From w_ang_temp at 163.com Thu Nov 1 08:47:25 2012 From: w_ang_temp at 163.com (w_ang_temp) Date: Thu, 1 Nov 2012 21:47:25 +0800 (CST) Subject: [petsc-users] How rto use multigrid? In-Reply-To: <01255FF7-A444-48E8-AB48-AE76C710197C@columbia.edu> References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <3fb03a6a.10633.13aa798827b.Coremail.w_ang_temp@163.com> <611bda2d.10ae0.13aac91f0d5.Coremail.w_ang_temp@163.com> <01255FF7-A444-48E8-AB48-AE76C710197C@columbia.edu> Message-ID: <5c4f7f1f.c7e0.13abc39f25e.Coremail.w_ang_temp@163.com> Hello, I have just used the latest version 'petsc-3.3-p4.tar.gz'. The codes which are ok under version 'petsc-3.2-p7.tar.gz' are not ok now. The error infomation is as follows. So if can I still use the original codes without any modification and also use multigrid with -pc_type gamg -pc_gamg_agg_nsmooths 1. Thanks. Jim [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Object is in wrong state! [0]PETSC ERROR: Must call MatXXXSetPreallocation() or MatSetUp() on argument 1 "mat" before MatGetOwnershipRange()! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 CDT 2012 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: ./ex4f on a arch-linu named ubuntu by ubu Thu Nov 1 06:10:23 2012 [0]PETSC ERROR: Libraries linked from /home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib [0]PETSC ERROR: Configure run at Thu Nov 1 05:54:48 2012 [0]PETSC ERROR: Configure options --with-mpi-dir=/home/ubu/soft/mpich2/ --download-f-blas-lapack =1 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: MatGetOwnershipRange() line 5992 in src/mat/interface/matrix.c [1]PETSC ERROR: [2]PETSC ERROR: --------------------- Error Message ------------------------------------ [2]PETSC ERROR: Object is in wrong state! [2]PETSC ERROR: Must call MatXXXSetPreallocation() or MatSetUp() on argument 1 "mat" before MatGetOwnershipRange()! [2]PETSC ERROR: ------------------------------------------------------------------------ [2]PETSC ERROR: Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 CDT 2012 [2]PETSC ERROR: See docs/changes/index.html for recent updates. [2]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [2]PETSC ERROR: See docs/index.html for manual pages. [2]PETSC ERROR: ------------------------------------------------------------------------ [2]PETSC ERROR: ./ex4f on a arch-linu named ubuntu by ubu Thu Nov 1 06:10:23 2012 [2]PETSC ERROR: Libraries linked from /home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib [2]PETSC ERROR: Configure run at Thu Nov 1 05:54:48 2012 [2]PETSC ERROR: Configure options --with-mpi-dir=/home/ubu/soft/mpich2/ --download-f-blas-lapack =1 [2]PETSC ERROR: ------------------------------------------------------------------------ [2]PETSC ERROR: MatGetOwnershipRange() line 5992 in src/mat/interface/matrix.c [3]PETSC ERROR: --------------------- Error Message ------------------------------------ [3]PETSC ERROR: Object is in wrong state! [3]PETSC ERROR: Must call MatXXXSetPreallocation() or MatSetUp() on argument 1 "mat" before MatGetOwnershipRange()! [3]PETSC ERROR: ------------------------------------------------------------------------ [3]PETSC ERROR: Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 CDT 2012 [3]PETSC ERROR: See docs/changes/index.html for recent updates. [3]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [3]PETSC ERROR: See docs/index.html for manual pages. [3]PETSC ERROR: ------------------------------------------------------------------------ [3]PETSC ERROR: ./ex4f on a arch-linu named ubuntu by ubu Thu Nov 1 06:10:23 2012 [3]PETSC ERROR: Libraries linked from /home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib [3]PETSC ERROR: Configure run at Thu Nov 1 05:54:48 2012 [3]PETSC ERROR: Configure options --with-mpi-dir=/home/ubu/soft/mpich2/ --download-f-blas-lapack =1 [3]PETSC ERROR: ------------------------------------------------------------------------ [3]PETSC ERROR: MatGetOwnershipRange() line 5992 in src/mat/interface/matrix.c --------------------- Error Message ------------------------------------ [1]PETSC ERROR: Object is in wrong state! [1]PETSC ERROR: Must call MatXXXSetPreallocation() or MatSetUp() on argument 1 "mat" before MatGetOwnershipRange()! [1]PETSC ERROR: ------------------------------------------------------------------------ [1]PETSC ERROR: Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 CDT 2012 [1]PETSC ERROR: See docs/changes/index.html for recent updates. [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [1]PETSC ERROR: See docs/index.html for manual pages. [1]PETSC ERROR: ------------------------------------------------------------------------ [1]PETSC ERROR: ./ex4f on a arch-linu named ubuntu by ubu Thu Nov 1 06:10:23 2012 [1]PETSC ERROR: Libraries linked from /home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib [1]PETSC ERROR: Configure run at Thu Nov 1 05:54:48 2012 [1]PETSC ERROR: Configure options --with-mpi-dir=/home/ubu/soft/mpich2/ --download-f-blas-lapack =1 [1]PETSC ERROR: ------------------------------------------------------------------------ [1]PETSC ERROR: MatGetOwnershipRange() line 5992 in src/mat/interface/matrix.c [1]PETSC ERROR: [2]PETSC ERROR: [3]PETSC ERROR: --------------------- Error Message ------------------------------------ [3]PETSC ERROR: Object is in wrong state! [3]PETSC ERROR: Matrix is missing diagonal entry 0! [3]PETSC ERROR: ------------------------------------------------------------------------ [3]PETSC ERROR: Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 CDT 2012 [3]PETSC ERROR: See docs/changes/index.html for recent updates. [3]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [3]PETSC ERROR: See docs/index.html for manual pages. [3]PETSC ERROR: ------------------------------------------------------------------------ [3]PETSC ERROR: ./ex4f on a arch-linu named ubuntu by ubu Thu Nov 1 06:10:23 2012 [3]PETSC ERROR: Libraries linked from /home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib [3]PETSC ERROR: Configure run at Thu Nov 1 05:54:48 2012 [3]PETSC ERROR: Configure options --with-mpi-dir=/home/ubu/soft/mpich2/ --download-f-blas-lapack =1 [3]PETSC ERROR: ------------------------------------------------------------------------ [3]PETSC ERROR: MatILUFactorSymbolic_SeqAIJ_ilu0() line 1641 in src/mat/impls/aij/seq/aijfact.c [3]PETSC ERROR: MatILUFactorSymbolic_SeqAIJ() line 1745 in src/mat/impls/aij/seq/aijfact.c [3]PETSC ERROR: MatILUFactorSymbolic() line 6130 in src/mat/interface/matrix.c [3]PETSC ERROR: PCSetUp_ILU() line 216 in src/ksp/pc/impls/factor/ilu/ilu.c [3]PETSC ERROR: PCSetUp() line 832 in src/ksp/pc/interface/precon.c [3]PETSC ERROR: KSPSetUp() line 278 in src/ksp/ksp/interface/itfunc.c [3]PETSC ERROR: PCSetUpOnBlocks_BJacobi_Singleblock() line 715 in src/ksp/pc/impls/bjacobi/bjacobi.c [3]PETSC ERROR: PCSetUpOnBlocks() line 865 in src/ksp/pc/interface/precon.c [3]PETSC ERROR: KSPSetUpOnBlocks() line 154 in src/ksp/ksp/interface/itfunc.c [3]PETSC ERROR: KSPSolve() line 403 in src/ksp/ksp/interface/itfunc.c Fatal error in MPI_Send: Invalid count, error stack: MPI_Send(173): MPI_Send(buf=0x100, count=-199040697, MPI_REAL, dest=0, tag=3, MPI_COMM_WORLD) failed MPI_Send(97).: Negative count, value is -199040697 >? 2012-10-29 21:57:49?"Mark F. Adams" ??? >You need an updated PETSc. (I thought 3.2 had an early version of gamg ? but you need 3.3 or dev) >Mark >On Oct 29, 2012, at 8:49 AM, w_ang_temp wrote: >Hello, Jed > I use the command: > mpiexec -n 4 ./ex4f -ksp_type cgs -pc_type gamg -pc_gamg_agg_nsmooths 1 -ksp_rtol 1.0e-15 -ksp_converged_reason > The error is as follows: >[0]PETSC ERROR: --------------------- Error Message ------------------------------------ >[0]PETSC ERROR: Unknown type. Check for miss-spelling or missing external package needed for type > seehttp://www.mcs.anl.gov/petsc/petsc-as/documentation/installation.html#external! >[0]PETSC ERROR: Unable to find requested PC type gamg! >[0]PETSC ERROR: ------------------------------------------------------------------------ >[0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 7, Thu Mar 15 09:30:51 CDT 2012 >[0]PETSC ERROR: See docs/changes/index.html for recent updates. >[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. >[0]PETSC ERROR: See docs/index.html for manual pages. >[0]PETSC ERROR: ------------------------------------------------------------------------ >[0]PETSC ERROR: ./ex4f on a arch-linu named ubuntu by geo Mon Oct 29 05:40:13 2012 >[0]PETSC ERROR: Libraries linked from /home /geo/soft/petsc/petsc-3.2-p7/arch-linux2-c-opt/lib >[0]PETSC ERROR: Configure run at Mon Jul 2 20:33:17 2012 >[0]PETSC ERROR: Configure options --with-mpi-dir=/home/geo/soft/mpich2 --download-f-blas-lapack=1 --with-x=1 --with-debugging=0 -->download-parmetis --download-mumps --download-scalapack --download-blacs >[0]PETSC ERROR: ------------------------------------------------------------------------ >[0]PETSC ERROR: PCSetType() line 67 in src/ksp/pc/interface/pcset.c >[0]PETSC ERROR: PCSetFromOptions() line 184 in src/ksp/pc/interface/pcset.c >[0]PETSC ERROR: KSPSetFromOptions() line 286 in src/ksp/ksp/interface/itcl.c > When I use 'mpiexec -n 4 ./ex4f -ksp_type cgs -pc_type sor -ksp_rtol 1.0e-15 -ksp_converged_reason', it is ok. So >what is the possible reason? > Thanks. > Jim >>At 2012-10-28 22:25:31,"Jed Brown" wrote: >>Try the simple option I just sent. >>On Oct 28, 2012 6:38 AM, "w_ang_temp" wrote: >>Hello, Jed >> Thanks for your timely reply. I deal with the soil-water coupled problem in geotechnical engineering, >>whose stiffness matrix is ill-conditioned. I have did some work about it, mainly finding the effective >>solvers and preconditioners. I used the command line option like this: >>mpiexec -n 4 ./ex4f -ksp_type cgs -pc_type sor -ksp_rtol 1.0e-15 -ksp_converged_reason. >> So, I also want to use the multigrid just like the simple command. There is only a little introduction >>about multigrid in the manual. Multigrid is complex and not a easy thing for me, so I just need to konw how >>to use it simply in PETSc to solve the Ax=b system. >> Thanks. Jim >At 2012-10-28 21:17:00,"Jed Brown" wrote: >Algebraic multigrid can be used directly, -pc_type gamg -pc_gamg_agg_nsmooths 1. Geometric either required that you use the PCMG interface to set >interpolation (and provide a coarse operator for non-Galerkin) or use a DM that provides coarsening capability. >What kind of problem are you solving? >>On Oct 28, 2012 6:09 AM, "w_ang_temp" wrote: >>Hello, >> I want to use the multigrid as a preconditioner. The introduction about it in the manual is little. >>So are there some typical examples or details about multigrid? Is it used just like other preconditioners >>like jacobi, sor, which can be simply used in the cammand line options? >> Thanks. >> Jim -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Thu Nov 1 08:49:35 2012 From: knepley at gmail.com (Matthew Knepley) Date: Thu, 1 Nov 2012 09:49:35 -0400 Subject: [petsc-users] How rto use multigrid? In-Reply-To: <5c4f7f1f.c7e0.13abc39f25e.Coremail.w_ang_temp@163.com> References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <3fb03a6a.10633.13aa798827b.Coremail.w_ang_temp@163.com> <611bda2d.10ae0.13aac91f0d5.Coremail.w_ang_temp@163.com> <01255FF7-A444-48E8-AB48-AE76C710197C@columbia.edu> <5c4f7f1f.c7e0.13abc39f25e.Coremail.w_ang_temp@163.com> Message-ID: On Thu, Nov 1, 2012 at 9:47 AM, w_ang_temp wrote: > Hello, > I have just used the latest version 'petsc-3.3-p4.tar.gz'. The codes > which are ok under version 'petsc-3.2-p7.tar.gz' > are not ok now. The error infomation is as follows. So if can I still use > the original codes without any > modification and also use multigrid with -pc_type gamg > -pc_gamg_agg_nsmooths 1. > Thanks. > Jim > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [0]PETSC ERROR: Object is in wrong state! > [0]PETSC ERROR: Must call MatXXXSetPreallocation() or MatSetUp() on > argument 1 "mat" before MatGetOwnershipRange()! > This says what is wrong. Now you must either preallocate your matrix or turn of this error using MatSetOption() Matt > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 > CDT 2012 > [0]PETSC ERROR: See docs/changes/index.html for recent updates. > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [0]PETSC ERROR: See docs/index.html for manual pages. > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: ./ex4f on a arch-linu named ubuntu by ubu Thu Nov 1 > 06:10:23 2012 > [0]PETSC ERROR: Libraries linked from > /home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib > [0]PETSC ERROR: Configure run at Thu Nov 1 05:54:48 2012 > [0]PETSC ERROR: Configure options --with-mpi-dir=/home/ubu/soft/mpich2/ > --download-f-blas-lapack =1 > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: MatGetOwnershipRange() line 5992 in > src/mat/interface/matrix.c > [1]PETSC ERROR: [2]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [2]PETSC ERROR: Object is in wrong state! > [2]PETSC ERROR: Must call MatXXXSetPreallocation() or MatSetUp() on > argument 1 "mat" before MatGetOwnershipRange()! > [2]PETSC ERROR: > ------------------------------------------------------------------------ > [2]PETSC ERROR: Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 > CDT 2012 > [2]PETSC ERROR: See docs/changes/index.html for recent updates. > [2]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [2]PETSC ERROR: See docs/index.html for manual pages. > [2]PETSC ERROR: > ------------------------------------------------------------------------ > [2]PETSC ERROR: ./ex4f on a arch-linu named ubuntu by ubu Thu Nov 1 > 06:10:23 2012 > [2]PETSC ERROR: Libraries linked from > /home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib > [2]PETSC ERROR: Configure run at Thu Nov 1 05:54:48 2012 > [2]PETSC ERROR: Configure options --with-mpi-dir=/home/ubu/soft/mpich2/ > --download-f-blas-lapack =1 > [2]PETSC ERROR: > ------------------------------------------------------------------------ > [2]PETSC ERROR: MatGetOwnershipRange() line 5992 in > src/mat/interface/matrix.c > [3]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [3]PETSC ERROR: Object is in wrong state! > [3]PETSC ERROR: Must call MatXXXSetPreallocation() or MatSetUp() on > argument 1 "mat" before MatGetOwnershipRange()! > [3]PETSC ERROR: > ------------------------------------------------------------------------ > [3]PETSC ERROR: Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 > CDT 2012 > [3]PETSC ERROR: See docs/changes/index.html for recent updates. > [3]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [3]PETSC ERROR: See docs/index.html for manual pages. > [3]PETSC ERROR: > ------------------------------------------------------------------------ > [3]PETSC ERROR: ./ex4f on a arch-linu named ubuntu by ubu Thu Nov 1 > 06:10:23 2012 > [3]PETSC ERROR: Libraries linked from > /home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib > [3]PETSC ERROR: Configure run at Thu Nov 1 05:54:48 2012 > [3]PETSC ERROR: Configure options --with-mpi-dir=/home/ubu/soft/mpich2/ > --download-f-blas-lapack =1 > [3]PETSC ERROR: > ------------------------------------------------------------------------ > [3]PETSC ERROR: MatGetOwnershipRange() line 5992 in > src/mat/interface/matrix.c > --------------------- Error Message ------------------------------------ > [1]PETSC ERROR: Object is in wrong state! > [1]PETSC ERROR: Must call MatXXXSetPreallocation() or MatSetUp() on > argument 1 "mat" before MatGetOwnershipRange()! > [1]PETSC ERROR: > ------------------------------------------------------------------------ > [1]PETSC ERROR: Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 > CDT 2012 > [1]PETSC ERROR: See docs/changes/index.html for recent updates. > [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [1]PETSC ERROR: See docs/index.html for manual pages. > [1]PETSC ERROR: > ------------------------------------------------------------------------ > [1]PETSC ERROR: ./ex4f on a arch-linu named ubuntu by ubu Thu Nov 1 > 06:10:23 2012 > [1]PETSC ERROR: Libraries linked from > /home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib > [1]PETSC ERROR: Configure run at Thu Nov 1 05:54:48 2012 > [1]PETSC ERROR: Configure options --with-mpi-dir=/home/ubu/soft/mpich2/ > --download-f-blas-lapack =1 > [1]PETSC ERROR: > ------------------------------------------------------------------------ > [1]PETSC ERROR: MatGetOwnershipRange() line 5992 in > src/mat/interface/matrix.c > [1]PETSC ERROR: [2]PETSC ERROR: [3]PETSC ERROR: --------------------- > Error Message ------------------------------------ > [3]PETSC ERROR: Object is in wrong state! > [3]PETSC ERROR: Matrix is missing diagonal entry 0! > [3]PETSC ERROR: > ------------------------------------------------------------------------ > [3]PETSC ERROR: Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 > CDT 2012 > [3]PETSC ERROR: See docs/changes/index.html for recent updates. > [3]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [3]PETSC ERROR: See docs/index.html for manual pages. > [3]PETSC ERROR: > ------------------------------------------------------------------------ > [3]PETSC ERROR: ./ex4f on a arch-linu named ubuntu by ubu Thu Nov 1 > 06:10:23 2012 > [3]PETSC ERROR: Libraries linked from > /home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib > [3]PETSC ERROR: Configure run at Thu Nov 1 05:54:48 2012 > [3]PETSC ERROR: Configure options --with-mpi-dir=/home/ubu/soft/mpich2/ > --download-f-blas-lapack =1 > [3]PETSC ERROR: > ------------------------------------------------------------------------ > [3]PETSC ERROR: MatILUFactorSymbolic_SeqAIJ_ilu0() line 1641 in > src/mat/impls/aij/seq/aijfact.c > [3]PETSC ERROR: MatILUFactorSymbolic_SeqAIJ() line 1745 in > src/mat/impls/aij/seq/aijfact.c > [3]PETSC ERROR: MatILUFactorSymbolic() line 6130 in > src/mat/interface/matrix.c > [3]PETSC ERROR: PCSetUp_ILU() line 216 in src/ksp/pc/impls/factor/ilu/ilu.c > [3]PETSC ERROR: PCSetUp() line 832 in src/ksp/pc/interface/precon.c > [3]PETSC ERROR: KSPSetUp() line 278 in src/ksp/ksp/interface/itfunc.c > [3]PETSC ERROR: PCSetUpOnBlocks_BJacobi_Singleblock() line 715 in > src/ksp/pc/impls/bjacobi/bjacobi.c > [3]PETSC ERROR: PCSetUpOnBlocks() line 865 in src/ksp/pc/interface/precon.c > [3]PETSC ERROR: KSPSetUpOnBlocks() line 154 in > src/ksp/ksp/interface/itfunc.c > [3]PETSC ERROR: KSPSolve() line 403 in src/ksp/ksp/interface/itfunc.c > Fatal error in MPI_Send: Invalid count, error stack: > MPI_Send(173): MPI_Send(buf=0x100, count=-199040697, MPI_REAL, dest=0, > tag=3, MPI_COMM_WORLD) failed > MPI_Send(97).: Negative count, value is -199040697 > > > > > > > > > >? 2012-10-29 21:57:49?"Mark F. Adams" ??? > > >You need an updated PETSc. (I thought 3.2 had an early version of gamg ? > but you need 3.3 or dev) > > >Mark > > >On Oct 29, 2012, at 8:49 AM, w_ang_temp wrote: > > >Hello, Jed > > I use the command: > > mpiexec -n 4 ./ex4f -ksp_type cgs -pc_type gamg -pc_gamg_agg_nsmooths > 1 -ksp_rtol 1.0e-15 -ksp_converged_reason > > The error is as follows: > >[0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > >[0]PETSC ERROR: Unknown type. Check for miss-spelling or missing external > package needed for type > > > seehttp://www.mcs.anl.gov/petsc/petsc-as/documentation/installation.html#external! > >[0]PETSC ERROR: Unable to find requested PC type gamg! > >[0]PETSC ERROR: > ------------------------------------------------------------------------ > >[0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 7, Thu Mar 15 09:30:51 > CDT 2012 > >[0]PETSC ERROR: See docs/changes/index.html for recent updates. > >[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > >[0]PETSC ERROR: See docs/index.html for manual pages. > >[0]PETSC ERROR: > ------------------------------------------------------------------------ > >[0]PETSC ERROR: ./ex4f on a arch-linu named ubuntu by geo Mon Oct 29 > 05:40:13 2012 > >[0]PETSC ERROR: Libraries linked from /home > /geo/soft/petsc/petsc-3.2-p7/arch-linux2-c-opt/lib > >[0]PETSC ERROR: Configure run at Mon Jul 2 20:33:17 2012 > >[0]PETSC ERROR: Configure options --with-mpi-dir=/home/geo/soft/mpich2 > --download-f-blas-lapack=1 --with-x=1 --with-debugging=0 > -->download-parmetis --download-mumps --download-scalapack --download-blacs > >[0]PETSC ERROR: > ------------------------------------------------------------------------ > >[0]PETSC ERROR: PCSetType() line 67 in src/ksp/pc/interface/pcset.c > >[0]PETSC ERROR: PCSetFromOptions() line 184 in > src/ksp/pc/interface/pcset.c > >[0]PETSC ERROR: KSPSetFromOptions() line 286 in > src/ksp/ksp/interface/itcl.c > > When I use 'mpiexec -n 4 ./ex4f -ksp_type cgs -pc_type sor -ksp_rtol > 1.0e-15 -ksp_converged_reason', it is ok. So > >what is the possible reason? > > Thanks. > > Jim > > > > > > >>At 2012-10-28 22:25:31,"Jed Brown" wrote: > > >>Try the simple option I just sent. > >>On Oct 28, 2012 6:38 AM, "w_ang_temp" wrote: > >> >>Hello, Jed >> >> Thanks for your timely reply. I deal with the soil-water coupled >> problem in geotechnical engineering, >> >>whose stiffness matrix is ill-conditioned. I have did some work about >> it, mainly finding the effective >> >>solvers and preconditioners. I used the command line option like this: >> >>mpiexec -n 4 ./ex4f -ksp_type cgs -pc_type sor -ksp_rtol 1.0e-15 >> -ksp_converged_reason. >> >> So, I also want to use the multigrid just like the simple command. >> There is only a little introduction >> >>about multigrid in the manual. Multigrid is complex and not a easy >> thing for me, so I just need to konw how >> >>to use it simply in PETSc to solve the Ax=b system. >> >> Thanks. >> Jim >> >> >> >> >> >> >At 2012-10-28 21:17:00,"Jed Brown" wrote: >> >> >Algebraic multigrid can be used directly, -pc_type gamg >> -pc_gamg_agg_nsmooths 1. Geometric either required that you use the PCMG >> interface to set >interpolation (and provide a coarse operator for >> non-Galerkin) or use a DM that provides coarsening capability. >> >> >What kind of problem are you solving? >> >>On Oct 28, 2012 6:09 AM, "w_ang_temp" wrote: >> >>> >>Hello, >>> >> I want to use the multigrid as a preconditioner. The introduction >>> about it in the manual is little. >>> >>So are there some typical examples or details about multigrid? Is it >>> used just like other preconditioners >>> >>like jacobi, sor, which can be simply used in the cammand line options? >>> >> Thanks. >>> >> >>> Jim >>> >>> >>> >> >> > > > > > -- 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From w_ang_temp at 163.com Thu Nov 1 08:57:51 2012 From: w_ang_temp at 163.com (w_ang_temp) Date: Thu, 1 Nov 2012 21:57:51 +0800 (CST) Subject: [petsc-users] How rto use multigrid? In-Reply-To: References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <3fb03a6a.10633.13aa798827b.Coremail.w_ang_temp@163.com> <611bda2d.10ae0.13aac91f0d5.Coremail.w_ang_temp@163.com> <01255FF7-A444-48E8-AB48-AE76C710197C@columbia.edu> <5c4f7f1f.c7e0.13abc39f25e.Coremail.w_ang_temp@163.com> Message-ID: <50cc9123.12a74.13abc43826a.Coremail.w_ang_temp@163.com> Hello, Matthew Do you mean that the two versions have a different in this point? If I use the new version, I have to make some modifications on my codes? Thanks. Jim >? 2012-11-01 21:49:35?"Matthew Knepley" ??? >On Thu, Nov 1, 2012 at 9:47 AM, w_ang_temp wrote: >Hello, > I have just used the latest version 'petsc-3.3-p4.tar.gz'. The codes which are ok under version 'petsc-3.2-p7.tar.gz' >are not ok now. The error infomation is as follows. So if can I still use the original codes without any >modification and also use multigrid with -pc_type gamg -pc_gamg_agg_nsmooths 1. > Thanks. Jim >[0]PETSC ERROR: --------------------- Error Message ------------------------------------ >[0]PETSC ERROR: Object is in wrong state! >[0]PETSC ERROR: Must call MatXXXSetPreallocation() or MatSetUp() on argument 1 "mat" before MatGetOwnershipRange()! >This says what is wrong. Now you must either preallocate your matrix or turn of this error using MatSetOption() > Matt >>[0]PETSC ERROR: ------------------------------------------------------------------------ >>[0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 CDT 2012 >>[0]PETSC ERROR: See docs/changes/index.html for recent updates. >>[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. >>[0]PETSC ERROR: See docs/index.html for manual pages. >>[0]PETSC ERROR: ------------------------------------------------------------------------ >>[0]PETSC ERROR: ./ex4f on a arch-linu named ubuntu by ubu Thu Nov 1 06:10:23 2012 >>[0]PETSC ERROR: Libraries linked from /home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib >>[0]PETSC ERROR: Configure run at Thu Nov 1 05:54:48 2012 >>[0]PETSC ERROR: Configure options --with-mpi-dir=/home/ubu/soft/mpich2/ --download-f-blas-lapack =1 >>[0]PETSC ERROR: ------------------------------------------------------------------------ >>[0]PETSC ERROR: MatGetOwnershipRange() line 5992 in src/mat/interface/matrix.c >>[1]PETSC ERROR: [2]PETSC ERROR: --------------------- Error Message ------------------------------------ >>[2]PETSC ERROR: Object is in wrong state! >>[2]PETSC ERROR: Must call MatXXXSetPreallocation() or MatSetUp() on argument 1 "mat" before MatGetOwnershipRange()! >>[2]PETSC ERROR: ------------------------------------------------------------------------ >>[2]PETSC ERROR: Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 CDT 2012 >>[2]PETSC ERROR: See docs/changes/index.html for recent updates. >>[2]PETSC ERROR: See docs/faq.html for hints about trouble shooting. >>[2]PETSC ERROR: See docs/index.html for manual pages. >>[2]PETSC ERROR: ------------------------------------------------------------------------ >>[2]PETSC ERROR: ./ex4f on a arch-linu named ubuntu by ubu Thu Nov 1 06:10:23 2012 >>[2]PETSC ERROR: Libraries linked from /home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib >>[2]PETSC ERROR: Configure run at Thu Nov 1 05:54:48 2012 >>[2]PETSC ERROR: Configure options --with-mpi-dir=/home/ubu/soft/mpich2/ --download-f-blas-lapack =1 >>[2]PETSC ERROR: ------------------------------------------------------------------------ >>[2]PETSC ERROR: MatGetOwnershipRange() line 5992 in src/mat/interface/matrix.c >>[3]PETSC ERROR: --------------------- Error Message ------------------------------------ >>[3]PETSC ERROR: Object is in wrong state! >>[3]PETSC ERROR: Must call MatXXXSetPreallocation() or MatSetUp() on argument 1 "mat" before MatGetOwnershipRange()! >>[3]PETSC ERROR: ------------------------------------------------------------------------ >>[3]PETSC ERROR: Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 CDT 2012 >>[3]PETSC ERROR: See docs/changes/index.html for recent updates. >>[3]PETSC ERROR: See docs/faq.html for hints about trouble shooting. >>[3]PETSC ERROR: See docs/index.html for manual pages. >>[3]PETSC ERROR: ------------------------------------------------------------------------ >>[3]PETSC ERROR: ./ex4f on a arch-linu named ubuntu by ubu Thu Nov 1 06:10:23 2012 >>[3]PETSC ERROR: Libraries linked from /home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib >>[3]PETSC ERROR: Configure run at Thu Nov 1 05:54:48 2012 >>[3]PETSC ERROR: Configure options --with-mpi-dir=/home/ubu/soft/mpich2/ --download-f-blas-lapack =1 >>[3]PETSC ERROR: ------------------------------------------------------------------------ >>[3]PETSC ERROR: MatGetOwnershipRange() line 5992 in src/mat/interface/matrix.c >>--------------------- Error Message ------------------------------------ >>[1]PETSC ERROR: Object is in wrong state! >>[1]PETSC ERROR: Must call MatXXXSetPreallocation() or MatSetUp() on argument 1 "mat" before MatGetOwnershipRange()! >>[1]PETSC ERROR: ------------------------------------------------------------------------ >>[1]PETSC ERROR: Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 CDT 2012 >>[1]PETSC ERROR: See docs/changes/index.html for recent updates. >>[1]PETSC ERROR: See docs/faq.html for hints about trouble shooting. >>[1]PETSC ERROR: See docs/index.html for manual pages. >>[1]PETSC ERROR: ------------------------------------------------------------------------ >>[1]PETSC ERROR: ./ex4f on a arch-linu named ubuntu by ubu Thu Nov 1 06:10:23 2012 >>[1]PETSC ERROR: Libraries linked from /home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib >>[1]PETSC ERROR: Configure run at Thu Nov 1 05:54:48 2012 >>[1]PETSC ERROR: Configure options --with-mpi-dir=/home/ubu/soft/mpich2/ --download-f-blas-lapack =1 >>[1]PETSC ERROR: ------------------------------------------------------------------------ >>[1]PETSC ERROR: MatGetOwnershipRange() line 5992 in src/mat/interface/matrix.c >>[1]PETSC ERROR: [2]PETSC ERROR: [3]PETSC ERROR: --------------------- Error Message ------------------------------------ >>[3]PETSC ERROR: Object is in wrong state! >>[3]PETSC ERROR: Matrix is missing diagonal entry 0! >>[3]PETSC ERROR: ------------------------------------------------------------------------ >>[3]PETSC ERROR: Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 CDT 2012 >>[3]PETSC ERROR: See docs/changes/index.html for recent updates. >>[3]PETSC ERROR: See docs/faq.html for hints about trouble shooting. >>[3]PETSC ERROR: See docs/index.html for manual pages. >>[3]PETSC ERROR: ------------------------------------------------------------------------ >>[3]PETSC ERROR: ./ex4f on a arch-linu named ubuntu by ubu Thu Nov 1 06:10:23 2012 >>[3]PETSC ERROR: Libraries linked from /home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib >>[3]PETSC ERROR: Configure run at Thu Nov 1 05:54:48 2012 >>[3]PETSC ERROR: Configure options --with-mpi-dir=/home/ubu/soft/mpich2/ --download-f-blas-lapack =1 >>[3]PETSC ERROR: ------------------------------------------------------------------------ >>[3]PETSC ERROR: MatILUFactorSymbolic_SeqAIJ_ilu0() line 1641 in src/mat/impls/aij/seq/aijfact.c >>[3]PETSC ERROR: MatILUFactorSymbolic_SeqAIJ() line 1745 in src/mat/impls/aij/seq/aijfact.c >>[3]PETSC ERROR: MatILUFactorSymbolic() line 6130 in src/mat/interface/matrix.c >>[3]PETSC ERROR: PCSetUp_ILU() line 216 in src/ksp/pc/impls/factor/ilu/ilu.c >>[3]PETSC ERROR: PCSetUp() line 832 in src/ksp/pc/interface/precon.c >>[3]PETSC ERROR: KSPSetUp() line 278 in src/ksp/ksp/interface/itfunc.c >>[3]PETSC ERROR: PCSetUpOnBlocks_BJacobi_Singleblock() line 715 in src/ksp/pc/impls/bjacobi/bjacobi.c >>[3]PETSC ERROR: PCSetUpOnBlocks() line 865 in src/ksp/pc/interface/precon.c >>[3]PETSC ERROR: KSPSetUpOnBlocks() line 154 in src/ksp/ksp/interface/itfunc.c >>[3]PETSC ERROR: KSPSolve() line 403 in src/ksp/ksp/interface/itfunc.c >>Fatal error in MPI_Send: Invalid count, error stack: >>MPI_Send(173): MPI_Send(buf=0x100, count=-199040697, MPI_REAL, dest=0, tag=3, MPI_COMM_WORLD) failed >>MPI_Send(97).: Negative count, value is -199040697 >? 2012-10-29 21:57:49?"Mark F. Adams" ??? >You need an updated PETSc. (I thought 3.2 had an early version of gamg ? but you need 3.3 or dev) >Mark >On Oct 29, 2012, at 8:49 AM, w_ang_temp wrote: >Hello, Jed > I use the command: > mpiexec -n 4 ./ex4f -ksp_type cgs -pc_type gamg -pc_gamg_agg_nsmooths 1 -ksp_rtol 1.0e-15 -ksp_converged_reason > The error is as follows: >[0]PETSC ERROR: --------------------- Error Message ------------------------------------ >[0]PETSC ERROR: Unknown type. Check for miss-spelling or missing external package needed for type > seehttp://www.mcs.anl.gov/petsc/petsc-as/documentation/installation.html#external! >[0]PETSC ERROR: Unable to find requested PC type gamg! >[0]PETSC ERROR: ------------------------------------------------------------------------ >[0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 7, Thu Mar 15 09:30:51 CDT 2012 >[0]PETSC ERROR: See docs/changes/index.html for recent updates. >[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. >[0]PETSC ERROR: See docs/index.html for manual pages. >[0]PETSC ERROR: ------------------------------------------------------------------------ >[0]PETSC ERROR: ./ex4f on a arch-linu named ubuntu by geo Mon Oct 29 05:40:13 2012 >[0]PETSC ERROR: Libraries linked from /home /geo/soft/petsc/petsc-3.2-p7/arch-linux2-c-opt/lib >[0]PETSC ERROR: Configure run at Mon Jul 2 20:33:17 2012 >[0]PETSC ERROR: Configure options --with-mpi-dir=/home/geo/soft/mpich2 --download-f-blas-lapack=1 --with-x=1 --with-debugging=0 -->download-parmetis --download-mumps --download-scalapack --download-blacs >[0]PETSC ERROR: ------------------------------------------------------------------------ >[0]PETSC ERROR: PCSetType() line 67 in src/ksp/pc/interface/pcset.c >[0]PETSC ERROR: PCSetFromOptions() line 184 in src/ksp/pc/interface/pcset.c >[0]PETSC ERROR: KSPSetFromOptions() line 286 in src/ksp/ksp/interface/itcl.c > When I use 'mpiexec -n 4 ./ex4f -ksp_type cgs -pc_type sor -ksp_rtol 1.0e-15 -ksp_converged_reason', it is ok. So >what is the possible reason? > Thanks. > Jim >>At 2012-10-28 22:25:31,"Jed Brown" wrote: >>Try the simple option I just sent. >>On Oct 28, 2012 6:38 AM, "w_ang_temp" wrote: >>Hello, Jed >> Thanks for your timely reply. I deal with the soil-water coupled problem in geotechnical engineering, >>whose stiffness matrix is ill-conditioned. I have did some work about it, mainly finding the effective >>solvers and preconditioners. I used the command line option like this: >>mpiexec -n 4 ./ex4f -ksp_type cgs -pc_type sor -ksp_rtol 1.0e-15 -ksp_converged_reason. >> So, I also want to use the multigrid just like the simple command. There is only a little introduction >>about multigrid in the manual. Multigrid is complex and not a easy thing for me, so I just need to konw how >>to use it simply in PETSc to solve the Ax=b system. >> Thanks. Jim >At 2012-10-28 21:17:00,"Jed Brown" wrote: >Algebraic multigrid can be used directly, -pc_type gamg -pc_gamg_agg_nsmooths 1. Geometric either required that you use the PCMG interface to set >interpolation (and provide a coarse operator for non-Galerkin) or use a DM that provides coarsening capability. >What kind of problem are you solving? >>On Oct 28, 2012 6:09 AM, "w_ang_temp" wrote: >>Hello, >> I want to use the multigrid as a preconditioner. The introduction about it in the manual is little. >>So are there some typical examples or details about multigrid? Is it used just like other preconditioners >>like jacobi, sor, which can be simply used in the cammand line options? >> Thanks. >> Jim -- 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Thu Nov 1 09:00:28 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Thu, 1 Nov 2012 09:00:28 -0500 Subject: [petsc-users] How rto use multigrid? In-Reply-To: <50cc9123.12a74.13abc43826a.Coremail.w_ang_temp@163.com> References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <3fb03a6a.10633.13aa798827b.Coremail.w_ang_temp@163.com> <611bda2d.10ae0.13aac91f0d5.Coremail.w_ang_temp@163.com> <01255FF7-A444-48E8-AB48-AE76C710197C@columbia.edu> <5c4f7f1f.c7e0.13abc39f25e.Coremail.w_ang_temp@163.com> <50cc9123.12a74.13abc43826a.Coremail.w_ang_temp@163.com> Message-ID: Yes, it's faster to understand this error message than to have "mysteriously slow performance". ** Preallocation routines now automatically set MAT_NEW_NONZERO_ALLOCATION_ERR, if you intentionally preallocate less than necessary then use MatSetOption(mat,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE) to disable the error generation. * http://www.mcs.anl.gov/petsc/documentation/changes/33.html On Thu, Nov 1, 2012 at 8:57 AM, w_ang_temp wrote: > Do you mean that the two versions have a different in this point? If I use > the new version, I have to > make some modifications on my codes? > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhaonanavril at gmail.com Thu Nov 1 11:49:50 2012 From: zhaonanavril at gmail.com (NAN ZHAO) Date: Thu, 1 Nov 2012 11:49:50 -0500 Subject: [petsc-users] KSP scale problems Message-ID: Dear all, I am using PETSC to solve a fairly large linear system, petsc sometimes give me a answer of 10E-8 (but it should be 0). I do some research and found if I scale some parts of the linear system to a very small scale (for example I scale the third equation I solve to 1e-6), and PETSC give me the right answer (I got zero at the place it should be zero). Is any one have some hint of how to set some parameter in PETSC to archieve this as the user is not able to set the scale easily. Thanks, Nan -------------- next part -------------- An HTML attachment was scrubbed... URL: From rupp at mcs.anl.gov Thu Nov 1 12:56:34 2012 From: rupp at mcs.anl.gov (Karl Rupp) Date: Thu, 01 Nov 2012 12:56:34 -0500 Subject: [petsc-users] [petsc-maint #138291] KSP