program /p/home/tmondrag/WORK/moose/scripts/../petsc/lib/petsc/bin/win32fe/mpiexec...not found Checking for program /p/home/tmondrag/WORK/moose/scripts/../petsc/lib/petsc/bin/win32fe/mpirun...not found Checking for program /p/home/tmondrag/WORK/moose/scripts/../petsc/lib/petsc/bin/win32fe/mprun...not found Checking for program /bin/false...found Executing: /bin/false -n 1 printenv **** Configure header /p/work/tmondrag/petsc-QqlF3n/confdefs.h **** #if !defined(INCLUDED_UNKNOWN) #define INCLUDED_UNKNOWN #define IS_COLORING_MAX USHRT_MAX #define MPIU_COLORING_VALUE MPI_UNSIGNED_SHORT #define PETSC_CLANGUAGE_C 1 #define PETSC_HAVE_ERF 1 #define PETSC_HAVE_FENV_H 1 #define PETSC_HAVE_LOG2 1 #define PETSC_HAVE_TGAMMA 1 #define PETSC_CXX_INLINE inline #define PETSC_CXX_RESTRICT __restrict #define PETSC_C_INLINE inline #define PETSC_C_RESTRICT __restrict #define PETSC_FORTRAN_CHARLEN_T int #define PETSC_HAVE_C99 1 #define PETSC_HAVE_CXX_DIALECT_CXX11 1 #define PETSC_HAVE_FORTRAN_UNDERSCORE 1 #define PETSC_HAVE_RTLD_GLOBAL 1 #define PETSC_HAVE_RTLD_LAZY 1 #define PETSC_HAVE_RTLD_LOCAL 1 #define PETSC_HAVE_RTLD_NOW 1 #define PETSC_HAVE_DLFCN_H 1 #define PETSC_HAVE_FCNTL_H 1 #define PETSC_HAVE_FLOAT_H 1 #define PETSC_HAVE_IMMINTRIN_H 1 #define PETSC_HAVE_INTTYPES_H 1 #define PETSC_HAVE_MALLOC_H 1 #define PETSC_HAVE_NETDB_H 1 #define PETSC_HAVE_NETINET_IN_H 1 #define PETSC_HAVE_PTHREAD_H 1 #define PETSC_HAVE_PWD_H 1 #define PETSC_HAVE_SETJMP_H 1 #define PETSC_HAVE_STDINT_H 1 #define PETSC_HAVE_STRINGS_H 1 #define PETSC_HAVE_SYS_PARAM_H 1 #define PETSC_HAVE_SYS_PROCFS_H 1 #define PETSC_HAVE_SYS_RESOURCE_H 1 #define PETSC_HAVE_SYS_SOCKET_H 1 #define PETSC_HAVE_SYS_SYSINFO_H 1 #define PETSC_HAVE_SYS_TIMES_H 1 #define PETSC_HAVE_SYS_TIME_H 1 #define PETSC_HAVE_SYS_TYPES_H 1 #define PETSC_HAVE_SYS_UTSNAME_H 1 #define PETSC_HAVE_SYS_WAIT_H 1 #define PETSC_HAVE_TIME_H 1 #define PETSC_HAVE_UNISTD_H 1 #define PETSC_HAVE_ISINF 1 #define PETSC_HAVE_ISNAN 1 #define PETSC_HAVE_ISNORMAL 1 #define PETSC_HAVE_REAL___FLOAT128 1 #define PETSC_USE_REAL_DOUBLE 1 #define PETSC_HAVE_C99_COMPLEX 1 #define PETSC_HAVE_CXX_COMPLEX 1 #define PETSC_HAVE_STRUCT_SIGACTION 1 #define PETSC_SIZEOF_INT 4 #define PETSC_SIZEOF_LONG 8 #define PETSC_SIZEOF_LONG_LONG 8 #define PETSC_SIZEOF_SHORT 2 #define PETSC_SIZEOF_SIZE_T 8 #define PETSC_SIZEOF_VOID_P 8 #define PETSC_USE_FORTRANKIND 1 #define PETSC_USE_VISIBILITY_C 1 #define PETSC_USE_VISIBILITY_CXX 1 #define PETSC_HAVE_ACCESS 1 #define PETSC_HAVE_BZERO 1 #define PETSC_HAVE_CLOCK 1 #define PETSC_HAVE_DLCLOSE 1 #define PETSC_HAVE_DLERROR 1 #define PETSC_HAVE_DLOPEN 1 #define PETSC_HAVE_DLSYM 1 #define PETSC_HAVE_DRAND48 1 #define PETSC_HAVE_FORK 1 #define PETSC_HAVE_GETCWD 1 #define PETSC_HAVE_GETDOMAINNAME 1 #define PETSC_HAVE_GETHOSTBYNAME 1 #define PETSC_HAVE_GETHOSTNAME 1 #define PETSC_HAVE_GETPAGESIZE 1 #define PETSC_HAVE_GETRUSAGE 1 #define PETSC_HAVE_GETWD 1 #define PETSC_HAVE_LSEEK 1 #define PETSC_HAVE_MEMALIGN 1 #define PETSC_HAVE_MEMMOVE 1 #define PETSC_HAVE_MMAP 1 #define PETSC_HAVE_NANOSLEEP 1 #define PETSC_HAVE_POPEN 1 #define PETSC_HAVE_RAND 1 #define PETSC_HAVE_READLINK 1 #define PETSC_HAVE_REALPATH 1 #define PETSC_HAVE_SLEEP 1 #define PETSC_HAVE_SNPRINTF 1 #define PETSC_HAVE_SOCKET 1 #define PETSC_HAVE_STRCASECMP 1 #define PETSC_HAVE_SYSINFO 1 #define PETSC_HAVE_TIME 1 #define PETSC_HAVE_UNAME 1 #define PETSC_HAVE_USLEEP 1 #define PETSC_HAVE_VA_COPY 1 #define PETSC_HAVE_VSNPRINTF 1 #define PETSC_SIGNAL_CAST #define PETSC_FORTRAN_TYPE_INITIALIZE = -2 #define PETSC_HAVE_FORTRAN_FLUSH 1 #define PETSC_HAVE_FORTRAN_TYPE_STAR 1 #define PETSC_USING_F2003 1 #define PETSC_USING_F90 1 #define PETSC_HAVE_DYNAMIC_LIBRARIES 1 #define PETSC_USE_SHARED_LIBRARIES 1 #define PETSC_USE_DEBUGGER "gdb" #define PETSC_VERSION_BRANCH_GIT "(HEAD detached at 5ea3abfa7f)" #define PETSC_VERSION_DATE_GIT "2019-10-29 13:35:52 +0000" #define PETSC_VERSION_GIT "v3.12.1-23-g5ea3abfa7f" #define PETSC_HAVE_MPICH_NUMVERSION 30200300 #define PETSC_HAVE_MPIIO 1 #define PETSC_HAVE_MPI_F90MODULE 1 #define PETSC_HAVE_MPI_FINALIZED 1 #define PETSC_HAVE_MPI_GET_LIBRARY_VERSION 1 #define PETSC_HAVE_MPI_IN_PLACE 1 #define PETSC_HAVE_MPI_NEIGHBORHOOD_COLLECTIVES 1 #define PETSC_HAVE_MPI_NONBLOCKING_COLLECTIVES 1 #define PETSC_HAVE_MPI_PROCESS_SHARED_MEMORY 1 #define PETSC_HAVE_MPI_REDUCE_LOCAL 1 #define PETSC_HAVE_MPI_WIN_CREATE 1 #define PETSC_Alignx(a,b) #define PETSC_IS_COLOR_VALUE_TYPE short #define PETSC_IS_COLOR_VALUE_TYPE_F integer2 #define PETSC_USE_AVX512_KERNELS 1 #define PETSC_USE_BACKWARD_LOOP 1 #define PETSC_USE_CTABLE 1 #define PETSC_USE_INFO 1 #define PETSC_USE_LOG 1 #define PETSC_USE_MALLOC_COALESCED 1 #define PETSC_MEMALIGN 16 #define PETSC_LEVEL1_DCACHE_LINESIZE 64 #define PETSC__BSD_SOURCE 1 #define PETSC__DEFAULT_SOURCE 1 #define PETSC__GNU_SOURCE 1 #define PETSC_HAVE_FORTRAN_GET_COMMAND_ARGUMENT 1 #define PETSC_USE_PROC_FOR_SIZE 1 #endif **** C specific Configure header /p/work/tmondrag/petsc-QqlF3n/conffix.h **** #if !defined(INCLUDED_UNKNOWN) #define INCLUDED_UNKNOWN #if defined(__cplusplus) extern "C" { } #else #endif #endif ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Unable to run /bin/false with option "-n 1" ******************************************************************************* File "/p/work/tmondrag/moose/petsc/config/configure.py", line 443, in petsc_configure framework.configure(out = sys.stdout) File "/p/work/tmondrag/moose/petsc/config/BuildSystem/config/framework.py", line 1190, in configure self.processChildren() File "/p/work/tmondrag/moose/petsc/config/BuildSystem/config/framework.py", line 1179, in processChildren self.serialEvaluation(self.childGraph) File "/p/work/tmondrag/moose/petsc/config/BuildSystem/config/framework.py", line 1154, in serialEvaluation child.configure() File "/p/work/tmondrag/moose/petsc/config/BuildSystem/config/package.py", line 1083, in configure self.executeTest(self.configureLibrary) File "/p/work/tmondrag/moose/petsc/config/BuildSystem/config/base.py", line 139, in executeTest ret = test(*args,**kargs) File "/p/work/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py", line 604, in configureLibrary self.executeTest(self.configureMPIEXEC) File "/p/work/tmondrag/moose/petsc/config/BuildSystem/config/base.py", line 139, in executeTest ret = test(*args,**kargs) File "/p/work/tmondrag/moose/petsc/config/BuildSystem/config/packages/MPI.py", line 222, in configureMPIEXEC if ret: raise RuntimeError('Unable to run '+self.mpiexec+' with option "-n 1"\n'+err) ================================================================================ Finishing configure run at Mon, 16 Dec 2019 16:37:38 -0600 ================================================================================ From sam.guo at cd-adapco.com Tue Dec 17 10:49:57 2019 From: sam.guo at cd-adapco.com (Sam Guo) Date: Tue, 17 Dec 2019 11:49:57 -0500 Subject: [petsc-users] win32fe icl won't work In-Reply-To: References: Message-ID: It is better but the configuration still failed. On Tue, Dec 17, 2019 at 8:42 AM Balay, Satish wrote: > Alternative is to update PATH so that link.exe from compiler is before the > one from cygwin. > > I have it at '/cygdrive/c/Program Files (x86)/Microsoft Visual Studio > 14.0/VC/BIN/amd64/link.exe' so would do: > > export PATH='/cygdrive/c/Program Files (x86)/Microsoft Visual Studio > 14.0/VC/BIN/amd64':$PATH > > And verify with: > > balay at ps4 ~ > $ which link.exe > /cygdrive/c/Program Files (x86)/Microsoft Visual Studio > 14.0/VC/BIN/amd64/link.exe > > balay at ps4 ~ > $ > > > Satish > > > On Tue, 17 Dec 2019, Sam Guo wrote: > > > I cannot move link.exe: > > $ mv link.exe link_cyg.exe > > mv: cannot move 'link.exe' to 'link_cyg.exe': Permission denied > > > > I figure I need admin privilege. > > > > On Mon, Dec 16, 2019 at 8:30 PM Balay, Satish wrote: > > > > > Try: > > > > > > mv /usr/bin/link.exe /usr/bin/link-cygwin.exe > > > > > > And rerun configure > > > > > > Satish > > > > > > ------ > > > > > > > > > On Mon, 16 Dec 2019, Sam Guo wrote: > > > > > > > Thanks for the quick response. I attach the configure.log again. > > > > > > > > icl is found > > > > $ icl > > > > Intel(R) C++ Intel(R) 64 Compiler for applications running on > Intel(R) > > > 64, > > > > Version 18.0.3.210 Build 20180410 > > > > Copyright (C) 1985-2018 Intel Corporation. All rights reserved. > > > > icl: command line error: no files specified; for help type "icl > /help" > > > > > > > > On Mon, Dec 16, 2019 at 7:03 PM Balay, Satish > wrote: > > > > > > > > > The attached configure.log is a link file. Can you resend the log > from > > > > > PETSC_ARCH/lib/petsc/conf > > > > > > > > > > Also can you verify that you followed instructions from > > > > > > https://www.mcs.anl.gov/petsc/documentation/installation.html#windows > > > > > [its not explicitly specified - but you need to run the correct cmd > > > that > > > > > sets up Intel compiler - instead of the MS compiler] > > > > > > > > > > i.e verify 'icl' works from cygwin/bash - before attempting > configure. > > > > > > > > > > Satish > > > > > > > > > > On Mon, 16 Dec 2019, Sam Guo wrote: > > > > > > > > > > > Dear PETSc dev team, > > > > > > I tried to compile petsc using intel compiler win32fe icl on > > > cygwin > > > > > but > > > > > > encountered error. By the way, I am able to compile using visual > > > studio > > > > > > compiler win32fe cl. > > > > > > > > > > > > > > > > > > > > > =============================================================================== > > > > > > Configuring PETSc to compile on your system > > > > > > > > > > > > > > > =============================================================================== > > > > > > > > > > > > > > > =============================================================================== > > > > > > Warning: "with-clean" is specified. Removing all build files from > > > > > > > > > > > > > > > arch-starccmplus_s=============================================================================== > > > > > > TESTING: checkCCompiler from > > > > > > > > > > > > > > > config.setCompilers(config/BuildSystem/config/setCompilers.py******************************************************************************* > > > > > > UNABLE to CONFIGURE with GIVEN OPTIONS (see > > > configure.log for > > > > > > details): > > > > > > > > > > > > > > > ------------------------------------------------------------------------------- > > > > > > C compiler you provided with -with-cc=win32fe icl does not work. > > > > > > Cannot compile/link C with > > > > > > /home/xianzhongg/dev/star/petsc/lib/petsc/bin/win32fe/win32fe > icl. > > > > > > > > > > > > > > > ******************************************************************************* > > > > > > > > > > > > BR, > > > > > > Sam > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: configure.log Type: application/octet-stream Size: 931265 bytes Desc: not available URL: From balay at mcs.anl.gov Tue Dec 17 10:51:16 2019 From: balay at mcs.anl.gov (Balay, Satish) Date: Tue, 17 Dec 2019 16:51:16 +0000 Subject: [petsc-users] Running moose/scripts/update_and_rebuild_petsc.sh on HPC In-Reply-To: References: <277eb13a-0590-4b1a-a089-09a7c35efd83@googlegroups.com> Message-ID: The recommendation is to use --with-batch=1 if there is working mpiexec Note: the option is --with-mpiexec="mpirun" where "mpirun" would work with "mpirun -n 