scale problems In-Reply-To: References: Message-ID: <5092B7D2.8080307@mcs.anl.gov> Hi, due to round-off errors it is essentially impossible to ensure 'true zeros' in general. If you know a-priori that some entries have to be zero, you might simply overwrite your solution vector after the solver run accordingly. Instead, you may also decide not to assemble the respective equations for these 'known unknowns' at all. Best regards, Karli On 11/01/2012 11:49 AM, NAN ZHAO wrote: > Dear all, > > I am using PETSC to solve a fairly large linear system, petsc sometimes > give me a answer of 10E-8 (but it should be 0). I do some research and > found if I scale some parts of the linear system to a very small scale (for > example I scale the third equation I solve to 1e-6), and PETSC give me the > right answer (I got zero at the place it should be zero). Is any one have > some hint of how to set some parameter in PETSC to archieve this as the > user is not able to set the scale easily. > > Thanks, > Nan > From zhaonanavril at gmail.com Fri Nov 2 09:15:28 2012 From: zhaonanavril at gmail.com (NAN ZHAO) Date: Fri, 2 Nov 2012 09:15:28 -0500 Subject: [petsc-users] small number (1e-23) in the matrix Message-ID: Dear all, I am using PETSC to solve a nonlinear system with newton's method. I actually calculate the jacobian matrix in each newton iteration and solve the linear system by KSPsolve. However, I found one thing really brothers me is the ultra small numbers in the matrix (MPIBAIJ matrix). In the sparse matrix I create some location should be zero but I got some small values like 1e-23 instead. I use matzeroentries each time I give new value to the matrix and this problem still exist. What makes me more confuse is that if I do not use matzeroentries each time I give new values to the matrix, the locations which should be zero get exactly 0.0000e0 (although other values is wrong, cause I add new value to the location when I assemble the matrix, I can not use insert as the procedure is like finite element assembling). Does anyone have insight of why this happens? P.S. I tried destroy the matrix each time I give the new value but same thing happens. Regards, Nan -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Fri Nov 2 09:21:12 2012 From: knepley at gmail.com (Matthew Knepley) Date: Fri, 2 Nov 2012 10:21:12 -0400 Subject: [petsc-users] small number (1e-23) in the matrix In-Reply-To: References: Message-ID: On Fri, Nov 2, 2012 at 10:15 AM, NAN ZHAO wrote: > Dear all, > > I am using PETSC to solve a nonlinear system with newton's method. I > actually calculate the jacobian matrix in each newton iteration and solve > the linear system by KSPsolve. However, I found one thing > really brothers me is the ultra small numbers in the matrix (MPIBAIJ > matrix). In the sparse matrix I create some location should be zero but I > got some small values like 1e-23 instead. I use matzeroentries each time I > give new value to the matrix and this problem still exist. What makes me > more confuse is that if I do not use matzeroentries each time I give new > values to the matrix, the locations which should be zero get exactly > 0.0000e0 (although other values is wrong, cause I add new value to the > location when I assemble the matrix, I can not use insert as the procedure > is like finite element assembling). Does anyone have insight of why this > happens? P.S. I tried destroy the matrix each time I give the new value but > same thing happens. > You are not doing what you think you are doing. This has nothing to do with MatZeroEntries(). You are inserting weird values in the matrix, probably by misspecifying a length, so that MatSetValues() reads off the end of an array. Run your code through valgrind. Matt > Regards, > Nan > -- 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From fd.kong at siat.ac.cn Fri Nov 2 16:41:56 2012 From: fd.kong at siat.ac.cn (Fande Kong) Date: Fri, 2 Nov 2012 15:41:56 -0600 Subject: [petsc-users] Are there any functions (objects ) for scattering and gathering 64-bit integers just like VecScatter for PetscScalar? Message-ID: Hi all, Are there any functions (objects ) for scattering and gathering 64-bit integers just like VecScatter for PetscScalar? The VecScatter is very useful for managing communication for PetscScalar. But I can't find any functions or objects to do similar things for PetscInt. Any suggestions? Regards, -- Fande Kong ShenZhen Institutes of Advanced Technology Chinese Academy of Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From fande.kong at colorado.edu Fri Nov 2 16:48:47 2012 From: fande.kong at colorado.edu (Fande Kong) Date: Fri, 2 Nov 2012 15:48:47 -0600 Subject: [petsc-users] Are there any functions (objects ) for scattering and gathering 64-bit integers just like VecScatter for PetscScalar? Message-ID: Hi all, Are there any functions (objects ) for scattering and gathering 64-bit integers just like VecScatter for PetscScalar? The VecScatter is very useful for managing communication for PetscScalar. But I can't find any functions or objects to do similar things for PetscInt. Any suggestions? Regards, -- Fande Kong Department of Computer Science University of Colorado at Boulder -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Fri Nov 2 16:50:35 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Fri, 2 Nov 2012 16:50:35 -0500 Subject: [petsc-users] Are there any functions (objects ) for scattering and gathering 64-bit integers just like VecScatter for PetscScalar? In-Reply-To: References: Message-ID: I am using PetscSF for this. You would need petsc-dev and the current implementation requires an MPI with non-broken data types. https://bitbucket.org/petsc/petsc-dev/issue/9/implement-petscsf-without-one-sided Here are some (dated) notes about the communication model. http://59A2.org/files/StarForest.pdf On Fri, Nov 2, 2012 at 4:41 PM, Fande Kong wrote: > Hi all, > > Are there any functions (objects ) for scattering and gathering 64-bit > integers just like VecScatter for PetscScalar? The VecScatter is very > useful for managing communication for PetscScalar. But I can't find any > functions or objects to do similar things for PetscInt. Any suggestions? > > Regards, > -- > Fande Kong > ShenZhen Institutes of Advanced Technology > Chinese Academy of Sciences > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From fd.kong at siat.ac.cn Fri Nov 2 17:01:47 2012 From: fd.kong at siat.ac.cn (Fande Kong) Date: Fri, 2 Nov 2012 16:01:47 -0600 Subject: [petsc-users] Are there any functions (objects ) for scattering and gathering 64-bit integers just like VecScatter for PetscScalar? In-Reply-To: References: Message-ID: did you remove horrible one-side communication? and did you make some tests with using 64-bit integers? On Fri, Nov 2, 2012 at 3:50 PM, Jed Brown wrote: > I am using PetscSF for this. You would need petsc-dev and the current > implementation requires an MPI with non-broken data types. > > > https://bitbucket.org/petsc/petsc-dev/issue/9/implement-petscsf-without-one-sided > > Here are some (dated) notes about the communication model. > http://59A2.org/files/StarForest.pdf > > > On Fri, Nov 2, 2012 at 4:41 PM, Fande Kong wrote: > >> Hi all, >> >> Are there any functions (objects ) for scattering and gathering 64-bit >> integers just like VecScatter for PetscScalar? The VecScatter is very >> useful for managing communication for PetscScalar. But I can't find any >> functions or objects to do similar things for PetscInt. Any suggestions? >> >> Regards, >> -- >> Fande Kong >> ShenZhen Institutes of Advanced Technology >> Chinese Academy of Sciences >> >> >> >> > -- Fande Kong ShenZhen Institutes of Advanced Technology Chinese Academy of Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Fri Nov 2 17:04:18 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Fri, 2 Nov 2012 17:04:18 -0500 Subject: [petsc-users] Are there any functions (objects ) for scattering and gathering 64-bit integers just like VecScatter for PetscScalar? In-Reply-To: References: Message-ID: The current implementation uses one-sided because that was a natural. I need a solid day to implement without one-sided. As stated in the issue I posted, this is necessary because Open MPI data types are broken. On Fri, Nov 2, 2012 at 5:01 PM, Fande Kong wrote: > did you remove horrible one-side communication? and did you make some > tests with using 64-bit integers? > > > On Fri, Nov 2, 2012 at 3:50 PM, Jed Brown wrote: > >> I am using PetscSF for this. You would need petsc-dev and the current >> implementation requires an MPI with non-broken data types. >> >> >> https://bitbucket.org/petsc/petsc-dev/issue/9/implement-petscsf-without-one-sided >> >> Here are some (dated) notes about the communication model. >> http://59A2.org/files/StarForest.pdf >> >> >> On Fri, Nov 2, 2012 at 4:41 PM, Fande Kong wrote: >> >>> Hi all, >>> >>> Are there any functions (objects ) for scattering and gathering 64-bit >>> integers just like VecScatter for PetscScalar? The VecScatter is very >>> useful for managing communication for PetscScalar. But I can't find any >>> functions or objects to do similar things for PetscInt. Any suggestions? >>> >>> Regards, >>> -- >>> Fande Kong >>> ShenZhen Institutes of Advanced Technology >>> Chinese Academy of Sciences >>> >>> >>> >>> >> > > > -- > Fande Kong > ShenZhen Institutes of Advanced Technology > Chinese Academy of Sciences > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From fd.kong at siat.ac.cn Fri Nov 2 17:24:08 2012 From: fd.kong at siat.ac.cn (Fande Kong) Date: Fri, 2 Nov 2012 16:24:08 -0600 Subject: [petsc-users] Are there any functions (objects ) for scattering and gathering 64-bit integers just like VecScatter for PetscScalar? In-Reply-To: References: Message-ID: I got it. You still didn't fix the bugs that I encountered a few months ago. All current MPI implementations couldn't support the function MPI_Accumulate or others well with one-sided communication when data is large. Thus, I have to hack your code (PetscSF) to use point-point communications. But I find it's not so easy. don't you want to change to use point-point? On Fri, Nov 2, 2012 at 4:04 PM, Jed Brown wrote: > The current implementation uses one-sided because that was a natural. I > need a solid day to implement without one-sided. As stated in the issue I > posted, this is necessary because Open MPI data types are broken. > > > On Fri, Nov 2, 2012 at 5:01 PM, Fande Kong wrote: > >> did you remove horrible one-side communication? and did you make some >> tests with using 64-bit integers? >> >> >> On Fri, Nov 2, 2012 at 3:50 PM, Jed Brown wrote: >> >>> I am using PetscSF for this. You would need petsc-dev and the current >>> implementation requires an MPI with non-broken data types. >>> >>> >>> https://bitbucket.org/petsc/petsc-dev/issue/9/implement-petscsf-without-one-sided >>> >>> Here are some (dated) notes about the communication model. >>> http://59A2.org/files/StarForest.pdf >>> >>> >>> On Fri, Nov 2, 2012 at 4:41 PM, Fande Kong wrote: >>> >>>> Hi all, >>>> >>>> Are there any functions (objects ) for scattering and gathering 64-bit >>>> integers just like VecScatter for PetscScalar? The VecScatter is very >>>> useful for managing communication for PetscScalar. But I can't find any >>>> functions or objects to do similar things for PetscInt. Any suggestions? >>>> >>>> Regards, >>>> -- >>>> Fande Kong >>>> ShenZhen Institutes of Advanced Technology >>>> Chinese Academy of Sciences >>>> >>>> >>>> >>>> >>> >> >> >> -- >> Fande Kong >> ShenZhen Institutes of Advanced Technology >> Chinese Academy of Sciences >> >> > -- Fande Kong ShenZhen Institutes of Advanced Technology Chinese Academy of Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Fri Nov 2 17:38:08 2012 From: knepley at gmail.com (Matthew Knepley) Date: Fri, 2 Nov 2012 18:38:08 -0400 Subject: [petsc-users] Are there any functions (objects ) for scattering and gathering 64-bit integers just like VecScatter for PetscScalar? In-Reply-To: References: Message-ID: On Fri, Nov 2, 2012 at 6:24 PM, Fande Kong wrote: > I got it. You still didn't fix the bugs that I encountered a few months > ago. All current MPI implementations couldn't support the function > MPI_Accumulate or others well with one-sided communication when data is > large. Thus, I have to hack your code (PetscSF) to use point-point > communications. But I find it's not so easy. Can't you just use MPICH since it does not have bugs? What is the point of using a buggy MPI? Thanks, Matt > > don't you want to change to use point-point? > > On Fri, Nov 2, 2012 at 4:04 PM, Jed Brown wrote: > >> The current implementation uses one-sided because that was a natural. I >> need a solid day to implement without one-sided. As stated in the issue I >> posted, this is necessary because Open MPI data types are broken. >> >> >> On Fri, Nov 2, 2012 at 5:01 PM, Fande Kong wrote: >> >>> did you remove horrible one-side communication? and did you make some >>> tests with using 64-bit integers? >>> >>> >>> On Fri, Nov 2, 2012 at 3:50 PM, Jed Brown wrote: >>> >>>> I am using PetscSF for this. You would need petsc-dev and the current >>>> implementation requires an MPI with non-broken data types. >>>> >>>> >>>> https://bitbucket.org/petsc/petsc-dev/issue/9/implement-petscsf-without-one-sided >>>> >>>> Here are some (dated) notes about the communication model. >>>> http://59A2.org/files/StarForest.pdf >>>> >>>> >>>> On Fri, Nov 2, 2012 at 4:41 PM, Fande Kong wrote: >>>> >>>>> Hi all, >>>>> >>>>> Are there any functions (objects ) for scattering and gathering 64-bit >>>>> integers just like VecScatter for PetscScalar? The VecScatter is very >>>>> useful for managing communication for PetscScalar. But I can't find any >>>>> functions or objects to do similar things for PetscInt. Any suggestions? >>>>> >>>>> Regards, >>>>> -- >>>>> Fande Kong >>>>> ShenZhen Institutes of Advanced Technology >>>>> Chinese Academy of Sciences >>>>> >>>>> >>>>> >>>>> >>>> >>> >>> >>> -- >>> Fande Kong >>> ShenZhen Institutes of Advanced Technology >>> Chinese Academy of Sciences >>> >>> >> > > > -- > Fande Kong > ShenZhen Institutes of Advanced Technology > Chinese Academy of Sciences > > -- 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Fri Nov 2 17:41:20 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Fri, 2 Nov 2012 17:41:20 -0500 Subject: [petsc-users] Are there any functions (objects ) for scattering and gathering 64-bit integers just like VecScatter for PetscScalar? In-Reply-To: References: Message-ID: On Nov 2, 2012 5:24 PM, "Fande Kong" wrote: > > I got it. You still didn't fix the bugs that I encountered a few months ago. All current MPI implementations couldn't support the function MPI_Accumulate or others well with one-sided communication when data is large. I have not had problems with MPICH. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Fri Nov 2 17:41:20 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Fri, 2 Nov 2012 17:41:20 -0500 Subject: [petsc-users] Are there any functions (objects ) for scattering and gathering 64-bit integers just like VecScatter for PetscScalar? In-Reply-To: References: Message-ID: Read the issue I linked. You can watch it to be notified of action. It should be obvious that I've known about the Open MPI problem for a long time. You can also ask them to fix their bug. They _should_ fix it regardless. On Nov 2, 2012 5:24 PM, "Fande Kong" wrote: > I got it. You still didn't fix the bugs that I encountered a few months > ago. All current MPI implementations couldn't support the function > MPI_Accumulate or others well with one-sided communication when data is > large. Thus, I have to hack your code (PetscSF) to use point-point > communications. But I find it's not so easy. > > don't you want to change to use point-point? > > On Fri, Nov 2, 2012 at 4:04 PM, Jed Brown wrote: > >> The current implementation uses one-sided because that was a natural. I >> need a solid day to implement without one-sided. As stated in the issue I >> posted, this is necessary because Open MPI data types are broken. >> >> >> On Fri, Nov 2, 2012 at 5:01 PM, Fande Kong wrote: >> >>> did you remove horrible one-side communication? and did you make some >>> tests with using 64-bit integers? >>> >>> >>> On Fri, Nov 2, 2012 at 3:50 PM, Jed Brown wrote: >>> >>>> I am using PetscSF for this. You would need petsc-dev and the current >>>> implementation requires an MPI with non-broken data types. >>>> >>>> >>>> https://bitbucket.org/petsc/petsc-dev/issue/9/implement-petscsf-without-one-sided >>>> >>>> Here are some (dated) notes about the communication model. >>>> http://59A2.org/files/StarForest.pdf >>>> >>>> >>>> On Fri, Nov 2, 2012 at 4:41 PM, Fande Kong wrote: >>>> >>>>> Hi all, >>>>> >>>>> Are there any functions (objects ) for scattering and gathering 64-bit >>>>> integers just like VecScatter for PetscScalar? The VecScatter is very >>>>> useful for managing communication for PetscScalar. But I can't find any >>>>> functions or objects to do similar things for PetscInt. Any suggestions? >>>>> >>>>> Regards, >>>>> -- >>>>> Fande Kong >>>>> ShenZhen Institutes of Advanced Technology >>>>> Chinese Academy of Sciences >>>>> >>>>> >>>>> >>>>> >>>> >>> >>> >>> -- >>> Fande Kong >>> ShenZhen Institutes of Advanced Technology >>> Chinese Academy of Sciences >>> >>> >> > > > -- > Fande Kong > ShenZhen Institutes of Advanced Technology > Chinese Academy of Sciences > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From fd.kong at siat.ac.cn Fri Nov 2 17:57:43 2012 From: fd.kong at siat.ac.cn (Fande Kong) Date: Fri, 2 Nov 2012 16:57:43 -0600 Subject: [petsc-users] Are there any functions (objects ) for scattering and gathering 64-bit integers just like VecScatter for PetscScalar? In-Reply-To: References: Message-ID: Yes. I haven't tested my code on MPICH. Because MPICH don't support infiniband in the supercomputer. But I have tested code on mvapich. It also has bugs, when the finite mesh is larger than 50M. Now, I just want to know if you will change to use point-point. If you would not, I will try to rewrite PetscSF for me. Thanks, On Fri, Nov 2, 2012 at 4:41 PM, Jed Brown wrote: > > On Nov 2, 2012 5:24 PM, "Fande Kong" wrote: > > > > I got it. You still didn't fix the bugs that I encountered a few months > ago. All current MPI implementations couldn't support the function > MPI_Accumulate or others well with one-sided communication when data is > large. > > I have not had problems with MPICH. > -- Fande Kong ShenZhen Institutes of Advanced Technology Chinese Academy of Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From fd.kong at siat.ac.cn Fri Nov 2 18:01:31 2012 From: fd.kong at siat.ac.cn (Fande Kong) Date: Fri, 2 Nov 2012 17:01:31 -0600 Subject: [petsc-users] Are there any functions (objects ) for scattering and gathering 64-bit integers just like VecScatter for PetscScalar? In-Reply-To: References: Message-ID: Thank you very much. I don't want to use one-sided communication. It's horrible with countless bugs in current mpi implementations. On Fri, Nov 2, 2012 at 4:41 PM, Jed Brown wrote: > Read the issue I linked. You can watch it to be notified of action. It > should be obvious that I've known about the Open MPI problem for a long > time. You can also ask them to fix their bug. They _should_ fix it > regardless. > On Nov 2, 2012 5:24 PM, "Fande Kong" wrote: > >> I got it. You still didn't fix the bugs that I encountered a few months >> ago. All current MPI implementations couldn't support the function >> MPI_Accumulate or others well with one-sided communication when data is >> large. Thus, I have to hack your code (PetscSF) to use point-point >> communications. But I find it's not so easy. >> >> don't you want to change to use point-point? >> >> On Fri, Nov 2, 2012 at 4:04 PM, Jed Brown wrote: >> >>> The current implementation uses one-sided because that was a natural. I >>> need a solid day to implement without one-sided. As stated in the issue I >>> posted, this is necessary because Open MPI data types are broken. >>> >>> >>> On Fri, Nov 2, 2012 at 5:01 PM, Fande Kong wrote: >>> >>>> did you remove horrible one-side communication? and did you make some >>>> tests with using 64-bit integers? >>>> >>>> >>>> On Fri, Nov 2, 2012 at 3:50 PM, Jed Brown wrote: >>>> >>>>> I am using PetscSF for this. You would need petsc-dev and the current >>>>> implementation requires an MPI with non-broken data types. >>>>> >>>>> >>>>> https://bitbucket.org/petsc/petsc-dev/issue/9/implement-petscsf-without-one-sided >>>>> >>>>> Here are some (dated) notes about the communication model. >>>>> http://59A2.org/files/StarForest.pdf >>>>> >>>>> >>>>> On Fri, Nov 2, 2012 at 4:41 PM, Fande Kong wrote: >>>>> >>>>>> Hi all, >>>>>> >>>>>> Are there any functions (objects ) for scattering and gathering >>>>>> 64-bit integers just like VecScatter for PetscScalar? The VecScatter is >>>>>> very useful for managing communication for PetscScalar. But I can't find >>>>>> any functions or objects to do similar things for PetscInt. Any suggestions? >>>>>> >>>>>> Regards, >>>>>> -- >>>>>> Fande Kong >>>>>> ShenZhen Institutes of Advanced Technology >>>>>> Chinese Academy of Sciences >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>> >>>> >>>> -- >>>> Fande Kong >>>> ShenZhen Institutes of Advanced Technology >>>> Chinese Academy of Sciences >>>> >>>> >>> >> >> >> -- >> Fande Kong >> ShenZhen Institutes of Advanced Technology >> Chinese Academy of Sciences >> >> -- Fande Kong ShenZhen Institutes of Advanced Technology Chinese Academy of Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Fri Nov 2 18:04:13 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Fri, 2 Nov 2012 18:04:13 -0500 Subject: [petsc-users] Are there any functions (objects ) for scattering and gathering 64-bit integers just like VecScatter for PetscScalar? In-Reply-To: References: Message-ID: For the third time, look at the title of the issue I linked. I'm not going to answer any more questions that are directly addressed in that issue because I don't have time to repeat myself so many times _and_ get useful things done. This is higher priority now because we are using PetscSF in some more visible places. On Nov 2, 2012 5:57 PM, "Fande Kong" wrote: > Yes. I haven't tested my code on MPICH. Because MPICH don't > support infiniband in the supercomputer. But I have tested code on mvapich. > It also has bugs, when the finite mesh is larger than 50M. > > Now, I just want to know if you will change to use point-point. If you > would not, I will try to rewrite PetscSF for me. > > Thanks, > > On Fri, Nov 2, 2012 at 4:41 PM, Jed Brown wrote: > >> >> On Nov 2, 2012 5:24 PM, "Fande Kong" wrote: >> > >> > I got it. You still didn't fix the bugs that I encountered a few months >> ago. All current MPI implementations couldn't support the function >> MPI_Accumulate or others well with one-sided communication when data is >> large. >> >> I have not had problems with MPICH. >> > > > > -- > Fande Kong > ShenZhen Institutes of Advanced Technology > Chinese Academy of Sciences > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From fd.kong at siat.ac.cn Fri Nov 2 18:08:41 2012 From: fd.kong at siat.ac.cn (Fande Kong) Date: Fri, 2 Nov 2012 17:08:41 -0600 Subject: [petsc-users] Are there any functions (objects ) for scattering and gathering 64-bit integers just like VecScatter for PetscScalar? In-Reply-To: References: Message-ID: Thank you. Now, I got it. Sorry for bothering you. On Fri, Nov 2, 2012 at 5:04 PM, Jed Brown wrote: > For the third time, look at the title of the issue I linked. I'm not going > to answer any more questions that are directly addressed in that issue > because I don't have time to repeat myself so many times _and_ get useful > things done. > > This is higher priority now because we are using PetscSF in some more > visible places. > On Nov 2, 2012 5:57 PM, "Fande Kong" wrote: > >> Yes. I haven't tested my code on MPICH. Because MPICH don't >> support infiniband in the supercomputer. But I have tested code on mvapich. >> It also has bugs, when the finite mesh is larger than 50M. >> >> Now, I just want to know if you will change to use point-point. If you >> would not, I will try to rewrite PetscSF for me. >> >> Thanks, >> >> On Fri, Nov 2, 2012 at 4:41 PM, Jed Brown wrote: >> >>> >>> On Nov 2, 2012 5:24 PM, "Fande Kong" wrote: >>> > >>> > I got it. You still didn't fix the bugs that I encountered a few >>> months ago. All current MPI implementations couldn't support the function >>> MPI_Accumulate or others well with one-sided communication when data is >>> large. >>> >>> I have not had problems with MPICH. >>> >> >> >> >> -- >> Fande Kong >> ShenZhen Institutes of Advanced Technology >> Chinese Academy of Sciences >> >> -- Fande Kong ShenZhen Institutes of Advanced Technology Chinese Academy of Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Fri Nov 2 21:25:53 2012 From: balay at mcs.anl.gov (Satish Balay) Date: Fri, 2 Nov 2012 21:25:53 -0500 (CDT) Subject: [petsc-users] Are there any functions (objects ) for scattering and gathering 64-bit integers just like VecScatter for PetscScalar? In-Reply-To: References: Message-ID: On Fri, 2 Nov 2012, Fande Kong wrote: > But I have tested code on mvapich. > It also has bugs, when the finite mesh is larger than 50M. Can you confirm this problem you see is with newer mvapich2 not some old mvapich1? I see the current release is: MVAPICH2 1.8.1 [MVAPICH is based on mpich - so presumably onesided stuff should work with it.] Satish From mirzadeh at gmail.com Fri Nov 2 21:54:59 2012 From: mirzadeh at gmail.com (Mohammad Mirzadeh) Date: Fri, 2 Nov 2012 19:54:59 -0700 Subject: [petsc-users] thread model Message-ID: Hi, To use the new thread model in PETSc, does it suffice to run the code with the following? -threadcomm_type -threadcomm_nthreads <#> When I run the code with openmp, only 1 processor/core is active (looking at top). When using pthread, all cores are active. Am I missing something? -------------- next part -------------- An HTML attachment was scrubbed... URL: From abhyshr at mcs.anl.gov Fri Nov 2 22:24:11 2012 From: abhyshr at mcs.anl.gov (Shri) Date: Fri, 2 Nov 2012 22:24:11 -0500 Subject: [petsc-users] thread model In-Reply-To: References: Message-ID: <602AE3C5-6970-4BCA-858E-DF1F1D159302@mcs.anl.gov> On Nov 2, 2012, at 9:54 PM, Mohammad Mirzadeh wrote: > Hi, > > To use the new thread model in PETSc, does it suffice to run the code with the following? > > -threadcomm_type -threadcomm_nthreads <#> > > When I run the code with openmp, only 1 processor/core is active (looking at top). When using pthread, all cores are active. Am I missing something? OpenMP defaults to binding all threads to a single core if the cpu affinity is not specified explicitly. If you are using GNU OpenMP then you can bind the threads to specific cores using the environment variable GOMP_CPU_AFFINITY http://gcc.gnu.org/onlinedocs/libgomp/GOMP_005fCPU_005fAFFINITY.html If you are some other OpenMP implementation then check its manual to see how to set cpu affinity. Shri From w_ang_temp at 163.com Sat Nov 3 10:27:10 2012 From: w_ang_temp at 163.com (w_ang_temp) Date: Sat, 3 Nov 2012 23:27:10 +0800 (CST) Subject: [petsc-users] How to use multigrid? In-Reply-To: References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <3fb03a6a.10633.13aa798827b.Coremail.w_ang_temp@163.com> <611bda2d.10ae0.13aac91f0d5.Coremail.w_ang_temp@163.com> <01255FF7-A444-48E8-AB48-AE76C710197C@columbia.edu> <5c4f7f1f.c7e0.13abc39f25e.Coremail.w_ang_temp@163.com> <50cc9123.12a74.13abc43826a.Coremail.w_ang_temp@163.com> Message-ID: <4f586efd.7cb3.13ac6e1fd4b.Coremail.w_ang_temp@163.com> Hello, I have tried AMG, but there are some problems. I use the command: mpiexec -n 4 ./ex4f -ksp_type gmres -pc_type gamg -pc_gamg_agg_nsmooths 1 -ksp_gmres_restart 170 -ksp_rtol 1.0e-15 -ksp_converged_reason. The matrix has a size of 30000. However, compared with -pc_type asm, the amg need more time:asm needs 4.9s, amg needs 13.7s. I did several tests and got the same conclusion. When it begins, the screen shows the information: [0]PCSetData_AGG bs=1 MM=7601. I do not know the meaning. And if there is some parameters that affect the performance of AMG? Besides, I want to confirm a conception. In my view, AMG itself can be a solver like gmres. It can also be used as a preconditioner like jacobi and is used by combining with other solver. Is it right? If it is right, how use AMG solver? My codes are attached. Thanks. Jim -----------codes------------------------------------------ call MatCreate(PETSC_COMM_WORLD,A,ierr) call MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,m,n,ierr) call MatSetType(A, MATMPIAIJ,ierr) call MatSetFromOptions(A,ierr) !premalloc !find the max non-zero numbers of all rows maxnonzero=0 do 19,II=1,m !no-zero numbers of this row maxnonzeroII=NROWIN(II+1)-NROWIN(II) if (maxnonzeroII>maxnonzero) then maxnonzero=maxnonzeroII endif 19 continue call MatMPIAIJSetPreallocation(A,maxnonzero,PETSC_NULL_INTEGER, & maxnonzero,PETSC_NULL_INTEGER,ierr) call MatGetOwnershipRange(A,Istart,Iend,ierr) !set values per row do 10,II=Istart+1,Iend !no-zero numbers of this row rowNum=NROWIN(II+1)-NROWIN(II) allocate(nColPerRow(rowNum)) allocate(valuePerRow(rowNum)) kValStart=NROWIN(II)+1-1 kValEnd=NROWIN(II)+rowNum-1 !column index nColPerRow=NNZIJ(kValStart:kValEnd)-1 valuePerRow=VALUE(kValStart:kValEnd) nRow=II-1 call MatSetValues(A,ione,nRow,rowNum,nColPerRow,valuePerRow, & INSERT_VALUES,ierr) deallocate(nColPerRow) deallocate(valuePerRow) 10 continue call MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY,ierr) call MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY,ierr) call VecCreateMPI(PETSC_COMM_WORLD,PETSC_DECIDE,m,b,ierr) call VecSetFromOptions(b,ierr) call VecDuplicate(b,u,ierr) call VecDuplicate(b,x,ierr) call KSPCreate(PETSC_COMM_WORLD,ksp,ierr) call KSPSetOperators(ksp,A,A,DIFFERENT_NONZERO_PATTERN,ierr) call PetscOptionsHasName(PETSC_NULL_CHARACTER,'-my_ksp_monitor', & & flg,ierr) if (flg) then call KSPMonitorSet(ksp,MyKSPMonitor,PETSC_NULL_OBJECT, & & PETSC_NULL_FUNCTION,ierr) endif call KSPSetFromOptions(ksp,ierr) call PetscOptionsHasName(PETSC_NULL_CHARACTER, & & '-my_ksp_convergence',flg,ierr) if (flg) then call KSPSetConvergenceTest(ksp,MyKSPConverged, & & PETSC_NULL_OBJECT,PETSC_NULL_FUNCTION,ierr) endif !Assing values to 'b' bTemp=Iend-Istart ioneb=1 do 12,II=Istart,Iend-1 voneb=F(II+1) call VecSetValues(b,ioneb,II,voneb,INSERT_VALUES,ierr) 12 continue call VecAssemblyBegin(b,ierr) call VecAssemblyEnd(b,ierr) call KSPSolve(ksp,b,x,ierr) ------codes------------------------------------------------- >At 2012-11-01 22:00:28,"Jed Brown" wrote: >Yes, it's faster to understand this error message than to have "mysteriously slow performance". >* Preallocation routines now automatically set MAT_NEW_NONZERO_ALLOCATION_ERR, if you intentionally preallocate less than necessary then >use MatSetOption(mat,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE) to disable the error generation. >http://www.mcs.anl.gov/petsc/documentation/changes/33.html >On Thu, Nov 1, 2012 at 8:57 AM, w_ang_temp wrote: >Do you mean that the two versions have a different in this point? If I use the new version, I have to >make some modifications on my codes? -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Sat Nov 3 10:31:52 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Sat, 3 Nov 2012 10:31:52 -0500 Subject: [petsc-users] How to use multigrid? In-Reply-To: <4f586efd.7cb3.13ac6e1fd4b.Coremail.w_ang_temp@163.com> References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <3fb03a6a.10633.13aa798827b.Coremail.w_ang_temp@163.com> <611bda2d.10ae0.13aac91f0d5.Coremail.w_ang_temp@163.com> <01255FF7-A444-48E8-AB48-AE76C710197C@columbia.edu> <5c4f7f1f.c7e0.13abc39f25e.Coremail.w_ang_temp@163.com> <50cc9123.12a74.13abc43826a.Coremail.w_ang_temp@163.com> <4f586efd.7cb3.13ac6e1fd4b.Coremail.w_ang_temp@163.com> Message-ID: 1. *Always* send -log_summary when asking about performance. 2. AMG setup costs more, the solve should be faster, especially for large problems. 3. 30k degrees of freedom is not large. On Sat, Nov 3, 2012 at 10:27 AM, w_ang_temp wrote: > Hello, > I have tried AMG, but there are some problems. I use the command: > mpiexec -n 4 ./ex4f -ksp_type gmres -pc_type gamg > -pc_gamg_agg_nsmooths 1 -ksp_gmres_restart 170 -ksp_rtol 1.0e-15 > -ksp_converged_reason. > The matrix has a size of 30000. However, compared with -pc_type asm, > the amg need more time:asm needs 4.9s, amg needs 13.7s. I did several tests > and got the same conclusion. When it begins, the screen shows the > information: > [0]PCSetData_AGG bs=1 MM=7601. I do not know the meaning. And if there is > some > parameters that affect the performance of AMG? > Besides, I want to confirm a conception. In my view, AMG itself can be > a solver > like gmres. It can also be used as a preconditioner like jacobi and is > used by combining > with other solver. Is it right? If it is right, how use AMG solver? > My codes are attached. > Thanks. > Jim > > -----------codes------------------------------------------ > call MatCreate(PETSC_COMM_WORLD,A,ierr) > call MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,m,n,ierr) > call MatSetType(A, MATMPIAIJ,ierr) > call MatSetFromOptions(A,ierr) > !premalloc > !find the max non-zero numbers of all rows > maxnonzero=0 > do 19,II=1,m > !no-zero numbers of this row > maxnonzeroII=NROWIN(II+1)-NROWIN(II) > if (maxnonzeroII>maxnonzero) then > maxnonzero=maxnonzeroII > endif > 19 continue > &nbs p; call > MatMPIAIJSetPreallocation(A,maxnonzero,PETSC_NULL_INTEGER, > & maxnonzero,PETSC_NULL_INTEGER,ierr) > call MatGetOwnershipRange(A,Istart,Iend,ierr) > !set values per row > do 10,II=Istart+1,Iend > !no-zero numbers of this row > rowNum=NROWIN(II+1)-NROWIN(II) > > allocate(nColPerRow(rowNum)) > allocate(valuePerRow(rowNum)) > > kValStart=NROWIN(II)+1-1 > kValEnd=NROWIN(II)+rowNum-1 > > !column index > nColPerRow=NNZIJ(kValStart:kValEnd)-1 > valuePerRow=VALUE(kValStart:kValEnd) > &nb sp; nRow=II-1 > call MatSetValues(A,ione,nRow,rowNum,nColPerRow,valuePerRow, > & INSERT_VALUES,ierr) > deallocate(nColPerRow) > deallocate(valuePerRow) > 10 continue > call MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY,ierr) > call MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY,ierr) > call VecCreateMPI(PETSC_COMM_WORLD,PETSC_DECIDE,m,b,ierr) > call VecSetFromOptions(b,ierr) > call VecDuplicate(b,u,ierr) > call VecDuplicate(b,x,ierr) > call KSPCreate(PETSC_COMM_WORLD,ksp,ierr) > call KSPSetOperators(ksp,A,A,DIF FERENT_NONZERO_PATTERN,ierr) > call PetscOptionsHasName(PETSC_NULL_CHARACTER,'-my_ksp_monitor', & > & flg,ierr) > if (flg) then > call KSPMonitorSet(ksp,MyKSPMonitor,PETSC_NULL_OBJECT, & > & PETSC_NULL_FUNCTION,ierr) > endif > call KSPSetFromOptions(ksp,ierr) > call PetscOptionsHasName(PETSC_NULL_CHARACTER, & > & '-my_ksp_convergence',flg,ierr) > if (flg) then > call KSPSetConvergenceTest(ksp,MyKSPConverged, & > & PETSC_NULL_OBJECT,PETSC_NULL_FUNCTION,ierr) > endif > !Assing values to 'b' > bTemp=Iend-Istart > ioneb=1 > > do 12,II=Istart,Iend-1 > voneb=F(II+1) > call VecSetValues(b,ioneb,II,voneb,INSERT_VALUES,ierr) > 12 continue > call VecAssemblyBegin(b,ierr) > call VecAssemblyEnd(b,ierr) > call KSPSolve(ksp,b,x,ierr) > ------codes------------------------------------------------- > > > > > > > > > > >At 2012-11-01 22:00:28,"Jed Brown" wrote: > > >Yes, it's faster to understand this error message than to have > "mysteriously slow performance". > > >** Preallocation routines now automatically set > MAT_NEW_NONZERO_ALLOCATION_ERR, if you intentionally preallocate less than > necessary then *>*use > MatSetOption(mat,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE) to disable the > error generation. > * > >http://www.mcs.anl.gov/petsc/documentation/changes/33.html > > >On Thu, Nov 1, 2012 at 8:57 AM, w_ang_temp wrote: > >> >Do you mean that the two versions have a different in this point? If I >> use the new version, I have to >> >make some modifications on my codes? >> > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From w_ang_temp at 163.com Sat Nov 3 10:52:22 2012 From: w_ang_temp at 163.com (w_ang_temp) Date: Sat, 3 Nov 2012 23:52:22 +0800 (CST) Subject: [petsc-users] How to use multigrid? In-Reply-To: References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <3fb03a6a.10633.13aa798827b.Coremail.w_ang_temp@163.com> <611bda2d.10ae0.13aac91f0d5.Coremail.w_ang_temp@163.com> <01255FF7-A444-48E8-AB48-AE76C710197C@columbia.edu> <5c4f7f1f.c7e0.13abc39f25e.Coremail.w_ang_temp@163.com> <50cc9123.12a74.13abc43826a.Coremail.w_ang_temp@163.com> <4f586efd.7cb3.13ac6e1fd4b.Coremail.w_ang_temp@163.com> Message-ID: <4bae45af.5608.13ac6f91024.Coremail.w_ang_temp@163.com> Is there something that need attention when setting up PETSc? The -log_summary is no use in my system. >At 2012-11-03 23:31:52,"Jed Brown" wrote: >1. Always send -log_summary when asking about performance. >2. AMG setup costs more, the solve should be faster, especially for large problems. >3. 30k degrees of freedom is not large. >>On Sat, Nov 3, 2012 at 10:27 AM, w_ang_temp wrote: >>Hello, >> I have tried AMG, but there are some problems. I use the command: >> mpiexec -n 4 ./ex4f -ksp_type gmres -pc_type gamg -pc_gamg_agg_nsmooths 1 -ksp_gmres_restart 170 -ksp_rtol 1.0e-15 ->>ksp_converged_reason. >> The matrix has a size of 30000. However, compared with -pc_type asm, >>the amg need more time:asm needs 4.9s, amg needs 13.7s. I did several tests >>and got the same conclusion. When it begins, the screen shows the information: >>[0]PCSetData_AGG bs=1 MM=7601. I do not know the meaning. And if there is some >>parameters that affect the performance of AMG? >> Besides, I want to confirm a conception. In my view, AMG itself can be a solver >>like gmres. It can also be used as a preconditioner like jacobi and is used by combining >>with other solver. Is it right? If it is right, how use AMG solver? >> My codes are attached. >> Thanks. >> Jim >At 2012-11-01 22:00:28,"Jed Brown" wrote: >Yes, it's faster to understand this error message than to have "mysteriously slow performance". >* Preallocation routines now automatically set MAT_NEW_NONZERO_ALLOCATION_ERR, if you intentionally preallocate less than necessary then >use MatSetOption(mat,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE) to disable the error generation. >http://www.mcs.anl.gov/petsc/documentation/changes/33.html >On Thu, Nov 1, 2012 at 8:57 AM, w_ang_temp wrote: >Do you mean that the two versions have a different in this point? If I use the new version, I have to >make some modifications on my codes? -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Sat Nov 3 10:53:42 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Sat, 3 Nov 2012 10:53:42 -0500 Subject: [petsc-users] How to use multigrid? In-Reply-To: <4bae45af.5608.13ac6f91024.Coremail.w_ang_temp@163.com> References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <3fb03a6a.10633.13aa798827b.Coremail.w_ang_temp@163.com> <611bda2d.10ae0.13aac91f0d5.Coremail.w_ang_temp@163.com> <01255FF7-A444-48E8-AB48-AE76C710197C@columbia.edu> <5c4f7f1f.c7e0.13abc39f25e.Coremail.w_ang_temp@163.com> <50cc9123.12a74.13abc43826a.Coremail.w_ang_temp@163.com> <4f586efd.7cb3.13ac6e1fd4b.Coremail.w_ang_temp@163.com> <4bae45af.5608.13ac6f91024.Coremail.w_ang_temp@163.com> Message-ID: Just pass it as a command line option. It gives profiling output in PetscFinalize(). On Sat, Nov 3, 2012 at 10:52 AM, w_ang_temp wrote: > Is there something that need attention when setting up PETSc? The > -log_summary > is no use in my system. > > > >At 2012-11-03 23:31:52,"Jed Brown" wrote: > > >1. *Always* send -log_summary when asking about performance. > >2. AMG setup costs more, the solve should be faster, especially for large > problems. > >3. 30k degrees of freedom is not large. > > > >>On Sat, Nov 3, 2012 at 10:27 AM, w_ang_temp wrote: > >> >>Hello, >> >> I have tried AMG, but there are some problems. I use the command: >> >> mpiexec -n 4 ./ex4f -ksp_type gmres -pc_type gamg >> -pc_gamg_agg_nsmooths 1 -ksp_gmres_restart 170 -ksp_rtol 1.0e-15 >> ->>ksp_converged_reason. >> >> The matrix has a size of 30000. However, compared with -pc_type asm, >> >>the amg need more time:asm needs 4.9s, amg needs 13.7s. I did several >> tests >> >>and got the same conclusion. When it begins, the screen shows the >> information: >> >>[0]PCSetData_AGG bs=1 MM=7601. I do not know the meaning. And if there >> is some >> >>parameters that affect the performance of AMG? >> >> Besides, I want to confirm a conception. In my view, AMG itself can >> be a solver >> >>like gmres. It can also be used as a preconditioner like jacobi and is >> used by combining >> >>with other solver. Is it right? If it is right, how use AMG solver? >> >> My codes are attached. >> >> Thanks. >> >> Jim >> >> >> >> >At 2012-11-01 22:00:28,"Jed Brown" wrote: >> >> >Yes, it's faster to understand this error message than to have >> "mysteriously slow performance". >> >> >** Preallocation routines now automatically set >> MAT_NEW_NONZERO_ALLOCATION_ERR, if you intentionally preallocate less than >> necessary then *>*use >> MatSetOption(mat,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE) to disable the >> error generation. >> * >> >http://www.mcs.anl.gov/petsc/documentation/changes/33.html >> >> >On Thu, Nov 1, 2012 at 8:57 AM, w_ang_temp wrote: >> >>> >Do you mean that the two versions have a different in this point? If I >>> use the new version, I have to >>> >make some modifications on my codes? >>> >> >> >> >> > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From w_ang_temp at 163.com Sat Nov 3 12:05:28 2012 From: w_ang_temp at 163.com (w_ang_temp) Date: Sun, 4 Nov 2012 01:05:28 +0800 (CST) Subject: [petsc-users] How to use multigrid? In-Reply-To: References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <3fb03a6a.10633.13aa798827b.Coremail.w_ang_temp@163.com> <611bda2d.10ae0.13aac91f0d5.Coremail.w_ang_temp@163.com> <01255FF7-A444-48E8-AB48-AE76C710197C@columbia.edu> <5c4f7f1f.c7e0.13abc39f25e.Coremail.w_ang_temp@163.com> <50cc9123.12a74.13abc43826a.Coremail.w_ang_temp@163.com> <4f586efd.7cb3.13ac6e1fd4b.Coremail.w_ang_temp@163.com> <4bae45af.5608.13ac6f91024.Coremail.w_ang_temp@163.com> Message-ID: <408a3dbe.585e.13ac73bfe97.Coremail.w_ang_temp@163.com> (1) using AMG [0]PCSetData_AGG bs=1 MM=7601 Linear solve converged due to CONVERGED_RTOL iterations 445 Norm of error 0.2591E+04 iterations 445 0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000 -2.105776715959587E-017 0.000000000000000E+000 0.000000000000000E+000 26.4211453778391 -3.262172452839194E-017 -2.114490133288630E-017 ************************************************************************************************************************ *** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r -fCourier9' to print this document *** ************************************************************************************************************************ ---------------------------------------------- PETSc Performance Summary: ---------------------------------------------- ./ex4f on a arch-linux2-c-debug named ubuntu with 4 processors, by ubu Sat Nov 3 09:29:28 2012 Using Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 CDT 2012 Max Max/Min Avg Total Time (sec): 3.198e+02 1.00002 3.198e+02 Objects: 4.480e+02 1.00000 4.480e+02 Flops: 2.296e+09 1.08346 2.172e+09 8.689e+09 Flops/sec: 7.181e+06 1.08344 6.792e+06 2.717e+07 Memory: 2.374e+07 1.04179 9.297e+07 MPI Messages: 6.843e+03 1.87582 5.472e+03 2.189e+04 MPI Message Lengths: 2.660e+07 2.08884 3.446e+03 7.542e+07 MPI Reductions: 6.002e+04 1.00000 Flop counting convention: 1 flop = 1 real number operation of type (multiply/divide/add/subtract) e.g., VecAXPY() for real vectors of length N --> 2N flops and VecAXPY() for complex vectors of length N --> 8N flops Summary of Stages: ----- Time ------ ----- Flops ----- --- Messages --- -- Message Lengths -- -- Reductions -- Avg %Total Avg %Total counts %Total Avg %Total counts %Total 0: Main Stage: 3.1981e+02 100.0% 8.6886e+09 100.0% 2.189e+04 100.0% 3.446e+03 100.0% 6.001e+04 100.0% ------------------------------------------------------------------------------------------------------------------------ See the 'Profiling' chapter of the users' manual for details on interpreting output. Phase summary info: Count: number of times phase was executed Time and Flops: Max - maximum over all processors Ratio - ratio of maximum to minimum over all processors Mess: number of messages sent Avg. len: average message length Reduct: number of global reductions Global: entire computation Stage: stages of a computation. Set stages with PetscLogStagePush() and PetscLogStagePop(). %T - percent time in this phase %f - percent flops in this phase %M - percent messages in this phase %L - percent message lengths in this phase %R - percent reductions in this phase Total Mflop/s: 10e-6 * (sum of flops over all processors)/(max time over all processors) ------------------------------------------------------------------------------------------------------------------------ ########################################################## # # # WARNING!!! # # # # This code was compiled with a debugging option, # # To get timing results run ./configure # # using --with-debugging=no, the performance will # # be generally two or three times faster. # # # ########################################################## Event Count Time (sec) Flops --- Global --- --- Stage --- Total Max Ratio Max Ratio Max Ratio Mess Avg len Reduct %T %f %M %L %R %T %f %M %L %R Mflop/s ------------------------------------------------------------------------------------------------------------------------ --- Event Stage 0: Main Stage MatMult 6291 1.0 2.1431e+01 4.2 1.01e+09 1.2 1.9e+04 3.4e+03 0.0e+00 4 42 86 85 0 4 42 86 85 0 170 MatMultAdd 896 1.0 4.8204e-01 1.1 2.79e+07 1.2 1.3e+03 3.4e+03 0.0e+00 0 1 6 6 0 0 1 6 6 0 208 MatMultTranspose 896 1.0 2.2052e+00 1.3 2.79e+07 1.2 1.3e+03 3.4e+03 1.8e+03 1 1 6 6 3 1 1 6 6 3 45 MatSolve 896 0.0 1.4953e-02 0.0 2.44e+06 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 163 MatLUFactorSym 1 1.0 1.7595e-04 4.7 0.00e+00 0.0 0.0e+00 0.0e+00 5.0e+00 0 0 0 0 0 0 0 0 0 0 0 MatLUFactorNum 1 1.0 1.3995e-0423.5 1.85e+04 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 132 MatConvert 2 1.0 3.1026e-02 1.7 0.00e+00 0.0 0.0e+00 0.0e+00 1.2e+01 0 0 0 0 0 0 0 0 0 0 0 MatScale 6 1.0 8.9679e-03 5.7 3.98e+05 1.2 6.0e+00 3.4e+03 4.0e+00 0 0 0 0 0 0 0 0 0 0 158 MatAssemblyBegin 37 1.0 2.1544e-01 1.7 0.00e+00 0.0 5.4e+01 6.4e+03 4.2e+01 0 0 0 0 0 0 0 0 0 0 0 MatAssemblyEnd 37 1.0 2.5336e-01 1.4 0.00e+00 0.0 9.0e+01 6.8e+02 3.1e+02 0 0 0 0 1 0 0 0 0 1 0 MatGetRow 26874 1.2 9.8243e-02 1.6 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 MatGetRowIJ 1 0.0 2.5988e-05 0.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 MatGetOrdering 1 0.0 1.5616e-04 0.0 0.00e+00 0.0 0.0e+00 0.0e+00 5.0e-01 0 0 0 0 0 0 0 0 0 0 0 MatCoarsen 2 1.0 2.9671e-02 1.0 0.00e+00 0.0 2.4e+01 7.0e+03 3.8e+01 0 0 0 0 0 0 0 0 0 0 0 MatAXPY 2 1.0 6.1393e-04 2.1 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 MatTranspose 2 1.0 1.8161e-01 1.1 0.00e+00 0.0 3.0e+01 7.1e+03 9.4e+01 0 0 0 0 0 0 0 0 0 0 0 MatMatMult 2 1.0 1.1968e-01 1.0 3.31e+05 1.2 3.6e+01 1.7e+03 1.1e+02 0 0 0 0 0 0 0 0 0 0 10 MatMatMultSym 2 1.0 9.8982e-02 1.0 0.00e+00 0.0 3.0e+01 1.4e+03 9.6e+01 0 0 0 0 0 0 0 0 0 0 0 MatMatMultNum 2 1.0 2.1248e-02 1.1 3.31e+05 1.2 6.0e+00 3.4e+03 1.2e+01 0 0 0 0 0 0 0 0 0 0 56 MatPtAP 2 1.0 1.7070e-01 1.1 2.36e+06 1.2 5.4e+01 3.3e+03 1.1e+02 0 0 0 0 0 0 0 0 0 0 50 MatPtAPSymbolic 2 1.0 1.3786e-01 1.1 0.00e+00 0.0 4.8e+01 3.1e+03 1.0e+02 0 0 0 0 0 0 0 0 0 0 0 MatPtAPNumeric 2 1.0 4.7638e-02 2.2 2.36e+06 1.2 6.0e+00 4.8e+03 1.2e+01 0 0 0 0 0 0 0 0 0 0 180 MatTrnMatMult 2 1.0 7.9914e-01 1.0 1.14e+07 1.3 3.6e+01 2.1e+04 1.2e+02 0 0 0 1 0 0 0 0 1 0 48 MatGetLocalMat 10 1.0 6.7852e-03 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 2.4e+01 0 0 0 0 0 0 0 0 0 0 0 MatGetBrAoCol 6 1.0 3.6962e-02 2.4 0.00e+00 0.0 4.2e+01 4.5e+03 1.6e+01 0 0 0 0 0 0 0 0 0 0 0 MatGetSymTrans 4 1.0 4.4394e-04 1.2 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecMDot 913 1.0 2.8472e+00 3.0 5.28e+08 1.0 0.0e+00 0.0e+00 9.1e+02 1 24 0 0 2 1 24 0 0 2 741 VecNorm 1367 1.0 2.7202e+00 1.6 7.12e+06 1.0 0.0e+00 0.0e+00 1.4e+03 1 0 0 0 2 1 0 0 0 2 10 VecScale 4950 1.0 6.0693e-02 1.2 1.96e+07 1.1 0.0e+00 0.0e+00 0.0e+00 0 1 0 0 0 0 1 0 0 0 1169 VecCopy 1349 1.0 7.8685e-03 1.4 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecSet 4972 1.0 1.2852e-02 1.3 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecAXPY 7624 1.0 1.3610e-01 1.1 6.44e+07 1.2 0.0e+00 0.0e+00 0.0e+00 0 3 0 0 0 0 3 0 0 0 1676 VecAYPX 7168 1.0 1.5877e-01 1.2 4.01e+07 1.2 0.0e+00 0.0e+00 0.0e+00 0 2 0 0 0 0 2 0 0 0 896 VecMAXPY 1366 1.0 6.3739e-01 1.3 5.35e+08 1.0 0.0e+00 0.0e+00 0.0e+00 0 25 0 0 0 0 25 0 0 0 3353 VecAssemblyBegin 21 1.0 4.7891e-02 1.2 0.00e+00 0.0 0.0e+00 0.0e+00 6.0e+01 0 0 0 0 0 0 0 0 0 0 0 VecAssemblyEnd 21 1.0 4.5776e-05 1.4 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecPointwiseMult 5398 1.0 1.2278e-01 1.3 2.42e+07 1.2 0.0e+00 0.0e+00 0.0e+00 0 1 0 0 0 0 1 0 0 0 698 VecScatterBegin 8107 1.0 3.9436e-02 1.3 0.00e+00 0.0 2.2e+04 3.4e+03 0.0e+00 0 0 99 98 0 0 0 99 98 0 0 VecScatterEnd 8107 1.0 1.5414e+01344.4 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 VecSetRandom 2 1.0 1.1868e-03 1.6 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecNormalize 1366 1.0 2.7266e+00 1.6 1.07e+07 1.0 0.0e+00 0.0e+00 1.4e+03 1 0 0 0 2 1 0 0 0 2 15 KSPGMRESOrthog 913 1.0 8.5743e+00 1.1 1.06e+09 1.0 0.0e+00 0.0e+00 3.6e+04 3 49 0 0 60 3 49 0 0 60 492 KSPSetUp 7 1.0 2.4805e-02 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 6.0e+00 0 0 0 0 0 0 0 0 0 0 0 KSPSolve 1 1.0 5.7656e+01 1.0 2.30e+09 1.1 2.2e+04 3.4e+03 6.0e+04 18100100100100 18100100100100 151 PCSetUp 2 1.0 2.1524e+00 1.0 2.03e+07 1.3 3.8e+02 6.0e+03 1.1e+03 1 1 2 3 2 1 1 2 3 2 33 PCSetUpOnBlocks 448 1.0 1.5607e-03 1.8 1.85e+04 0.0 0.0e+00 0.0e+00 8.0e+00 0 0 0 0 0 0 0 0 0 0 12 PCApply 448 1.0 4.4331e+01 1.1 1.08e+09 1.2 1.9e+04 3.4e+03 2.3e+04 14 44 86 85 38 14 44 86 85 38 87 PCGAMGgraph_AGG 2 1.0 6.1282e-01 1.0 3.36e+05 1.2 6.6e+01 5.7e+03 1.9e+02 0 0 0 0 0 0 0 0 0 0 2 PCGAMGcoarse_AGG 2 1.0 8.8854e-01 1.0 1.14e+07 1.3 9.0e+01 1.2e+04 2.1e+02 0 0 0 1 0 0 0 0 1 0 44 PCGAMGProl_AGG 2 1.0 6.3711e-02 1.1 0.00e+00 0.0 4.2e+01 2.3e+03 1.0e+02 0 0 0 0 0 0 0 0 0 0 0 PCGAMGPOpt_AGG 2 1.0 3.4247e-01 1.0 6.22e+06 1.2 9.6e+01 2.8e+03 3.3e+02 0 0 0 0 1 0 0 0 0 1 65 ------------------------------------------------------------------------------------------------------------------------ Memory usage is given in bytes: Object Type Creations Destructions Memory Descendants' Mem. Reports information only for process 0. --- Event Stage 0: Main Stage Matrix 68 68 27143956 0 Matrix Coarsen 2 2 704 0 Vector 296 296 13385864 0 Vector Scatter 18 18 11304 0 Index Set 47 47 34816 0 Krylov Solver 7 7 554688 0 Preconditioner 7 7 3896 0 PetscRandom 2 2 704 0 Viewer 1 0 0 0 ======================================================================================================================== Average time to get PetscTime(): 1.3113e-06 Average time for MPI_Barrier(): 9.62257e-05 Average time for zero size MPI_Send(): 0.00019449 #PETSc Option Table entries: -ksp_converged_reason -ksp_gmres_restart 170 -ksp_rtol 1.0e-15 -ksp_type gmres -log_summary -pc_gamg_agg_nsmooths 1 -pc_type gamg #End of PETSc Option Table entries Compiled without FORTRAN kernels Compiled with full precision matrices (default) sizeof(short) 2 sizeof(int) 4 sizeof(long) 4 sizeof(void*) 4 sizeof(PetscScalar) 8 sizeof(PetscInt) 4 Configure run at: Thu Nov 1 05:54:48 2012 Configure options: --with-mpi-dir=/home/ubu/soft/mpich2/ --download-f-blas-lapack =1 ----------------------------------------- Libraries compiled on Thu Nov 1 05:54:48 2012 on ubuntu Machine characteristics: Linux-2.6.32-38-generic-i686-with-Ubuntu-10.04-lucid Using PETSc directory: /home/ubu/soft/petsc/petsc-3.3-p4 Using PETSc arch: arch-linux2-c-debug ----------------------------------------- Using C compiler: /home/ubu/soft/mpich2/bin/mpicc -wd1572 -g ${COPTFLAGS} ${CFLAGS} Using Fortran compiler: /home/ubu/soft/mpich2/bin/mpif90 -g ${FOPTFLAGS} ${FFLAGS} ----------------------------------------- Using include paths: -I/home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/include -I/home/ubu/soft/petsc/petsc-3.3-p4/include -I/home/ubu/soft/petsc/petsc-3.3-p4/include -I/home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/include -I/home/ubu/soft/mpich2/include ----------------------------------------- Using C linker: /home/ubu/soft/mpich2/bin/mpicc Using Fortran linker: /home/ubu/soft/mpich2/bin/mpif90 Using libraries: -Wl,-rpath,/home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib -L/home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib -lpetsc -lpthread -Wl,-rpath,/home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib -L/home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib -lflapack -lfblas -L/home/ubu/soft/mpich2/lib -L/opt/intel/composer_xe_2011_sp1.10.319/compiler/lib/ia32 -L/opt/intel/composer_xe_2011_sp1.10.319/ipp/lib/ia32 -L/opt/intel/composer_xe_2011_sp1.10.319/mkl/lib/ia32 -L/opt/intel/composer_xe_2011_sp1.10.319/tbb/lib/ia32/cc4.1.0_libc2.4_kernel2.6.16.21 -L/opt/intel/composer_xe_2011_sp1.9.293/compiler/lib/ia32 -L/opt/intel/composer_xe_2011_sp1.9.293/mkl/lib/ia32 -L/usr/lib/gcc/i486-linux-gnu/4.4.3 -L/usr/lib/i486-linux-gnu -lmpichf90 -lifport -lifcore -lm -lm -ldl -lmpich -lopa -lmpl -lrt -lpthread -limf -lsvml -lipgo -ldecimal -lcilkrts -lstdc++ -lgcc_s -lirc -lirc_s -ldl ----------------------------------------- time 14.4289010000000 time 14.4289020000000 time 14.4449030000000 time 14.4809050000000 (2) using asm Linear solve converged due to CONVERGED_RTOL iterations 483 Norm of error 0.2591E+04 iterations 483 0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000 4.866092420969481E-018 0.000000000000000E+000 0.000000000000000E+000 26.4211453778395 -4.861214483821431E-017 5.379151535696287E-018 ************************************************************************************************************************ *** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r -fCourier9' to print this document *** ************************************************************************************************************************ ---------------------------------------------- PETSc Performance Summary: ---------------------------------------------- ./ex4f on a arch-linux2-c-debug named ubuntu with 4 processors, by ubu Sat Nov 3 10:00:43 2012 Using Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 CDT 2012 Max Max/Min Avg Total Time (sec): 2.952e+02 1.00006 2.952e+02 Objects: 2.040e+02 1.00000 2.040e+02 Flops: 1.502e+09 1.00731 1.496e+09 5.983e+09 Flops/sec: 5.088e+06 1.00734 5.067e+06 2.027e+07 Memory: 2.036e+07 1.01697 8.073e+07 MPI Messages: 1.960e+03 2.00000 1.470e+03 5.880e+03 MPI Message Lengths: 7.738e+06 3.12820 3.474e+03 2.042e+07 MPI Reductions: 4.236e+04 1.00000 Flop counting convention: 1 flop = 1 real number operation of type (multiply/divide/add/subtract) e.g., VecAXPY() for real vectors of length N --> 2N flops and VecAXPY() for complex vectors of length N --> 8N flops Summary of Stages: ----- Time ------ ----- Flops ----- --- Messages --- -- Message Lengths -- -- Reductions -- Avg %Total Avg %Total counts %Total Avg %Total counts %Total 0: Main Stage: 2.9517e+02 100.0% 5.9826e+09 100.0% 5.880e+03 100.0% 3.474e+03 100.0% 4.236e+04 100.0% ------------------------------------------------------------------------------------------------------------------------ See the 'Profiling' chapter of the users' manual for details on interpreting output. Phase summary info: Count: number of times phase was executed Time and Flops: Max - maximum over all processors Ratio - ratio of maximum to minimum over all processors Mess: number of messages sent Avg. len: average message length Reduct: number of global reductions Global: entire computation Stage: stages of a computation. Set stages with PetscLogStagePush() and PetscLogStagePop(). %T - percent time in this phase %f - percent flops in this phase %M - percent messages in this phase %L - percent message lengths in this phase %R - percent reductions in this phase Total Mflop/s: 10e-6 * (sum of flops over all processors)/(max time over all processors) ------------------------------------------------------------------------------------------------------------------------ ########################################################## # # # WARNING!!! # # # # This code was compiled with a debugging option, # # To get timing results run ./configure # # using --with-debugging=no, the performance will # # be generally two or three times faster. # # # ########################################################## Event Count Time (sec) Flops --- Global --- --- Stage --- Total Max Ratio Max Ratio Max Ratio Mess Avg len Reduct %T %f %M %L %R %T %f %M %L %R Mflop/s ------------------------------------------------------------------------------------------------------------------------ --- Event Stage 0: Main Stage MatMult 485 1.0 3.1170e+00 5.9 1.36e+08 1.0 2.9e+03 3.4e+03 0.0e+00 1 9 49 48 0 1 9 49 48 0 173 MatSolve 486 1.0 6.8313e-01 1.3 1.49e+08 1.1 0.0e+00 0.0e+00 0.0e+00 0 10 0 0 0 0 10 0 0 0 842 MatLUFactorNum 1 1.0 6.0117e-02 1.2 1.54e+06 1.1 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 99 MatILUFactorSym 1 1.0 1.5973e-01 2.5 0.00e+00 0.0 0.0e+00 0.0e+00 1.0e+00 0 0 0 0 0 0 0 0 0 0 0 MatAssemblyBegin 2 1.0 6.0572e-02 9.5 0.00e+00 0.0 0.0e+00 0.0e+00 2.0e+00 0 0 0 0 0 0 0 0 0 0 0 MatAssemblyEnd 2 1.0 1.7764e-02 1.6 0.00e+00 0.0 1.2e+01 8.5e+02 1.9e+01 0 0 0 0 0 0 0 0 0 0 0 MatGetRowIJ 1 1.0 3.8147e-06 1.3 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 MatGetSubMatrice 1 1.0 1.9829e-01 2.1 0.00e+00 0.0 3.0e+01 2.1e+04 1.0e+01 0 0 1 3 0 0 0 1 3 0 0 MatGetOrdering 1 1.0 1.2739e-02 5.8 0.00e+00 0.0 0.0e+00 0.0e+00 4.0e+00 0 0 0 0 0 0 0 0 0 0 0 MatIncreaseOvrlp 1 1.0 1.8877e-02 1.2 0.00e+00 0.0 0.0e+00 0.0e+00 2.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecMDot 483 1.0 4.5957e+00 2.5 5.98e+08 1.0 0.0e+00 0.0e+00 4.8e+02 1 40 0 0 1 1 40 0 0 1 521 VecNorm 487 1.0 2.0843e+00 1.2 7.40e+06 1.0 0.0e+00 0.0e+00 4.9e+02 1 0 0 0 1 1 0 0 0 1 14 VecScale 486 1.0 1.2140e-02 1.1 3.69e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 1217 VecCopy 3 1.0 4.2915e-05 1.2 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecSet 979 1.0 8.1432e-03 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecAXPY 6 1.0 2.3413e-04 1.3 9.12e+04 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 1558 VecMAXPY 486 1.0 7.0027e-01 1.2 6.06e+08 1.0 0.0e+00 0.0e+00 0.0e+00 0 41 0 0 0 0 41 0 0 0 3460 VecAssemblyBegin 1 1.0 5.7101e-03 2.5 0.00e+00 0.0 0.0e+00 0.0e+00 3.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecAssemblyEnd 1 1.0 3.0994e-06 1.6 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecScatterBegin 1457 1.0 9.1357e-02 2.6 0.00e+00 0.0 5.8e+03 3.4e+03 0.0e+00 0 0 99 97 0 0 0 99 97 0 0 VecScatterEnd 1457 1.0 2.5327e+00323.7 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecNormalize 486 1.0 2.0858e+00 1.2 1.11e+07 1.0 0.0e+00 0.0e+00 4.9e+02 1 1 0 0 1 1 1 0 0 1 21 KSPGMRESOrthog 483 1.0 1.1152e+01 1.2 1.20e+09 1.0 0.0e+00 0.0e+00 4.0e+04 3 80 0 0 94 3 80 0 0 94 429 KSPSetUp 2 1.0 1.1989e-02 1.4 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 KSPSolve 1 1.0 2.0990e+01 1.0 1.50e+09 1.0 5.9e+03 3.5e+03 4.2e+04 7100100100100 7100100100100 285 PCSetUp 2 1.0 3.5928e-01 1.0 1.54e+06 1.1 4.2e+01 1.5e+04 3.5e+01 0 0 1 3 0 0 0 1 3 0 17 PCSetUpOnBlocks 1 1.0 2.2166e-01 1.7 1.54e+06 1.1 0.0e+00 0.0e+00 6.0e+00 0 0 0 0 0 0 0 0 0 0 27 PCApply 486 1.0 5.9831e+00 2.8 1.49e+08 1.1 2.9e+03 3.4e+03 1.5e+03 1 10 50 48 3 1 10 50 48 3 96 ------------------------------------------------------------------------------------------------------------------------ Memory usage is given in bytes: Object Type Creations Destructions Memory Descendants' Mem. Reports information only for process 0. --- Event Stage 0: Main Stage Matrix 5 5 8051336 0 Vector 182 182 11109304 0 Vector Scatter 2 2 1256 0 Index Set 10 10 121444 0 Krylov Solver 2 2 476844 0 Preconditioner 2 2 1088 0 Viewer 1 0 0 0 ======================================================================================================================== Average time to get PetscTime(): 9.05991e-07 Average time for MPI_Barrier(): 0.000297785 Average time for zero size MPI_Send(): 0.000174284 #PETSc Option Table entries: -ksp_converged_reason -ksp_gmres_restart 170 -ksp_rtol 1.0e-15 -ksp_type gmres -log_summary -pc_type asm #End of PETSc Option Table entries Compiled without FORTRAN kernels Compiled with full precision matrices (default) sizeof(short) 2 sizeof(int) 4 sizeof(long) 4 sizeof(void*) 4 sizeof(PetscScalar) 8 sizeof(PetscInt) 4 Configure run at: Thu Nov 1 05:54:48 2012 Configure options: --with-mpi-dir=/home/ubu/soft/mpich2/ --download-f-blas-lapack =1 ----------------------------------------- Libraries compiled on Thu Nov 1 05:54:48 2012 on ubuntu Machine characteristics: Linux-2.6.32-38-generic-i686-with-Ubuntu-10.04-lucid Using PETSc directory: /home/ubu/soft/petsc/petsc-3.3-p4 Using PETSc arch: arch-linux2-c-debug ----------------------------------------- Using C compiler: /home/ubu/soft/mpich2/bin/mpicc -wd1572 -g ${COPTFLAGS} ${CFLAGS} Using Fortran compiler: /home/ubu/soft/mpich2/bin/mpif90 -g ${FOPTFLAGS} ${FFLAGS} ----------------------------------------- Using include paths: -I/home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/include -I/home/ubu/soft/petsc/petsc-3.3-p4/include -I/home/ubu/soft/petsc/petsc-3.3-p4/include -I/home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/include -I/home/ubu/soft/mpich2/include ----------------------------------------- Using C linker: /home/ubu/soft/mpich2/bin/mpicc Using Fortran linker: /home/ubu/soft/mpich2/bin/mpif90 Using libraries: -Wl,-rpath,/home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib -L/home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib -lpetsc -lpthread -Wl,-rpath,/home/u bu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib -L/home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib -lflapack -lfblas -L/home/ubu/soft/mpich2/lib -L/opt/intel/composer_xe_2011_sp1.10.319/compiler/lib/ia32 -L/opt/intel/composer_xe_2011_sp1.10.319/ipp/lib/ia32 -L/opt/intel/composer_xe_2011_sp1.10.319/mkl/lib/ia32 -L/opt/intel/composer_xe_2011_sp1.10.319/tbb/lib/ia32/cc4.1.0_libc2.4_kernel2.6.16.21 -L/opt/intel/composer_xe_2011_sp1.9.293/compiler/lib/ia32 -L/opt/intel/composer_xe_2011_sp1.9.293/mkl/lib/ia32 -L/usr/lib/gcc/i486-linux-gnu/4.4.3 -L/usr/lib/i486-linux-gnu -lmpichf90 -lifport -lifcore -lm -lm -ldl -lmpich -lopa -lmpl -lrt -lpthread -limf -lsvml -lipgo -ldecimal -lcilkrts -lstdc++ -lgcc_s -lirc -lirc_s -ldl ----------------------------------------- time 5.72435800000000 time 5.40433800000000 time 5.39233700000000 time 5.51634499999999 >At 2012-11-03 23:53:42,"Jed Brown" wrote: >Just pass it as a command line option. It gives profiling output in PetscFinalize(). >On Sat, Nov 3, 2012 at 10:52 AM, w_ang_temp wrote: >Is there something that need attention when setting up PETSc? The -log_summary >is no use in my system. >At 2012-11-03 23:31:52,"Jed Brown" wrote: >1. Always send -log_summary when asking about performance. >2. AMG setup costs more, the solve should be faster, especially for large problems. >3. 30k degrees of freedom is not large. >>On Sat, Nov 3, 2012 at 10:27 AM, w_ang_temp wrote: >>Hello, >> I have tried AMG, but there are some problems. I use the command: >> mpiexec -n 4 ./ex4f -ksp_type gmres -pc_type gamg -pc_gamg_agg_nsmooths 1 -ksp_gmres_restart 170 -ksp_rtol 1.0e-15 ->>ksp_converged_reason. >> The matrix has a size of 30000. However, compared with -pc_type asm, >>the amg need more time:asm needs 4.9s, amg needs 13.7s. I did several tests >>and got the same conclusion. When it begins, the screen shows the information: >>[0]PCSetData_AGG bs=1 MM=7601. I do not know the meaning. And if there is some >>parameters that affect the performance of AMG? >> Besides, I want to confirm a conception. In my view, AMG itself can be a solver >>like gmres. It can also be used as a preconditioner like jacobi and is used by combining >>with other solver. Is it right? If it is right, how use AMG solver? >> My codes are attached. >> Thanks. >> Jim >At 2012-11-01 22:00:28,"Jed Brown" wrote: >Yes, it's faster to understand this error message than to have "mysteriously slow performance". >* Preallocation routines now automatically set MAT_NEW_NONZERO_ALLOCATION_ERR, if you intentionally preallocate less than necessary then >use MatSetOption(mat,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE) to disable the error generation. >http://www.mcs.anl.gov/petsc/documentation/changes/33.html >On Thu, Nov 1, 2012 at 8:57 AM, w_ang_temp wrote: >Do you mean that the two versions have a different in this point? If I use the new version, I have to >make some modifications on my codes? -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Sat Nov 3 12:08:26 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Sat, 3 Nov 2012 12:08:26 -0500 Subject: [petsc-users] How to use multigrid? In-Reply-To: <408a3dbe.585e.13ac73bfe97.Coremail.w_ang_temp@163.com> References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <3fb03a6a.10633.13aa798827b.Coremail.w_ang_temp@163.com> <611bda2d.10ae0.13aac91f0d5.Coremail.w_ang_temp@163.com> <01255FF7-A444-48E8-AB48-AE76C710197C@columbia.edu> <5c4f7f1f.c7e0.13abc39f25e.Coremail.w_ang_temp@163.com> <50cc9123.12a74.13abc43826a.Coremail.w_ang_temp@163.com> <4f586efd.7cb3.13ac6e1fd4b.Coremail.w_ang_temp@163.com> <4bae45af.5608.13ac6f91024.Coremail.w_ang_temp@163.com> <408a3dbe.585e.13ac73bfe97.Coremail.w_ang_temp@163.com> Message-ID: 1. What kind of equation are you solving? AMG is not working well if it takes that many iterations. 2. * ##########################################################* * # #* * # WARNING!!! #* * # #* * # This code was compiled with a debugging option, #* * # To get timing results run ./configure #* * # using --with-debugging=no, the performance will #* * # be generally two or three times faster. #* * # #* * ##########################################################* On Sat, Nov 3, 2012 at 12:05 PM, w_ang_temp wrote: > (1) using AMG > [0]PCSetData_AGG bs=1 MM=7601 > Linear solve converged due to CONVERGED_RTOL iterations 445 > Norm of error 0.2591E+04 iterations 445 > 0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000 > -2.105776715959587E-017 0.000000000000000E+000 0.000000000000000E+000 > 26.4211453778391 -3.262172452839194E-017 -2.114490133288630E-017 > > ************************************************************************************************************************ > *** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r > -fCourier9' to print this document *** > ******************************************************************** > **************************************************** > ---------------------------------------------- PETSc Performance Summary: > ---------------------------------------------- > ./ex4f on a arch-linux2-c-debug named ubuntu with 4 processors, by ubu Sat > Nov 3 09:29:28 2012 > Using Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 CDT 2012 > Max Max/Min Avg Total > Time (sec): 3.198e+02 1.00002 3.198e+02 > Objects: 4.480e+02 1.00000 4.480e+02 > Flops: 2.296e+09 1.08346 2.172e+09 8.689e+09 > Flops/sec: 7.181e+06 1.08344 6.792e+06 2.717e+07 > Memory: 2.374e+07 1.04179 9.297e+07 > MPI Messages: 6.843e+03 1.87582 5.472e+03 2.189e+04 > MPI Message Lengths: 2.660e+07 2.08884 3.446e+03 7.542e+07 > MPI Reductions: 6.002e+04 1.00000 > Flop counting convention: 1 flop = 1 real number operation of type > (multiply/divide/add/subtract) > e.g., VecAXPY() for real vectors of length N > --> 2N flops > and VecAXPY() for complex vectors of length N > --> 8N flops > Summary of Stages: ----- Time ------ ----- Flops ----- --- Messages > --- -- Message Lengths -- -- Reductions -- > Avg %Total Avg %Total counts > %Total Avg %Total counts %Total > 0: Main Stage: 3.1981e+02 100.0% 8.6886e+09 100.0% 2.189e+04 > 100.0% 3.446e+03 100.0% 6.001e+04 100.0% > > ------------------------------------------------------------------------------------------------------------------------ > See the 'Profiling' chapter of the users' manual for details on > interpreting output. > Phase summary info: > &n bsp; Count: number of times phase was executed > Time and Flops: Max - maximum over all processors > Ratio - ratio of maximum to minimum over all processors > Mess: number of messages sent > Avg. len: average message length > Reduct: number of global reductions > Global: entire computation > Stage: stages of a computation. Set stages with PetscLogStagePush() and > PetscLogStagePop(). > %T - percent time in this phase %f - percent flops in this > phase > %M - percent messages in this phase %L - percent message lengths > in this phase > %R - percent reductions in this phase > Total Mflop/s: 10e-6 * (sum of flops o ver all processors)/(max time > over all processors) > > ------------------------------------------------------------------------------------------------------------------------ > > ########################################################## > # # > # WARNING!!! # > # & nbsp; # > # This code was compiled with a debugging option, # > # To get timing results run ./configure # > # using --with-debugging=no, the performance will # > # be generally two or three times faster. # > # &n bsp; # > ########################################################## > > Event Count Time (sec) > Flops --- Global --- --- Stage --- Total > Max Ratio Max Ratio Max Ratio Mess Avg len > Reduct %T %f %M %L %R %T %f %M %L %R Mflop/s > > ------------------------------------------------------------------------------------------------------------------------ > --- Event Stage 0: Main Stage > MatMult 6291 1.0 2.1431e+01 4.2 1.01e+09 1.2 1.9e+04 3.4e+03 > 0.0e+00 4 42 86 85 0 4 42 86 85 0 170 > MatMultAdd 896 1.0 4.8204e-01 1.1 2.79e+07 1.2 1.3e+03 3.4e+03 > 0.0e+00 0 1 6 6 0 0 1 6 6 0 208 > MatMultTranspose 896 1.0 2.2052e+00 1.3 2.79e+07 1.2 1.3e+03 3.4e+03 > 1.8e+03 1 1 6 6 3 1 1 6 6 3 45 > MatSolve 896 0.0 1.4953e-02 0.0 2.44e+06 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 163 > MatLUFactorSym 1 1.0 1.7595e -04 4.7 0.00e+00 0.0 0.0e+00 0.0e+00 > 5.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatLUFactorNum 1 1.0 1.3995e-0423.5 1.85e+04 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 132 > MatConvert 2 1.0 3.1026e-02 1.7 0.00e+00 0.0 0.0e+00 0.0e+00 > 1.2e+01 0 0 0 0 0 0 0 0 0 0 0 > MatScale 6 1.0 8.9679e-03 5.7 3.98e+05 1.2 6.0e+00 3.4e+03 > 4.0e+00 0 0 0 0 0 0 0 0 0 0 158 > MatAssemblyBegin 37 1.0 2.1544e-01 1.7 0.00e+00 0.0 5.4e+01 6 .4e+03 > 4.2e+01 0 0 0 0 0 0 0 0 0 0 0 > MatAssemblyEnd 37 1.0 2.5336e-01 1.4 0.00e+00 0.0 9.0e+01 6.8e+02 > 3.1e+02 0 0 0 0 1 0 0 0 0 1 0 > MatGetRow 26874 1.2 9.8243e-02 1.6 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatGetRowIJ 1 0.0 2.5988e-05 0.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatGetOrdering 1 0.0 1.5616e-04 0.