1 ./binary" Satish On Tue, 17 Dec 2019, Fande Kong wrote: > Are you able to run your MPI code using " mpiexec_mpt -n 1 ./yourbinary"? > You need to use --with-mpiexec to specify what exactly command lines you > can run, e.g., --with-mpiexec="mpirun -n 1". > > I am also CCing the email to PETSc guys who may know the answer to these > questions. > > Thanks, > > Fande, > > On Mon, Dec 16, 2019 at 3:52 PM Tomas Mondragon < > tom.alex.mondragon at gmail.com> wrote: > > > I have attached the configure.log file from when I ran > > update_and_rebuild_petsc.sh on both machines. In the log from jim is from > > an attempt to rebuild after adding --with-mpiexec=mpiexec_mpt to the call > > to pets/configure in the update and rebuild script > > > > -- > > You received this message because you are subscribed to the Google Groups > > "moose-users" group. > > To unsubscribe from this group and stop receiving emails from it, send an > > email to moose-users+unsubscribe at googlegroups.com. > > To view this discussion on the web visit > > https://groups.google.com/d/msgid/moose-users/edd3a169-5012-4e46-a060-5088a199603c%40googlegroups.com > > > > . > > > From balay at mcs.anl.gov Tue Dec 17 10:58:15 2019 From: balay at mcs.anl.gov (Balay, Satish) Date: Tue, 17 Dec 2019 16:58:15 +0000 Subject: [petsc-users] win32fe icl won't work In-Reply-To: References: Message-ID: You don't need --with-batch for this usage [esp with --with-mpi=0] Also suggest using latest petsc version [and update your code to it] Satish On Tue, 17 Dec 2019, Sam Guo wrote: > It is better but the configuration still failed. > > On Tue, Dec 17, 2019 at 8:42 AM Balay, Satish wrote: > > > Alternative is to update PATH so that link.exe from compiler is before the > > one from cygwin. > > > > I have it at '/cygdrive/c/Program Files (x86)/Microsoft Visual Studio > > 14.0/VC/BIN/amd64/link.exe' so would do: > > > > export PATH='/cygdrive/c/Program Files (x86)/Microsoft Visual Studio > > 14.0/VC/BIN/amd64':$PATH > > > > And verify with: > > > > balay at ps4 ~ > > $ which link.exe > > /cygdrive/c/Program Files (x86)/Microsoft Visual Studio > > 14.0/VC/BIN/amd64/link.exe > > > > balay at ps4 ~ > > $ > > > > > > Satish > > > > > > On Tue, 17 Dec 2019, Sam Guo wrote: > > > > > I cannot move link.exe: > > > $ mv link.exe link_cyg.exe > > > mv: cannot move 'link.exe' to 'link_cyg.exe': Permission denied > > > > > > I figure I need admin privilege. > > > > > > On Mon, Dec 16, 2019 at 8:30 PM Balay, Satish wrote: > > > > > > > Try: > > > > > > > > mv /usr/bin/link.exe /usr/bin/link-cygwin.exe > > > > > > > > And rerun configure > > > > > > > > Satish > > > > > > > > ------ > > > > > > > > > > > > On Mon, 16 Dec 2019, Sam Guo wrote: > > > > > > > > > Thanks for the quick response. I attach the configure.log again. > > > > > > > > > > icl is found > > > > > $ icl > > > > > Intel(R) C++ Intel(R) 64 Compiler for applications running on > > Intel(R) > > > > 64, > > > > > Version 18.0.3.210 Build 20180410 > > > > > Copyright (C) 1985-2018 Intel Corporation. All rights reserved. > > > > > icl: command line error: no files specified; for help type "icl > > /help" > > > > > > > > > > On Mon, Dec 16, 2019 at 7:03 PM Balay, Satish > > wrote: > > > > > > > > > > > The attached configure.log is a link file. Can you resend the log > > from > > > > > > PETSC_ARCH/lib/petsc/conf > > > > > > > > > > > > Also can you verify that you followed instructions from > > > > > > > > https://www.mcs.anl.gov/petsc/documentation/installation.html#windows > > > > > > [its not explicitly specified - but you need to run the correct cmd > > > > that > > > > > > sets up Intel compiler - instead of the MS compiler] > > > > > > > > > > > > i.e verify 'icl' works from cygwin/bash - before attempting > > configure. > > > > > > > > > > > > Satish > > > > > > > > > > > > On Mon, 16 Dec 2019, Sam Guo wrote: > > > > > > > > > > > > > Dear PETSc dev team, > > > > > > > I tried to compile petsc using intel compiler win32fe icl on > > > > cygwin > > > > > > but > > > > > > > encountered error. By the way, I am able to compile using visual > > > > studio > > > > > > > compiler win32fe cl. > > > > > > > > > > > > > > > > > > > > > > > > > > =============================================================================== > > > > > > > Configuring PETSc to compile on your system > > > > > > > > > > > > > > > > > > > =============================================================================== > > > > > > > > > > > > > > > > > > > =============================================================================== > > > > > > > Warning: "with-clean" is specified. Removing all build files from > > > > > > > > > > > > > > > > > > > arch-starccmplus_s=============================================================================== > > > > > > > TESTING: checkCCompiler from > > > > > > > > > > > > > > > > > > > config.setCompilers(config/BuildSystem/config/setCompilers.py******************************************************************************* > > > > > > > UNABLE to CONFIGURE with GIVEN OPTIONS (see > > > > configure.log for > > > > > > > details): > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------------- > > > > > > > C compiler you provided with -with-cc=win32fe icl does not work. > > > > > > > Cannot compile/link C with > > > > > > > /home/xianzhongg/dev/star/petsc/lib/petsc/bin/win32fe/win32fe > > icl. > > > > > > > > > > > > > > > > > > > ******************************************************************************* > > > > > > > > > > > > > > BR, > > > > > > > Sam > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > From sam.guo at cd-adapco.com Tue Dec 17 11:00:17 2019 From: sam.guo at cd-adapco.com (Sam Guo) Date: Tue, 17 Dec 2019 12:00:17 -0500 Subject: [petsc-users] win32fe icl won't work In-Reply-To: References: Message-ID: Yes, removing --with-batch works. Thanks a lot. On Tue, Dec 17, 2019 at 11:58 AM Balay, Satish wrote: > You don't need --with-batch for this usage [esp with --with-mpi=0] > > > Also suggest using latest petsc version [and update your code to it] > > Satish > > > On Tue, 17 Dec 2019, Sam Guo wrote: > > > It is better but the configuration still failed. > > > > On Tue, Dec 17, 2019 at 8:42 AM Balay, Satish wrote: > > > > > Alternative is to update PATH so that link.exe from compiler is before > the > > > one from cygwin. > > > > > > I have it at '/cygdrive/c/Program Files (x86)/Microsoft Visual Studio > > > 14.0/VC/BIN/amd64/link.exe' so would do: > > > > > > export PATH='/cygdrive/c/Program Files (x86)/Microsoft Visual Studio > > > 14.0/VC/BIN/amd64':$PATH > > > > > > And verify with: > > > > > > balay at ps4 ~ > > > $ which link.exe > > > /cygdrive/c/Program Files (x86)/Microsoft Visual Studio > > > 14.0/VC/BIN/amd64/link.exe > > > > > > balay at ps4 ~ > > > $ > > > > > > > > > Satish > > > > > > > > > On Tue, 17 Dec 2019, Sam Guo wrote: > > > > > > > I cannot move link.exe: > > > > $ mv link.exe link_cyg.exe > > > > mv: cannot move 'link.exe' to 'link_cyg.exe': Permission denied > > > > > > > > I figure I need admin privilege. > > > > > > > > On Mon, Dec 16, 2019 at 8:30 PM Balay, Satish > wrote: > > > > > > > > > Try: > > > > > > > > > > mv /usr/bin/link.exe /usr/bin/link-cygwin.exe > > > > > > > > > > And rerun configure > > > > > > > > > > Satish > > > > > > > > > > ------ > > > > > > > > > > > > > > > On Mon, 16 Dec 2019, Sam Guo wrote: > > > > > > > > > > > Thanks for the quick response. I attach the configure.log again. > > > > > > > > > > > > icl is found > > > > > > $ icl > > > > > > Intel(R) C++ Intel(R) 64 Compiler for applications running on > > > Intel(R) > > > > > 64, > > > > > > Version 18.0.3.210 Build 20180410 > > > > > > Copyright (C) 1985-2018 Intel Corporation. All rights reserved. > > > > > > icl: command line error: no files specified; for help type "icl > > > /help" > > > > > > > > > > > > On Mon, Dec 16, 2019 at 7:03 PM Balay, Satish > > > > wrote: > > > > > > > > > > > > > The attached configure.log is a link file. Can you resend the > log > > > from > > > > > > > PETSC_ARCH/lib/petsc/conf > > > > > > > > > > > > > > Also can you verify that you followed instructions from > > > > > > > > > > https://www.mcs.anl.gov/petsc/documentation/installation.html#windows > > > > > > > [its not explicitly specified - but you need to run the > correct cmd > > > > > that > > > > > > > sets up Intel compiler - instead of the MS compiler] > > > > > > > > > > > > > > i.e verify 'icl' works from cygwin/bash - before attempting > > > configure. > > > > > > > > > > > > > > Satish > > > > > > > > > > > > > > On Mon, 16 Dec 2019, Sam Guo wrote: > > > > > > > > > > > > > > > Dear PETSc dev team, > > > > > > > > I tried to compile petsc using intel compiler win32fe icl > on > > > > > cygwin > > > > > > > but > > > > > > > > encountered error. By the way, I am able to compile using > visual > > > > > studio > > > > > > > > compiler win32fe cl. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > =============================================================================== > > > > > > > > Configuring PETSc to compile on your system > > > > > > > > > > > > > > > > > > > > > > > > =============================================================================== > > > > > > > > > > > > > > > > > > > > > > > > =============================================================================== > > > > > > > > Warning: "with-clean" is specified. Removing all build files > from > > > > > > > > > > > > > > > > > > > > > > > > arch-starccmplus_s=============================================================================== > > > > > > > > TESTING: checkCCompiler from > > > > > > > > > > > > > > > > > > > > > > > > config.setCompilers(config/BuildSystem/config/setCompilers.py******************************************************************************* > > > > > > > > UNABLE to CONFIGURE with GIVEN OPTIONS (see > > > > > configure.log for > > > > > > > > details): > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------------- > > > > > > > > C compiler you provided with -with-cc=win32fe icl does not > work. > > > > > > > > Cannot compile/link C with > > > > > > > > /home/xianzhongg/dev/star/petsc/lib/petsc/bin/win32fe/win32fe > > > icl. > > > > > > > > > > > > > > > > > > > > > > > > ******************************************************************************* > > > > > > > > > > > > > > > > BR, > > > > > > > > Sam > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mail2amneet at gmail.com Tue Dec 17 12:05:10 2019 From: mail2amneet at gmail.com (Amneet Bhalla) Date: Tue, 17 Dec 2019 10:05:10 -0800 Subject: [petsc-users] Tenure-track faculty positions at San Diego State University Message-ID: Dear Colleagues, Apologies in advance if you are reading these job ads from multiple mailing lists. The Department of Mechanical Engineering at San Diego State University seeks to fill two tenure-track positions at the Assistant Professor level in the areas of computational mechanics and renewable energy conversion and storage starting Fall 2020. Candidates having expertise in large scale computations and state-of-the-art machine learning and data-driven model development techniques in these areas are particularly encouraged to apply. Applicants must have an earned Ph.D. degree in mechanical engineering or a closely related discipline. Applications