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 5.0e-01 0 0 0 0 0 0 0 0 0 0 0 > MatCoarsen 2 1.0 2.9671e-02 1.0 0.00e+00 0.0 2.4e+01 7.0e+03 > 3.8e+01 0 0 0 0 0 0 0 0 0 0 0 > MatAXPY 2 1.0 6.1393e-04 2.1 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatTranspose 2 1.0 1.8161e-01 1.1 0.00e+00 0.0 3.0e+01 7.1e+03 > 9.4e+01 0 0 0 0 0 0 0 0 0 0 0 > MatMatMult 2 1.0 1.1968e-01 1.0 3.31e+05 1.2 3.6e+01 1.7e+03 > 1.1e+02 0 0 0 0 0 0 0 0 0 0 10 > MatMatMultSym 2 1.0 9.8982e-02 1.0 0.00e+00 0.0 3.0e+01 1.4e+03 > 9.6e+01 0 0 0 0 0 0 0 0 0 0 0 > MatMatMultNum 2 1.0 2.1248e-02 1.1 3.31e+05 1.2 6.0e+00 3.4e+03 > 1.2e+01 0 0 0 0 0 0 0 0 0 0 56 > MatPtAP 2 1.0 1.7070e-01 1.1 2.36e+06 1.2 5.4e+01 3.3e+03 > 1.1e+02 0 0 0 0 0 0 0 0 0 0 50 > MatPtAPSymbolic 2 1.0 1.3786e-01 1.1 0.00e+00 0.0 4.8e+01 3.1e+03 > 1.0 e+02 0 0 0 0 0 0 0 0 0 0 0 > MatPtAPNumeric 2 1.0 4.7638e-02 2.2 2.36e+06 1.2 6.0e+00 4.8e+03 > 1.2e+01 0 0 0 0 0 0 0 0 0 0 180 > MatTrnMatMult 2 1.0 7.9914e-01 1.0 1.14e+07 1.3 3.6e+01 2.1e+04 > 1.2e+02 0 0 0 1 0 0 0 0 1 0 48 > MatGetLocalMat 10 1.0 6.7852e-03 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 > 2.4e+01 0 0 0 0 0 0 0 0 0 0 0 > MatGetBrAoCol 6 1.0 3.6962e-02 2.4 0.00e+00 0.0 4.2e+01 4.5e+03 > 1.6e+01 0 0 0 0 0   ; 0 0 0 0 0 0 > MatGetSymTrans 4 1.0 4.4394e-04 1.2 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > VecMDot 913 1.0 2.8472e+00 3.0 5.28e+08 1.0 0.0e+00 0.0e+00 > 9.1e+02 1 24 0 0 2 1 24 0 0 2 741 > VecNorm 1367 1.0 2.7202e+00 1.6 7.12e+06 1.0 0.0e+00 0.0e+00 > 1.4e+03 1 0 0 0 2 1 0 0 0 2 10 > VecScale 4950 1.0 6.0693e-02 1.2 1.96e+07 1.1 0.0e+00 0.0e+00 > 0.0e+00 0 1 0 0 0 0 1 0 0 0 1169 > VecCopy 1349 1.0 7.8685e-03 1.4 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > VecSet 4972 1.0 1.2852e-02 1.3 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > VecAXPY 7624 1.0 1.3610e-01 1.1 6.44e+07 1.2 0.0e+00 0.0e+00 > 0.0e+00 0 3 0 0 0 0 3 0 0 0 1676 > VecAYPX 7168 1.0 1.5877e-01 1.2 4.01e+07 1.2 0.0e+00 0.0e+00 > 0.0e+00 0 2 0 0 0   ; 0 2 0 0 0 896 > VecMAXPY 1366 1.0 6.3739e-01 1.3 5.35e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 0 25 0 0 0 0 25 0 0 0 3353 > VecAssemblyBegin 21 1.0 4.7891e-02 1.2 0.00e+00 0.0 0.0e+00 0.0e+00 > 6.0e+01 0 0 0 0 0 0 0 0 0 0 0 > VecAssemblyEnd 21 1.0 4.5776e-05 1.4 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > VecPointwiseMult 5398 1.0 1.2278e-01 1.3 2.42e+07 1.2 0.0e+00 0.0e+00 > 0.0e+00 0 1 0 0 0 0 1 0 0 0 698 > VecScatterBegin 8107 1.0 3.9436 e-02 1.3 0.00e+00 0.0 2.2e+04 3.4e+03 > 0.0e+00 0 0 99 98 0 0 0 99 98 0 0 > VecScatterEnd 8107 1.0 1.5414e+01344.4 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 > VecSetRandom 2 1.0 1.1868e-03 1.6 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > VecNormalize 1366 1.0 2.7266e+00 1.6 1.07e+07 1.0 0.0e+00 0.0e+00 > 1.4e+03 1 0 0 0 2 1 0 0 0 2 15 > KSPGMRESOrthog 913 1.0 8.5743e+00 1.1 1.06e+09 1.0 0.0e+00 0.0e+00 > 3.6e+04 3 49 0 0 60 &nb sp; 3 49 0 0 60 492 > KSPSetUp 7 1.0 2.4805e-02 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 > 6.0e+00 0 0 0 0 0 0 0 0 0 0 0 > KSPSolve 1 1.0 5.7656e+01 1.0 2.30e+09 1.1 2.2e+04 3.4e+03 > 6.0e+04 18100100100100 18100100100100 151 > PCSetUp 2 1.0 2.1524e+00 1.0 2.03e+07 1.3 3.8e+02 6.0e+03 > 1.1e+03 1 1 2 3 2 1 1 2 3 2 33 > PCSetUpOnBlocks 448 1.0 1.5607e-03 1.8 1.85e+04 0.0 0.0e+00 0.0e+00 > 8.0e+00 0 0 0 0 0 0 0 0 0 0 & nbsp; 12 > PCApply 448 1.0 4.4331e+01 1.1 1.08e+09 1.2 1.9e+04 3.4e+03 > 2.3e+04 14 44 86 85 38 14 44 86 85 38 87 > PCGAMGgraph_AGG 2 1.0 6.1282e-01 1.0 3.36e+05 1.2 6.6e+01 5.7e+03 > 1.9e+02 0 0 0 0 0 0 0 0 0 0 2 > PCGAMGcoarse_AGG 2 1.0 8.8854e-01 1.0 1.14e+07 1.3 9.0e+01 1.2e+04 > 2.1e+02 0 0 0 1 0 0 0 0 1 0 44 > PCGAMGProl_AGG 2 1.0 6.3711e-02 1.1 0.00e+00 0.0 4.2e+01 2.3e+03 > 1.0e+02 0 0 0 0 0 0 0 0 0 0 0 > PCGAMGPOpt_AGG 2 1.0 3.4247e-01 1.0 6.22e+06 1.2 9.6e+01 2.8e+03 > 3.3e+02 0 0 0 0 1 0 0 0 0 1 65 > > ------------------------------------------------------------------------------------------------------------------------ > Memory usage is given in bytes: > Object Type Creations Destructions Memory Descendants' Mem. > Reports information only for process 0. > --- Event Stage 0: Main Stage > Matrix 68 68 27143956 0 > Matrix Coarsen 2 2 704 0 > Vector 296 296 13385864 0 > Vector Scatter 18 18 11304 0 > & nbsp; Index Set 47 47 34816 0 > Krylov Solver 7 7 554688 0 > Preconditioner 7 7 3896 0 > PetscRandom 2 2 704 0 >   ; Viewer 1 0 0 0 > > ======================================================================================================================== > Average time to get PetscTime(): 1.3113e-06 > Average time for MPI_Barrier(): 9.62257e-05 > Average time for zero size MPI_Send(): 0.00019449 > #PETSc Option Table entries: > -ksp_converged_reason > -ksp_gmres_restart 170 > -ksp_rtol 1.0e-15 > -ksp_type gmres > -log_summary > -pc_gamg_agg_nsmooths 1 > -pc_type gamg > #End of PETSc Option Table entries > Compiled without FORTRAN kernels > Compiled with full precision matrices (default) > sizeof(short) 2 sizeof(int) 4 sizeof(long) 4 sizeof(void*) 4 > sizeof(PetscScalar) 8 sizeof(PetscInt) 4 > Configure run at: Thu Nov 1 05:54:48 2012 > Configure options: --with-mpi-dir=/home/ub u/soft/mpich2/ > --download-f-blas-lapack =1 > ----------------------------------------- > Libraries compiled on Thu Nov 1 05:54:48 2012 on ubuntu > Machine characteristics: > Linux-2.6.32-38-generic-i686-with-Ubuntu-10.04-lucid > Using PETSc directory: /home/ubu/soft/petsc/petsc-3.3-p4 > Using PETSc arch: arch-linux2-c-debug > ----------------------------------------- > Using C compiler: /home/ubu/soft/mpich2/bin/mpicc -wd1572 -g > ${COPTFLAGS} ${CFLAGS} > Using Fortran compiler: /home/ubu/soft/mpich2/bin/mpif90 -g > ${FOPTFLAGS} ${FFLAGS} > ----------------------------------------- > Using include paths: > -I/home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/include > -I/home/ubu/soft/petsc/petsc-3.3-p4/include > -I/home/ubu/soft/petsc/petsc-3.3-p4/include > -I/home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/include > -I/home/ubu/soft/mpich2/include > ----------------------------------------- > Using C linker: /home/ubu/soft/mpich2/bin/mpicc > Using Fortran linker: /home/ubu/soft/mpich2/bin/mpif90 > Using libraries: > -Wl,-rpath,/home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib > -L/home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib -lpetsc > -lpthread > -Wl,-rpath,/home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib > -L/home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib -lflapack > -lfblas -L/home/ubu/soft/mpich2/lib > -L/opt/intel/composer_xe_2011_sp1.10.319/compiler/lib/ia32 > -L/opt/intel/composer_xe_2011_sp1.10.319/ipp/lib/ia32 > -L/opt/intel/composer_xe_2011_sp1.10.319/mkl/lib/ia32 > -L/opt/intel/composer_xe_2011_sp1.10.319/tbb/lib/ia32/cc4.1.0_libc2.4_kernel2.6.16.21 > -L/opt/intel/composer_xe_2011_sp1.9.293/compiler/lib/ia32 > -L/opt/intel/composer_xe_2011_sp1.9.293/mkl/lib/ia32 > -L/usr/lib/gcc/i486-linux-gnu/4.4.3 -L/usr/lib/i486-linux-gnu -lmpichf90 > -lifport -lifcore -lm -lm -ldl -lmpich -lopa -lmpl -lrt -lpthread -limf > -lsvml -lipgo -ldecimal -lci lkrts -lstdc++ -lgcc_s -lirc -lirc_s -ldl > ----------------------------------------- > time 14.4289010000000 > time 14.4289020000000 > time 14.4449030000000 > time 14.4809050000000 > > > (2) using asm > Linear solve converged due to CONVERGED_RTOL iterations 483 > Norm of error 0.2591E+04 iterations 483 > 0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000 > 4.866092420969481E-018 0.000000000000000E+000 0.000000000000000E+000 > 26.4211453778395 -4.861214483821431E-017 5.379151535696287E-018 > > ************************************************************************************************************************ > *** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r > -fCourier9' to print this document *** > > ************************************************************************************************************************ > ---------------------------------------------- PETSc Performance Summary: > ---------------------------------------------- > ./ex4f on a arch-linux2-c-debug named ubuntu with 4 processors, by ubu Sat > Nov 3 10:00:43 2012 > Using Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 CDT 2012 > Max Max/Min Avg Total > Time (sec): 2.952e+02 1.00006 2.952e+02 > Objects: 2.040e+02 1.00000 2.040e+02 > Flops: 1.502e+09 1.00731 1.496e+09 5.983e+09 > Flops/sec: 5.088e+06 1.00734 5.067e+06 2.027e+07 > Memory: 2.036e+07 1.01697 8.073e+07 > MPI Messages: 1.960e+03 2.00000 1.470e+03 5.880e+03 > MPI Message Lengths: 7.738e+06 3.12820 3.474e+03 2.042e+07 > MPI Reductions: 4.236e+04 1.00000 > Flop counting convention: 1 flop = 1 real number operation of type > (multiply/divide/add/subtract) > e.g., VecAXPY() for real vectors of length N > --> 2N flops > and VecAXPY() for complex vectors of length N > --> 8N flops > Summary of Stages: ----- Time ------ ----- Flops ----- --- Messages > --- -- Message Lengths -- -- Reductions -- > Avg %Total Avg %Total counts > %Total Avg %Total counts %Total > 0: Main Stage: 2.9517e+02 100.0% 5.9826e+09 100.0% 5.880e+03 > 100.0% 3.474e+03 100.0% 4.236e+04 100.0% > > ------------------------------------------------------------------------------------------------------------------------ > See the 'Profiling' chapter of the users' manual for details on > interpreting output. > Phase summary info: > Count: number of times phase was executed > Time and Flops: Max - maximum over all processors > Ratio - ratio of maximum to minimum over all processors > Mess: number of messages sent > Avg. len: average message length > Reduct: number of global reductions > Global: entire computation > Stage: stages of a computation. Set stages with PetscLogStagePush() and > PetscLogStagePop(). > %T - percent time in this phase %f - percent flops in this > phase > & nbsp; %M - percent messages in this phase %L - percent message > lengths in this phase > %R - percent reductions in this phase > Total Mflop/s: 10e-6 * (sum of flops over all processors)/(max time > over all processors) > > ------------------------------------------------------------------------------------------------------------------------ > > ########################################################## > # # > # WARNING!!! # > # & nbsp; # > # This code was compiled with a debugging option, # > # To get timing results run ./configure # > # using --with-debugging=no, the performance will # > # be generally two or three times faster. # > # &n bsp; # > ########################################################## > > Event Count Time (sec) > Flops --- Global --- --- Stage --- Total > Max Ratio Max Ratio Max Ratio Mess Avg len > Reduct %T %f %M %L %R %T %f %M %L %R Mflop/s > > ------------------------------------------------------------------------------------------------------------------------ > --- Event Stage 0: Main Stage > MatMult 485 1.0 3.1170e+00 5.9 1.36e+08 1.0 2.9e+03 3.4e+03 > 0.0e+00 1 9 49 48 0 1 9 49 48 0 173 > MatSolve 486 1.0 6.8313e-01 1.3 1.49e+08 1.1 0.0e+00 0.0e+00 > 0.0e+00 0 10 0 0 0 0 10 0 0 0 842 > MatLUFactorNum 1 1.0 6.0117e-02 1.2 1.54e+06 1.1 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 99 > MatILUFactorSym 1 1.0 1.5973e-01 2.5 0.00e+00 0.0 0.0e+00 0.0e+00 > 1.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatAssemblyBegin 2 1 .0 6.0572e-02 9.5 0.00e+00 0.0 0.0e+00 0.0e+00 > 2.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatAssemblyEnd 2 1.0 1.7764e-02 1.6 0.00e+00 0.0 1.2e+01 8.5e+02 > 1.9e+01 0 0 0 0 0 0 0 0 0 0 0 > MatGetRowIJ 1 1.0 3.8147e-06 1.3 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatGetSubMatrice 1 1.0 1.9829e-01 2.1 0.00e+00 0.0 3.0e+01 2.1e+04 > 1.0e+01 0 0 1 3 0 0 0 1 3 0 0 > MatGetOrdering 1 1.0 1.2739e-02 5.8 0.00e+00 0.0 0.0e+00 0 .0e+00 > 4.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatIncreaseOvrlp 1 1.0 1.8877e-02 1.2 0.00e+00 0.0 0.0e+00 0.0e+00 > 2.0e+00 0 0 0 0 0 0 0 0 0 0 0 > VecMDot 483 1.0 4.5957e+00 2.5 5.98e+08 1.0 0.0e+00 0.0e+00 > 4.8e+02 1 40 0 0 1 1 40 0 0 1 521 > VecNorm 487 1.0 2.0843e+00 1.2 7.40e+06 1.0 0.0e+00 0.0e+00 > 4.9e+02 1 0 0 0 1 1 0 0 0 1 14 > VecScale 486 1.0 1.2140e-02 1.1 3.69e+06 1.0 0.0e+00 0.0e+00 > 0.0 e+00 0 0 0 0 0 0 0 0 0 0 1217 > VecCopy 3 1.0 4.2915e-05 1.2 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > VecSet 979 1.0 8.1432e-03 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > VecAXPY 6 1.0 2.3413e-04 1.3 9.12e+04 1.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 1558 > VecMAXPY 486 1.0 7. 0027e-01 1.2 6.06e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 0 41 0 0 0 0 41 0 0 0 3460 > VecAssemblyBegin 1 1.0 5.7101e-03 2.5 0.00e+00 0.0 0.0e+00 0.0e+00 > 3.0e+00 0 0 0 0 0 0 0 0 0 0 0 > VecAssemblyEnd 1 1.0 3.0994e-06 1.6 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > VecScatterBegin 1457 1.0 9.1357e-02 2.6 0.00e+00 0.0 5.8e+03 3.4e+03 > 0.0e+00 0 0 99 97 0 0 0 99 97 0 0 > VecScatterEnd 1457 1.0 2.5327e+00323.7 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0&n bsp; 0 0 > VecNormalize 486 1.0 2.0858e+00 1.2 1.11e+07 1.0 0.0e+00 0.0e+00 > 4.9e+02 1 1 0 0 1 1 1 0 0 1 21 > KSPGMRESOrthog 483 1.0 1.1152e+01 1.2 1.20e+09 1.0 0.0e+00 0.0e+00 > 4.0e+04 3 80 0 0 94 3 80 0 0 94 429 > KSPSetUp 2 1.0 1.1989e-02 1.4 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > KSPSolve 1 1.0 2.0990e+01 1.0 1.50e+09 1.0 5.9e+03 3.5e+03 > 4.2e+04 7100100100100 7100100100100 285 > PCSetUp & nbsp; 2 1.0 3.5928e-01 1.0 1.54e+06 1.1 4.2e+01 > 1.5e+04 3.5e+01 0 0 1 3 0 0 0 1 3 0 17 > PCSetUpOnBlocks 1 1.0 2.2166e-01 1.7 1.54e+06 1.1 0.0e+00 0.0e+00 > 6.0e+00 0 0 0 0 0 0 0 0 0 0 27 > PCApply 486 1.0 5.9831e+00 2.8 1.49e+08 1.1 2.9e+03 3.4e+03 > 1.5e+03 1 10 50 48 3 1 10 50 48 3 96 > > ------------------------------------------------------------------------------------------------------------------------ > Memory usage is given in bytes: > Object Type Creations Destructions Memory Descendants' Mem. > Reports information only for process 0. > --- Event Stage 0: Main Stage > Matrix 5 5 8051336 0 > Vector 182 182 11109304 0 > Vector Scatter 2 2 1256 0 > Index Set 10 10 121444 0 > & nbsp; Krylov Solver 2 2 476844 0 > Preconditioner 2 2 1088 0 > Viewer 1 0 0 0 > > ======================================================================================================================== > Average time to get PetscTime(): 9.05991e-07 > Average time for MPI_Barrier(): 0.000297785 > Average time for zero size MPI_Send() : 0.000174284 > #PETSc Option Table entries: > -ksp_converged_reason > -ksp_gmres_restart 170 > -ksp_rtol 1.0e-15 > -ksp_type gmres > -log_summary > -pc_type asm > #End of PETSc Option Table entries > Compiled without FORTRAN kernels > Compiled with full precision matrices (default) > sizeof(short) 2 sizeof(int) 4 sizeof(long) 4 sizeof(void*) 4 > sizeof(PetscScalar) 8 sizeof(PetscInt) 4 > Configure run at: Thu Nov 1 05:54:48 2012 > Configure options: --with-mpi-dir=/home/ubu/soft/mpich2/ > --download-f-blas-lapack =1 > ----------------------------------------- > Libraries compiled on Thu Nov 1 05:54:48 2012 on ubuntu > Machine characteristics: > Linux-2.6.32-38-generic-i686-with-Ubuntu-10.04-lucid > Using PETSc directory: /home/ubu/soft/petsc/petsc-3.3-p4 > Using PETSc arch: arch-linux2-c-debug > ----------------------------------------- > Using C compiler: /home/ubu/soft/mpich2/bin/mpicc -wd1572 -g > ${COPTFLAGS} ${CFLAGS} > Using Fortran compiler: /home/ubu/soft/mpich2/bin/mpif90 -g > ${FOPTFLAGS} ${FFLAGS} > ----------------------------------------- > Using include paths: > -I/home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/include > -I/home/ubu/soft/petsc/petsc-3.3-p4/include > -I/home/ubu/soft/petsc/petsc-3.3-p4/include > -I/home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/include > -I/home/ubu/soft/mpich2/include > ----------------------------------------- > Using C linker: /home/ubu/soft/mpich2/bin/mpicc > Using Fortran linker: /home/ubu/soft/mpich2/bin/mpif90 > Using libraries: > -Wl,-rpath,/home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib > -L/home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib -lpetsc > -lpthread -Wl,-rpath,/home/u > bu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib > -L/home/ubu/soft/petsc/petsc-3.3-p4/arch-linux2-c-debug/lib -lflapack > -lfblas -L/home/ubu/soft/mpich2/lib > -L/opt/intel/composer_xe_2011_sp1.10.319/compiler/lib/ia32 > -L/opt/intel/composer_xe_2011_sp1.10.319/ipp/lib/ia32 > -L/opt/intel/composer_xe_2011_sp1.10.319/mkl/lib/ia32 > -L/opt/intel/composer_xe_2011_sp1.10.319/tbb/lib/ia32/cc4.1.0_libc2.4_kernel2.6.16.21 > -L/opt/intel/composer_xe_2011_sp1.9.293/compiler/lib/ia32 > -L/opt/intel/composer_xe_2011_sp1.9.293/mkl/lib/ia32 > -L/usr/lib/gcc/i486-linux-gnu/4.4.3 -L/usr/lib/i486-linux-gnu -lmpichf90 > -lifport -lifcore -lm -lm -ldl -lmpich -lopa -lmpl -lrt -lpthread -limf > -lsvml -lipgo -ldecimal -lcilkrts -lstdc++ -lgcc_s -lirc -lirc_s -ldl > ----------------------------------------- > time 5.72435800000000 > time 5.40433800000000 > time 5.39233700000000 > time 5.51634499999999 > > > > > >At 2012-11-03 23:53:42,"Jed Brown" wrote: > > >Just pass it as a command line option. It gives profiling output in > PetscFinalize(). > > > >On Sat, Nov 3, 2012 at 10:52 AM, w_ang_temp wrote: > >> >Is there something that need attention when setting up PETSc? The >> -log_summary >> >is no use in my system. >> >> >> >At 2012-11-03 23:31:52,"Jed Brown" wrote: >> >> >1. *Always* send -log_summary when asking about performance. >> >2. AMG setup costs more, the solve should be faster, especially for >> large problems. >> >3. 30k degrees of freedom is not large. >> >> >> >>On Sat, Nov 3, 2012 at 10:27 AM, w_ang_temp wrote: >> >>> >>Hello, >>> >> I have tried AMG, but there are some problems. I use the command: >>> >> mpiexec -n 4 ./ex4f -ksp_type gmres -pc_type gamg >>> -pc_gamg_agg_nsmooths 1 -ksp_gmres_restart 170 -ksp_rtol 1.0e-15 >>> ->>ksp_converged_reason. >>> >> The matrix has a size of 30000. However, compared with -pc_type >>> asm, >>> >>the amg need more time:asm needs 4.9s, amg needs 13.7s. I did several >>> tests >>> >>and got the same conclusion. When it begins, the screen shows the >>> information: >>> >>[0]PCSetData_AGG bs=1 MM=7601. I do not know the meaning. And if there >>> is some >>> >>parameters that affect the performance of AMG? >>> >> Besides, I want to confirm a conception. In my view, AMG itself >>> can be a solver >>> >>like gmres. It can also be used as a preconditioner like jacobi and is >>> used by combining >>> >>with other solver. Is it right? If it is right, how use AMG solver? >>> >> My codes are attached. >>> >> Thanks. >>> >> Jim >>> >>> >>> >>> >At 2012-11-01 22:00:28,"Jed Brown" wrote: >>> >>> >Yes, it's faster to understand this error message than to have >>> "mysteriously slow performance". >>> >>> >** Preallocation routines now automatically set >>> MAT_NEW_NONZERO_ALLOCATION_ERR, if you intentionally preallocate less than >>> necessary then *>*use >>> MatSetOption(mat,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE) to disable the >>> error generation. >>> * >>> >http://www.mcs.anl.gov/petsc/documentation/changes/33.html >>> >>> >On Thu, Nov 1, 2012 at 8:57 AM, w_ang_temp wrote: >>> >>>> >Do you mean that the two versions have a different in this point? If I >>>> use the new version, I have to >>>> >make some modifications on my codes? >>>> >>> >>> >>> >>> >> >> >> > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From w_ang_temp at 163.com Sat Nov 3 12:17:47 2012 From: w_ang_temp at 163.com (w_ang_temp) Date: Sun, 4 Nov 2012 01:17:47 +0800 (CST) Subject: [petsc-users] How to use multigrid? In-Reply-To: References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <3fb03a6a.10633.13aa798827b.Coremail.w_ang_temp@163.com> <611bda2d.10ae0.13aac91f0d5.Coremail.w_ang_temp@163.com> <01255FF7-A444-48E8-AB48-AE76C710197C@columbia.edu> <5c4f7f1f.c7e0.13abc39f25e.Coremail.w_ang_temp@163.com> <50cc9123.12a74.13abc43826a.Coremail.w_ang_temp@163.com> <4f586efd.7cb3.13ac6e1fd4b.Coremail.w_ang_temp@163.com> <4bae45af.5608.13ac6f91024.Coremail.w_ang_temp@163.com> <408a3dbe.585e.13ac73bfe97.Coremail.w_ang_temp@163.com> Message-ID: >At 2012-11-04 01:08:26,"Jed Brown" wrote: >1. What kind of equation are you solving? AMG is not working well if it takes that many iterations. I just deal with the typical soil-water coupled geotechnical problems. It is a typical finite element equation. The matrix is 30000X30000 and ill-conditioned. 2. ########################################################## # # # WARNING!!! # # # # This code was compiled with a debugging option, # # To get timing results run ./configure # # using --with-debugging=no, the performance will # # be generally two or three times faster. # # # ########################################################## It is true a debugging version. And I used the same version dealing with the same problem, one preconditioner is asm and the other is amg. The time with amg is about 3 times as with asm. I do not know the reason. And I also do not know the meaning of '[0]PCSetData_AGG bs=1 MM=7601'. -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Sat Nov 3 12:21:59 2012 From: knepley at gmail.com (Matthew Knepley) Date: Sat, 3 Nov 2012 13:21:59 -0400 Subject: [petsc-users] How to use multigrid? In-Reply-To: References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <3fb03a6a.10633.13aa798827b.Coremail.w_ang_temp@163.com> <611bda2d.10ae0.13aac91f0d5.Coremail.w_ang_temp@163.com> <01255FF7-A444-48E8-AB48-AE76C710197C@columbia.edu> <5c4f7f1f.c7e0.13abc39f25e.Coremail.w_ang_temp@163.com> <50cc9123.12a74.13abc43826a.Coremail.w_ang_temp@163.com> <4f586efd.7cb3.13ac6e1fd4b.Coremail.w_ang_temp@163.com> <4bae45af.5608.13ac6f91024.Coremail.w_ang_temp@163.com> <408a3dbe.585e.13ac73bfe97.Coremail.w_ang_temp@163.com> Message-ID: On Sat, Nov 3, 2012 at 1:17 PM, w_ang_temp wrote: > >At 2012-11-04 01:08:26,"Jed Brown" wrote: > > >1. What kind of equation are you solving? AMG is not working well if it > takes that many iterations. > > I just deal with the typical soil-water coupled geotechnical problems. It > is a typical finite element equation. The matrix is 30000X30000 and > ill-conditioned. > > We are now at the root of your problem. Solvers do not work on discretizations, they work on equations. No solver is designed for "finite elements", and there is no typical finite element problem. Multigrid works best on elliptic equations with smooth coefficients. Without that, you have to do special things. I can tell from the above discussion that you have not spent a lot of time researching successful preconditioning strategies for your problem in the literature. This is always the first step to building a high performance solver. Thanks, Matt > 2. > > * ##########################################################* > * # #* > * # WARNING!!! #* > * # #* > * # This code was compiled with a debugging option, #* > * # To get timing results run ./configure #* > * # using --with-debugging=no, the performance will #* > * # be generally two or three times faster. #* > * # #* > * ##########################################################* > It is true a debugging version. And I used the same version dealing with > the same problem, one preconditioner is asm > and the other is amg. The time with amg is about 3 times as with asm. I do > not know the reason. And I also do not know the > meaning of '[0]PCSetData_AGG bs=1 MM=7601'. > > > > -- 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From w_ang_temp at 163.com Sat Nov 3 12:38:33 2012 From: w_ang_temp at 163.com (w_ang_temp) Date: Sun, 4 Nov 2012 01:38:33 +0800 (CST) Subject: [petsc-users] How to use multigrid? In-Reply-To: References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <3fb03a6a.10633.13aa798827b.Coremail.w_ang_temp@163.com> <611bda2d.10ae0.13aac91f0d5.Coremail.w_ang_temp@163.com> <01255FF7-A444-48E8-AB48-AE76C710197C@columbia.edu> <5c4f7f1f.c7e0.13abc39f25e.Coremail.w_ang_temp@163.com> <50cc9123.12a74.13abc43826a.Coremail.w_ang_temp@163.com> <4f586efd.7cb3.13ac6e1fd4b.Coremail.w_ang_temp@163.com> <4bae45af.5608.13ac6f91024.Coremail.w_ang_temp@163.com> <408a3dbe.585e.13ac73bfe97.Coremail.w_ang_temp@163.com> Message-ID: <43c9d390.8b48.13ac75a4779.Coremail.w_ang_temp@163.com> Hello, Matthew I just mean that the problem that I am resolving is a finite element problem. The linear system of it is true elliptic equations. I heared that AMG was an efficient solver, so I just want to have a try about AMG and find that if it is efficient. By the way, I want to confirm a conception. In my view, AMG itself can be a solver like gmres. It can also be used as a preconditioner like jacobi and is used by combining with other solver. Is it right? If it is right, how use AMG solver? Thanks. Jim >? 2012-11-04 01:21:59?"Matthew Knepley" ??? > wrote: >At 2012-11-04 01:08:26,"Jed Brown" wrote: >1. What kind of equation are you solving? AMG is not working well if it takes that many iterations. >I just deal with the typical soil-water coupled geotechnical problems. It is a typical finite element equation. The matrix is 30000X30000 and ill-conditioned. >We are now at the root of your problem. Solvers do not work on discretizations, they work on equations. No >solver is designed for "finite elements", and there is no typical finite element problem. >Multigrid works best on elliptic equations with smooth coefficients. Without that, you have to do special things. >I can tell from the above discussion that you have not spent a lot of time researching successful preconditioning >strategies for your problem in the literature. This is always the first step to building a high performance solver. > Thanks, > Matt >2. ########################################################## # # # WARNING!!! # # # # This code was compiled with a debugging option, # # To get timing results run ./configure # # using --with-debugging=no, the performance will # # be generally two or three times faster. # # # ########################################################## >It is true a debugging version. And I used the same version dealing with the same problem, one preconditioner is asm >and the other is amg. The time with amg is about 3 times as with asm. I do not know the reason. And I also do not know the >meaning of '[0]PCSetData_AGG bs=1 MM=7601'. -- 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Sat Nov 3 12:52:13 2012 From: knepley at gmail.com (Matthew Knepley) Date: Sat, 3 Nov 2012 13:52:13 -0400 Subject: [petsc-users] How to use multigrid? In-Reply-To: <43c9d390.8b48.13ac75a4779.Coremail.w_ang_temp@163.com> References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <3fb03a6a.10633.13aa798827b.Coremail.w_ang_temp@163.com> <611bda2d.10ae0.13aac91f0d5.Coremail.w_ang_temp@163.com> <01255FF7-A444-48E8-AB48-AE76C710197C@columbia.edu> <5c4f7f1f.c7e0.13abc39f25e.Coremail.w_ang_temp@163.com> <50cc9123.12a74.13abc43826a.Coremail.w_ang_temp@163.com> <4f586efd.7cb3.13ac6e1fd4b.Coremail.w_ang_temp@163.com> <4bae45af.5608.13ac6f91024.Coremail.w_ang_temp@163.com> <408a3dbe.585e.13ac73bfe97.Coremail.w_ang_temp@163.com> <43c9d390.8b48.13ac75a4779.Coremail.w_ang_temp@163.com> Message-ID: On Sat, Nov 3, 2012 at 1:38 PM, w_ang_temp wrote: > Hello, Matthew > > I just mean that the problem that I am resolving is a finite > element problem. The linear system of it is true elliptic equations. > I heared that AMG was an efficient solver, so I just want to have a try > about AMG and find that if it is efficient. > And I meant it when I said, you MUST look it up .Next time you ask us what AMG can do, please include a reference for a paper in which they are attacking this problem with it and we can help. > By the way, I want to confirm a conception. In my view, AMG > itself can be a solver like gmres. It can also be used as a preconditioner > like jacobi and is used by combining with other solver. Is it right? If it > is right, how use AMG solver? > This is true of almost all KSP and PC objects. These are all jsut approximate solvers. Matt > > Thanks. > > > Jim > > > >? 2012-11-04 01:21:59?"Matthew Knepley" ??? > > > wrote: > >> >At 2012-11-04 01:08:26,"Jed Brown" wrote: >> >> >1. What kind of equation are you solving? AMG is not working well if it >> takes that many iterations. >> >> >I just deal with the typical soil-water coupled geotechnical problems. >> It is a typical finite element equation. The matrix is 30000X30000 and >> ill-conditioned. >> >> > >We are now at the root of your problem. Solvers do not work on > discretizations, they work on equations. No > >solver is designed for "finite elements", and there is no typical finite > element problem. > > >Multigrid works best on elliptic equations with smooth coefficients. > Without that, you have to do special things. > > >I can tell from the above discussion that you have not spent a lot of > time researching successful preconditioning > >strategies for your problem in the literature. This is always the first > step to building a high performance solver. > > > Thanks, > > > Matt > > >> >2. >> >> * ##########################################################* >> * # #* >> * # WARNING!!! #* >> * # #* >> * # This code was compiled with a debugging option, #* >> * # To get timing results run ./configure #* >> * # using --with-debugging=no, the performance will #* >> * # be generally two or three times faster. #* >> * # #* >> * ##########################################################* >> >It is true a debugging version. And I used the same version dealing with >> the same problem, one preconditioner is asm >> >and the other is amg. The time with amg is about 3 times as with asm. I >> do not know the reason. And I also do not know the >> >meaning of '[0]PCSetData_AGG bs=1 MM=7601'. >> >> >> >> > > > -- > 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 > > > > -- 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mirzadeh at gmail.com Sat Nov 3 20:20:41 2012 From: mirzadeh at gmail.com (Mohammad Mirzadeh) Date: Sat, 3 Nov 2012 18:20:41 -0700 Subject: [petsc-users] thread model In-Reply-To: <602AE3C5-6970-4BCA-858E-DF1F1D159302@mcs.anl.gov> References: <602AE3C5-6970-4BCA-858E-DF1F1D159302@mcs.anl.gov> Message-ID: Hum ... That did not help. I found this -threadcomm_affinities 0,1,2,3,4,5,6,7 but that also did nothing. Is that option any relevant? Another question: the linux box I'm testing on has 2 quad-cores (8 cores/2 sockets). If I run the code with mpirun -np 8, I get about 3X which makes sense to me. However, If I run with either pthread (which seems to use all cores) or openmp (which always defaults to 1 no matter what) I get the same performance as serial. Does this mean there is something messed up with the hardware and/or how mpi/openmp/pthread is set up? On Fri, Nov 2, 2012 at 8:24 PM, Shri wrote: > > On Nov 2, 2012, at 9:54 PM, Mohammad Mirzadeh wrote: > > > Hi, > > > > To use the new thread model in PETSc, does it suffice to run the code > with the following? > > > > -threadcomm_type -threadcomm_nthreads <#> > > > > When I run the code with openmp, only 1 processor/core is active > (looking at top). When using pthread, all cores are active. Am I missing > something? > OpenMP defaults to binding all threads to a single core if the cpu > affinity is not specified explicitly. If you > are using GNU OpenMP then you can bind the threads to specific cores using > the environment variable GOMP_CPU_AFFINITY > http://gcc.gnu.org/onlinedocs/libgomp/GOMP_005fCPU_005fAFFINITY.html > If you are some other OpenMP implementation then check its manual to see > how to set cpu affinity. > > Shri > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From abhyshr at mcs.anl.gov Sat Nov 3 23:50:15 2012 From: abhyshr at mcs.anl.gov (Shri) Date: Sat, 3 Nov 2012 23:50:15 -0500 Subject: [petsc-users] thread model In-Reply-To: References: <602AE3C5-6970-4BCA-858E-DF1F1D159302@mcs.anl.gov> Message-ID: <46D4ADAB-B58E-46F3-BD03-8D28DCB0B418@mcs.anl.gov> On Nov 3, 2012, at 8:20 PM, Mohammad Mirzadeh wrote: > Hum ... That did not help. I found this -threadcomm_affinities 0,1,2,3,4,5,6,7 but that also did nothing. Is that option any relevant? This option currently only works with pthreads. > > Another question: the linux box I'm testing on has 2 quad-cores (8 cores/2 sockets). If I run the code with mpirun -np 8, I get about 3X which makes sense to me. However, If I run with either pthread (which seems to use all cores) or openmp (which always defaults to 1 no matter what) As I said before you have to set the core affinity for OpenMP through environment variables. > I get the same performance as serial. i) Which example are you running? Please send output of -log_summary. ii) Only the vector and a few matrix operations are threaded currently. There are no threaded preconditioners yet. > Does this mean there is something messed up with the hardware and/or how mpi/openmp/pthread is set up? Shri > > > On Fri, Nov 2, 2012 at 8:24 PM, Shri wrote: > > On Nov 2, 2012, at 9:54 PM, Mohammad Mirzadeh wrote: > > > Hi, > > > > To use the new thread model in PETSc, does it suffice to run the code with the following? > > > > -threadcomm_type -threadcomm_nthreads <#> > > > > When I run the code with openmp, only 1 processor/core is active (looking at top). When using pthread, all cores are active. Am I missing something? > OpenMP defaults to binding all threads to a single core if the cpu affinity is not specified explicitly. If you > are using GNU OpenMP then you can bind the threads to specific cores using the environment variable GOMP_CPU_AFFINITY http://gcc.gnu.org/onlinedocs/libgomp/GOMP_005fCPU_005fAFFINITY.html > If you are some other OpenMP implementation then check its manual to see how to set cpu affinity. > > Shri > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mark.adams at columbia.edu Sun Nov 4 07:52:23 2012 From: mark.adams at columbia.edu (Mark F. Adams) Date: Sun, 4 Nov 2012 08:52:23 -0500 Subject: [petsc-users] How to use multigrid? In-Reply-To: References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <3fb03a6a.10633.13aa798827b.Coremail.w_ang_temp@163.com> <611bda2d.10ae0.13aac91f0d5.Coremail.w_ang_temp@163.com> <01255FF7-A444-48E8-AB48-AE76C710197C@columbia.edu> <5c4f7f1f.c7e0.13abc39f25e.Coremail.w_ang_temp@163.com> <50cc9123.12a74.13abc43826a.Coremail.w_ang_temp@163.com> <4f586efd.7cb3.13ac6e1fd4b.Coremail.w_ang_temp@163.com> <4bae45af.5608.13ac6f91024.Coremail.w_ang_temp@163.com> <408a3dbe.585e.13ac73bfe97.Coremail.w_ang_temp@163.com> <43c9d390.8b48.13ac75a4779.Coremail.w_ang_temp@163.com> Message-ID: <738F35E6-39C6-4C26-80A1-2130EDC76070@columbia.edu> Just to add to Jed and Matt's comments: 1) What are your equations (I really don't care what physics you are modeling, its the equations that we see). Is is a scalar div (alpha(x) grad ) u? 2) Try using hyper (-pc_type hyper -pc_hypre_type boomeramg). Look at "PCApply 448", this should be like 10-20. Configure your systems with --download-hyper=1 if you do not have it. 3) Why do you say it is ill conditioned? Stretched grids? large jumps in material coefficients? Why do you think it is illoconditioned? On Nov 3, 2012, at 1:52 PM, Matthew Knepley wrote: > On Sat, Nov 3, 2012 at 1:38 PM, w_ang_temp wrote: > Hello, Matthew > > I just mean that the problem that I am resolving is a finite element problem. The linear system of it is true elliptic equations. > I heared that AMG was an efficient solver, so I just want to have a try about AMG and find that if it is efficient. > > And I meant it when I said, you MUST look it up .Next time you ask us what AMG can do, please include > a reference for a paper in which they are attacking this problem with it and we can help. > > > By the way, I want to confirm a conception. In my view, AMG itself can be a solver like gmres. It can also be used as a preconditioner > like jacobi and is used by combining with other solver. Is it right? If it is right, how use AMG solver? > > This is true of almost all KSP and PC objects. These are all jsut approximate solvers. > > Matt > > > Thanks. > > Jim > > > >? 2012-11-04 01:21:59?"Matthew Knepley" ??? > > wrote: > >At 2012-11-04 01:08:26,"Jed Brown" wrote: > >1. What kind of equation are you solving? AMG is not working well if it takes that many iterations. > > >I just deal with the typical soil-water coupled geotechnical problems. It is a typical finite element equation. The matrix is 30000X30000 and ill-conditioned. > > > >We are now at the root of your problem. Solvers do not work on discretizations, they work on equations. No > >solver is designed for "finite elements", and there is no typical finite element problem. > > >Multigrid works best on elliptic equations with smooth coefficients. Without that, you have to do special things. > > >I can tell from the above discussion that you have not spent a lot of time researching successful preconditioning > >strategies for your problem in the literature. This is always the first step to building a high performance solver. > > > Thanks, > > > Matt > > >2. > > > ########################################################## > # # > # WARNING!!! # > # # > # This code was compiled with a debugging option, # > # To get timing results run ./configure # > # using --with-debugging=no, the performance will # > # be generally two or three times faster. # > # # > ########################################################## > >It is true a debugging version. And I used the same version dealing with the same problem, one preconditioner is asm > >and the other is amg. The time with amg is about 3 times as with asm. I do not know the reason. And I also do not know the > >meaning of '[0]PCSetData_AGG bs=1 MM=7601'. > > > > > > > -- > 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 > > > > > > -- > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Sun Nov 4 08:24:13 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Sun, 4 Nov 2012 08:24:13 -0600 Subject: [petsc-users] How to use multigrid? In-Reply-To: <738F35E6-39C6-4C26-80A1-2130EDC76070@columbia.edu> References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <3fb03a6a.10633.13aa798827b.Coremail.w_ang_temp@163.com> <611bda2d.10ae0.13aac91f0d5.Coremail.w_ang_temp@163.com> <01255FF7-A444-48E8-AB48-AE76C710197C@columbia.edu> <5c4f7f1f.c7e0.13abc39f25e.Coremail.w_ang_temp@163.com> <50cc9123.12a74.13abc43826a.Coremail.w_ang_temp@163.com> <4f586efd.7cb3.13ac6e1fd4b.Coremail.w_ang_temp@163.com> <4bae45af.5608.13ac6f91024.Coremail.w_ang_temp@163.com> <408a3dbe.585e.13ac73bfe97.Coremail.w_ang_temp@163.com> <43c9d390.8b48.13ac75a4779.Coremail.w_ang_temp@163.com> <738F35E6-39C6-4C26-80A1-2130EDC76070@columbia.edu> Message-ID: On Sun, Nov 4, 2012 at 7:52 AM, Mark F. Adams wrote: > 2) Try using hyper (-pc_type hyper -pc_hypre_type boomeramg). Look at "PCApply > 448", this should be like 10-20. Configure your systems with > --download-hyper=1 if you do not have it. > Jim, you can use -pc_type hypre (note the spelling "hypre", not "hyper"). > > 3) Why do you say it is ill conditioned? Stretched grids? large jumps in > material coefficients? Why do you think it is illoconditioned? > This question is important. PETSc devs, we may need to write an FAQ about how saying that your problem is "ill-conditioned" is useless, and explaining the sort of context that is necessary to say something useful. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mirzadeh at gmail.com Sun Nov 4 13:43:03 2012 From: mirzadeh at gmail.com (Mohammad Mirzadeh) Date: Sun, 4 Nov 2012 11:43:03 -0800 Subject: [petsc-users] thread model In-Reply-To: <46D4ADAB-B58E-46F3-BD03-8D28DCB0B418@mcs.anl.gov> References: <602AE3C5-6970-4BCA-858E-DF1F1D159302@mcs.anl.gov> <46D4ADAB-B58E-46F3-BD03-8D28DCB0B418@mcs.anl.gov> Message-ID: > > As I said before you have to set the core affinity for OpenMP through > environment variables. > > Well I tried 'export GOMP_CPU_AFFINITY="0-7" ' before running the code but that did not help. I'm using gcc. Am I doing it wrong. i) Which example are you running? Please send output of -log_summary. > This was my own code. Will try on some of the examples and report back. > ii) Only the vector and a few matrix operations are threaded currently. > There are no threaded preconditioners yet. > Aah! That may actually be it. I'm using hypre and I think that is not threaded. Will try with -pc_type none to see if that makes any difference. -------------- next part -------------- An HTML attachment was scrubbed... URL: From w_ang_temp at 163.com Sun Nov 4 19:52:26 2012 From: w_ang_temp at 163.com (w_ang_temp) Date: Mon, 5 Nov 2012 09:52:26 +0800 (CST) Subject: [petsc-users] How to use multigrid? In-Reply-To: <738F35E6-39C6-4C26-80A1-2130EDC76070@columbia.edu> References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <3fb03a6a.10633.13aa798827b.Coremail.w_ang_temp@163.com> <611bda2d.10ae0.13aac91f0d5.Coremail.w_ang_temp@163.com> <01255FF7-A444-48E8-AB48-AE76C710197C@columbia.edu> <5c4f7f1f.c7e0.13abc39f25e.Coremail.w_ang_temp@163.com> <50cc9123.12a74.13abc43826a.Coremail.w_ang_temp@163.com> <4f586efd.7cb3.13ac6e1fd4b.Coremail.w_ang_temp@163.com> <4bae45af.5608.13ac6f91024.Coremail.w_ang_temp@163.com> <408a3dbe.585e.13ac73bfe97.Coremail.w_ang_temp@163.com> <43c9d390.8b48.13ac75a4779.Coremail.w_ang_temp@163.com> <738F35E6-39C6-4C26-80A1-2130EDC76070@columbia.edu> Message-ID: <3fe23fa1.2738.13ace44ce07.Coremail.w_ang_temp@163.com> >At 2012-11-04 21:52:23,"Mark F. Adams" wrote: >Just to add to Jed and Matt's comments: >1) What are your equations (I really don't care what physics you are modeling, its the equations that we see). Is is a scalar div (alpha(x) grad ) u? The linear system Ax=b is resulted from the finite element discretization. It is a algebraic equation, based from a elliptic equation, my opinion. >2) Try using hyper (-pc_type hyper -pc_hypre_type boomeramg). Look at "PCApply 448", this should be like 10-20. Configure your systems with -->download-hyper=1 if you do not have it. >3) Why do you say it is ill conditioned? Stretched grids? large jumps in material coefficients? Why do you think it is illoconditioned? Pragmatic geotechnical problems often involve materials with highly varied material zones, such as in soil-structure interaction problems or soil-water coupled problems.([1]summary;[2-4]) Reference: [1]Krishna Bahadur Chaudhary. Preconditioners for soil-structure interaction problems with significant material stiffness contrast[D]. [2]S.H.Chan. A modified Jacobi preconditioner for solving ill-conditioned Biot's consolidation equations using symmetric quasi-minimal residual method.International journal for numerical and analytical methods in geomechanics[J]. [3]Kok-Kwang Phoon. Iterative solution of large-scale consolidation and constraint finite element equations for 3D problems.International e-Conference on Modern Trends in Foundation Engineering[J]. [4]Massimiliano, etc. Ill-conditioning of finite element poroelasticity equations. International Journal of Solids and Structures[J]. Thanks. Jim -------------- next part -------------- An HTML attachment was scrubbed... URL: From Gregor.Matura at dlr.de Mon Nov 5 07:10:41 2012 From: Gregor.Matura at dlr.de (Gregor.Matura at dlr.de) Date: Mon, 5 Nov 2012 13:10:41 +0000 Subject: [petsc-users] Block matrix data layout and access In-Reply-To: References: <2ED7073FE68F3F40B2D8739A46A7971B01537D28@dlrexmbx02.intra.dlr.de> Message-ID: <2ED7073FE68F3F40B2D8739A46A7971B01539383@dlrexmbx02.intra.dlr.de> Strongly recommend using MatSetValues[Blocked][Local]() instead of MatCreateMPIAIJWithSplitArrays(). Just preallocate and set the values from wherever you know them. This way, the same code will work immediately with different matrix formats and it's easier to transition to generating the matrix on-the-fly (rather than reading from disk which is always a bottleneck). Maybe I have not explained my situation well enough: I do already have a matrix on the disk. This makes generating the matrix on-the-fly either a burden for the filesystem (because of to many accesses in a short time) or for the memory (because data has to be duplicated). I want to avoid both, thus read in my matrix in one go and pass this data conveniently to PETSc. As far as my insights go, there are two possibilities with certain drawbacks, maybe you could uncover more details on both (like convenience of data layout, assembly time, solution speed, ?). 1.)MatCreateBAIJ (includes MatSetBlockSize and MatMPIBAIJSetPreallocation) > MatSetLocalToGlobalMapping > MatSetValuesBlockedLocal drawbacks: - data is copied (thus doubles memory needs) - ALL local rows has to be read in to get information for preallocation - but: SetValuesBlockedLocal requires "square" layout of data (not suited for sparse matrices). In my case this leads to setting values (block) row by (block) row. - and: value array does not match block structure (cf. documentation example of MatSetValuesBlocked): my values are sorted sequentially by blocks, i.e. v[] = [1,2,5,6,3,4,7,8,...] 2.)MatCreateMPIAIJWithSplitArrays drawbacks: ? doesn't match PETSc data layout -> slower? - not blocked (conversion to MPIBAIJ possible?) Regards, Gregor Matura ?????????????????????????? Deutsches Zentrum f?r Luft- und Raumfahrt e.V. (DLR) German Aerospace Center -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Mon Nov 5 08:08:26 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Mon, 5 Nov 2012 08:08:26 -0600 Subject: [petsc-users] Block matrix data layout and access In-Reply-To: <2ED7073FE68F3F40B2D8739A46A7971B01539383@dlrexmbx02.intra.dlr.de> References: <2ED7073FE68F3F40B2D8739A46A7971B01537D28@dlrexmbx02.intra.dlr.de> <2ED7073FE68F3F40B2D8739A46A7971B01539383@dlrexmbx02.intra.dlr.de> Message-ID: On Mon, Nov 5, 2012 at 7:10 AM, wrote: > Maybe I have not explained my situation well enough: I do already have a > matrix on the disk. > First a warning: 99% of the time, storing large matrices on disk represents a flawed workflow. Putting a matrix on disk is an epic scalability bottleneck that almost no amount of computation can escape. It takes most of today's supercomputers more than half an hour to read or write their contents to disk, assuming that they sustain maximum theoretical bandwidth for the entire operation. > This makes generating the matrix on-the-fly either a burden for the > filesystem (because of to many accesses in a short time) or for the memory > (because data has to be duplicated). > 1. File IO APIs read in chunks, not entire files. Just read one chunk at a time, loop through rows in the chunk, and call MatSetValues[Blocked][Local](). 2. Be aware that independent file IO will scale terribly. 3. Recall that it's _terrible_ for your workflow to partition the matrix entirely up-front for a specific number of processors. This means that you can't store the matrix data in a way that could be used directly anyway. > I want to avoid both, thus read in my matrix in one go and pass this data > conveniently to PETSc. As far as my insights go, there are two > possibilities with certain drawbacks, maybe you could uncover more details > on both (like convenience of data layout, assembly time, solution speed, ?). > **** > > ** ** > > 1.)MatCreateBAIJ (includes MatSetBlockSize and MatMPIBAIJSetPreallocation) > > MatSetLocalToGlobalMapping > MatSetValuesBlockedLocal**** > > drawbacks:**** > > - data is copied (thus doubles memory needs) > Disk doesn't work like this, see above. > **** > > - ALL local rows has to be read in to get information for preallocation > Row lengths are stored explicitly anyway, in a dedicated array if you use a CSR-type format. > **** > > - but: SetValuesBlockedLocal requires "square" layout of data (not suited > for sparse matrices). In my case this leads to setting values (block) row > by (block) row. > That is intentional. It inserts a _logically dense_ block. In typical PDE problems, that is a row (for FD schemes) or an element stiffness matrix for FE schemes. > **** > > - and: value array does not match block structure (cf. documentation > example of MatSetValuesBlocked): my values are sorted sequentially by > blocks, i.e. v[] = [1,2,5,6,3,4,7,8,...] > Just unpack row-by-row before calling MatSetValuesBlocked(). It's vanishingly little time. > **** > > ** ** > > 2.)MatCreateMPIAIJWithSplitArrays**** > > drawbacks:**** > > ? doesn't match PETSc data layout -> slower?**** > > - not blocked (conversion to MPIBAIJ possible?) > This routine exists for rare and peculiar workflows. It's only used by a handful of people and most of them shouldn't be using it. You shouldn't use it either. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Mon Nov 5 21:44:07 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Mon, 5 Nov 2012 21:44:07 -0600 Subject: [petsc-users] How to use multigrid? In-Reply-To: <3fe23fa1.2738.13ace44ce07.Coremail.w_ang_temp@163.com> References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <3fb03a6a.10633.13aa798827b.Coremail.w_ang_temp@163.com> <611bda2d.10ae0.13aac91f0d5.Coremail.w_ang_temp@163.com> <01255FF7-A444-48E8-AB48-AE76C710197C@columbia.edu> <5c4f7f1f.c7e0.13abc39f25e.Coremail.w_ang_temp@163.com> <50cc9123.12a74.13abc43826a.Coremail.w_ang_temp@163.com> <4f586efd.7cb3.13ac6e1fd4b.Coremail.w_ang_temp@163.com> <4bae45af.5608.13ac6f91024.Coremail.w_ang_temp@163.com> <408a3dbe.585e.13ac73bfe97.Coremail.w_ang_temp@163.com> <43c9d390.8b48.13ac75a4779.Coremail.w_ang_temp@163.com> <738F35E6-39C6-4C26-80A1-2130EDC76070@columbia.edu> <3fe23fa1.2738.13ace44ce07.Coremail.w_ang_temp@163.com> Message-ID: On Sun, Nov 4, 2012 at 7:52 PM, w_ang_temp wrote: > > > >At 2012-11-04 21:52:23,"Mark F. Adams" wrote: > > >Just to add to Jed and Matt's comments: > > >1) What are your equations (I really don't care what physics you are > modeling, its the equations that we see). Is is a scalar div (alpha(x) > grad ) u? > > The linear system Ax=b is resulted from the finite element discretization. > It is a algebraic equation, based from a elliptic equation, my opinion. > > If you use the formulation in the first cited reference, then you have a saddle point problem. This is extremely important and explains why naive application of algebraic multigrid did not work. AMG can handle the variable coefficients (and "ill-conditioning"), but it can't "automatically" handle the saddle. You can use PCFIELDSPLIT for these problems, but it's not a black box and it requires that you _understand_ what you are trying to do. You need to choose a respectable reference on preconditioners for saddle point problems. Best would be a review paper written since 2000 and with more than 100 citations. (There are a handful, almost any will be fine.) Read it first, then read a couple papers specific to poroelasticity and frame those methods in the context from the saddle point paper. Also read section 4.5 of the PETSc user's manual on PCFIELDSPLIT. Yes, this takes time, but if you want to solve these problems robustly, you have to understand enough about the methods to troubleshoot. >2) Try using hyper (-pc_type hyper -pc_hypre_type boomeramg). Look at "PCApply > 448", this should be like 10-20. Configure your systems with > -->download-hyper=1 if you do not have it. > > >3) Why do you say it is ill conditioned? Stretched grids? large jumps in > material coefficients? Why do you think it is illoconditioned? > > Pragmatic geotechnical problems often involve materials with highly > varied material zones, such as in soil-structure interaction problems or > soil-water > coupled problems.([1]summary;[2-4]) > Reference: > [1]Krishna Bahadur Chaudhary. Preconditioners for soil-structure > interaction problems with significant material stiffness contrast[D]. > [2]S.H.Chan. A modified Jacobi preconditioner for solving ill-conditioned > Biot's consolidation equations using symmetric quasi-minimal residual > method.International journal for numerical and analytical methods in > geomechanics[J]. > [3]Kok-Kwang Phoon. Iterative solution of large-scale consolidation and > constraint finite element equations for 3D problems.International > e-Conference on > Modern Trends in Foundation Engineering[J]. > [4]Massimiliano, etc. Ill-conditioning of finite element poroelasticity > equations. International Journal of Solids and Structures[J]. > > Thanks. > > > Jim > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhaonanavril at gmail.com Tue Nov 6 11:38:49 2012 From: zhaonanavril at gmail.com (NAN ZHAO) Date: Tue, 6 Nov 2012 11:38:49 -0600 Subject: [petsc-users] Wrong answers from KSPSolve Message-ID: Dear all, I tried to solve a 18 by 18 linear system with KSPsolve, the right hand vector and matrix can be found in the file in the attachment. The right hand vector has several zeros and the corresponding row in the matrix only have values in diagonal, I expected zero at this element but got -1 for the answer. I am using the tutorial code in petsc-3.2-p6/src/ksp/ksp/examples/tutorials/ex1.c as an example to assemble the matrix and vector and to solve the system. I also include the code in the attachment. I am working on a solution now but have run out of ideas. If you have any hint on the potential solution to this problems let me know. Thanks, Nan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: J_p64.m Type: application/octet-stream Size: 7414 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: R_p64.m Type: application/octet-stream Size: 440 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ex1.c Type: text/x-csrc Size: 13007 bytes Desc: not available URL: From ckhuangf at gmail.com Tue Nov 6 13:56:40 2012 From: ckhuangf at gmail.com (Chung-Kan Huang) Date: Tue, 6 Nov 2012 13:56:40 -0600 Subject: [petsc-users] Expecting zeros in solution when A_{I, I} != 0 A_{I, J} = 0. where I!=J and B_I = 0. In-Reply-To: References: Message-ID: Barry, We have tried tiny tol and lu but the problem is still there. It doesn't make sense to us that this problem is expected and common in iterative solvers instead we think this might be caused by some mistakes we made when we setup the ksp, pc or even the linear system. On Sat, Oct 27, 2012 at 6:07 PM, Barry Smith wrote: > > > PETSc, by default, using iterative solvers which only solve the problem > within a certain accuracy. You can control this accuracy by using -ksp_rtol > tol where for example you could pick tol = 1.0e-12 You can also use a > direct solver > -pc_type lu Run with -ksp_monitor_true_residual -ksp_converged_reason to > see if the linear solver is solving to the requested accuracy. > > Barry > > On Oct 27, 2012, at 3:46 PM, Chung-Kan Huang wrote: > > > Hi, > > > > I am solving a linear system A * X = B that sometime contains A_{I,I} != > 0 A_{I,J} = 0. where I!=J and B_I = 0. so I would expect X_i to be perfect > zero not some tiny small value. The same linear system is solved by other > solvers but they gave zero for aforementioned situation even the system is > fair large to our applications. I have tried several configurations in > PETSc hoping that problem can be solved but all attempts failed. I wonder > if someone can give me some pointers that help to solve this issue. Thanks, > > > > Chung-Kan > > > > > > > > -- > > Cheers > > > > > > -- *Cheers* -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Tue Nov 6 13:58:20 2012 From: bsmith at mcs.anl.gov (Barry Smith) Date: Tue, 6 Nov 2012 13:58:20 -0600 Subject: [petsc-users] Expecting zeros in solution when A_{I, I} != 0 A_{I, J} = 0. where I!=J and B_I = 0. In-Reply-To: References: Message-ID: <53D2DA2E-E1FB-4DE1-BD89-84F0C39F990D@mcs.anl.gov> Ok send the code to petsc-maint at mcs.anl.gov Barry On Nov 6, 2012, at 1:56 PM, Chung-Kan Huang wrote: > Barry, > > We have tried tiny tol and lu but the problem is still there. It doesn't make sense to us that this problem is expected and common in iterative solvers instead we think this might be caused by some mistakes we made when we setup the ksp, pc or even the linear system. > > > > > > On Sat, Oct 27, 2012 at 6:07 PM, Barry Smith wrote: > > > PETSc, by default, using iterative solvers which only solve the problem within a certain accuracy. You can control this accuracy by using -ksp_rtol tol where for example you could pick tol = 1.0e-12 You can also use a direct solver > -pc_type lu Run with -ksp_monitor_true_residual -ksp_converged_reason to see if the linear solver is solving to the requested accuracy. > > Barry > > On Oct 27, 2012, at 3:46 PM, Chung-Kan Huang wrote: > > > Hi, > > > > I am solving a linear system A * X = B that sometime contains A_{I,I} != 0 A_{I,J} = 0. where I!=J and B_I = 0. so I would expect X_i to be perfect zero not some tiny small value. The same linear system is solved by other solvers but they gave zero for aforementioned situation even the system is fair large to our applications. I have tried several configurations in PETSc hoping that problem can be solved but all attempts failed. I wonder if someone can give me some pointers that help to solve this issue. Thanks, > > > > Chung-Kan > > > > > > > > -- > > Cheers > > > > > > > > > -- > Cheers > > From petsc-maint at mcs.anl.gov Tue Nov 6 16:02:43 2012 From: petsc-maint at mcs.anl.gov (Matthew Knepley) Date: Tue, 6 Nov 2012 17:02:43 -0500 Subject: [petsc-users] Wrong answers from KSPSolve In-Reply-To: References: Message-ID: On Tue, Nov 6, 2012 at 12:38 PM, NAN ZHAO wrote: > Dear all, > > I tried to solve a 18 by 18 linear system with KSPsolve, the right hand > vector and matrix can be found in the file in the attachment. The right > hand vector has several zeros and the corresponding row in the matrix only > have values in diagonal, I expected zero at this element but got -1 for the > answer. I am using the tutorial code > in petsc-3.2-p6/src/ksp/ksp/examples/tutorials/ex1.c as an example to > assemble the matrix and vector and to solve the system. I also include the > code in the attachment. I am working on a solution now but have run out of > ideas. > > If you have any hint on the potential solution to this problems let me > know. > There are just so many errors here its hard to begin: 1) Your exact solution u does not match the rhs 2) I changed b to match u 3) The solver you chose was not solving the problem. The default works fine Here is the fixed up code. Our job is not to debug your code. Matt > Thanks, > Nan > -- 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ex1.c Type: text/x-csrc Size: 12961 bytes Desc: not available URL: From w_ang_temp at 163.com Wed Nov 7 07:41:42 2012 From: w_ang_temp at 163.com (w_ang_temp) Date: Wed, 7 Nov 2012 21:41:42 +0800 (CST) Subject: [petsc-users] Some change in 3.3 about --with-x? Message-ID: <241e703e.f52f.13adb1adfab.Coremail.w_ang_temp@163.com> Hello, I get a problem when configuring about the command "--with-x=1" in version 3.3. The command "./configure --with-mpi-dir=/home/ubu/soft/mpich2/ --download-f-blas-lapack=1 --with-x=1 --with-hypre=1 --download-hypre=1" is ok in version 3.2 but makes an error in 3.3:"Could not locate X *development* package. Perhaps its not installed". I do not find the detail about the change in "Documentation/Changes". Do I need "--with-x=1 --download-x=1"? The configure.log: ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Could not locate X *development* package. Perhaps its not installed ******************************************************************************* File "./config/configure.py", line 311, in petsc_configure framework.configure(out = sys.stdout) File "/home/ubu/soft/petsc/petsc-3.3-p4/config/BuildSystem/config/framework.py", line 933, in configure child.configure() File "/home/ubu/soft/petsc/petsc-3.3-p4/config/PETSc/packages/X.py", line 263, in configure self.executeTest(self.configureLibrary) File "/home/ubu/soft/petsc/petsc-3.3-p4/config/BuildSystem/config/base.py", line 115, in executeTest ret = apply(test, args,kargs) File "/home/ubu/soft/petsc/petsc-3.3-p4/config/PETSc/packages/X.py", line 247, in configureLibrary raise RuntimeError("Could not locate X *development* package. Perhaps its not installed") Thanks. Jim -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Wed Nov 7 07:45:16 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Wed, 7 Nov 2012 07:45:16 -0600 Subject: [petsc-users] Some change in 3.3 about --with-x? In-Reply-To: <241e703e.f52f.13adb1adfab.Coremail.w_ang_temp@163.com> References: <241e703e.f52f.13adb1adfab.Coremail.w_ang_temp@163.com> Message-ID: 1. Don't use both --with-hypre and --download-hypre. You probably only want the latter. 2. If you want to use X, you have to install it. PETSc can't install it for you so there is no --download-x. Look for the development headers in your package manager. On Wed, Nov 7, 2012 at 7:41 AM, w_ang_temp wrote: > Hello, > I get a problem when configuring about the command "--with-x=1" in > version 3.3. > The command "./configure --with-mpi-dir=/home/ubu/soft/mpich2/ > --download-f-blas-lapack=1 --with-x=1 --with-hypre=1 --download-hypre=1" > is ok in version 3.2 but makes an error in 3.3:"Could not locate X > *development* package. Perhaps its not installed". > I do not find the detail about the change in "Documentation/Changes". Do I > need "--with-x=1 --download-x=1"? > The configure.log: > > ******************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > details): > > ------------------------------------------------------------------------------- > Could not locate X *development* package. Perhaps its not installed > > ******************************************************************************* > File "./config/configure.py", line 311, in petsc_configure > framework.configure(out = sys.stdout) > File > "/home/ubu/soft/petsc/petsc-3.3-p4/config/BuildSystem/config/framework.py", > line 933, in configure > child.configure() > File "/home/ubu/soft/petsc/petsc-3.3-p4/config/PETSc/packages/X.py", > line 263, in configure > self.executeTest(self.configureLibrary) > File "/home/ubu/soft/petsc/petsc-3.3-p4/config/ > BuildSystem/config/base.py", line 115, in executeTest > ret = apply(test, args,kargs) > File "/home/ubu/soft/petsc/petsc-3.3-p4/config/PETSc/packages/X.py", > line 247, in configureLibrary > raise RuntimeError("Could not locate X *development* package. Perhaps > its not installed") > > Thanks. > Jim > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From als88 at cam.ac.uk Wed Nov 7 07:58:49 2012 From: als88 at cam.ac.uk (A.L. Siahaan) Date: 07 Nov 2012 13:58:49 +0000 Subject: [petsc-users] unable to set type "agg" in GAMG preconditioner Message-ID: Hi, I am experimenting with GAMG by changing some of its parameters. I tried to set the GAMG type into "agg" using : PCGAMGSetType(pc,"agg"); and I get the following error : ========================================================================== Solving linear system of size 108972 x 108972 (PETSc Krylov solver). demo_elasticity: /usr/local/packages/src/petsc-3.3/src/ksp/pc/impls/gamg/agg.c:1522: PCCreateGAMG_AGG: Assertion `!pc_gamg->subctx' failed. ========================================================================== Is there any other parameter which needs to be set to enable "agg" ? And what is the default type if I don't set to either "agg" or "geo" ? Thanks, Antony From arun.kamath.m at gmail.com Wed Nov 7 08:31:07 2012 From: arun.kamath.m at gmail.com (Arun Kamath) Date: Wed, 7 Nov 2012 15:31:07 +0100 Subject: [petsc-users] CFD code with immersed boundary method Message-ID: Hi! I am working with a CFD code where I need to solve the Poisson Pressure equation. We solve a two phase flow problem which results in a jump in the coefficients and a non symmetric system. The boundary conditions are fulfilled using immersed boundary method ghost cells at the solid boundaries of the domain. I read about the DAs to deal with the boundary conditions, but they are applicable to only "IJK" matrices as per my understanding. So when I am using the "Aij" (CSR) matrix, how would you suggest I deal with the ghost cells of the physical domain while forming the matrix and the vector? Thanks a lot. -- Arun Kamath PhD Stipendiat NTNU, Trondheim -------------- next part -------------- An HTML attachment was scrubbed... URL: From w_ang_temp at 163.com Wed Nov 7 08:43:12 2012 From: w_ang_temp at 163.com (w_ang_temp) Date: Wed, 7 Nov 2012 22:43:12 +0800 (CST) Subject: [petsc-users] About the use of MatMPIAIJSetPreallocation in 3.3 Message-ID: <1501d8a0.fe1e.13adb532d4c.Coremail.w_ang_temp@163.com> Hello, Version3.3 makes some change on Preallocation. (1)In version 3.2, my codes are as follows: call MatGetOwnershipRange(A,Istart,Iend,ierr) !premalloc !find the max non-zero numbers of all rows maxnonzero=0 do 19,II=Istart+1,Iend !no-zero numbers of this row maxnonzeroII=NROWIN(II+1)-NROWIN(II) if (maxnonzeroII>maxnonzero) then maxnonzero=maxnonzeroII endif 19 continue call MatMPIAIJSetPreallocation(A,maxnonzero,PETSC_NULL_INTEGER,maxnonzero,PETSC_NULL_INTEGER,ierr) (2)In version 3.3, my codes are as follows: !premalloc !find the max non-zero numbers of all rows maxnonzero=0 do 19,II=1,m !no-zero numbers of this row maxnonzeroII=NROWIN(II+1)-NROWIN(II) if (maxnonzeroII>maxnonzero) then maxnonzero=maxnonzeroII endif 19 continue call MatMPIAIJSetPreallocation(A,maxnonzero,PETSC_NULL_INTEGER,maxnonzero,PETSC_NULL_INTEGER,ierr) call MatGetOwnershipRange(A,Istart,Iend,ierr) The modification is:in version3.3, MatMPIAIJSetPreallocation must be in the front of MatGetOwnershipRange. And then when I call MatMPIAIJSetPreallocation, I cannot get "Istart&Iend". So I have to use "do 19,II=1,m" instead of "do 19,II=Istart+1,Iend" to get the maximum non-zero number of all rows for the use of MatMPIAIJSetPreallocation. Is this reasonable of using MatMPIAIJSetPreallocation? Thanks. Jim -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Wed Nov 7 08:55:02 2012 From: knepley at gmail.com (Matthew Knepley) Date: Wed, 7 Nov 2012 09:55:02 -0500 Subject: [petsc-users] CFD code with immersed boundary method In-Reply-To: References: Message-ID: On Wed, Nov 7, 2012 at 9:31 AM, Arun Kamath wrote: > Hi! > I am working with a CFD code where I need to solve the Poisson Pressure > equation. We solve a two phase flow problem which results in a jump in the > coefficients and a non symmetric system. > > The boundary conditions are fulfilled using immersed boundary method ghost > cells at the solid boundaries of the domain. > I read about the DAs to deal with the boundary conditions, but they are > applicable to only "IJK" matrices as per my understanding. > So when I am using the "Aij" (CSR) matrix, how would you suggest I deal > with the ghost cells of the physical domain while forming the matrix and > the vector? > Are you saying that you have an unstructured grid with ghost cells, and you would like PETSc to produce a Vec of the correct size and Mat with the correct preallocation for that grid and discretization, just as DA does for structured grids? Thanks, Matt > Thanks a lot. > -- > Arun Kamath > PhD Stipendiat > NTNU, Trondheim > > -- 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mark.adams at columbia.edu Wed Nov 7 09:56:47 2012 From: mark.adams at columbia.edu (Mark F. Adams) Date: Wed, 7 Nov 2012 10:56:47 -0500 Subject: [petsc-users] unable to set type "agg" in GAMG preconditioner In-Reply-To: References: Message-ID: <04835331-C8F5-4483-BDEC-5E49D946522D@columbia.edu> On Nov 7, 2012, at 8:58 AM, A.L. Siahaan wrote: > Hi, I am experimenting with GAMG by changing some of its parameters. I tried to set the GAMG type into "agg" using : PCGAMGSetType(pc,"agg"); > > and I get the following error : > ========================================================================== Solving linear system of size 108972 x 108972 (PETSc Krylov solver). demo_elasticity: /usr/local/packages/src/petsc-3.3/src/ksp/pc/impls/gamg/agg.c:1522: PCCreateGAMG_AGG: Assertion `!pc_gamg->subctx' failed. ========================================================================== > I've pushed a fix into petsc-dev. > Is there any other parameter which needs to be set to enable "agg" ? This is usually set from the command line but you are doing it correctly as far as I can tell. > And what is the default type if I don't set to either "agg" or "geo" ? 'agg' is the default. Thanks, Mark > > Thanks, > Antony > From arun.kamath.m at gmail.com Wed Nov 7 09:59:01 2012 From: arun.kamath.m at gmail.com (Arun Kamath) Date: Wed, 7 Nov 2012 16:59:01 +0100 Subject: [petsc-users] CFD code with immersed boundary method In-Reply-To: References: Message-ID: Yes, I would like to know if it is possible to do what DA does for an unstructured grid. Thanks. On Wed, Nov 7, 2012 at 3:31 PM, Arun Kamath wrote: > Hi! > I am working with a CFD code where I need to solve the Poisson Pressure > equation. We solve a two phase flow problem which results in a jump in the > coefficients and a non symmetric system. > > The boundary conditions are fulfilled using immersed boundary method ghost > cells at the solid boundaries of the domain. > I read about the DAs to deal with the boundary conditions, but they are > applicable to only "IJK" matrices as per my understanding. > So when I am using the "Aij" (CSR) matrix, how would you suggest I deal > with the ghost cells of the physical domain while forming the matrix and > the vector? > > Thanks a lot. > -- > Arun Kamath > PhD Stipendiat > NTNU, Trondheim > > -- Arun Kamath PhD Stipendiat NTNU, Trondheim -------------- next part -------------- An HTML attachment was scrubbed... URL: From als88 at cam.ac.uk Wed Nov 7 10:23:57 2012 From: als88 at cam.ac.uk (A.L. Siahaan) Date: 07 Nov 2012 16:23:57 +0000 Subject: [petsc-users] unable to set type "agg" in GAMG preconditioner In-Reply-To: <04835331-C8F5-4483-BDEC-5E49D946522D@columbia.edu> References: <04835331-C8F5-4483-BDEC-5E49D946522D@columbia.edu> Message-ID: On Nov 7 2012, Mark F. Adams wrote: > >I've pushed a fix into petsc-dev. > Thank's a lot, Mark ! > >> And what is the default type if I don't set to either "agg" or "geo" ? > >'agg' is the default. > In the previous version (before you pushed a fix), when I didn't set anything, it worked fine. Only when I set it specifically to "agg" did the problem occur. Antony From bsmith at mcs.anl.gov Wed Nov 7 11:34:20 2012 From: bsmith at mcs.anl.gov (Barry Smith) Date: Wed, 7 Nov 2012 11:34:20 -0600 Subject: [petsc-users] About the use of MatMPIAIJSetPreallocation in 3.3 In-Reply-To: <1501d8a0.fe1e.13adb532d4c.Coremail.w_ang_temp@163.com> References: <1501d8a0.fe1e.13adb532d4c.Coremail.w_ang_temp@163.com> Message-ID: Normally we expect the user, based on grid information, etc to decide how many rows to assign to each process. Thus they have the local sizes to pass to the Mat. If you want to have PETSc decide how many rows to assign to each process you can call PetscSplitOwnership() to determine the number of rows to be assigned for each process. Barry On Nov 7, 2012, at 8:43 AM, w_ang_temp wrote: > Hello, > Version3.3 makes some change on Preallocation. > (1)In version 3.2, my codes are as follows: > > call MatGetOwnershipRange(A,Istart,Iend,ierr) > !premalloc > !find the max non-zero numbers of all rows > maxnonzero=0 > do 19,II=Istart+1,Iend > !no-zero numbers of this row > maxnonzeroII=NROWIN(II+1)-NROWIN(II) > if (maxnonzeroII>maxnonzero) then > maxnonzero=maxnonzeroII > endif > 19 continue > call MatMPIAIJSetPreallocation(A,maxnonzero,PETSC_NULL_INTEGER,maxnonzero,PETSC_NULL_INTEGER,ierr) > > (2)In version 3.3, my codes are as follows: > > !premalloc > !find the max non-zero numbers of all rows > maxnonzero=0 > do 19,II=1,m > !no-zero numbers of this row > maxnonzeroII=NROWIN(II+1)-NROWIN(II) > if (maxnonzeroII>maxnonzero) then > maxnonzero=maxnonzeroII > endif > 19 continue > call MatMPIAIJSetPreallocation(A,maxnonzero,PETSC_NULL_INTEGER,maxnonzero,PETSC_NULL_INTEGER,ierr) > call MatGetOwnershipRange(A,Istart,Iend,ierr) > > The modification is:in version3.3, MatMPIAIJSetPreallocation must be in the front of MatGetOwnershipRange. > And then when I call MatMPIAIJSetPreallocation, I cannot get "Istart&Iend". So I have to use "do 19,II=1,m" > instead of "do 19,II=Istart+1,Iend" to get the maximum non-zero number of all rows for the use of > MatMPIAIJSetPreallocation. > Is this reasonable of using MatMPIAIJSetPreallocation? > Thanks. > Jim > > From jefonseca at gmail.com Wed Nov 7 12:46:10 2012 From: jefonseca at gmail.com (Jim Fonseca) Date: Wed, 7 Nov 2012 13:46:10 -0500 Subject: [petsc-users] diagonalizing dense matrix with LAPACK Message-ID: Hi, Given a dense PETSc matrix, what is the most computationally efficient way to use LAPACK to diagonalize it? Thanks, Jim -- Jim Fonseca, PhD Research Scientist Network for Computational Nanotechnology Purdue University 765-496-6495 www.jimfonseca.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Wed Nov 7 12:52:28 2012 From: bsmith at mcs.anl.gov (Barry Smith) Date: Wed, 7 Nov 2012 12:52:28 -0600 Subject: [petsc-users] diagonalizing dense matrix with LAPACK In-Reply-To: References: Message-ID: On Nov 7, 2012, at 12:46 PM, Jim Fonseca wrote: > Hi, > Given a dense PETSc matrix, what is the most computationally efficient way to use LAPACK to diagonalize it? This seems to be a question about sequential matrix since LAPACK is sequential. Call MatGetArray() (MatDenseGetArray() in petsc-dev) and MatGetSizes() and pass the resulting info into the lapack routines (this will not involve a copy of the data). Barry > > Thanks, > Jim > > -- > Jim Fonseca, PhD > Research Scientist > Network for Computational Nanotechnology > Purdue University > 765-496-6495 > www.jimfonseca.com > > > From arun.kamath.m at gmail.com Wed Nov 7 14:18:46 2012 From: arun.kamath.m at gmail.com (Arun Kamath) Date: Wed, 7 Nov 2012 21:18:46 +0100 Subject: [petsc-users] CFD code with immersed boundary Message-ID: My previous post gave a completely wrong meaning I guess, with a missing punctuation. Matt, you got it right. I wanted to know how do I deal with the ghost cells arising from the physical domain, when I am using an unstructured grid. Since DA works with structured grids only, as far as I understood. Thanks. Are you saying that you have an unstructured grid with ghost cells, and you would like PETSc to produce a Vec of the correct size and Mat with the correct preallocation for that grid and discretization, just as DA does for structured grids? Thanks, Matt On Wed, Nov 7, 2012 at 9:31 AM, Arun Kamath > wrote: >* Hi!