received by January 20, 2020 will receive full consideration; the position will remain open until filled. Candidates must apply via Interfolio at https://apply.interfolio.com/72480 [computational mechanics position] and https://apply.interfolio.com/72479 [renewable energy conversion and storage position]. Questions related to this search may be addressed to mech.engineering at sdsu.edu. Please refer to the attached job ads for further information. Thanks and kind regards, -- Amneet Bhalla Assistant Professor, Department of Mechanical Engineering San Diego State University 5500 Campanile Drive San Diego, CA 92182 USA Web: https://bhallagroup.wixsite.com/cfdlab -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Computational Mechanics.pdf Type: application/pdf Size: 120830 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Renewable Energy Conversion and Storage.pdf Type: application/pdf Size: 121270 bytes Desc: not available URL: From eda.oktay at metu.edu.tr Wed Dec 18 01:24:41 2019 From: eda.oktay at metu.edu.tr (Eda Oktay) Date: Wed, 18 Dec 2019 10:24:41 +0300 Subject: [petsc-users] Noncomforming object sizes error in MatEqual Message-ID: Hello everyone, In a part of my code, I am trying to understand whether a matrix is equal to its transpose, that is why I am using MatEqual(). However, for most of the matrices I took from University of Florida State Sparse Matrix Library, I get the following error for more than 2 processes, where main() line 155 is MatEqual: [2]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [2]PETSC ERROR: Nonconforming object sizes [2]PETSC ERROR: Mat A,Mat B: global dim 6 6 8 5 [2]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [2]PETSC ERROR: Petsc Release Version 3.11.1, Apr, 12, 2019 [2]PETSC ERROR: ./yeni_vertexweight_imbalance_without_spectral on a arch-linux2-c-debug named d1e.wls.metu.edu.tr by edaoktay Wed Dec 18 10:18:30 2019 [2]PETSC ERROR: Configure options --download-mpich --download-openblas --download-slepc --download-metis --download-parmetis --download-chaco --with-X=1 [2]PETSC ERROR: #1 MatEqual() line 5130 in /home/edaoktay/petsc-3.11.1/src/mat/interface/matrix.c [2]PETSC ERROR: #2 MatEqual_MPIAIJ() line 2112 in /home/edaoktay/petsc-3.11.1/src/mat/impls/aij/mpi/mpiaij.c [2]PETSC ERROR: #3 MatEqual() line 5136 in /home/edaoktay/petsc-3.11.1/src/mat/interface/matrix.c [2]PETSC ERROR: #4 main() line 115 in /home/edaoktay/petsc-3.11.1/arch-linux2-c-debug/share/slepc/examples/src/eda/yeni_vertexweight_imbalance_without_spectral.c [2]PETSC ERROR: PETSc Option Table entries: [2]PETSC ERROR: -f /home/edaoktay/petsc-3.11.1/share/petsc/datafiles/matrices/binary_files/Ragusa16_binary [2]PETSC ERROR: -mat_partitioning_type parmetis [2]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- And this is the part of my code: ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; /* Determine files from which we read matrix */ ierr = PetscOptionsGetString(NULL,NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr); if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate binary file with the -f option"); /* Open binary file. Note that we use FILE_MODE_READ to indicate reading from this file. */ ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr); /* Load the matrix; then destroy the viewer. */ ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr); ierr = MatSetOptionsPrefix(A,"a_");CHKERRQ(ierr); ierr = MatSetFromOptions(A);CHKERRQ(ierr); ierr = MatLoad(A,fd);CHKERRQ(ierr); ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr); /* PetscLogDouble v1,v2,elapsed_time; PetscTime(&v1); */ /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create Partitioning - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = MatConvert(A,MATMPIADJ,MAT_INITIAL_MATRIX,&AL);CHKERRQ(ierr); ierr = MatPartitioningCreate(MPI_COMM_WORLD,&part);CHKERRQ(ierr); ierr = MatPartitioningSetAdjacency(part,AL);CHKERRQ(ierr); /* Symmetry check */ Mat Atr,SymmA,Atrabs,Aabs; PetscBool isEqual; Vec D; PetscInt i; ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&Atr);CHKERRQ(ierr); ierr = MatDuplicate(Atr,MAT_COPY_VALUES,&SymmA);CHKERRQ(ierr); flg = PETSC_TRUE; PetscOptionsGetBool(NULL,NULL, "-check_symmetry", &flg,NULL); if (flg) { ierr = MatEqual(A,Atr,&isEqual);CHKERRQ(ierr); For this specific error, the matrix is of size 24*24. When I checked, I couldn't understand what is wrong when it comes to 3rd process. I will be glad if someone can tell me what is wrong with my code that I get this dimension error. Thanks, Eda -------------- next part -------------- An HTML attachment was scrubbed... URL: From mo7ammedmostafa at gmail.com Wed Dec 18 01:32:24 2019 From: mo7ammedmostafa at gmail.com (Mohammed Mostafa) Date: Wed, 18 Dec 2019 16:32:24 +0900 Subject: [petsc-users] Strange Memory Increase in PCHYPRE BOOMERAMG Message-ID: Hello everyone, I seem to have a problem of increasing memory size with the linear solver. I double check every single part of my code and I isolated the problem to KSPSolve command. A bit of context/background regarding my algorithm. I am writing a finite volume numerical solver for incompressible two phase flow. I am mainly solving liquid sloshing and waves impact problems. Until recently most of simulations were 2D with max cell count of 100K cells but now I am considering solving 3D problems with cell counts between 6M~10M cells. The algorithm is as follows: setup ksp setup pc loop 1 ? number of timesteps 1- // do some work 2- create the pressure poisson matrix 3 ? loop: iloop 1 to 4 4-1- solve the matrix if ( iloop == 1) update the precond 4-2- // do some work 4-3- update rhs(no matrix or precond update) 4- do the next timestep and go back to step 1 *From many online posts many people recommended KSPCG with PCHYPRE with the following options* // PC Setup PCCreate(PETSC_COMM_WORLD, &preconditioner); PCSetType(preconditioner, PCHYPRE); PCHYPRESetType(preconditioner, "boomeramg"); PetscOptionsSetValue(NULL, "-pc_hypre_boomeramg_strong_threshold", "0.4"); PetscOptionsSetValue(NULL, "-pc_hypre_boomeramg_agg_nl", "3"); PetscOptionsSetValue(NULL, "-pc_hypre_boomeramg_agg_num_paths", "4"); PetscOptionsSetValue(NULL, "-pc_hypre_boomeramg_interp_type", "ext+i"); PetscOptionsSetValue(NULL, "-pc_hypre_boomeramg_truncfactor", "0.3"); PetscOptionsSetValue(NULL, "-pc_hypre_boomeramg_max_iter", "1"); PetscOptionsSetValue(NULL, "-pc_hypre_boomeramg_relax_type_all", "SOR/Jacobi"); PetscOptionsSetValue(NULL, "-pc_hypre_boomeramg_grid_sweeps_down", "1"); PetscOptionsSetValue(NULL, "-pc_hypre_boomeramg_max_iter", "1"); PetscOptionsSetValue(NULL, "-pc_hypre_boomeramg_rtol", "0"); KSPSetPC(iterSolver, preconditioner); KSPSetOperators(iterSolver, A, A); // KSP Setup KSPSetType(iterSolver, KSPCG); KSPSetInitialGuessNonzero(iterSolver, PETSC_TRUE); KSPSetNormType(iterSolver, KSP_NORM_UNPRECONDITIONED); KSPSetFromOptions(iterSolver); PCSetUp(preconditioner); KSPSetUp(iterSolver); KSPSetTolerances(iterSolver, 1e-18 /*reltol*/, 1e-12 /*abstol*/, 1e5 /*divergencetol*/, 50); *When solving the linear system for the first time during the timestep (iloop =1), the following commands are used so that the preconditioner is reconstructed based on the new matrix values.* KSPSetReusePreconditioner(iterSolver, PETSC_FALSE); KSPSetOperators(iterSolver, A, A); // set the new matrix KSPSolve(iterSolver, *RHS, *x); *Otherwise* KSPSetReusePreconditioner(iterSolver, PETSC_TRUE); KSPSolve(iterSolver, *RHS, *x); *It should be noted that matrix non-zero structure remains the same throught the simulation but the values change every timestep.* Now My problem is that memory size keep changing throught the simulation utill my workstation evetually runs out of memory. I tracked down the memory increase to the step which solve the linear system of equations. * KSPSetReusePreconditioner(iterSolver, PETSC_FALSE);* * KSPSetOperators(iterSolver, A, A); // set the new matrix* * KSPSolve(iterSolver, *RHS, *x);* My current problem is a sloshing problem with cell count of 1.2M cells running on workstation with 40 Cores and 94GB of RAM. The memory increase I observed did not occur every single time step but more like every 3-10 time step. The increase each time is somewhere from 0.51MB~3.0MB per mpi process and not not all process show memory change. For example in time step id 14 , proc0, proc6, proc13, proc24 show change but the others don?t. On average 10~15 processes show memory change while the others do not. Over 1000 time steps the solver use up additional 10GB of memory and still increasing until the system runs out of memory after nearly 10K time steps. I wanted to try another preconditioner PCJACOBI which ultimately failed due to max number of iterations but at least no memory change was observed over 50 time steps. Since I am using multigrid I expected the increase in memory required by the linear solver, I just assumed that after enough number of timesteps it would settle on some value. But it just kept increasing util finally the system ran out of memory. I monitored the memory usage of other parts/components of the code and no memory change occurs at all except at code section above. I configure PETSC with following options PETSC_ARCH=release3 -with-debugging=0 COPTFLAGS="-O3 -march=native -mtune=native" CXXOPTFLAGS="-O3 -march=native -mtune=native" FOPTFLAGS="-O3 -march=native -mtune=native" --with-cc=mpicc --w ith-cxx=mpicxx --with-fc=mpif90 --download-metis --download-hypre I tried configuring it in debug and compiling my code also in debug mode and running as the FAQ suggests but the code ended up being too slow so I shut it down after running it for 50mins and not even one timestep was completed. So to track down the memory leak/increase I used PetscMemoryGetCurrentUsage(&mem1); // some code PetscMemoryGetCurrentUsage(&mem2); memChnge = mem2 ? mem1; I believe it could be one of the following possibilities: 1. A memory leak (bug) in the petsc library ( unlikely otherwise someone would have found it by now ) 2. Some thing to do with setting of the boomerAMG Hypre preconditioner which makes it unnecessarily add additional levels. The settings I am using, I got from an online post I found so I don?t really understand it. https://mooseframework.inl.gov/application_development/hypre.html 3. Some problem with the sequence of commands I am using for the solution of linear system of eqns that makes allocate additional memory with freeing the old one. Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From eda.oktay at metu.edu.tr Wed Dec 18 04:21:04 2019 From: eda.oktay at metu.edu.tr (Eda Oktay) Date: Wed, 18 Dec 2019 13:21:04 +0300 Subject: [petsc-users] Bad Termination error in MatPartitioningApply with ParMETIS Message-ID: Hi all, I am trying to partition a matrix in multiple processes. However, at some point I get the following eror: [ 0] ***ASSERTION failed on line 176 of file /home/edaoktay/petsc-3.11.1/arch-linux2-c-debug/externalpackages/git.parmetis/libparmetis/comm.c: j == nnbrs [ 2] [ 3] ***ASSERTION failed on line 176 of file /home/edaoktay/petsc-3.11.1/arch-linux2-c-debug/externalpackages/git.parmetis/libparmetis/comm.c: j == nnbrs enson_unweighted_yeni_vertexweight_imbalance_without_spectral: /home/edaoktay/petsc-3.11.1/arch-linux2-c-debug/externalpackages/git.parmetis/libparmetis/comm.c:176: libparmetis__CommSetup: Assertion `j == nnbrs' failed. enson_unweighted_yeni_vertexweight_imbalance_without_spectral: /home/edaoktay/petsc-3.11.1/arch-linux2-c-debug/externalpackages/git.parmetis/libparmetis/comm.c:176: libparmetis__CommSetup: Assertion `j == nnbrs' failed. ***ASSERTION failed on line 176 of file /home/edaoktay/petsc-3.11.1/arch-linux2-c-debug/externalpackages/git.parmetis/libparmetis/comm.c: j == nnbrs enson_unweighted_yeni_vertexweight_imbalance_without_spectral: /home/edaoktay/petsc-3.11.1/arch-linux2-c-debug/externalpackages/git.parmetis/libparmetis/comm.c:176: libparmetis__CommSetup: Assertion `j == nnbrs' failed. =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = PID 13751 RUNNING AT d1e.wls.metu.edu.tr = EXIT CODE: 134 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES =================================================================================== YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6) This typically refers to a problem with your application. Please see the FAQ page for debugging suggestions I get the error for example in 9*9 matrix for 4 processes. Why a I getting this message, it is working with 2 processes for all matrices but when I increase process number, it starts to give this message at some point. Thanks! Eda -------------- next part -------------- An HTML attachment was scrubbed... URL: From eda.oktay at metu.edu.tr Wed Dec 18 05:42:15 2019 From: eda.oktay at metu.edu.tr (Eda Oktay) Date: Wed, 18 Dec 2019 14:42:15 +0300 Subject: [petsc-users] Noncomforming object sizes error in MatEqual In-Reply-To: References: Message-ID: Hi all, I solved the problem by using different routine. Thanks anyway! Eda Eda Oktay , 18 Ara 2019 ?ar, 10:24 tarihinde ?unu yazd?: > Hello everyone, > > In a part of my code, I am trying to understand whether a matrix is equal > to its transpose, that is why I am using MatEqual(). However, for most of > the matrices I took from University of Florida State Sparse Matrix Library, > I get the following error for more than 2 processes, where main() line 155 > is MatEqual: > > [2]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [2]PETSC ERROR: Nonconforming object sizes > [2]PETSC ERROR: Mat A,Mat B: global dim 6 6 8 5 > [2]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > [2]PETSC ERROR: Petsc Release Version 3.11.1, Apr, 12, 2019 > [2]PETSC ERROR: ./yeni_vertexweight_imbalance_without_spectral on a > arch-linux2-c-debug named d1e.wls.metu.edu.tr by edaoktay Wed Dec 18 > 10:18:30 2019 > [2]PETSC ERROR: Configure options --download-mpich --download-openblas > --download-slepc --download-metis --download-parmetis --download-chaco > --with-X=1 > [2]PETSC ERROR: #1 MatEqual() line 5130 in > /home/edaoktay/petsc-3.11.1/src/mat/interface/matrix.c > [2]PETSC ERROR: #2 MatEqual_MPIAIJ() line 2112 in > /home/edaoktay/petsc-3.11.1/src/mat/impls/aij/mpi/mpiaij.c > [2]PETSC ERROR: #3 MatEqual() line 5136 in > /home/edaoktay/petsc-3.11.1/src/mat/interface/matrix.c > [2]PETSC ERROR: #4 main() line 115 in > /home/edaoktay/petsc-3.11.1/arch-linux2-c-debug/share/slepc/examples/src/eda/yeni_vertexweight_imbalance_without_spectral.c > [2]PETSC ERROR: PETSc Option Table entries: > [2]PETSC ERROR: -f > /home/edaoktay/petsc-3.11.1/share/petsc/datafiles/matrices/binary_files/Ragusa16_binary > [2]PETSC ERROR: -mat_partitioning_type parmetis > [2]PETSC ERROR: ----------------End of Error Message -------send entire > error message to petsc-maint at mcs.anl.gov---------- > > And this is the part of my code: > > ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; > > /* > Determine files from which we read matrix > */ > > ierr = > PetscOptionsGetString(NULL,NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr); > if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate binary file with the > -f option"); > > /* > Open binary file. Note that we use FILE_MODE_READ to indicate > reading from this file. > */ > > ierr = > PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr); > > /* > Load the matrix; then destroy the viewer. > */ > > ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr); > > ierr = MatSetOptionsPrefix(A,"a_");CHKERRQ(ierr); > ierr = MatSetFromOptions(A);CHKERRQ(ierr); > ierr = MatLoad(A,fd);CHKERRQ(ierr); > ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr); > > /* PetscLogDouble v1,v2,elapsed_time; > > PetscTime(&v1); */ > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > Create Partitioning > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > ierr = MatConvert(A,MATMPIADJ,MAT_INITIAL_MATRIX,&AL);CHKERRQ(ierr); > > > ierr = MatPartitioningCreate(MPI_COMM_WORLD,&part);CHKERRQ(ierr); > ierr = MatPartitioningSetAdjacency(part,AL);CHKERRQ(ierr); > > /* Symmetry check */ > > Mat Atr,SymmA,Atrabs,Aabs; > PetscBool isEqual; > Vec D; > PetscInt i; > > ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&Atr);CHKERRQ(ierr); > ierr = MatDuplicate(Atr,MAT_COPY_VALUES,&SymmA);CHKERRQ(ierr); > flg = PETSC_TRUE; > > PetscOptionsGetBool(NULL,NULL, "-check_symmetry", &flg,NULL); > if (flg) { > ierr = MatEqual(A,Atr,&isEqual);CHKERRQ(ierr); > > For this specific error, the matrix is of size 24*24. When I checked, I > couldn't understand what is wrong when it comes to 3rd process. I will be > glad if someone can tell me what is wrong with my code that I get this > dimension error. > > Thanks, > > Eda > -------------- next part -------------- An HTML attachment was scrubbed... URL: From eda.oktay at metu.edu.tr Wed Dec 18 05:42:34 2019 From: eda.oktay at metu.edu.tr (Eda Oktay) Date: Wed, 18 Dec 2019 14:42:34 +0300 Subject: [petsc-users] Bad Termination error in MatPartitioningApply with ParMETIS In-Reply-To: References: Message-ID: Hi all, I solved the problem by using different routine. Thanks anyway! Eda Eda Oktay , 18 Ara 2019 ?ar, 13:21 tarihinde ?unu yazd?: > Hi all, > > I am trying to partition a matrix in multiple processes. However, at some > point I get the following eror: > > [ 0] ***ASSERTION failed on line 176 of file > /home/edaoktay/petsc-3.11.1/arch-linux2-c-debug/externalpackages/git.parmetis/libparmetis/comm.c: > j == nnbrs > [ 2] [ 3] ***ASSERTION failed on line 176 of file > /home/edaoktay/petsc-3.11.1/arch-linux2-c-debug/externalpackages/git.parmetis/libparmetis/comm.c: > j == nnbrs > enson_unweighted_yeni_vertexweight_imbalance_without_spectral: > /home/edaoktay/petsc-3.11.1/arch-linux2-c-debug/externalpackages/git.parmetis/libparmetis/comm.c:176: > libparmetis__CommSetup: Assertion `j == nnbrs' failed. > enson_unweighted_yeni_vertexweight_imbalance_without_spectral: > /home/edaoktay/petsc-3.11.1/arch-linux2-c-debug/externalpackages/git.parmetis/libparmetis/comm.c:176: > libparmetis__CommSetup: Assertion `j == nnbrs' failed. > ***ASSERTION failed on line 176 of file > /home/edaoktay/petsc-3.11.1/arch-linux2-c-debug/externalpackages/git.parmetis/libparmetis/comm.c: > j == nnbrs > enson_unweighted_yeni_vertexweight_imbalance_without_spectral: > /home/edaoktay/petsc-3.11.1/arch-linux2-c-debug/externalpackages/git.parmetis/libparmetis/comm.c:176: > libparmetis__CommSetup: Assertion `j == nnbrs' failed. > > > =================================================================================== > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = PID 13751 RUNNING AT d1e.wls.metu.edu.tr > = EXIT CODE: 134 > = CLEANING UP REMAINING PROCESSES > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > > =================================================================================== > YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6) > This typically refers to a problem with your application. > Please see the FAQ page for debugging suggestions > > I get the error for example in 9*9 matrix for 4 processes. Why a I getting > this message, it is working with 2 processes for all matrices but when I > increase process number, it starts to give this message at some point. > > Thanks! > > Eda > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Wed Dec 18 09:00:33 2019 From: bsmith at mcs.anl.gov (Smith, Barry F.) Date: Wed, 18 Dec 2019 15:00:33 +0000 Subject: [petsc-users] Bad Termination error in MatPartitioningApply with ParMETIS In-Reply-To: References: Message-ID: Can you please send use the exact code and data file that causes the crash? And any options. There are bugs in Metis/Parmetis that we need to track down and eliminate since it is so central to PETSc's work flow. Barry > On Dec 18, 2019, at 4:21 AM, Eda Oktay wrote: > > Hi all, > > I am trying to partition a matrix in multiple processes. However, at some point I get the following eror: > > [ 0] ***ASSERTION failed on line 176 of file /home/edaoktay/petsc-3.11.1/arch-linux2-c-debug/externalpackages/git.parmetis/libparmetis/comm.c: j == nnbrs > [ 2] [ 3] ***ASSERTION failed on line 176 of file /home/edaoktay/petsc-3.11.1/arch-linux2-c-debug/externalpackages/git.parmetis/libparmetis/comm.c: j == nnbrs > enson_unweighted_yeni_vertexweight_imbalance_without_spectral: /home/edaoktay/petsc-3.11.1/arch-linux2-c-debug/externalpackages/git.parmetis/libparmetis/comm.c:176: libparmetis__CommSetup: Assertion `j == nnbrs' failed. > enson_unweighted_yeni_vertexweight_imbalance_without_spectral: /home/edaoktay/petsc-3.11.1/arch-linux2-c-debug/externalpackages/git.parmetis/libparmetis/comm.c:176: libparmetis__CommSetup: Assertion `j == nnbrs' failed. > ***ASSERTION failed on line 176 of file /home/edaoktay/petsc-3.11.1/arch-linux2-c-debug/externalpackages/git.parmetis/libparmetis/comm.c: j == nnbrs > enson_unweighted_yeni_vertexweight_imbalance_without_spectral: /home/edaoktay/petsc-3.11.1/arch-linux2-c-debug/externalpackages/git.parmetis/libparmetis/comm.c:176: libparmetis__CommSetup: Assertion `j == nnbrs' failed. > > =================================================================================== > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = PID 13751 RUNNING AT d1e.wls.metu.edu.tr > = EXIT CODE: 134 > = CLEANING UP REMAINING PROCESSES > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > =================================================================================== > YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6) > This typically refers to a problem with your application. > Please see the FAQ page for debugging suggestions > > I get the error for example in 9*9 matrix for 4 processes. Why a I getting this message, it is working with 2 processes for all matrices but when I increase process number, it starts to give this message at some point. > > Thanks! > > Eda From griesser.jan at googlemail.com Wed Dec 18 10:58:15 2019 From: griesser.jan at googlemail.com (=?UTF-8?B?SmFuIEdyaWXDn2Vy?