*>* I am working with a CFD code where I need to solve the Poisson Pressure*>* equation. We solve a two phase flow problem which results in a jump in the*>* coefficients and a non symmetric system.*>**>* The boundary conditions are fulfilled using immersed boundary method ghost*>* cells at the solid boundaries of the domain.*>* I read about the DAs to deal with the boundary conditions, but they are*>* applicable to only "IJK" matrices as per my understanding.*>* So when I am using the "Aij" (CSR) matrix, how would you suggest I deal*>* with the ghost cells of the physical domain while forming the matrix and*>* the vector?*>** >* Thanks a lot.*>* --*>* Arun Kamath*>* PhD Stipendiat*>* NTNU, Trondheim*>**> -- Arun Kamath PhD Stipendiat NTNU, Trondheim -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Wed Nov 7 15:40:58 2012 From: knepley at gmail.com (Matthew Knepley) Date: Wed, 7 Nov 2012 16:40:58 -0500 Subject: [petsc-users] CFD code with immersed boundary method In-Reply-To: References: Message-ID: On Wed, Nov 7, 2012 at 10:59 AM, Arun Kamath wrote: > Yes, I would like to know if it is possible to do what DA does for an > unstructured grid. There is a way to do this now. You can use DMComplex, from petsc-dev. Here is the idea: 1) You must input the topology of your mesh as a DMComplex object 2) You make a PetscSection object encoding your data layout 3) You call DMSetDefaultSection(dm, section) 4) Now the regular DMGetGlobal/LocalVector() and DMCreateMatrix() work as normal I am almost finished with the manual section on this. I will push it soon. First, how is your mesh expressed, since we have helper functions for importing meshes. Matt > Thanks. > > > On Wed, Nov 7, 2012 at 3:31 PM, Arun Kamath wrote: >> >> Hi! >> I am working with a CFD code where I need to solve the Poisson Pressure >> equation. We solve a two phase flow problem which results in a jump in the >> coefficients and a non symmetric system. >> >> The boundary conditions are fulfilled using immersed boundary method ghost >> cells at the solid boundaries of the domain. >> I read about the DAs to deal with the boundary conditions, but they are >> applicable to only "IJK" matrices as per my understanding. >> So when I am using the "Aij" (CSR) matrix, how would you suggest I deal >> with the ghost cells of the physical domain while forming the matrix and the >> vector? >> >> Thanks a lot. >> -- >> Arun Kamath >> PhD Stipendiat >> NTNU, Trondheim >> > > > > -- > Arun Kamath > PhD Stipendiat > NTNU, Trondheim > -- 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 From zhenglun.wei at gmail.com Wed Nov 7 18:50:30 2012 From: zhenglun.wei at gmail.com (Alan) Date: Wed, 07 Nov 2012 18:50:30 -0600 Subject: [petsc-users] Non-uniform Cartisian Grid Message-ID: <509B01D6.9030501@gmail.com> Dear folks, I hope you're having a nice day. I'm testing the Poisson solver in /src/ksp/ksp/examples/tutorials/ex45. It uses the 'DMDACreate3d' to generate a Cartisian structured grid and solve it with uniform grid size. However, I attempt to modify it to obtain solution with a Cartsian structured grid and non-uniform grid (It is not unstructured local refined mesh). Should I still use the 'DMDACreate3d' and implement different grid size in 'ComputeMatrix' and 'ComputeRHS'? In other words, does 'DMDACreate3d' itself include any mesh size information? thanks, Alan From bsmith at mcs.anl.gov Wed Nov 7 18:55:45 2012 From: bsmith at mcs.anl.gov (Barry Smith) Date: Wed, 7 Nov 2012 18:55:45 -0600 Subject: [petsc-users] Non-uniform Cartisian Grid In-Reply-To: <509B01D6.9030501@gmail.com> References: <509B01D6.9030501@gmail.com> Message-ID: <818369A9-2984-4133-A62F-E5DCEE283EA1@mcs.anl.gov> On Nov 7, 2012, at 6:50 PM, Alan wrote: > Dear folks, > I hope you're having a nice day. > I'm testing the Poisson solver in /src/ksp/ksp/examples/tutorials/ex45. > It uses the 'DMDACreate3d' to generate a Cartisian structured grid and > solve it with uniform grid size. However, I attempt to modify it to > obtain solution with a Cartsian structured grid and non-uniform grid (It > is not unstructured local refined mesh). Should I still use the > 'DMDACreate3d' and implement different grid size in 'ComputeMatrix' and > 'ComputeRHS'? In other words, does 'DMDACreate3d' itself include any > mesh size information? You can use DMDASetCoordinates() and DMDAGetCoordinates() (called DMSetCoordinates() and DMGetCoordinates() in petsc-dev) to keep track of the coordinates but you are responsible for generating the correctly scaled entries in the matrix etc. Barry > > thanks, > Alan From zhenglun.wei at gmail.com Wed Nov 7 19:10:30 2012 From: zhenglun.wei at gmail.com (Alan) Date: Wed, 07 Nov 2012 19:10:30 -0600 Subject: [petsc-users] Non-uniform Cartisian Grid In-Reply-To: <818369A9-2984-4133-A62F-E5DCEE283EA1@mcs.anl.gov> References: <509B01D6.9030501@gmail.com> <818369A9-2984-4133-A62F-E5DCEE283EA1@mcs.anl.gov> Message-ID: <509B0686.8050502@gmail.com> Thank you so much, Dr. Smith. Alan > On Nov 7, 2012, at 6:50 PM, Alan wrote: > >> Dear folks, >> I hope you're having a nice day. >> I'm testing the Poisson solver in /src/ksp/ksp/examples/tutorials/ex45. >> It uses the 'DMDACreate3d' to generate a Cartisian structured grid and >> solve it with uniform grid size. However, I attempt to modify it to >> obtain solution with a Cartsian structured grid and non-uniform grid (It >> is not unstructured local refined mesh). Should I still use the >> 'DMDACreate3d' and implement different grid size in 'ComputeMatrix' and >> 'ComputeRHS'? In other words, does 'DMDACreate3d' itself include any >> mesh size information? > You can use DMDASetCoordinates() and DMDAGetCoordinates() (called DMSetCoordinates() and DMGetCoordinates() in petsc-dev) to keep track of the coordinates but you are responsible for generating the correctly scaled entries in the matrix etc. > > Barry > >> thanks, >> Alan From arun.kamath.m at gmail.com Thu Nov 8 05:22:11 2012 From: arun.kamath.m at gmail.com (Arun Kamath) Date: Thu, 8 Nov 2012 12:22:11 +0100 Subject: [petsc-users] CFD code with immersed boundary method Message-ID: <7D1380BE-4A91-4EF4-BFD7-3664DFC671F3@gmail.com> Matt, Before I delve further, I wanted to make sure that there is no way to work with an AIJ matrix structure in combination with the something like DMDA_BOUNDARY_GHOSTED without using pets-dev. I am a little disinclined to use the dev version as once I can confirm things are working for my code, we plan to use a supercomputer and its operators have the normal releases on the system. Since DMComplexCreate and the other functions in the procedure you have described are listed in the set of DM routines manual, I assume it works in the common release of PETSc? From jedbrown at mcs.anl.gov Thu Nov 8 07:24:32 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Thu, 8 Nov 2012 07:24:32 -0600 Subject: [petsc-users] CFD code with immersed boundary method In-Reply-To: <7D1380BE-4A91-4EF4-BFD7-3664DFC671F3@gmail.com> References: <7D1380BE-4A91-4EF4-BFD7-3664DFC671F3@gmail.com> Message-ID: On Thu, Nov 8, 2012 at 5:22 AM, Arun Kamath wrote: > Matt, > Before I delve further, I wanted to make sure that there is no way to work > with an AIJ matrix structure in combination with the something like > DMDA_BOUNDARY_GHOSTED without using pets-dev. > > I am a little disinclined to use the dev version as once I can confirm > things are working for my code, we plan to use a supercomputer and its > operators have the normal releases on the system. > You can build your own PETSc there, it's not a big deal. Since DMComplexCreate and the other functions in the procedure you have > described are listed in the set of DM routines manual, I assume it works in > the common release of PETSc? > DMComplex is very new and still evolving so you really need to use petsc-dev. Of course you can write your own unstructured mesh management, and many projects do. There are also many third-party libraries. -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Thu Nov 8 07:24:55 2012 From: knepley at gmail.com (Matthew Knepley) Date: Thu, 8 Nov 2012 08:24:55 -0500 Subject: [petsc-users] CFD code with immersed boundary method In-Reply-To: <7D1380BE-4A91-4EF4-BFD7-3664DFC671F3@gmail.com> References: <7D1380BE-4A91-4EF4-BFD7-3664DFC671F3@gmail.com> Message-ID: On Thu, Nov 8, 2012 at 6:22 AM, Arun Kamath wrote: > Matt, > Before I delve further, I wanted to make sure that there is no way to work with an AIJ matrix structure in combination with the something like DMDA_BOUNDARY_GHOSTED without using pets-dev. 1) This is a Cartesian mesh, so it will not work with unstructured stuff 2) This boundary condition only works for cell centered, but I think you have that > I am a little disinclined to use the dev version as once I can confirm things are working for my code, we plan to use a supercomputer and its operators have the normal releases on the system. > > Since DMComplexCreate and the other functions in the procedure you have described are listed in the set of DM routines manual, I assume it works in the common release of PETSc? The reason I suggested petsc-dev is that you would get all the updates. With new components, this is usually much much easier. You can install it yourself on the supercomputer, using the MPI and BLAS/LAPACK they have there very easily. Moreover, I do not know of a single place that would not install dev for you. 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 From arun.kamath.m at gmail.com Thu Nov 8 08:19:34 2012 From: arun.kamath.m at gmail.com (Arun Kamath) Date: Thu, 8 Nov 2012 15:19:34 +0100 Subject: [petsc-users] CFD code with immersed boundary method Message-ID: The fact is I do use a uniform cartesian grid, but the data structure in the code is in "AIJ" instead of the "IJK" format. This was done because the ghost cells (from the immersed boundary method) were updated from multiple directions and this cannot be handled using the "ijk" format. The computational grid is a staggered grid with velocities at the cell edges and pressure at cell centres. I guess , that puts the DMDA out of the solution then. So, though I am on a structured uniform cartesian grid (planning on local mesh refinement in the future), the boundary treatment doesn't allow me to use the procedure that would be normally followed. Am I right in this assessment? So then I wait for the manual on DMComplex and get pets-dev. What do you suggest? Thanks a lot! -- Arun Kamath PhD Stipendiat NTNU, Trondheim -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Thu Nov 8 10:11:51 2012 From: knepley at gmail.com (Matthew Knepley) Date: Thu, 8 Nov 2012 11:11:51 -0500 Subject: [petsc-users] CFD code with immersed boundary method In-Reply-To: References: Message-ID: On Thu, Nov 8, 2012 at 9:19 AM, Arun Kamath wrote: > The fact is I do use a uniform cartesian grid, but the data structure in the > code is in "AIJ" instead of the "IJK" format. I do not understand what you mean by AIJ and IJK. AIJ is a storage format. IJK does not mean anything to me. > This was done because the ghost cells (from the immersed boundary method) > were updated from multiple directions and this cannot be handled using the > "ijk" format. > The computational grid is a staggered grid with velocities at the cell edges > and pressure at cell centres. > I guess , that puts the DMDA out of the solution then. Okay, the default DMDA defines variables only at vertices. You can try telling DA that they are at vertices, but calculating like they are at edges, which is what SNES ex30 does. However, then you have to make the DA bigger and handle BCs yourself. Matt > So, though I am on a structured uniform cartesian grid (planning on local > mesh refinement in the future), the boundary treatment doesn't allow me to > use the procedure that would be normally followed. > Am I right in this assessment? So then I wait for the manual on DMComplex > and get pets-dev. > What do you suggest? > Thanks a lot! > -- > Arun Kamath > PhD Stipendiat > NTNU, Trondheim > -- 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 From ghegde at purdue.edu Thu Nov 8 11:55:03 2012 From: ghegde at purdue.edu (Ganesh Hegde) Date: Thu, 8 Nov 2012 12:55:03 -0500 Subject: [petsc-users] Conjugate transpose for rectangular complex matrices Message-ID: Hi, I have been using the MatHermitianTranspose method to get the conjugate transpose for complex square matrices. To optimize code, I needed to make my matrix rectangular. Doing so and using the same function call gave me the following error with code 60: 'Nonconforming object sizes' I then decided to do this in two steps - get the conjugate of the rectangular complex matrix and then call MatTranspose. The error still persists. Can you suggest any alternatives to this problem? Regards, -- Ganesh -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhenglun.wei at gmail.com Thu Nov 8 12:27:18 2012 From: zhenglun.wei at gmail.com (Zhenglun (Alan) Wei) Date: Thu, 08 Nov 2012 12:27:18 -0600 Subject: [petsc-users] Fwd: error messages while updating petsc-dev In-Reply-To: <509BF8B8.6090104@gmail.com> References: <509BF8B8.6090104@gmail.com> Message-ID: <509BF986.7080801@gmail.com> Dear folks, I came across an error while making a code: makefile:7: *** missing separator. Stop. This happens after I was tying to update the petsc-dev with some error message; the configure.log, error.log and make.log are attached. I've already sent it to petsc-maint list. Is this makefile error related to the fail update? thanks, Alan -------------- next part -------------- filevf.c:3:33: error: private/fortranimpl.h: No such file or directory filevf.c:67: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerasciisettab_? filevf.c:71: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerasciiaddtab_? filevf.c:75: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerasciisubtracttab_? filevf.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerasciipushtab_? filevf.c:83: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerasciipoptab_? filevf.c:87: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerasciiusetabs_? /usr/bin/ar: filevf.o: No such file or directory binvf.c:3:33: error: private/fortranimpl.h: No such file or directory binvf.c:67: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerbinaryskipinfo_? binvf.c:71: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerbinarysetskipoptions_? binvf.c:75: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerbinarygetskipoptions_? binvf.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerbinarysetskipheader_? binvf.c:83: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerbinarygetskipheader_? binvf.c:87: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerbinarysetmpiio_? /usr/bin/ar: binvf.o: No such file or directory drawvf.c:3:33: error: private/fortranimpl.h: No such file or directory drawvf.c:67: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerdrawclear_? drawvf.c:71: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerdrawgetpause_? drawvf.c:75: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerdrawsetpause_? drawvf.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerdrawsethold_? drawvf.c:83: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerdrawgethold_? drawvf.c:87: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerdrawsetbounds_? /usr/bin/ar: drawvf.o: No such file or directory viewf.c:3:33: error: private/fortranimpl.h: No such file or directory viewf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerdestroy_? viewf.c:50: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewersetup_? viewregf.c:3:33: error: private/fortranimpl.h: No such file or directory viewregf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewercreate_? flushf.c:3:33: error: private/fortranimpl.h: No such file or directory flushf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerflush_? duplf.c:3:33: error: private/fortranimpl.h: No such file or directory duplf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewergetsingleton_? duplf.c:61: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerrestoresingleton_? duplf.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewergetsubcomm_? duplf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerrestoresubcomm_? /usr/bin/ar: viewf.o: No such file or directory drectf.c:3:33: error: private/fortranimpl.h: No such file or directory drectf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawrectangle_? drectf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawsave_? dmousef.c:3:33: error: private/fortranimpl.h: No such file or directory dmousef.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawgetmousebutton_? dmousef.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawsynchronizedgetmousebutton_? dellipsef.c:3:33: error: private/fortranimpl.h: No such file or directory dellipsef.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawellipse_? dcoorf.c:3:33: error: private/fortranimpl.h: No such file or directory dcoorf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawsetcoordinates_? dtrif.c:3:33: error: private/fortranimpl.h: No such file or directory dtrif.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawtriangle_? dtrif.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawscalepopup_? dtrif.c:61: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawtensorcontourpatch_? dpointsf.c:3:33: error: private/fortranimpl.h: No such file or directory dpointsf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawpointsetsize_? dlinegwf.c:3:33: error: private/fortranimpl.h: No such file or directory dlinegwf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlinegetwidth_? dflushf.c:3:33: error: private/fortranimpl.h: No such file or directory dflushf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawflush_? dpausef.c:3:33: error: private/fortranimpl.h: No such file or directory dpausef.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawpause_? dsclearf.c:3:33: error: private/fortranimpl.h: No such file or directory dsclearf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawsynchronizedclear_? dbufff.c:3:33: error: private/fortranimpl.h: No such file or directory dbufff.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawisnull_? dbufff.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawsetdoublebuffer_? dgpausef.c:3:33: error: private/fortranimpl.h: No such file or directory dgpausef.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawgetpause_? dsflushf.c:3:33: error: private/fortranimpl.h: No such file or directory dsflushf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawsynchronizedflush_? dtextsf.c:3:33: error: private/fortranimpl.h: No such file or directory dtextsf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawstringsetsize_? dsetpausef.c:3:33: error: private/fortranimpl.h: No such file or directory dsetpausef.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawsetpause_? dgcoorf.c:3:33: error: private/fortranimpl.h: No such file or directory dgcoorf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawgetcoordinates_? dviewpf.c:3:33: error: private/fortranimpl.h: No such file or directory dviewpf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawsetviewport_? dviewpf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawsplitviewport_? dlinewf.c:3:33: error: private/fortranimpl.h: No such file or directory dlinewf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlinesetwidth_? drawf.c:3:33: error: private/fortranimpl.h: No such file or directory drawf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawresizewindow_? drawf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawcheckresizedwindow_? drawf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawdestroy_? drawf.c:73: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawgetpopup_? drawf.c:77: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawsetdisplay_? dtextgsf.c:3:33: error: private/fortranimpl.h: No such file or directory dtextgsf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawstringgetsize_? dclearf.c:3:33: error: private/fortranimpl.h: No such file or directory dclearf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawclear_? dclearf.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawbop_? dclearf.c:60: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdraweop_? dpointf.c:3:33: error: private/fortranimpl.h: No such file or directory dpointf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawpoint_? dlinef.c:3:33: error: private/fortranimpl.h: No such file or directory dlinef.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawline_? dlinef.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawarrow_? /usr/bin/ar: drectf.o: No such file or directory lgcf.c:3:33: error: private/fortranimpl.h: No such file or directory lgcf.c:91: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlggetaxis_? lgcf.c:95: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlggetdraw_? lgcf.c:99: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlgspdraw_? lgcf.c:104: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlgcreate_? lgcf.c:108: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlgsetcolors_? lgcf.c:112: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlgsetdimension_? lgcf.c:116: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlgreset_? lgcf.c:120: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlgdestroy_? lgcf.c:123: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlgindicatedatapoints_? lgcf.c:127: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlgdraw_? lgcf.c:131: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlgprint_? lgf.c:3:33: error: private/fortranimpl.h: No such file or directory lgf.c:46: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlgaddpoint_? lgf.c:50: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlgsetlimits_? histsf.c:3:33: error: private/fortranimpl.h: No such file or directory histsf.c:82: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawhgsetnumberbins_? histsf.c:86: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawhgreset_? histsf.c:90: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawhgaddvalue_? histsf.c:94: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawhgdraw_? histsf.c:98: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawhgprint_? histsf.c:102: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawhgsetcolor_? histsf.c:106: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawhgsetlimits_? histsf.c:110: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawhgcalcstats_? histsf.c:114: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawhgintegerbins_? axisf.c:3:33: error: private/fortranimpl.h: No such file or directory axisf.c:41: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawaxissetlimits_? dscatterf.c:3:33: error: private/fortranimpl.h: No such file or directory dscatterf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawspsetdimension_? dscatterf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawspreset_? dscatterf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawspaddpoint_? dscatterf.c:74: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawspdraw_? dscatterf.c:78: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawspsetlimits_? axiscf.c:3:33: error: private/fortranimpl.h: No such file or directory axiscf.c:61: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawaxiscreate_? axiscf.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawaxisdestroy_? axiscf.c:68: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawaxissetcolors_? axiscf.c:72: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawaxissetholdlimits_? axiscf.c:76: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawaxisdraw_? /usr/bin/ar: lgcf.o: No such file or directory errf.c:3:33: error: private/fortranimpl.h: No such file or directory errf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscpoperrorhandler_? adebugf.c:3:33: error: private/fortranimpl.h: No such file or directory adebugf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsetdefaultdebugger_? adebugf.c:50: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscattachdebugger_? fpf.c:3:33: error: private/fortranimpl.h: No such file or directory fpf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsetfptrap_? signalf.c:3:33: error: private/fortranimpl.h: No such file or directory signalf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdefaultsignalhandler_? signalf.c:50: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscpopsignalhandler_? /usr/bin/ar: errf.o: No such file or directory regf.c:3:33: error: private/fortranimpl.h: No such file or directory regf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscflistdestroy_? regf.c:60: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscflistview_? regf.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscflistget_? regf.c:69: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscflistduplicate_? /usr/bin/ar: regf.o: No such file or directory mpiuopenf.c:3:33: error: private/fortranimpl.h: No such file or directory mpiuopenf.c:41: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscfclose_? mprintf.c:3:33: error: private/fortranimpl.h: No such file or directory mprintf.c:41: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsynchronizedflush_? sysiof.c:3:33: error: private/fortranimpl.h: No such file or directory sysiof.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscbinaryread_? sysiof.c:59: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscbinarywrite_? sysiof.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscbinaryclose_? sysiof.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscbinaryseek_? /usr/bin/ar: mpiuopenf.o: No such file or directory memf.c:3:33: error: private/fortranimpl.h: No such file or directory memf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscmemorygetcurrentusage_? memf.c:50: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscmemorygetmaximumusage_? /usr/bin/ar: memf.o: No such file or directory gcommf.c:3:33: error: private/fortranimpl.h: No such file or directory gcommf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscobjectgettablevel_? gcommf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscobjectincrementtablevel_? optionsf.c:3:33: error: private/fortranimpl.h: No such file or directory optionsf.c:67: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscoptionsvalidkey_? optionsf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscoptionsprefixpush_? optionsf.c:73: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscoptionsprefixpop_? optionsf.c:76: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscoptionsleft_? optionsf.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscoptionssetfromoptions_? optionsf.c:82: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscoptionsmonitorcancel_? tagmf.c:3:33: error: private/fortranimpl.h: No such file or directory tagmf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsccommgetnewtag_? destroyf.c:3:33: error: private/fortranimpl.h: No such file or directory destroyf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscobjectdestroy_? ptypef.c:3:33: error: private/fortranimpl.h: No such file or directory ptypef.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdatatypegetsize_? inheritf.c:3:33: error: private/fortranimpl.h: No such file or directory inheritf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscobjectreference_? inheritf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscobjectgetreference_? inheritf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscobjectdereference_? inheritf.c:74: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscobjectsetfromoptions_? inheritf.c:78: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscobjectsetup_? pinitf.c:3:33: error: private/fortranimpl.h: No such file or directory pinitf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscinitialized_? pinitf.c:50: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscfinalized_? /usr/bin/ar: gcommf.o: No such file or directory cputimef.c:3:33: error: private/fortranimpl.h: No such file or directory cputimef.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscgetcputime_? ptimef.c:3:33: error: private/fortranimpl.h: No such file or directory ptimef.c:41: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscgettime_? /usr/bin/ar: cputimef.o: No such file or directory sortdf.c:3:33: error: private/fortranimpl.h: No such file or directory sortdf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsortreal_? sortdf.c:55: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsortsplit_? sortdf.c:58: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsortsplitreal_? mpiuf.c:3:33: error: private/fortranimpl.h: No such file or directory mpiuf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsequentialphasebegin_? mpiuf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsequentialphaseend_? sortif.c:3:33: error: private/fortranimpl.h: No such file or directory sortif.c:67: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsortint_? sortif.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsortremovedupsint_? sortif.c:73: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsortintwitharray_? sortif.c:76: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsortmpiintwitharray_? sortif.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsortintwithscalararray_? sortif.c:82: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscprocesstree_? psplitf.c:3:33: error: private/fortranimpl.h: No such file or directory psplitf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsplitownershipblock_? psplitf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsplitownership_? memcf.c:3:33: error: private/fortranimpl.h: No such file or directory memcf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscmemcmp_? memcf.c:50: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscmemmove_? psleepf.c:3:33: error: private/fortranimpl.h: No such file or directory psleepf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsleep_? sortipf.c:3:33: error: private/fortranimpl.h: No such file or directory sortipf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsortintwithpermutation_? sortipf.c:50: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsortrealwithpermutation_? /usr/bin/ar: sortdf.o: No such file or directory plogf.c:3:33: error: private/fortranimpl.h: No such file or directory plogf.c:103: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogtracebegin_? plogf.c:107: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogactions_? plogf.c:110: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogobjects_? plogf.c:113: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogstagesetactive_? plogf.c:116: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogstagegetactive_? plogf.c:119: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogstagesetvisible_? plogf.c:122: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogstagegetvisible_? plogf.c:125: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogeventactivate_? plogf.c:128: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogeventdeactivate_? plogf.c:131: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogeventsetactiveall_? plogf.c:134: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogeventactivateclass_? plogf.c:137: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogeventdeactivateclass_? plogf.c:140: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogviewpython_? /usr/bin/ar: plogf.o: No such file or directory randomf.c:3:33: error: private/fortranimpl.h: No such file or directory randomf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscrandomgetvalue_? randomf.c:61: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscrandomgetvaluereal_? randomf.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscrandomgetinterval_? randomf.c:69: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscrandomsetinterval_? randomcf.c:3:33: error: private/fortranimpl.h: No such file or directory randomcf.c:72: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscrandomdestroy_? randomcf.c:75: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscrandomgetseed_? randomcf.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscrandomsetseed_? randomcf.c:83: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscrandomsetfromoptions_? randomcf.c:87: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscrandomviewfromoptions_? randomcf.c:92: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscrandomcreate_? randomcf.c:96: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscrandomseed_? /usr/bin/ar: randomf.o: No such file or directory bagf.c:3:33: error: private/fortranimpl.h: No such file or directory bagf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscbagcreate_? /usr/bin/ar: bagf.o: No such file or directory verboseinfof.c:3:33: error: private/fortranimpl.h: No such file or directory verboseinfof.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscinfodeactivateclass_? verboseinfof.c:50: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscinfoactivateclass_? /usr/bin/ar: verboseinfof.o: No such file or directory vpscatf.c:3:33: error: private/fortranimpl.h: No such file or directory vpscatf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecscattercreatelocal_? combf.c:3:33: error: private/fortranimpl.h: No such file or directory combf.c:87: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecdotbegin_? combf.c:92: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecdotend_? combf.c:97: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vectdotbegin_? combf.c:102: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vectdotend_? combf.c:107: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecnormbegin_? combf.c:111: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecnormend_? combf.c:115: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecmdotbegin_? combf.c:119: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecmdotend_? combf.c:123: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecmtdotbegin_? combf.c:127: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecmtdotend_? vecmpitoseqf.c:3:33: error: private/fortranimpl.h: No such file or directory vecmpitoseqf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecscattercreatetoall_? vecmpitoseqf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecscattercreatetozero_? cmeshf.c:3:33: error: private/fortranimpl.h: No such file or directory cmeshf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?veccontourscale_? vinvf.c:3:33: error: private/fortranimpl.h: No such file or directory vinvf.c:147: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstrideset_? vinvf.c:151: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstridescale_? vinvf.c:155: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstridenorm_? vinvf.c:159: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstridemax_? vinvf.c:163: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstridemin_? vinvf.c:167: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstridescaleall_? vinvf.c:171: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstridenormall_? vinvf.c:175: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstridemaxall_? vinvf.c:179: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstrideminall_? vinvf.c:183: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstridegatherall_? vinvf.c:187: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstridescatterall_? vinvf.c:191: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstridegather_? vinvf.c:196: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstridescatter_? vinvf.c:201: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecexp_? vinvf.c:205: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?veclog_? vinvf.c:209: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsqrtabs_? vinvf.c:213: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecdotnorm2_? vinvf.c:218: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsum_? vinvf.c:222: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecshift_? vinvf.c:226: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecabs_? vinvf.c:230: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecpermute_? vinvf.c:235: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecequal_? vscatf.c:3:33: error: private/fortranimpl.h: No such file or directory vscatf.c:63: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecscattergetmerged_? vscatf.c:67: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecscatterbegin_? vscatf.c:73: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecscatterend_? vscatf.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecscattercopy_? vscatf.c:83: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecscatterview_? /usr/bin/ar: vpscatf.o: No such file or directory veccreatef.c:3:33: error: private/fortranimpl.h: No such file or directory veccreatef.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?veccreate_? vectorf.c:3:33: error: private/fortranimpl.h: No such file or directory vectorf.c:197: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstashgetinfo_? vectorf.c:201: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetlocaltoglobalmapping_? vectorf.c:206: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetlocaltoglobalmappingblock_? vectorf.c:211: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecgetlocaltoglobalmapping_? vectorf.c:215: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecgetlocaltoglobalmappingblock_? vectorf.c:219: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecassemblybegin_? vectorf.c:223: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecassemblyend_? vectorf.c:227: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecpointwisemax_? vectorf.c:233: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecpointwisemin_? vectorf.c:239: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecpointwisemaxabs_? vectorf.c:245: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecpointwisedivide_? vectorf.c:251: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecduplicate_? vectorf.c:255: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecdestroy_? vectorf.c:258: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecviewfromoptions_? vectorf.c:262: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecgetsize_? vectorf.c:266: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecgetlocalsize_? vectorf.c:270: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetoption_? vectorf.c:274: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecresetarray_? vectorf.c:278: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecreciprocal_? vectorf.c:282: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstashsetinitialsize_? vectorf.c:286: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecconjugate_? vectorf.c:290: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecpointwisemult_? vectorf.c:296: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetrandom_? vectorf.c:301: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?veczeroentries_? vectorf.c:305: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetfromoptions_? vectorf.c:309: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetsizes_? vectorf.c:313: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetblocksize_? vectorf.c:317: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecgetblocksize_? vectorf.c:321: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetup_? vectorf.c:325: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?veccopy_? vectorf.c:330: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecswap_? vectorf.c:335: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstashview_? rvectorf.c:3:33: error: private/fortranimpl.h: No such file or directory rvectorf.c:162: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecmaxpointwisedivide_? rvectorf.c:167: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecdot_? rvectorf.c:172: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecnorm_? rvectorf.c:176: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecnormavailable_? rvectorf.c:180: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecnormalize_? rvectorf.c:184: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecmin_? rvectorf.c:188: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vectdot_? rvectorf.c:193: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecscale_? rvectorf.c:197: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecset_? rvectorf.c:201: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecaxpy_? rvectorf.c:206: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecaxpby_? rvectorf.c:211: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecaxpbypcz_? rvectorf.c:217: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecaypx_? rvectorf.c:222: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecwaxpy_? rvectorf.c:228: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetvalues_? rvectorf.c:232: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecgetvalues_? rvectorf.c:236: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetvaluesblocked_? rvectorf.c:240: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetvalueslocal_? rvectorf.c:244: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetvaluesblockedlocal_? rvectorf.c:248: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecmtdot_? rvectorf.c:252: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecmdot_? rvectorf.c:256: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecmaxpy_? rvectorf.c:260: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecgetsubvector_? rvectorf.c:265: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecrestoresubvector_? rvectorf.c:270: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecplacearray_? /usr/bin/ar: veccreatef.o: No such file or directory vseqcrf.c:3:33: error: private/fortranimpl.h: No such file or directory vseqcrf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?veccreateseq_? /usr/bin/ar: vseqcrf.o: No such file or directory pbvecf.c:3:33: error: private/fortranimpl.h: No such file or directory pbvecf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?veccreateghost_? pbvecf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?veccreateghostblock_? commonmpvecf.c:3:33: error: private/fortranimpl.h: No such file or directory commonmpvecf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecghostgetlocalform_? commonmpvecf.c:61: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecghostrestorelocalform_? commonmpvecf.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecghostupdatebegin_? commonmpvecf.c:69: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecghostupdateend_? vmpicrf.c:3:33: error: private/fortranimpl.h: No such file or directory vmpicrf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?veccreatempi_? /usr/bin/ar: pbvecf.o: No such file or directory shvecf.c:3:33: error: private/fortranimpl.h: No such file or directory shvecf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?veccreateshared_? /usr/bin/ar: shvecf.o: No such file or directory vecnestf.c:3:33: error: private/fortranimpl.h: No such file or directory vecnestf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?veccreatenest_? /usr/bin/ar: vecnestf.o: No such file or directory isregf.c:3:33: error: private/fortranimpl.h: No such file or directory isregf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?iscreate_? indexf.c:3:33: error: private/fortranimpl.h: No such file or directory indexf.c:132: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isidentity_? indexf.c:136: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?issetidentity_? indexf.c:140: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?iscontiguouslocal_? indexf.c:144: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?ispermutation_? indexf.c:148: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?issetpermutation_? indexf.c:152: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isdestroy_? indexf.c:155: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isinvertpermutation_? indexf.c:159: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isgetsize_? indexf.c:163: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isgetlocalsize_? indexf.c:167: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isgetnonlocalis_? indexf.c:171: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isrestorenonlocalis_? indexf.c:175: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?issort_? indexf.c:179: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?istogeneral_? indexf.c:183: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?issorted_? indexf.c:187: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isduplicate_? indexf.c:191: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?iscopy_? indexf.c:196: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isoncomm_? indexf.c:201: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?issetblocksize_? indexf.c:205: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isgetblocksize_? /usr/bin/ar: isregf.o: No such file or directory generalf.c:3:33: error: private/fortranimpl.h: No such file or directory generalf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?iscreategeneral_? generalf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isgeneralsetindices_? /usr/bin/ar: generalf.o: No such file or directory stridef.c:3:33: error: private/fortranimpl.h: No such file or directory stridef.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isstridegetinfo_? stridef.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isstridesetstride_? stridef.c:60: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?iscreatestride_? /usr/bin/ar: stridef.o: No such file or directory blockf.c:3:33: error: private/fortranimpl.h: No such file or directory blockf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isblocksetindices_? blockf.c:61: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?iscreateblock_? blockf.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isblockgetlocalsize_? blockf.c:69: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isblockgetsize_? /usr/bin/ar: blockf.o: No such file or directory isdifff.c:3:33: error: private/fortranimpl.h: No such file or directory isdifff.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isdifference_? isdifff.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?issum_? isdifff.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isexpand_? isltogf.c:3:33: error: private/fortranimpl.h: No such file or directory isltogf.c:73: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?islocaltoglobalmappingcreateis_? isltogf.c:77: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?islocaltoglobalmappingcreate_? isltogf.c:81: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?islocaltoglobalmappingblock_? isltogf.c:85: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?islocaltoglobalmappingunblock_? isltogf.c:89: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?islocaltoglobalmappingdestroy_? isltogf.c:92: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?islocaltoglobalmappingapplyis_? isltogf.c:97: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isglobaltolocalmappingapply_? iscompf.c:3:33: error: private/fortranimpl.h: No such file or directory iscompf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isequal_? iscoloringf.c:3:33: error: private/fortranimpl.h: No such file or directory iscoloringf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?iscoloringdestroy_? iscoloringf.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?ispartitioningtonumbering_? iscoloringf.c:69: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?ispartitioningcount_? iscoloringf.c:73: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isallgather_? iscoloringf.c:77: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?iscomplement_? /usr/bin/ar: isdifff.o: No such file or directory pff.c:3:33: error: private/fortranimpl.h: No such file or directory pff.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pfapplyvec_? pff.c:63: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pfapply_? pff.c:67: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pfview_? pff.c:72: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pfsetfromoptions_? /usr/bin/ar: pff.o: No such file or directory matrixf.c:3:33: error: private/fortranimpl.h: No such file or directory matrixf.c:547: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetdiagonalblock_? matrixf.c:551: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgettrace_? matrixf.c:555: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matrealpart_? matrixf.c:559: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matimaginarypart_? matrixf.c:563: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmissingdiagonal_? matrixf.c:567: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matconjugate_? matrixf.c:571: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetrowuppertriangular_? matrixf.c:575: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matrestorerowuppertriangular_? matrixf.c:579: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetup_? matrixf.c:583: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matscalesystem_? matrixf.c:589: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matunscalesystem_? matrixf.c:595: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matusescaledform_? matrixf.c:599: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matdestroy_? matrixf.c:602: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetvalues_? matrixf.c:606: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetvaluesrowlocal_? matrixf.c:610: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetvaluesrow_? matrixf.c:614: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetvaluesstencil_? matrixf.c:618: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetstencil_? matrixf.c:622: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetvaluesblocked_? matrixf.c:626: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetvalues_? matrixf.c:630: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetvaluesbatch_? matrixf.c:634: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetlocaltoglobalmapping_? matrixf.c:640: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetlocaltoglobalmappingblock_? matrixf.c:646: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetlocaltoglobalmapping_? matrixf.c:650: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetlocaltoglobalmappingblock_? matrixf.c:654: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetvalueslocal_? matrixf.c:658: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetvaluesblockedlocal_? matrixf.c:662: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmultdiagonalblock_? matrixf.c:668: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmult_? matrixf.c:674: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmulttranspose_? matrixf.c:680: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmulthermitiantranspose_? matrixf.c:686: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmultadd_? matrixf.c:693: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmulttransposeadd_? matrixf.c:700: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmulthermitiantransposeadd_? matrixf.c:707: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmultconstrained_? matrixf.c:713: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmulttransposeconstrained_? matrixf.c:719: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsolve_? matrixf.c:725: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmatsolve_? matrixf.c:731: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matforwardsolve_? matrixf.c:737: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matbackwardsolve_? matrixf.c:743: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsolveadd_? matrixf.c:750: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsolvetranspose_? matrixf.c:756: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsolvetransposeadd_? matrixf.c:763: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsor_? matrixf.c:769: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcopy_? matrixf.c:774: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matduplicate_? matrixf.c:778: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetdiagonal_? matrixf.c:783: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetrowmin_? matrixf.c:788: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetrowminabs_? matrixf.c:793: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetrowmax_? matrixf.c:798: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetrowmaxabs_? matrixf.c:803: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetrowsum_? matrixf.c:808: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?mattranspose_? matrixf.c:812: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matistranspose_? matrixf.c:817: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?mathermitiantranspose_? matrixf.c:821: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matishermitiantranspose_? matrixf.c:826: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matpermute_? matrixf.c:832: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matequal_? matrixf.c:837: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matdiagonalscale_? matrixf.c:843: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matscale_? matrixf.c:847: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matnorm_? matrixf.c:851: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matassemblybegin_? matrixf.c:855: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matassembled_? matrixf.c:859: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matassemblyend_? matrixf.c:863: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetoption_? matrixf.c:867: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matzeroentries_? matrixf.c:871: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetsize_? matrixf.c:875: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetlocalsize_? matrixf.c:879: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetownershiprangecolumn_? matrixf.c:883: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetownershiprange_? matrixf.c:887: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matincreaseoverlap_? matrixf.c:891: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetblocksize_? matrixf.c:895: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetblocksize_? matrixf.c:899: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetunfactored_? matrixf.c:903: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetsubmatrix_? matrixf.c:909: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matstashsetinitialsize_? matrixf.c:913: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matinterpolateadd_? matrixf.c:920: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matinterpolate_? matrixf.c:926: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matrestrict_? matrixf.c:932: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetnullspace_? matrixf.c:937: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetvaluesadic_? matrixf.c:941: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetcoloring_? matrixf.c:946: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetvaluesadifor_? matrixf.c:950: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matdiagonalscalelocal_? matrixf.c:955: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetinertia_? matrixf.c:959: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matissymmetric_? matrixf.c:963: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matishermitian_? matrixf.c:967: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matissymmetricknown_? matrixf.c:971: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matishermitianknown_? matrixf.c:975: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matisstructurallysymmetric_? matrixf.c:979: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matstashgetinfo_? matrixf.c:983: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matptap_? matrixf.c:988: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matptapnumeric_? matrixf.c:994: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matptapsymbolic_? matrixf.c:999: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmatmult_? matrixf.c:1004: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmatmultsymbolic_? matrixf.c:1009: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmatmultnumeric_? matrixf.c:1015: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmatmulttranspose_? matrixf.c:1020: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetlocalsubmatrix_? matrixf.c:1026: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matrestorelocalsubmatrix_? matrixf.c:1032: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matfindzerodiagonals_? matrixf.c:1036: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matinvertblockdiagonal_? mhasf.c:3:33: error: private/fortranimpl.h: No such file or directory mhasf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?mathasoperation_? matnullf.c:3:33: error: private/fortranimpl.h: No such file or directory matnullf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matnullspacecreate_? matnullf.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matnullspacedestroy_? matnullf.c:59: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matnullspacetest_? /usr/bin/ar: matrixf.o: No such file or directory mpidensef.c:3:33: error: private/fortranimpl.h: No such file or directory mpidensef.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matdensegetlocalmatrix_? /usr/bin/ar: mpidensef.o: No such file or directory aijf.c:3:33: error: private/fortranimpl.h: No such file or directory aijf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matseqaijsetcolumnindices_? aijf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matstorevalues_? aijf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matretrievevalues_? aijf.c:74: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matseqaijsetpreallocationcsr_? aijf.c:78: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreateseqaijwitharrays_? /usr/bin/ar: aijf.o: No such file or directory mpiaijf.c:3:33: error: private/fortranimpl.h: No such file or directory mpiaijf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmpiaijsetpreallocationcsr_? mpiaijf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatempiaijwitharrays_? mpiaijf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmerge_? mpiaijf.c:75: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmpiaijgetlocalmat_? mpiaijf.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatempiaijwithsplitarrays_? /usr/bin/ar: mpiaijf.o: No such file or directory shellf.c:3:33: error: private/fortranimpl.h: No such file or directory shellf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matshellsetcontext_? /usr/bin/ar: shellf.o: No such file or directory baijf.c:3:33: error: private/fortranimpl.h: No such file or directory baijf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matseqbaijsetcolumnindices_? baijf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreateseqbaijwitharrays_? /usr/bin/ar: baijf.o: No such file or directory mpibaijf.c:3:33: error: private/fortranimpl.h: No such file or directory mpibaijf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmpibaijsethashtablefactor_? mpibaijf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatempibaijwitharrays_? /usr/bin/ar: mpibaijf.o: No such file or directory matisf.c:3:33: error: private/fortranimpl.h: No such file or directory matisf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matisgetlocalmat_? matisf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreateis_? /usr/bin/ar: matisf.o: No such file or directory sbaijf.c:3:33: error: private/fortranimpl.h: No such file or directory sbaijf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matseqsbaijsetcolumnindices_? sbaijf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreateseqsbaijwitharrays_? /usr/bin/ar: sbaijf.o: No such file or directory mpisbaijf.c:3:33: error: private/fortranimpl.h: No such file or directory mpisbaijf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatempisbaijwitharrays_? /usr/bin/ar: mpisbaijf.o: No such file or directory normmf.c:3:33: error: private/fortranimpl.h: No such file or directory normmf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatenormal_? /usr/bin/ar: normmf.o: No such file or directory lrcf.c:3:33: error: private/fortranimpl.h: No such file or directory lrcf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatelrc_? /usr/bin/ar: lrcf.o: No such file or directory mscatterf.c:3:33: error: private/fortranimpl.h: No such file or directory mscatterf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matscattergetvecscatter_? mscatterf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matscattersetvecscatter_? /usr/bin/ar: mscatterf.o: No such file or directory mcompositef.c:3:33: error: private/fortranimpl.h: No such file or directory mcompositef.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcompositeaddmat_? /usr/bin/ar: mcompositef.o: No such file or directory mffddeff.c:3:33: error: private/fortranimpl.h: No such file or directory mffddeff.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmffddssetumin_? wpf.c:3:33: error: private/fortranimpl.h: No such file or directory wpf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmffdwpsetcomputenormu_? mffdf.c:3:33: error: private/fortranimpl.h: No such file or directory mffdf.c:82: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatemffd_? mffdf.c:86: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmffdgeth_? mffdf.c:90: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmffdsetperiod_? mffdf.c:94: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmffdsetfunctionerror_? mffdf.c:98: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmffdaddnullspace_? mffdf.c:103: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmffdsethhistory_? mffdf.c:107: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmffdresethhistory_? mffdf.c:111: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmffdsetbase_? mffdf.c:117: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmffdcheckpositivity_? /usr/bin/ar: mffddeff.o: No such file or directory transmf.c:3:33: error: private/fortranimpl.h: No such file or directory transmf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatetranspose_? /usr/bin/ar: transmf.o: No such file or directory submatf.c:3:33: error: private/fortranimpl.h: No such file or directory submatf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatesubmatrix_? submatf.c:53: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsubmatrixupdate_? /usr/bin/ar: submatf.o: No such file or directory mlocalreff.c:3:33: error: private/fortranimpl.h: No such file or directory mlocalreff.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatelocalref_? /usr/bin/ar: mlocalreff.o: No such file or directory matnestf.c:3:33: error: private/fortranimpl.h: No such file or directory matnestf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matnestsetsubmats_? matnestf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatenest_? /usr/bin/ar: matnestf.o: No such file or directory fftf.c:3:33: error: private/fortranimpl.h: No such file or directory fftf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatefft_? /usr/bin/ar: fftf.o: No such file or directory zerodiagf.c:3:33: error: private/fortranimpl.h: No such file or directory zerodiagf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matreorderfornonzerodiagonal_? gcreatef.c:3:33: error: private/fortranimpl.h: No such file or directory gcreatef.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreate_? gcreatef.c:61: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetsizes_? gcreatef.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetfromoptions_? gcreatef.c:69: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetuppreallocation_? multequalf.c:3:33: error: private/fortranimpl.h: No such file or directory multequalf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmultequal_? multequalf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmultaddequal_? multequalf.c:67: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmulttransposeequal_? multequalf.c:72: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmulttransposeaddequal_? axpyf.c:3:33: error: private/fortranimpl.h: No such file or directory axpyf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?mataxpy_? axpyf.c:67: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matshift_? axpyf.c:71: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matdiagonalset_? axpyf.c:76: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?mataypx_? axpyf.c:81: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcomputeexplicitoperator_? getcolvf.c:3:33: error: private/fortranimpl.h: No such file or directory getcolvf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetcolumnvector_? getcolvf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetcolumnnorms_? /usr/bin/ar: zerodiagf.o: No such file or directory fdmatrixf.c:3:33: error: private/fortranimpl.h: No such file or directory fdmatrixf.c:67: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matfdcoloringsetparameters_? fdmatrixf.c:71: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matfdcoloringsetfromoptions_? fdmatrixf.c:75: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matfdcoloringcreate_? fdmatrixf.c:80: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matfdcoloringdestroy_? fdmatrixf.c:83: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matfdcoloringapply_? fdmatrixf.c:89: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matfdcoloringapplyts_? /usr/bin/ar: fdmatrixf.o: No such file or directory partitionf.c:3:33: error: private/fortranimpl.h: No such file or directory partitionf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matpartitioningapply_? partitionf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matpartitioningsetadjacency_? partitionf.c:71: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matpartitioningdestroy_? partitionf.c:74: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matpartitioningcreate_? partitionf.c:78: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matpartitioningsetfromoptions_? /usr/bin/ar: partitionf.o: No such file or directory sorderf.c:3:33: error: private/fortranimpl.h: No such file or directory sorderf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matorderingregisterdestroy_? /usr/bin/ar: sorderf.o: No such file or directory aof.c:3:33: error: private/fortranimpl.h: No such file or directory aof.c:77: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?aopetsctoapplicationis_? aof.c:82: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?aoapplicationtopetscis_? aof.c:87: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?aopetsctoapplication_? aof.c:91: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?aoapplicationtopetsc_? aof.c:95: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?aopetsctoapplicationpermuteint_? aof.c:99: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?aoapplicationtopetscpermuteint_? aof.c:103: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?aopetsctoapplicationpermutereal_? aof.c:107: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?aoapplicationtopetscpermutereal_? /usr/bin/ar: aof.o: No such file or directory aomappingf.c:3:33: error: private/fortranimpl.h: No such file or directory aomappingf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?aomappinghaspetscindex_? /usr/bin/ar: aomappingf.o: No such file or directory dacreatef.c:3:33: error: private/fortranimpl.h: No such file or directory dacreatef.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdacreate_? dainterpf.c:3:33: error: private/fortranimpl.h: No such file or directory dainterpf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmgetinterpolationscale_? dagtonaf.c:3:33: error: private/fortranimpl.h: No such file or directory dagtonaf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdaglobaltonaturalallcreate_? dagtonaf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdanaturalalltoglobalcreate_? dagetarrayf.c:3:33: error: private/fortranimpl.h: No such file or directory dagetarrayf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdavecrestorearray_? dagetarrayf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdavecrestorearraydof_? dagtolf.c:3:33: error: private/fortranimpl.h: No such file or directory dagtolf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdaglobaltonaturalbegin_? dagtolf.c:63: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdaglobaltonaturalend_? dagtolf.c:69: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdanaturaltoglobalbegin_? dagtolf.c:75: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdanaturaltoglobalend_? daltolf.c:3:33: error: private/fortranimpl.h: No such file or directory daltolf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdalocaltolocalbegin_? daltolf.c:53: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdalocaltolocalend_? fddaf.c:3:33: error: private/fortranimpl.h: No such file or directory fddaf.c:48: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetblockfills_? fddaf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetdm_? gr1f.c:3:33: error: private/fortranimpl.h: No such file or directory gr1f.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetuniformcoordinates_? daindexf.c:3:33: error: private/fortranimpl.h: No such file or directory daindexf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdagetao_? dadistf.c:3:33: error: private/fortranimpl.h: No such file or directory dadistf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdacreatenaturalvector_? da2f.c:3:33: error: private/fortranimpl.h: No such file or directory da2f.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdaformfunction_? da2f.c:68: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdaformfunction1_? da2f.c:74: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdaformfunctioni1_? da2f.