=) Date: Wed, 18 Dec 2019 17:58:15 +0100 Subject: [petsc-users] Corrrect usage of MatMumpsGetInverse() In-Reply-To: References: Message-ID: Hey, i tested the fix today and ran the same code as above. It is now working fine and my results are in agreement with my analytical solutions. Although i have to tranpose the computed entries afterwards. This should be the correct behaviour or ? ierr = MatTranspose(spRHST, MAT_INPLACE_MATRIX, &spRHST);CHKERRQ(ierr); Am Mo., 16. Dez. 2019 um 22:57 Uhr schrieb Zhang, Hong : > Jan: > You found a bug in our interface. I pushed a fix > https://gitlab.com/petsc/petsc/commit/6fa4709e1488f7c58b0a4ecbdf34b75ae4ac64d2 > in branch hzhang/fix-mumps-GetInverse. > You may give it a try by 'git checkout hzhang/fix-mumps-GetInverse' at > PETSC_DIR and rebuild petsc. > Let me know if it fixes the issue. > Hong > > Hello, everybody, >> I am using PETSc version 3.12 together with MUMPS to calculate a part of >> an inverse from a matrix A. For this I used the example >> mat/examples/tests/ex214.c as suggested here in the forum. For test >> purposes I read a matrix with the dimension 10x10, which only has entries >> on the main diagonal, because I know the inverse of it. >> But now I have a problem using the MatMumpsGetInverse() function. I get >> the error message: >> Error reported by MUMPS in solve phase: INFOG(1)=-47 INFO(2)=1 ACcording >> to the MUMPS Docu this message tells me that I would ignored the constraint >> NRHS= N. I checked the shape of spRHST but they appear to be correct. Does >> anyone see the error? >> My code is appended below. >> static char help[] ="Compute a part of the inverse of a sparse matrix. >> This code requires that PETSc was configured with MUMPS since we are >> dealing with large matrices \ >> and therefore use a parallel LU factorization. We compute the inverse >> by solving the equation A*X=RHS. Where A is our Matrix, X is the inverse >> and RHS is the identity matrix.\ >> Note that the number of columns nrhs of X can be chosen smaller than >> the number of columns N in A. Therefore only a part of the inverse is >> computed in X. \n \ >> In this code we use a sparse representation of the RHS matrix in >> MUMPS in csr format. Computation of selected entries in inv(A) is done >> using MatMumpsGetInverse. \n \ >> Input parameters: \n\ >> -fin : file to load \n \ >> -fout : file to load \n \ >> -nrhs : Number of columns to compute \n \ >> -displ : Print matrices to terminal \n\ >> Example usage: \n \ >> mpiexec -np 2 ./compute_inverse_sparse_rhs -fin >> ../../convert_to_binary_petsc_matrix/identity_matrix_prefactor3_ncols10 >> -nrhs 5 -displ"; >> >> #include >> #include >> #include >> >> int main(int argc, char **args){ >> PetscErrorCode ierr; // Datatype used for return error code >> PetscMPIInt size,rank; // Datatype used to represent 'int' parameters >> to MPI functions. >> #if defined(PETSC_HAVE_MUMPS) >> Mat A,F,spRHST; // Abstract PETSc matrix object used to manage all >> linear operators in PETSc >> PetscViewer fd; // Abstract PETSc object that helps view (in ASCII, >> binary, graphically etc) other PETSc objects >> PetscBool flg1,flg2; // Logical variable. Actually an int in C. >> PetscBool displ=PETSC_FALSE; // Display matrices >> PetscInt M,N,m,n,rstart,rend,nrhs,i; // PETSc type that represents an >> integer, used primarily to represent size of arrays and indexing into >> arrays. >> PetscScalar v; // PETSc type >> that represents either a double precision real number,... >> char inputfile[1][PETSC_MAX_PATH_LEN]; // Input file name >> // char outputfile[1][PETSC_MAX_PATH_LEN]; // Outputfile file name >> #endif >> >> // Initializes PETSc and MPI. Get size and rank of MPI. >> ierr = PetscInitialize(&argc, &args, (char*)0, help);if (ierr){return >> ierr;} >> ierr = MPI_Comm_size(PETSC_COMM_WORLD, &size);CHKERRQ(ierr); >> ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); >> >> //Check if PETSc was configured with MUMPS. If not print error >> message and exit >> #if !defined(PETSC_HAVE_MUMPS) >> if (!=rank){ierr = PetscPrintf(PETSC_COMM_SELF, "This code requires >> MUMPS, exit...\n");CHKERRQ(ierr); >> ierr = PetscFinalize(); >> return ierr; >> } >> #else >> >> // Check if displ is set. If True the matrices are printed to the >> terminal >> ierr = PetscOptionsGetBool(NULL, NULL, "-displ", &displ, >> NULL);CHKERRQ(ierr); >> >> // Load matrix A from file >> ierr = PetscOptionsGetString(NULL, NULL, "-fin" ,inputfile[0], >> PETSC_MAX_PATH_LEN, &flg1);CHKERRQ(ierr); >> ierr = PetscPrintf(PETSC_COMM_WORLD, "Load matrix in: %s \n", >> inputfile[0]);CHKERRQ(ierr); >> ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD, inputfile[0], >> FILE_MODE_READ, &fd);CHKERRQ(ierr); >> ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr); >> ierr = MatSetType(A, MATAIJ);CHKERRQ(ierr); >> ierr = MatLoad(A, fd);CHKERRQ(ierr); >> // Print matrix A >> if (displ){ >> ierr = PetscPrintf(PETSC_COMM_WORLD, >> "\n---------------\n");CHKERRQ(ierr); >> ierr = PetscPrintf(PETSC_COMM_WORLD,"Matrix A from file:\n", >> nrhs); >> ierr = MatView(A, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); >> ierr = PetscPrintf(PETSC_COMM_WORLD, "\n");CHKERRQ(ierr); >> } >> // Check if matrix is quadratic >> ierr = MatGetSize(A, &M, &N);CHKERRQ(ierr); >> ierr = MatGetLocalSize(A, &m, &n);CHKERRQ(ierr); >> if (M != N){ >> //Macro that is called when an error has been detected. >> SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Detected a >> rectangular matrix: (%d, %d)", M, N); >> } >> ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr); >> ierr = PetscPrintf(PETSC_COMM_WORLD, >> "---------------\n");CHKERRQ(ierr); >> ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD, "Ownership ranges >> for Matrix A, rank: %i, size: %i, rstart: %i, rend: %i \n", rank, size, >> rstart, rend);CHKERRQ(ierr); >> ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD, >> PETSC_STDOUT);CHKERRQ(ierr); >> ierr = PetscPrintf(PETSC_COMM_WORLD, >> "---------------\n");CHKERRQ(ierr); >> >> // Set the number of columns of the inverse to be computed. >> nrhs = N; >> ierr = PetscOptionsGetInt(NULL, NULL, "-nrhs", &nrhs, >> &flg2);CHKERRQ(ierr); >> >> // Create SpRHST for inv(A) with sparse RHS stored in the host. >> // PETSc does not support compressed column format which is required >> by MUMPS for sparse RHS matrix, >> // thus user must create spRHST=spRHS^T and call >> MatMatTransposeSolve() >> // User must create B^T in sparse compressed row format on the host >> processor and call MatMatTransposeSolve() to implement MUMPS' MatMatSolve(). >> // MUMPS requires nrhs = N >> ierr = MatCreate(PETSC_COMM_WORLD, &spRHST);CHKERRQ(ierr); >> if (!rank){ >> ierr = >> MatSetSizes(spRHST,N,M,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); >> } >> else{ >> ierr = >> MatSetSizes(spRHST,0,0,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); >> } >> ierr = MatSetType(spRHST,MATAIJ);CHKERRQ(ierr); >> ierr = MatSetFromOptions(spRHST);CHKERRQ(ierr); >> ierr = MatSetUp(spRHST);CHKERRQ(ierr); >> if (!rank){ >> v = 1.0; >> for(i=0;i> ierr = >> MatSetValues(spRHST,1,&i,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr); >> } >> } >> ierr = MatAssemblyBegin(spRHST,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); >> ierr = MatAssemblyEnd(spRHST, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); >> >> // Print matrix spRHST >> if (displ){ >> ierr = PetscPrintf(PETSC_COMM_WORLD, >> "\n---------------\n");CHKERRQ(ierr); >> ierr = PetscPrintf(PETSC_COMM_WORLD,"Matrix spRHST:\n", nrhs); >> ierr = MatView(spRHST, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); >> ierr = PetscPrintf(PETSC_COMM_WORLD, "\n");CHKERRQ(ierr); >> } >> >> // Print information >> ierr = PetscPrintf(PETSC_COMM_WORLD, "\nCompute %i columns of the >> inverse using LU-factorization in MUMPS!\n", nrhs); >> >> // Factorize the Matrix using a parallel LU factorization in MUMPS >> ierr = MatGetFactor(A, MATSOLVERMUMPS, MAT_FACTOR_LU, >> &F);CHKERRQ(ierr); >> ierr = MatLUFactorSymbolic(F, A, NULL, NULL, NULL);CHKERRQ(ierr); >> ierr = MatLUFactorNumeric(F, A, NULL);CHKERRQ(ierr); >> >> // Create spRHS >> Mat spRHS = NULL; >> >> // Create spRHS = spRHS^T. Two matrices that share internal matrix >> data structure. >> // Creates a new matrix object that behaves like A'. >> ierr = MatCreateTranspose(spRHST,&spRHS);CHKERRQ(ierr); >> >> // Get user-specified set of entries in inverse of A >> ierr = MatMumpsGetInverse(F,spRHS);CHKERRQ(ierr); >> >> if (displ){ >> ierr = PetscPrintf(PETSC_COMM_WORLD, >> "\n---------------\n");CHKERRQ(ierr); >> ierr = PetscPrintf(PETSC_COMM_WORLD,"First %D columns of inv(A) >> with sparse RHS:\n", nrhs); >> ierr = MatView(spRHS,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); >> ierr = PetscPrintf(PETSC_COMM_WORLD, >> "---------------\n");CHKERRQ(ierr); >> } >> >> // Free data structures >> ierr = MatDestroy(&A);CHKERRQ(ierr); >> ierr = MatDestroy(&spRHS);CHKERRQ(ierr); >> ierr = MatDestroy(&spRHST);CHKERRQ(ierr); >> ierr = PetscFinalize(); >> return ierr; >> >> #endif >> } >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Wed Dec 18 11:00:06 2019 From: bsmith at mcs.anl.gov (Smith, Barry F.) Date: Wed, 18 Dec 2019 17:00:06 +0000 Subject: [petsc-users] Strange Memory Increase in PCHYPRE BOOMERAMG In-Reply-To: References: Message-ID: <4B697DF4-D2BA-4A6F-99E5-426B5DABA872@anl.gov> Thank you for the full and detailed report. The memory leak could be anywhere but my guess is it is in the interface between PETSc and Hyper. The first thing to check is if PETSc memory keeps increasing. The simplest way to do this is run your code 3 independent times with -malloc_debug -log_view and say 5 steps, then 10 steps, then 15 steps. Now look at the information at the end of the -log_view report. It shows how many PETSc objects are created and how much memory they use. Are the numbers getting larger? The -malloc_debug flag will cause PETSc to print at the end of the run all the memory it has allocated but not freed. If your code is properly freeing everything it will print nothing indicating PETSc has no object leaps in your code. Let us know how it goes and we can direct you how to debug memory leaks between PETSc and hypre or in hypre if that is where they are. Barry > On Dec 18, 2019, at 1:32 AM, Mohammed Mostafa wrote: > > Hello everyone, > I seem to have a problem of increasing memory size with the linear solver. I double check every single part of my code and I isolated the problem to KSPSolve command. > A bit of context/background regarding my algorithm. > I am writing a finite volume numerical solver for incompressible two phase flow. I am mainly solving liquid sloshing and waves impact problems. Until recently most of simulations were 2D with max cell count of 100K cells but now I am considering solving 3D problems with cell counts between 6M~10M cells. > The algorithm is as follows: > > setup ksp > setup pc > > loop 1 ? number of timesteps > 1- // do some work > 2- create the pressure poisson matrix > > 3 ? loop: iloop 1 to 4 > 4-1- solve the matrix if ( iloop == 1) update the precond > 4-2- // do some work > 4-3- update rhs(no matrix or precond update) > 4- do the next timestep and go back to step 1 > > From many online posts many people recommended KSPCG with PCHYPRE with the following options > > // PC Setup > PCCreate(PETSC_COMM_WORLD, &preconditioner); > PCSetType(preconditioner, PCHYPRE); > PCHYPRESetType(preconditioner, "boomeramg"); > > PetscOptionsSetValue(NULL, "-pc_hypre_boomeramg_strong_threshold", "0.4"); > PetscOptionsSetValue(NULL, "-pc_hypre_boomeramg_agg_nl", "3"); > PetscOptionsSetValue(NULL, "-pc_hypre_boomeramg_agg_num_paths", "4"); > > PetscOptionsSetValue(NULL, "-pc_hypre_boomeramg_interp_type", "ext+i"); > PetscOptionsSetValue(NULL, "-pc_hypre_boomeramg_truncfactor", "0.3"); > PetscOptionsSetValue(NULL, "-pc_hypre_boomeramg_max_iter", "1"); > PetscOptionsSetValue(NULL, "-pc_hypre_boomeramg_relax_type_all", > "SOR/Jacobi"); > PetscOptionsSetValue(NULL, "-pc_hypre_boomeramg_grid_sweeps_down", "1"); > PetscOptionsSetValue(NULL, "-pc_hypre_boomeramg_max_iter", "1"); > PetscOptionsSetValue(NULL, "-pc_hypre_boomeramg_rtol", "0"); > KSPSetPC(iterSolver, preconditioner); > KSPSetOperators(iterSolver, A, A); > // KSP