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdaformfunctionib1_? da2f.c:84: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdacomputejacobian1_? daghostf.c:3:33: error: private/fortranimpl.h: No such file or directory daghostf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdagetghostcorners_? dalocalf.c:3:33: error: private/fortranimpl.h: No such file or directory dalocalf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmgetlocalvector_? dalocalf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmrestorelocalvector_? dalocalf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmgetglobalvector_? dalocalf.c:74: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmclearglobalvectors_? dalocalf.c:78: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmrestoreglobalvector_? daf.c:3:33: error: private/fortranimpl.h: No such file or directory daf.c:92: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetdim_? daf.c:96: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetsizes_? daf.c:100: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetnumprocs_? daf.c:104: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetboundarytype_? daf.c:108: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetdof_? daf.c:112: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetstenciltype_? daf.c:116: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetstencilwidth_? daf.c:120: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetownershipranges_? daf.c:124: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetinterpolationtype_? daf.c:128: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdagetinterpolationtype_? daf.c:133: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetrefinementfactor_? dacornf.c:3:33: error: private/fortranimpl.h: No such file or directory dacornf.c:82: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetcoordinates_? dacornf.c:87: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetghostedcoordinates_? dacornf.c:92: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdagetcoordinates_? dacornf.c:96: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdagetcoordinateda_? dacornf.c:100: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdagetghostedcoordinates_? dacornf.c:104: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdagetcorners_? dacornf.c:108: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdagetlocalboundingbox_? dacornf.c:112: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdagetboundingbox_? dacornf.c:116: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdagetreducedda_? /usr/bin/ar: dacreatef.o: No such file or directory addaf.c:3:33: error: private/fortranimpl.h: No such file or directory addaf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmaddagetmatrixns_? addaf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmaddasetrefinement_? addaf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmaddagetcorners_? addaf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmaddagetghostcorners_? /usr/bin/ar: addaf.o: No such file or directory dmf.c:3:33: error: private/fortranimpl.h: No such file or directory dmf.c:197: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmcreate_? dmf.c:201: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdestroy_? dmf.c:204: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmsetup_? dmf.c:208: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmsetfromoptions_? dmf.c:212: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmcreateglobalvector_? dmf.c:216: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmcreatelocalvector_? dmf.c:220: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmgetlocaltoglobalmapping_? dmf.c:224: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmgetlocaltoglobalmappingblock_? dmf.c:228: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmgetblocksize_? dmf.c:232: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmgetinterpolation_? dmf.c:237: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmgetinjection_? dmf.c:242: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmsetmatrixpreallocateonly_? dmf.c:246: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmrefine_? dmf.c:251: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmgetrefinelevel_? dmf.c:255: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmglobaltolocalbegin_? dmf.c:261: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmglobaltolocalend_? dmf.c:267: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmlocaltoglobalbegin_? dmf.c:273: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmlocaltoglobalend_? dmf.c:279: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmcomputejacobiandefault_? dmf.c:286: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmcoarsen_? dmf.c:291: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmgetaggregates_? dmf.c:296: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmsetapplicationcontext_? dmf.c:300: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmgetapplicationcontext_? dmf.c:304: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmsetinitialguess_? dmf.c:308: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmsetfunction_? dmf.c:312: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmsetjacobian_? dmf.c:316: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmcomputeinitialguess_? dmf.c:321: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmhasinitialguess_? dmf.c:325: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmhasfunction_? dmf.c:329: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmhasjacobian_? dmf.c:333: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmcomputefunction_? dmf.c:339: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmcomputejacobian_? /usr/bin/ar: dmf.o: No such file or directory pcsetf.c:3:33: error: private/fortranimpl.h: No such file or directory pcsetf.c:67: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcregisterdestroy_? pcsetf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsetfromoptions_? pcsetf.c:74: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsetdm_? pcsetf.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcgetdm_? pcsetf.c:83: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsetapplicationcontext_? pcsetf.c:87: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcgetapplicationcontext_? preconf.c:3:33: error: private/fortranimpl.h: No such file or directory preconf.c:157: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcreset_? preconf.c:161: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcdestroy_? preconf.c:164: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsetdiagonalscale_? preconf.c:169: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcdiagonalscaleleft_? preconf.c:175: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcdiagonalscaleright_? preconf.c:181: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pccreate_? preconf.c:185: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcapply_? preconf.c:191: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcapplysymmetricleft_? preconf.c:197: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcapplysymmetricright_? preconf.c:203: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcapplytranspose_? preconf.c:209: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcapplytransposeexists_? preconf.c:213: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcapplybaorab_? preconf.c:220: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcapplybaorabtranspose_? preconf.c:227: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcapplyrichardsonexists_? preconf.c:231: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcapplyrichardson_? preconf.c:239: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsetup_? preconf.c:243: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsetuponblocks_? preconf.c:247: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsetoperators_? preconf.c:253: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorgetmatrix_? preconf.c:257: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcpresolve_? preconf.c:262: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcpostsolve_? preconf.c:267: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsetinitialguessnonzero_? preconf.c:271: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pccomputeexplicitoperator_? preconf.c:275: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsetcoordinates_? /usr/bin/ar: pcsetf.o: No such file or directory jacobif.c:3:33: error: private/fortranimpl.h: No such file or directory jacobif.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcjacobisetuseabs_? jacobif.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcjacobisetuserowmax_? jacobif.c:60: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcjacobisetuserowsum_? /usr/bin/ar: jacobif.o: No such file or directory sorf.c:3:33: error: private/fortranimpl.h: No such file or directory sorf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsorsetsymmetric_? sorf.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsorsetomega_? sorf.c:60: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsorsetiterations_? /usr/bin/ar: sorf.o: No such file or directory shellpcf.c:3:33: error: private/fortranimpl.h: No such file or directory shellpcf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcshellsetcontext_? /usr/bin/ar: shellpcf.o: No such file or directory bjacobif.c:3:33: error: private/fortranimpl.h: No such file or directory bjacobif.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcbjacobisetusetruelocal_? bjacobif.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcbjacobisettotalblocks_? bjacobif.c:60: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcbjacobisetlocalblocks_? /usr/bin/ar: bjacobif.o: No such file or directory mgfuncf.c:3:33: error: private/fortranimpl.h: No such file or directory mgfuncf.c:93: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmggetcoarsesolve_? mgfuncf.c:97: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsetinterpolation_? mgfuncf.c:102: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsetrestriction_? mgfuncf.c:107: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsetrscale_? mgfuncf.c:112: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmggetsmoother_? mgfuncf.c:116: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmggetsmootherup_? mgfuncf.c:120: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmggetsmootherdown_? mgfuncf.c:124: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsetcyclesonlevel_? mgfuncf.c:128: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsetrhs_? mgfuncf.c:133: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsetx_? mgfuncf.c:138: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsetr_? mgf.c:3:33: error: private/fortranimpl.h: No such file or directory mgf.c:77: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmggetlevels_? mgf.c:81: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsettype_? mgf.c:85: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsetcycletype_? mgf.c:89: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgmultiplicativesetcycles_? mgf.c:93: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsetgalerkin_? mgf.c:97: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmggetgalerkin_? mgf.c:101: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsetnumbersmoothdown_? mgf.c:105: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsetnumbersmoothup_? /usr/bin/ar: mgfuncf.o: No such file or directory eisenf.c:3:33: error: private/fortranimpl.h: No such file or directory eisenf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pceisenstatsetomega_? eisenf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pceisenstatnodiagonalscaling_? /usr/bin/ar: eisenf.o: No such file or directory asmf.c:3:33: error: private/fortranimpl.h: No such file or directory asmf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcasmsetoverlap_? asmf.c:61: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcasmsettype_? asmf.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcasmsetsortindices_? asmf.c:69: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcasmcreatesubdomains2d_? /usr/bin/ar: asmf.o: No such file or directory pckspf.c:3:33: error: private/fortranimpl.h: No such file or directory pckspf.c:48: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pckspsetusetrue_? pckspf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pckspgetksp_? /usr/bin/ar: pckspf.o: No such file or directory compositef.c:3:33: error: private/fortranimpl.h: No such file or directory compositef.c:58: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pccompositesettype_? compositef.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pccompositespecialsetalpha_? compositef.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pccompositegetpc_? compositef.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pccompositesetusetrue_? /usr/bin/ar: compositef.o: No such file or directory redundantf.c:3:33: error: private/fortranimpl.h: No such file or directory redundantf.c:58: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcredundantsetnumber_? redundantf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcredundantsetscatter_? redundantf.c:68: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcredundantgetksp_? redundantf.c:72: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcredundantgetoperators_? /usr/bin/ar: redundantf.o: No such file or directory fieldsplitf.c:3:33: error: private/fortranimpl.h: No such file or directory fieldsplitf.c:68: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfieldsplitsetfields_? fieldsplitf.c:72: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfieldsplitsetis_? fieldsplitf.c:77: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfieldsplitgetis_? fieldsplitf.c:81: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfieldsplitsetblocksize_? fieldsplitf.c:85: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfieldsplitschurprecondition_? fieldsplitf.c:90: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfieldsplitsettype_? /usr/bin/ar: fieldsplitf.o: No such file or directory choleskyf.c:3:33: error: private/fortranimpl.h: No such file or directory choleskyf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetreuseordering_? /usr/bin/ar: choleskyf.o: No such file or directory factorf.c:3:33: error: private/fortranimpl.h: No such file or directory factorf.c:97: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetupmatsolverpackage_? factorf.c:101: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetzeropivot_? factorf.c:105: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetshifttype_? factorf.c:109: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetshiftamount_? factorf.c:113: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetlevels_? factorf.c:117: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetallowdiagonalfill_? factorf.c:121: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorreorderfornonzerodiagonal_? factorf.c:125: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetfill_? factorf.c:129: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetuseinplace_? factorf.c:133: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetcolumnpivot_? factorf.c:137: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetpivotinblocks_? factorf.c:141: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetreusefill_? /usr/bin/ar: factorf.o: No such file or directory galerkinf.c:3:33: error: private/fortranimpl.h: No such file or directory galerkinf.c:53: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcgalerkinsetrestriction_? galerkinf.c:58: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcgalerkinsetinterpolation_? galerkinf.c:63: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcgalerkingetksp_? /usr/bin/ar: galerkinf.o: No such file or directory wbf.c:3:33: error: private/fortranimpl.h: No such file or directory wbf.c:43: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcexoticsettype_? /usr/bin/ar: wbf.o: No such file or directory redistributef.c:3:33: error: private/fortranimpl.h: No such file or directory redistributef.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcredistributegetksp_? /usr/bin/ar: redistributef.o: No such file or directory gasmf.c:3:33: error: private/fortranimpl.h: No such file or directory gasmf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcgasmsetoverlap_? gasmf.c:61: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcgasmsettype_? gasmf.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcgasmsetsortindices_? gasmf.c:69: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcgasmcreatesubdomains2d_? /usr/bin/ar: gasmf.o: No such file or directory itcreatef.c:3:33: error: private/fortranimpl.h: No such file or directory itcreatef.c:92: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetnormtype_? itcreatef.c:96: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetchecknormiteration_? itcreatef.c:100: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetlagnorm_? itcreatef.c:104: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetsupportednorm_? itcreatef.c:108: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetnormtype_? itcreatef.c:113: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetoperators_? itcreatef.c:119: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetoperators_? itcreatef.c:123: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspcreate_? itcreatef.c:127: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspregisterdestroy_? itcreatef.c:130: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetnullspace_? itcreatef.c:135: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetnullspace_? eigef.c:3:33: error: private/fortranimpl.h: No such file or directory eigef.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspcomputeexplicitoperator_? eigef.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspcomputeeigenvaluesexplicitly_? iterativf.c:3:33: error: private/fortranimpl.h: No such file or directory iterativf.c:87: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetresidualnorm_? iterativf.c:91: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetiterationnumber_? iterativf.c:95: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspdefaultconvergedsetuirnorm_? iterativf.c:99: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspdefaultconvergedsetumirnorm_? iterativf.c:103: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetconvergedreason_? iterativf.c:107: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetdm_? iterativf.c:112: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetdmactive_? iterativf.c:116: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetdm_? iterativf.c:120: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetapplicationcontext_? iterativf.c:124: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetapplicationcontext_? xmonf.c:3:33: error: private/fortranimpl.h: No such file or directory xmonf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspmonitorlgdestroy_? xmonf.c:50: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspmonitorlgrangedestroy_? itfuncf.c:3:33: error: private/fortranimpl.h: No such file or directory itfuncf.c:202: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspcomputeextremesingularvalues_? itfuncf.c:206: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspcomputeeigenvalues_? itfuncf.c:210: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetuponblocks_? itfuncf.c:214: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetup_? itfuncf.c:218: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsolve_? itfuncf.c:225: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsolvetranspose_? itfuncf.c:231: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspreset_? itfuncf.c:235: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspdestroy_? itfuncf.c:238: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetpcside_? itfuncf.c:242: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetpcside_? itfuncf.c:247: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgettolerances_? itfuncf.c:251: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsettolerances_? itfuncf.c:255: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetinitialguessnonzero_? itfuncf.c:259: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetinitialguessnonzero_? itfuncf.c:263: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspseterrorifnotconverged_? itfuncf.c:267: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgeterrorifnotconverged_? itfuncf.c:271: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetinitialguessknoll_? itfuncf.c:275: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetinitialguessknoll_? itfuncf.c:279: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetcomputesingularvalues_? itfuncf.c:283: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetcomputesingularvalues_? itfuncf.c:287: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetcomputeeigenvalues_? itfuncf.c:291: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetcomputeeigenvalues_? itfuncf.c:295: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetrhs_? itfuncf.c:299: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetsolution_? itfuncf.c:303: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetpc_? itfuncf.c:308: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetpc_? itfuncf.c:312: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspmonitor_? itfuncf.c:316: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspmonitorcancel_? itfuncf.c:320: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetresidualhistory_? itfuncf.c:324: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetdiagonalscale_? itfuncf.c:328: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetdiagonalscale_? itfuncf.c:332: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetdiagonalscalefix_? itfuncf.c:336: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetdiagonalscalefix_? itclf.c:3:33: error: private/fortranimpl.h: No such file or directory itclf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetfromoptions_? itresf.c:3:33: error: private/fortranimpl.h: No such file or directory itresf.c:48: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspinitialresidual_? itresf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspunwindpreconditioner_? /usr/bin/ar: itcreatef.o: No such file or directory bcgslf.c:3:33: error: private/fortranimpl.h: No such file or directory bcgslf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspbcgslsetxres_? bcgslf.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspbcgslsetpol_? bcgslf.c:60: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspbcgslsetell_? /usr/bin/ar: bcgslf.o: No such file or directory gltrf.c:3:33: error: private/fortranimpl.h: No such file or directory gltrf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgltrsetradius_? gltrf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgltrgetnormd_? gltrf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgltrgetobjfcn_? gltrf.c:74: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgltrgetmineig_? gltrf.c:78: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgltrgetlambda_? /usr/bin/ar: gltrf.o: No such file or directory nashf.c:3:33: error: private/fortranimpl.h: No such file or directory nashf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspnashsetradius_? nashf.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspnashgetnormd_? nashf.c:60: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspnashgetobjfcn_? /usr/bin/ar: nashf.o: No such file or directory stcgf.c:3:33: error: private/fortranimpl.h: No such file or directory stcgf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspstcgsetradius_? stcgf.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspstcggetnormd_? stcgf.c:60: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspstcggetobjfcn_? /usr/bin/ar: stcgf.o: No such file or directory cgtypef.c:3:33: error: private/fortranimpl.h: No such file or directory cgtypef.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspcgsettype_? cgtypef.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspcgusesinglereduction_? /usr/bin/ar: cgtypef.o: No such file or directory modpcff.c:3:33: error: private/fortranimpl.h: No such file or directory modpcff.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspfgmresmodifypcnochange_? modpcff.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspfgmresmodifypcksp_? /usr/bin/ar: modpcff.o: No such file or directory gmresf.c:3:33: error: private/fortranimpl.h: No such file or directory gmresf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgmressetcgsrefinementtype_? gmresf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgmresgetcgsrefinementtype_? gmresf.c:71: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgmressetrestart_? gmresf.c:75: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgmresgetrestart_? gmresf.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgmressethaptol_? gmpref.c:3:33: error: private/fortranimpl.h: No such file or directory gmpref.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgmressetpreallocatevectors_? /usr/bin/ar: gmresf.o: No such file or directory chebyf.c:3:33: error: private/fortranimpl.h: No such file or directory chebyf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspchebychevseteigenvalues_? chebyf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspchebychevsetestimateeigenvalues_? /usr/bin/ar: chebyf.o: No such file or directory richscalef.c:3:33: error: private/fortranimpl.h: No such file or directory richscalef.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?ksprichardsonsetscale_? richscalef.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?ksprichardsonsetselfscale_? /usr/bin/ar: richscalef.o: No such file or directory qcgf.c:3:33: error: private/fortranimpl.h: No such file or directory qcgf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspqcgsettrustregionradius_? qcgf.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspqcggettrialstepnorm_? qcgf.c:60: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspqcggetquadratic_? /usr/bin/ar: qcgf.o: No such file or directory schurmf.c:3:33: error: private/fortranimpl.h: No such file or directory schurmf.c:58: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreateschurcomplement_? schurmf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matschurcomplementgetksp_? schurmf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matschurcomplementupdate_? schurmf.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetschurcomplement_? /usr/bin/ar: schurmf.o: No such file or directory snesf.c:3:33: error: private/fortranimpl.h: No such file or directory snesf.c:277: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesseterrorifnotconverged_? snesf.c:281: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgeterrorifnotconverged_? snesf.c:285: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetfunctiondomainerror_? snesf.c:289: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetfromoptions_? snesf.c:293: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetcomputeapplicationcontext_? snesf.c:297: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetapplicationcontext_? snesf.c:301: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetapplicationcontext_? snesf.c:305: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetiterationnumber_? snesf.c:309: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetfunctionnorm_? snesf.c:313: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetnonlinearstepfailures_? snesf.c:317: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetmaxnonlinearstepfailures_? snesf.c:321: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetmaxnonlinearstepfailures_? snesf.c:325: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetnumberfunctionevals_? snesf.c:329: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetlinearsolvefailures_? snesf.c:333: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetmaxlinearsolvefailures_? snesf.c:337: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetmaxlinearsolvefailures_? snesf.c:341: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetlinearsolveiterations_? snesf.c:345: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetksp_? snesf.c:349: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetksp_? snesf.c:354: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snescreate_? snesf.c:358: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snescomputefunction_? snesf.c:364: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snescomputejacobian_? snesf.c:369: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetup_? snesf.c:373: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesreset_? snesf.c:377: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesdestroy_? snesf.c:380: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetlagpreconditioner_? snesf.c:384: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetgridsequence_? snesf.c:388: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetlagpreconditioner_? snesf.c:392: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetlagjacobian_? snesf.c:396: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetlagjacobian_? snesf.c:400: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessettolerances_? snesf.c:404: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgettolerances_? snesf.c:408: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessettrustregiontolerance_? snesf.c:412: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesmonitor_? snesf.c:416: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetconvergedreason_? snesf.c:420: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetconvergencehistory_? snesf.c:424: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesdefaultupdate_? snesf.c:428: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesregisterdestroy_? snesf.c:431: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetsolution_? snesf.c:435: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetsolutionupdate_? snesf.c:439: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?sneskspsetuseew_? snesf.c:443: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?sneskspgetuseew_? snesf.c:447: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?sneskspsetparametersew_? snesf.c:452: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?sneskspgetparametersew_? snesf.c:457: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetdm_? snesf.c:462: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetdm_? snesf.c:466: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetpc_? snesf.c:471: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetpc_? snesutf.c:3:33: error: private/fortranimpl.h: No such file or directory snesutf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesdefaultgetwork_? /usr/bin/ar: snesf.o: No such file or directory snesmfjf.c:3:33: error: private/fortranimpl.h: No such file or directory snesmfjf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatesnesmf_? /usr/bin/ar: snesmfjf.o: No such file or directory lsparamsf.c:3:33: error: private/fortranimpl.h: No such file or directory lsparamsf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?sneslinesearchsetparams_? /usr/bin/ar: lsparamsf.o: No such file or directory vif.c:3:33: error: private/fortranimpl.h: No such file or directory vif.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesvisetvariablebounds_? /usr/bin/ar: vif.o: No such file or directory snesshellf.c:3:33: error: private/fortranimpl.h: No such file or directory snesshellf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesshellsetcontext_? /usr/bin/ar: snesshellf.o: No such file or directory tsf.c:3:33: error: private/fortranimpl.h: No such file or directory tsf.c:237: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssetfromoptions_? tsf.c:241: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tscomputerhsjacobian_? tsf.c:246: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tscomputerhsfunction_? tsf.c:252: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tscomputeifunction_? tsf.c:259: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tscomputeijacobian_? tsf.c:265: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssetapplicationcontext_? tsf.c:269: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgetapplicationcontext_? tsf.c:273: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgettimestepnumber_? tsf.c:277: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssetinitialtimestep_? tsf.c:281: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssettimestep_? tsf.c:285: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssetexactfinaltime_? tsf.c:289: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgettimestep_? tsf.c:293: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgetsolution_? tsf.c:297: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssetproblemtype_? tsf.c:301: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssetup_? tsf.c:305: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsreset_? tsf.c:309: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsdestroy_? tsf.c:312: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgetsnes_? tsf.c:316: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgetksp_? tsf.c:320: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgetduration_? tsf.c:324: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssetduration_? tsf.c:328: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssetsolution_? tsf.c:333: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsprestep_? tsf.c:337: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tspoststep_? tsf.c:341: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsmonitordefault_? tsf.c:346: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssetretainstages_? tsf.c:350: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsinterpolate_? tsf.c:355: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsstep_? tsf.c:359: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssolve_? tsf.c:364: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsmonitor_? tsf.c:369: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgettime_? tsf.c:373: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssettime_? tsf.c:377: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssetdm_? tsf.c:382: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgetdm_? tsf.c:386: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snestsformfunction_? tsf.c:392: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snestsformjacobian_? tsf.c:397: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgetconvergedreason_? tsf.c:402: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgetnonlinearsolveiterations_? tsf.c:406: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgetlinearsolveiterations_? tsf.c:410: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsvisetvariablebounds_? /usr/bin/ar: tsf.o: No such file or directory rkf.c:3:33: error: private/fortranimpl.h: No such file or directory rkf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsrksettolerance_? /usr/bin/ar: rkf.o: No such file or directory sspf.c:3:33: error: private/fortranimpl.h: No such file or directory sspf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssspsetnumstages_? sspf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssspgetnumstages_? /usr/bin/ar: sspf.o: No such file or directory thetaf.c:3:33: error: private/fortranimpl.h: No such file or directory thetaf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsthetagettheta_? thetaf.c:61: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsthetasettheta_? thetaf.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsthetagetendpoint_? thetaf.c:69: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsthetasetendpoint_? /usr/bin/ar: thetaf.o: No such file or directory alphaf.c:3:33: error: private/fortranimpl.h: No such file or directory alphaf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsalphasetradius_? alphaf.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsalphasetparams_? alphaf.c:60: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsalphagetparams_? /usr/bin/ar: alphaf.o: No such file or directory posindepf.c:3:33: error: private/fortranimpl.h: No such file or directory posindepf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tspseudocomputetimestep_? posindepf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tspseudoverifytimestep_? posindepf.c:71: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tspseudosettimestepincrement_? posindepf.c:75: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tspseudosetmaxtimestep_? posindepf.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tspseudoincrementdtfrominitialdt_? /usr/bin/ar: posindepf.o: No such file or directory characteristicf.c:3:33: error: private/fortranimpl.h: No such file or directory characteristicf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?characteristicsetup_? /usr/bin/ar: characteristicf.o: No such file or directory -------------- next part -------------- ========================================== See documentation/faq.html and documentation/bugreporting.html for help with installation problems. Please send EVERYTHING printed out below when reporting problems To subscribe to the PETSc announcement list, send mail to majordomo at mcs.anl.gov with the message: subscribe petsc-announce To subscribe to the PETSc users mailing list, send mail to majordomo at mcs.anl.gov with the message: subscribe petsc-users ========================================== On Thu Nov 8 11:42:29 CST 2012 on l2118a-linux.soecs.ku.edu Machine characteristics: Linux l2118a-linux.soecs.ku.edu 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux ----------------------------------------- Using PETSc directory: /home/zlwei/soft/mercurial/petsc-dev Using PETSc arch: arch-linux2-c-debug ----------------------------------------- PETSC_VERSION_RELEASE 0 PETSC_VERSION_MAJOR 3 PETSC_VERSION_MINOR 3 PETSC_VERSION_SUBMINOR 0 PETSC_VERSION_PATCH 4 PETSC_VERSION_DATE "Jun, 5, 2012" PETSC_VERSION_PATCH_DATE "unknown" PETSC_VERSION_HG "unknown" PETSC_VERSION_DATE_HG "unknown" PETSC_VERSION_(MAJOR,MINOR,SUBMINOR) \ PETSC_VERSION_LT(MAJOR,MINOR,SUBMINOR) \ PETSC_VERSION_LE(MAJOR,MINOR,SUBMINOR) \ ----------------------------------------- Using configure Options: --download-f-blas-lapack=1 --download-mpich=1 --with-cc=gcc --with-fc=gfortran PETSC_ARCH=arch-linux2-c-debug Using configuration flags: #define INCLUDED_PETSCCONF_H #define IS_COLORING_MAX 65535 #define STDC_HEADERS 1 #define MPIU_COLORING_VALUE MPI_UNSIGNED_SHORT #define PETSC_UINTPTR_T uintptr_t #define PETSC_HAVE_PTHREAD 1 #define PETSC_STATIC_INLINE static inline #define PETSC_REPLACE_DIR_SEPARATOR '\\' #define PETSC_RESTRICT __restrict__ #define PETSC_HAVE_MPI 1 #define PETSC_PREFETCH_HINT_T2 _MM_HINT_T2 #define PETSC_PREFETCH_HINT_T0 _MM_HINT_T0 #define PETSC_PREFETCH_HINT_T1 _MM_HINT_T1 #define PETSC_HAVE_FORTRAN 1 