Setup > KSPSetType(iterSolver, KSPCG); > KSPSetInitialGuessNonzero(iterSolver, PETSC_TRUE); > KSPSetNormType(iterSolver, KSP_NORM_UNPRECONDITIONED); > KSPSetFromOptions(iterSolver); > > PCSetUp(preconditioner); > KSPSetUp(iterSolver); > KSPSetTolerances(iterSolver, 1e-18 /*reltol*/, 1e-12 /*abstol*/, > 1e5 /*divergencetol*/, 50); > > When solving the linear system for the first time during the timestep (iloop =1), the following commands are used so that the preconditioner is reconstructed based on the new matrix values. > > KSPSetReusePreconditioner(iterSolver, PETSC_FALSE); > KSPSetOperators(iterSolver, A, A); // set the new matrix > KSPSolve(iterSolver, *RHS, *x); > Otherwise > KSPSetReusePreconditioner(iterSolver, PETSC_TRUE); > KSPSolve(iterSolver, *RHS, *x); > It should be noted that matrix non-zero structure remains the same throught the simulation but the values change every timestep. > Now My problem is that memory size keep changing throught the simulation utill my workstation evetually runs out of memory. > I tracked down the memory increase to the step which solve the linear system of equations. > KSPSetReusePreconditioner(iterSolver, PETSC_FALSE); > KSPSetOperators(iterSolver, A, A); // set the new matrix > KSPSolve(iterSolver, *RHS, *x); > My current problem is a sloshing problem with cell count of 1.2M cells running on workstation with 40 Cores and 94GB of RAM. > The memory increase I observed did not occur every single time step but more like every 3-10 time step. The increase each time is somewhere from 0.51MB~3.0MB per mpi process and not not all process show memory change. For example in time step id 14 , proc0, proc6, proc13, proc24 show change but the others don?t. On average 10~15 processes show memory change while the others do not. > Over 1000 time steps the solver use up additional 10GB of memory and still increasing until the system runs out of memory after nearly 10K time steps. > I wanted to try another preconditioner PCJACOBI which ultimately failed due to max number of iterations but at least no memory change was observed over 50 time steps. > Since I am using multigrid I expected the increase in memory required by the linear solver, I just assumed that after enough number of timesteps it would settle on some value. But it just kept increasing util finally the system ran out of memory. > I monitored the memory usage of other parts/components of the code and no memory change occurs at all except at code section above. > I configure PETSC with following options > PETSC_ARCH=release3 -with-debugging=0 COPTFLAGS="-O3 -march=native -mtune=native" CXXOPTFLAGS="-O3 -march=native -mtune=native" FOPTFLAGS="-O3 -march=native -mtune=native" --with-cc=mpicc --w > ith-cxx=mpicxx --with-fc=mpif90 --download-metis --download-hypre > > I tried configuring it in debug and compiling my code also in debug mode and running as the FAQ suggests but the code ended up being too slow so I shut it down after running it for 50mins and not even one timestep was completed. > > So to track down the memory leak/increase I used > PetscMemoryGetCurrentUsage(&mem1); > // some code > PetscMemoryGetCurrentUsage(&mem2); > memChnge = mem2 ? mem1; > > I believe it could be one of the following possibilities: > ? A memory leak (bug) in the petsc library ( unlikely otherwise someone would have found it by now ) > ? Some thing to do with setting of the boomerAMG Hypre preconditioner which makes it unnecessarily add additional levels. The settings I am using, I got from an online post I found so I don?t really understand it. > https://mooseframework.inl.gov/application_development/hypre.html > ? Some problem with the sequence of commands I am using for the solution of linear system of eqns that makes allocate additional memory with freeing the old one. > Thanks > From hzhang at mcs.anl.gov Wed Dec 18 12:11:04 2019 From: hzhang at mcs.anl.gov (Zhang, Hong) Date: Wed, 18 Dec 2019 18:11:04 +0000 Subject: [petsc-users] Corrrect usage of MatMumpsGetInverse() In-Reply-To: References: Message-ID: Jan: Hey, i tested the fix today and ran the same code as above. It is now working fine and my results are in agreement with my analytical solutions. Good. I'll push the fix to the petsc release after regression tests. Although i have to tranpose the computed entries afterwards. This should be the correct behaviour or ? ierr = MatTranspose(spRHST, MAT_INPLACE_MATRIX, &spRHST);CHKERRQ(ierr); Yes, you have to do so. The issue is, mumps uses centralized compressed COLUMN format for RHS, while pestc only supports compressed ROW format. A hack is to have user create spRHST, then call MatTranspose(spRHST, MAT_INPLACE_MATRIX, &spRHS); Note: there is no copying in this routine. spRHST and spRHS share same data structure using column-wise and row-wise orderings. If you have a better suggestion, let us know. Thanks for reporting the bug. Hong Am Mo., 16. Dez. 2019 um 22:57 Uhr schrieb Zhang, Hong >: Jan: You found a bug in our interface. I pushed a fix https://gitlab.com/petsc/petsc/commit/6fa4709e1488f7c58b0a4ecbdf34b75ae4ac64d2 in branch hzhang/fix-mumps-GetInverse. You may give it a try by 'git checkout hzhang/fix-mumps-GetInverse' at PETSC_DIR and rebuild petsc. Let me know if it fixes the issue. Hong Hello, everybody, I am using PETSc version 3.12 together with MUMPS to calculate a part of an inverse from a matrix A. For this I used the example mat/examples/tests/ex214.c as suggested here in the forum. For test purposes I read a matrix with the dimension 10x10, which only has entries on the main diagonal, because I know the inverse of it. But now I have a problem using the MatMumpsGetInverse() function. I get the error message: Error reported by MUMPS in solve phase: INFOG(1)=-47 INFO(2)=1 ACcording to the MUMPS Docu this message tells me that I would ignored the constraint NRHS= N. I checked the shape of spRHST but they appear to be correct. Does anyone see the error? My code is appended below. static char help[] ="Compute a part of the inverse of a sparse matrix. This code requires that PETSc was configured with MUMPS since we are dealing with large matrices \ and therefore use a parallel LU factorization. We compute the inverse by solving the equation A*X=RHS. Where A is our Matrix, X is the inverse and RHS is the identity matrix.\ Note that the number of columns nrhs of X can be chosen smaller than the number of columns N in A. Therefore only a part of the inverse is computed in X. \n \ In this code we use a sparse representation of the RHS matrix in MUMPS in csr format. Computation of selected entries in inv(A) is done using MatMumpsGetInverse. \n \ Input parameters: \n\ -fin : file to load \n \ -fout : file to load \n \ -nrhs : Number of columns to compute \n \ -displ : Print matrices to terminal \n\ Example usage: \n \ mpiexec -np 2 ./compute_inverse_sparse_rhs -fin ../../convert_to_binary_petsc_matrix/identity_matrix_prefactor3_ncols10 -nrhs 5 -displ"; #include #include #include int main(int argc, char **args){ PetscErrorCode ierr; // Datatype used for return error code PetscMPIInt size,rank; // Datatype used to represent 'int' parameters to MPI functions. #if defined(PETSC_HAVE_MUMPS) Mat A,F,spRHST; // Abstract PETSc matrix object used to manage all linear operators in PETSc PetscViewer fd; // Abstract PETSc object that helps view (in ASCII, binary, graphically etc) other PETSc objects PetscBool flg1,flg2; // Logical variable. Actually an int in C. PetscBool displ=PETSC_FALSE; // Display matrices PetscInt M,N,m,n,rstart,rend,nrhs,i; // PETSc type that represents an integer, used primarily to represent size of arrays and indexing into arrays. PetscScalar v; // PETSc type that represents either a double precision real number,... char inputfile[1][PETSC_MAX_PATH_LEN]; // Input file name // char outputfile[1][PETSC_MAX_PATH_LEN]; // Outputfile file name #endif // Initializes PETSc and MPI. Get size and rank of MPI. ierr = PetscInitialize(&argc, &args, (char*)0, help);if (ierr){return ierr;} ierr = MPI_Comm_size(PETSC_COMM_WORLD, &size);CHKERRQ(ierr); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); //Check if PETSc was configured with MUMPS. If not print error message and exit #if !defined(PETSC_HAVE_MUMPS) if (!=rank){ierr = PetscPrintf(PETSC_COMM_SELF, "This code requires MUMPS, exit...\n");CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; } #else // Check if displ is set. If True the matrices are printed to the terminal ierr = PetscOptionsGetBool(NULL, NULL, "-displ", &displ, NULL);CHKERRQ(ierr); // Load matrix A from file ierr = PetscOptionsGetString(NULL, NULL, "-fin" ,inputfile[0], PETSC_MAX_PATH_LEN, &flg1);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Load matrix in: %s \n", inputfile[0]);CHKERRQ(ierr); ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD, inputfile[0], FILE_MODE_READ, &fd);CHKERRQ(ierr); ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr); ierr = MatSetType(A, MATAIJ);CHKERRQ(ierr); ierr = MatLoad(A, fd);CHKERRQ(ierr); // Print matrix A if (displ){ ierr = PetscPrintf(PETSC_COMM_WORLD, "\n---------------\n");CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"Matrix A from file:\n", nrhs); ierr = MatView(A, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "\n");CHKERRQ(ierr); } // Check if matrix is quadratic ierr = MatGetSize(A, &M, &N);CHKERRQ(ierr); ierr = MatGetLocalSize(A, &m, &n);CHKERRQ(ierr); if (M != N){ //Macro that is called when an error has been detected. SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Detected a rectangular matrix: (%d, %d)", M, N); } ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "---------------\n");CHKERRQ(ierr); ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD, "Ownership ranges for Matrix A, rank: %i, size: %i, rstart: %i, rend: %i \n", rank, size, rstart, rend);CHKERRQ(ierr); ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD, PETSC_STDOUT);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "---------------\n");CHKERRQ(ierr); // Set the number of columns of the inverse to be computed. nrhs = N; ierr = PetscOptionsGetInt(NULL, NULL, "-nrhs", &nrhs, &flg2);CHKERRQ(ierr); // Create SpRHST for inv(A) with sparse RHS stored in the host. // PETSc does not support compressed column format which is required by MUMPS for sparse RHS matrix, // thus user must create spRHST=spRHS^T and call MatMatTransposeSolve() // User must create B^T in sparse compressed row format on the host processor and call MatMatTransposeSolve() to implement MUMPS' MatMatSolve(). // MUMPS requires nrhs = N ierr = MatCreate(PETSC_COMM_WORLD, &spRHST);CHKERRQ(ierr); if (!rank){ ierr = MatSetSizes(spRHST,N,M,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); } else{ ierr = MatSetSizes(spRHST,0,0,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); } ierr = MatSetType(spRHST,MATAIJ);CHKERRQ(ierr); ierr = MatSetFromOptions(spRHST);CHKERRQ(ierr); ierr = MatSetUp(spRHST);CHKERRQ(ierr); if (!rank){ v = 1.0; for(i=0;i From fdkong.jd at gmail.com Thu Dec 19 10:00:35 2019 From: fdkong.jd at gmail.com (Fande Kong) Date: Thu, 19 Dec 2019 09:00:35 -0700 Subject: [petsc-users] Running moose/scripts/update_and_rebuild_petsc.sh on HPC In-Reply-To: <641b2c64-0e88-47e7-b33a-e2528287095a@googlegroups.com> References: <277eb13a-0590-4b1a-a089-09a7c35efd83@googlegroups.com> <641b2c64-0e88-47e7-b33a-e2528287095a@googlegroups.com> Message-ID: Did you try "--with-batch=1"? A suggestion was proposed by Satish earlier (CCing here). Fande, On Wed, Dec 18, 2019 at 12:36 PM Tomas Mondragon < tom.alex.mondragon at gmail.com> wrote: > Yes, but now that I have tried this a couple of different ways with > different --with-mpiexec options, I am beginning to suspect that I need to > run this as a PBS job on compute nodes rather than a shell script on login > nodes. Also, running it with --with-mpiexec="mpirun -n 1" and with > --with-mpiexec="path/to/mpirun" don't get me results any different from > using --with-mpiexec="mpirun" > > I have attached my modified update_and_rebuild_petsc.sh scripts from both > machines plus their respective configure.log files. > > -- > You received this message because you are subscribed to the Google Groups > "moose-users" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to moose-users+unsubscribe at googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/moose-users/641b2c64-0e88-47e7-b33a-e2528287095a%40googlegroups.com > > . > -------------- next part -------------- An HTML attachment was scrubbed... URL: From repepo at gmail.com Mon Dec 23 14:13:08 2019 From: repepo at gmail.com (Santiago Andres Triana) Date: Mon, 23 Dec 2019 21:13:08 +0100 Subject: [petsc-users] killed 9 signal after upgrade from petsc 3.9.4 to 3.12.2 Message-ID: Dear all, After upgrading to petsc 3.12.2 my solver program crashes consistently. Before the upgrade I was using petsc 3.9.4 with no problems. My application deals with a complex-valued, generalized eigenvalue problem. The matrices involved are relatively large, typically 2 to 10 Gb in size, which is no problem for petsc 3.9.4. However, after the upgrade I can only obtain solutions when the matrices are small, the solver crashes when the matrices' size exceed about 1.5 Gb: [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. and so on for each cpu. I tried using valgrind and this is the typical output: ==2874== Conditional jump or move depends on uninitialised value(s) ==2874== at 0x4018178: index (in /lib64/ld-2.22.so) ==2874== by 0x400752D: expand_dynamic_string_token (in /lib64/ld-2.22.so) ==2874== by 0x4008009: _dl_map_object (in /lib64/ld-2.22.so) ==2874== by 0x40013E4: map_doit (in /lib64/ld-2.22.so) ==2874== by 0x400EA53: _dl_catch_error (in /lib64/ld-2.22.so) ==2874== by 0x4000ABE: do_preload (in /lib64/ld-2.22.so) ==2874== by 0x4000EC0: handle_ld_preload (in /lib64/ld-2.22.so) ==2874== by 0x40034F0: dl_main (in /lib64/ld-2.22.so) ==2874== by 0x4016274: _dl_sysdep_start (in /lib64/ld-2.22.so) ==2874== by 0x4004A99: _dl_start (in /lib64/ld-2.22.so) ==2874== by 0x40011F7: ??? (in /lib64/ld-2.22.so) ==2874== by 0x12: ??? ==2874== These are my configuration options. Identical for both petsc 3.9.4 and 3.12.2: ./configure --with-scalar-type=complex --download-mumps --download-parmetis --download-metis --download-scalapack=1 --download-fblaslapack=1 --with-debugging=0 --download-superlu_dist=1 --download-ptscotch=1 CXXOPTFLAGS='-O3 -march=native' FOPTFLAGS='-O3 -march=native' COPTFLAGS='-O3 -march=native' Thanks in advance for any comments or ideas! Cheers, Santiago -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Mon Dec 23 16:18:53 2019 From: knepley at gmail.com (Matthew Knepley) Date: Mon, 23 Dec 2019 17:18:53 -0500 Subject: [petsc-users] killed 9 signal after upgrade from petsc 3.9.4 to 3.12.2 In-Reply-To: References: Message-ID: On Mon, Dec 23, 2019 at 3:14 PM Santiago Andres Triana wrote: > Dear all, > > After upgrading to petsc 3.12.2 my solver program crashes consistently. > Before the upgrade I was using petsc 3.9.4 with no problems. > > My application deals with a complex-valued, generalized eigenvalue > problem. The matrices involved are relatively large, typically 2 to 10 Gb > in size, which is no problem for petsc 3.9.4. > Are you sure that your indices do not exceed 4B? If so, you need to configure using --with-64-bit-indices Also, it would be nice if you ran with the debugger so we can get a stack trace for the SEGV. Thanks, Matt > However, after the upgrade I can only obtain solutions when the matrices > are small, the solver crashes when the matrices' size exceed about 1.5 Gb: > > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the > batch system) has told this process to end > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [0]PETSC ERROR: or see > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind > [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS > X to find memory corruption errors > [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and > run > [0]PETSC ERROR: to get more information on the crash. > > and so on for each cpu. > > > I tried using valgrind and this is the typical output: > > ==2874== Conditional jump or move depends on uninitialised value(s) > ==2874== at 0x4018178: index (in /lib64/ld-2.22.so) > ==2874== by 0x400752D: expand_dynamic_string_token (in /lib64/ > ld-2.22.so) > ==2874== by 0x4008009: _dl_map_object (in /lib64/ld-2.22.so) > ==2874== by 0x40013E4: map_doit (in /lib64/ld-2.22.so) > ==2874== by 0x400EA53: _dl_catch_error (in /lib64/ld-2.22.so) > ==2874== by 0x4000ABE: do_preload (in /lib64/ld-2.22.so) > ==2874== by 0x4000EC0: handle_ld_preload (in /lib64/ld-2.22.so) > ==2874== by 0x40034F0: dl_main (in /lib64/ld-2.22.so) > ==2874== by 0x4016274: _dl_sysdep_start (in /lib64/ld-2.22.so) > ==2874== by 0x4004A99: _dl_start (in /lib64/ld-2.22.so) > ==2874== by 0x40011F7: ??? (in /lib64/ld-2.22.so) > ==2874== by 0x12: ??? > ==2874== > > > These are my configuration options. Identical for both petsc 3.9.4 and > 3.12.2: > > ./configure --with-scalar-type=complex --download-mumps > --download-parmetis --download-metis --download-scalapack=1 > --download-fblaslapack=1 --with-debugging=0 --download-superlu_dist=1 > --download-ptscotch=1 CXXOPTFLAGS='-O3 -march=native' FOPTFLAGS='-O3 > -march=native' COPTFLAGS='-O3 -march=native' > > > Thanks in advance for any comments or ideas! > > Cheers, > Santiago > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From mbuerkle at web.de Tue Dec 24 01:27:30 2019 From: mbuerkle at web.de (Marius Buerkle) Date: Tue, 24 Dec 2019 08:27:30 +0100 Subject: [petsc-users] possible memory leak Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: memory_leak.f90 Type: text/x-fortran Size: 2237 bytes Desc: not available URL: From mfadams at lbl.gov Tue Dec 24 08:56:23 2019 From: mfadams at lbl.gov (Mark Adams) Date: Tue, 24 Dec 2019 09:56:23 -0500 Subject: [petsc-users] possible memory leak In-Reply-To: References: Message-ID: Try running with -malloc_debug This should print out where unfreed memory was allocated. See what pops up. Mark On Tue, Dec 24, 2019 at 2:27 AM Marius Buerkle wrote: > Hi, > > > > In my code I create and destroy during one run a lot of MPIAIJ matrices > and it seems that not all memory is freed when I destroy the matrices. > Moreover, it looks like the amount of ?disappearing? memory increases with > the number of processes. I am not so sure if I am doing something wrong or > if it is really a memory leak. I have attached a simple reproducer. > > > > Best, > > Marius > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mbuerkle at web.de Tue Dec 24 09:47:36 2019 From: mbuerkle at web.de (Marius Buerkle) Date: Tue, 24 Dec 2019 16:47:36 +0100 Subject: [petsc-users] possible memory leak In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Tue Dec 24 09:53:27 2019 From: bsmith at mcs.anl.gov (Smith, Barry F.) Date: Tue, 24 Dec 2019 15:53:27 +0000 Subject: [petsc-users] possible memory leak In-Reply-To: References: Message-ID: There are no leaks but it appears what is happening is that rather than recycle the memory PETSc is returning to the system the system is generating new space as needed. Since the old PETSc pages are never used again this should be harmless. Barry > On Dec 24, 2019, at 9:47 AM, Marius Buerkle wrote: > > thanks for the swift reply. This didn't give any output. > > > Gesendet: Dienstag, 24. Dezember 2019 um 23:56 Uhr > Von: "Mark Adams" > An: "Marius Buerkle" > Cc: "petsc-usersmcs.anl.gov" > Betreff: Re: [petsc-users] possible memory leak > Try running with -malloc_debug > > This should print out where unfreed memory was allocated. See what pops up. > > Mark > > On Tue, Dec 24, 2019 at 2:27 AM Marius Buerkle wrote: > Hi, > > > In my code I create and destroy during one run a lot of MPIAIJ matrices and it seems that not all memory is freed when I destroy the matrices. Moreover, it looks like the amount of ?disappearing? memory increases with the number of processes. I am not so sure if I am doing something wrong or if it is really a memory leak. I have attached a simple reproducer. > > > Best, > > Marius > From mbuerkle at web.de Tue Dec 24 10:03:43 2019 From: mbuerkle at web.de (Marius Buerkle) Date: Tue, 24 Dec 2019 17:03:43 +0100 Subject: [petsc-users] possible memory leak In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Tue Dec 24 11:25:34 2019 From: bsmith at mcs.anl.gov (Smith, Barry F.) Date: Tue, 24 Dec 2019 17:25:34 +0000 Subject: [petsc-users] possible memory leak In-Reply-To: References: Message-ID: <4281C254-A947-4A4C-8C45-AD9AA4743F38@mcs.anl.gov> I see, What version of MPI are you using? Some versions of OpenMPI have serious memory leaks. Maybe try the exact same version of OpenMPI you used previously with success? You can also use valgrind with some options to track the memory usage. Barry > On Dec 24, 2019, at 10:03 AM, Marius Buerkle wrote: > > I see. For actual production runs on 512 processes with larger matrices this causes eventually a seg fault due to running out of memory. I am not sure but think this did not happen with some "older" version of PETSC. I am not sure which one (or which revision), I wil check it. > > > Gesendet: Mittwoch, 25. Dezember 2019 um 00:53 Uhr > Von: "Smith, Barry F." > An: "Marius Buerkle" > Cc: "Mark Adams" , "petsc-usersmcs.anl.gov" > Betreff: Re: [petsc-users] possible memory leak > > There are no leaks but it appears what is happening is that rather than recycle the memory PETSc is returning to the system the system is generating new space as needed. Since the old PETSc pages are never used again this should be harmless. > > Barry > > > > > On Dec 24, 2019, at 9:47 AM, Marius Buerkle wrote: > > > > thanks for the swift reply. This didn't give any output. > > > > > > Gesendet: Dienstag, 24. Dezember 2019 um 23:56 Uhr > > Von: "Mark Adams" > > An: "Marius Buerkle" > > Cc: "petsc-usersmcs.anl.gov" > > Betreff: Re: [petsc-users] possible memory leak > > Try running with -malloc_debug > > > > This should print out where unfreed memory was allocated. See what pops up. > > > > Mark > > > > On Tue, Dec 24, 2019 at 2:27 AM Marius Buerkle wrote: > > Hi, > > > > > > In my code I create and destroy during one run a lot of MPIAIJ matrices and it seems that not all memory is freed when I destroy the matrices. Moreover, it looks like the amount of ?disappearing? memory increases with the number of processes. I am not so sure if I am doing something wrong or if it is really a memory leak. I have attached a simple reproducer. > > > > > > Best, > > > > Marius > > > From mbuerkle at web.de Tue Dec 24 19:04:45 2019 From: mbuerkle at web.de (Marius Buerkle) Date: Wed, 25 Dec 2019 02:04:45 +0100 Subject: [petsc-users] possible memory leak In-Reply-To: <4281C254-A947-4A4C-8C45-AD9AA4743F38@mcs.anl.gov> References: <4281C254-A947-4A4C-8C45-AD9AA4743F38@mcs.anl.gov> Message-ID: An HTML attachment was scrubbed... URL: From mark.cunningham at ariacoustics.com Thu Dec 26 12:34:55 2019 From: mark.cunningham at ariacoustics.com (Mark Cunningham) Date: Thu, 26 Dec 2019 13:34:55 -0500 Subject: [petsc-users] KSPComputeOperator in petsc4py Message-ID: I have an application written in python and using petsc4py. I would like to study the effects of different preconditioners on my eigenvalue spectrum and thought to use KSPComputeOperator to obtain the preconditioned matrix. This, apparently, is not disclosed through the petsc4py implementation. I found KSP.pyx, where I believe that the KSP object is defined, and added a definition for the function but, after a pip install, my updated library still says that ksp.computeOperator is not known. What else must I touch to include this function? Thanks for your help, Mark ------------------------------------------------------ Mark A Cunningham, PhD Senior Scientist Applied Research in Acoustics LLC -------------- next part -------------- An HTML attachment was scrubbed... URL: From mfadams at lbl.gov Sun Dec 29 09:53:26 2019 From: mfadams at lbl.gov (Mark Adams) Date: Sun, 29 Dec 2019 10:53:26 -0500 Subject: [petsc-users] [petsc-maint] Error during compile In-Reply-To: <1b1b4b0b.670d.16f51fd1f9e.Coremail.asachoo@shu.edu.cn> References: <2e973c39.658e.16f51511ad4.Coremail.asachoo@shu.edu.cn> <1b1b4b0b.670d.16f51fd1f9e.Coremail.asachoo@shu.edu.cn> Message-ID: On Sun, Dec 29, 2019 at 9:09 AM ??? wrote: > I'm sorry that I have deleted the gnu-opt directory and made from scratch, > the same errors still occur. So, could you tell me what will you do if you > face this problem? > I now see that you are using a very old version of PETSc. Unless someone else can diagnose this you may have to upgrade PETSc. PETSc is very reliable after you get configure done, but perhaps someone else can help. Meanwhile I would just upgrade your PETSc version. Your old configure captions should work, although some 3rd party packages are no longer supported. > -----????----- > *???:*"Mark Adams" > *????:*2019-12-29 21:28:07 (???) > *???:* "???" > *??:* petsc-maint > *??:* Re: [petsc-maint] Error during compile > > First thing I would do is start from scratch. Delete the gnu-opt > directory, reconfigure and make. > > On Sun, Dec 29, 2019 at 6:02 AM ??? wrote: > >> I tried to install PETSc , but it had an error ,could you please tell me >> how to deal it. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ???? 2019-12-29 ??10.05.11.png Type: image/png Size: 459527 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ???? 2019-12-29 ??6.54.57.png Type: image/png Size: 572787 bytes Desc: not available URL: From knepley at gmail.com Sun Dec 29 15:31:21 2019 From: knepley at gmail.com (Matthew Knepley) Date: Sun, 29 Dec 2019 16:31:21 -0500 Subject: [petsc-users] [petsc-maint] Error during compile In-Reply-To: References: <2e973c39.658e.16f51511ad4.Coremail.asachoo@shu.edu.cn> <1b1b4b0b.670d.16f51fd1f9e.Coremail.asachoo@shu.edu.cn> Message-ID: The problem is that your PETSc is old and your MPI is new. That type has been removed from MPI. As Mark points out, please upgrade PETSc and it will work. You could also try using an ancient MPI, but that seems counterproductive. Thanks, Matt On Sun, Dec 29, 2019 at 10:54 AM Mark Adams wrote: > > > On Sun, Dec 29, 2019 at 9:09 AM ??? wrote: > >> I'm sorry that I have deleted the gnu-opt directory and made from >> scratch, the same errors still occur. So, could you tell me what will you >> do if you face this problem? >> > > I now see that you are using a very old version of PETSc. Unless someone > else can diagnose this you may have to upgrade PETSc. PETSc is very > reliable after you get configure done, but perhaps someone else can help. > > Meanwhile I would just upgrade your PETSc version. Your old configure > captions should work, although some 3rd party packages are no longer > supported. > > > >> -----????----- >> *???:*"Mark Adams" >> *????:*2019-12-29 21:28:07 (???) >> *???:* "???" >> *??:* petsc-maint >> *??:* Re: [petsc-maint] Error during compile >> >> First thing I would do is start from scratch. Delete the gnu-opt >> directory, reconfigure and make. >> >> On Sun, Dec 29, 2019 at 6:02 AM ??? wrote: >> >>> I tried to install PETSc , but it had an error ,could you please tell me >>> how to deal it. >> >> -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ???? 2019-12-29 ??6.54.57.png Type: image/png Size: 572787 bytes Desc: not available URL: From matt.landreman at gmail.com Mon Dec 30 08:44:01 2019 From: matt.landreman at gmail.com (Matt Landreman) Date: Mon, 30 Dec 2019 09:44:01 -0500 Subject: [petsc-users] Redundant Jacobian evaluations in tao-brgn Message-ID: Hi, I have a question about the TAO BRGN algorithm for least-squares optimization. It seems to be calling the user-supplied Jacobian routine twice for each point in the parameter space, unnecessarily increasing the amount of computation. This can be seen by inserting the lines printf("EvaluateFunction called at x = %.15e, %.15e, %.15e\n",x[0],x[1],x[2]); and printf("EvaluateJacobian called at x = %.15e, %.15e, %.15e\n",x[0],x[1],x[2]); into the petsc example src/tao/leastsquares/examples/tutorials/chwirut1.c at line numbers 128 and 150 respectively. Then running ./chwirut1 -tao_type brgn the output is EvaluateFunction called at x = 1.500000000000000e-01, 8.000000000000000e-03, 1.000000000000000e-02 EvaluateJacobian called at x = 1.500000000000000e-01, 8.000000000000000e-03, 1.000000000000000e-02 EvaluateJacobian called at x = 1.500000000000000e-01, 8.000000000000000e-03, 1.000000000000000e-02 EvaluateFunction called at x = 1.678609230300274e-01, 5.606199685573443e-03, 1.143975621188315e-02 EvaluateJacobian called at x = 1.678609230300274e-01, 5.606199685573443e-03, 1.143975621188315e-02 EvaluateJacobian called at x = 1.678609230300274e-01, 5.606199685573443e-03, 1.143975621188315e-02 EvaluateFunction called at x = 1.895677598936882e-01, 6.141611118905459e-03, 1.052387574144709e-02 EvaluateJacobian called at x = 1.895677598936882e-01, 6.141611118905459e-03, 1.052387574144709e-02 EvaluateJacobian called at x = 1.895677598936882e-01, 6.141611118905459e-03, 1.052387574144709e-02 EvaluateFunction called at x = 1.901553874099915e-01, 6.129649283393148e-03, 1.053528933460132e-02 EvaluateJacobian called at x = 1.901553874099915e-01, 6.129649283393148e-03, 1.053528933460132e-02 EvaluateJacobian called at x = 1.901553874099915e-01, 6.129649283393148e-03, 1.053528933460132e-02 EvaluateFunction called at x = 1.902758303510814e-01, 6.131413563754055e-03, 1.053093200323840e-02 EvaluateJacobian called at x = 1.902758303510814e-01, 6.131413563754055e-03, 1.053093200323840e-02 EvaluateJacobian called at x = 1.902758303510814e-01, 6.131413563754055e-03, 1.053093200323840e-02 EvaluateFunction called at x = 1.902779152522651e-01, 6.131396913966817e-03, 1.053091761136939e-02 EvaluateJacobian called at x = 1.902779152522651e-01, 6.131396913966817e-03, 1.053091761136939e-02 EvaluateJacobian called at x = 1.902779152522651e-01, 6.131396913966817e-03, 1.053091761136939e-02 EvaluateFunction called at x = 1.902781772105115e-01, 6.131400452825695e-03, 1.053090850459907e-02 EvaluateJacobian called at x = 1.902781772105115e-01, 6.131400452825695e-03, 1.053090850459907e-02 EvaluateJacobian called at x = 1.902781772105115e-01, 6.131400452825695e-03, 1.053090850459907e-02 EvaluateFunction called at x = 1.902781831060656e-01, 6.131400440501068e-03, 1.053090841847083e-02 EvaluateJacobian called at x = 1.902781831060656e-01, 6.131400440501068e-03, 1.053090841847083e-02 EvaluateJacobian called at x = 1.902781831060656e-01, 6.131400440501068e-03, 1.053090841847083e-02 EvaluateFunction called at x = 1.902781836794117e-01, 6.131400447676857e-03, 1.053090839927484e-02 EvaluateJacobian called at x = 1.902781836794117e-01, 6.131400447676857e-03, 1.053090839927484e-02 EvaluateJacobian called at x = 1.902781836794117e-01, 6.131400447676857e-03, 1.053090839927484e-02 EvaluateFunction called at x = 1.902781836950446e-01, 6.131400447696052e-03, 1.053090839897943e-02 EvaluateJacobian called at x = 1.902781836950446e-01, 6.131400447696052e-03, 1.053090839897943e-02 This shows that every call to EvaluateJacobian (except the last) is actually two calls at the same point. Is there a way to eliminate these redundant Jacobian evaluations? Thanks, Matt Landreman P.S. I'm using petsc 3.12.2, and in case it's helpful, the output of -tao_view is copied here: Tao Object: 1 MPI processes type: brgn Tao Object: (tao_brgn_subsolver_) 1 MPI processes type: bnls Rejected BFGS updates: 0 CG steps: 0 Newton steps: 9 BFGS steps: 0 Scaled gradient steps: 0 Gradient steps: 0 KSP termination reasons: atol: 0 rtol: 9 ctol: 0 negc: 0 dtol: 0 iter: 0 othr: 0 TaoLineSearch Object: (tao_brgn_subsolver_) 1 MPI processes type: more-thuente maximum function evaluations=30 tolerances: ftol=0.0001, rtol=1e-10, gtol=0.9 total number of function evaluations=0 total number of gradient evaluations=0 total number of function/gradient evaluations=1 Termination reason: 1 KSP Object: (tao_brgn_subsolver_) 1 MPI processes type: stcg maximum iterations=10000, initial guess is zero tolerances: relative=1e-05, absolute=1e-50, divergence=10000. left preconditioning using UNPRECONDITIONED norm type for convergence test PC Object: (tao_brgn_subsolver_) 1 MPI processes type: lmvm Mat Object: (pc_lmvm_) 1 MPI processes type: lmvmbfgs rows=3, cols=3 Scale type: diagonal Scale history: 1 Scale params: alpha=1., beta=0.5, rho=1. Convex factors: phi=0., theta=0.125 Max. storage: 5 Used storage: 5 Number of updates: 8 Number of rejects: 0 Number of resets: 0 Mat Object: (J0_) 1 MPI processes type: lmvmdiagbrdn rows=3, cols=3 Scale history: 1 Scale params: alpha=1., beta=0.5, rho=1. Convex factor: theta=0.125 Max. storage: 1 Used storage: 1 Number of updates: 8 Number of rejects: 0 Number of resets: 0 linear system matrix = precond matrix: Mat Object: 1 MPI processes type: shell rows=3, cols=3 total KSP iterations: 27 Active Set subset type: subvec convergence tolerances: gatol=1e-08, steptol=0., gttol=0. Residual in Function/Gradient:=4.30981e-07 Objective value=1192.24 total number of iterations=9, (max: 2000) total number of function evaluations=10, max: 4000 total number of function/gradient evaluations=10, (max: 4000) total number of Hessian evaluations=9 total number of Jacobian evaluations=19 Solution converged: ||g(X)||/|f(X)| <= grtol convergence tolerances: gatol=1e-08, steptol=0., gttol=0. Residual in Function/Gradient:=0. Objective value=0. total number of iterations=9, (max: 2000) total number of function evaluations=10, max: 4000 total number of function/gradient evaluations=10, (max: 4000) total number of Hessian evaluations=9 Solution converged: ||g(X)||/|f(X)| <= grtol -- ======================================= Dr. Matt Landreman Associate Research Scientist Institute for Research in Electronics & Applied Physics University of Maryland 8223 Paint Branch Drive, College Park MD 20742, USA (+1) 651-366-9306 mattland at umd.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: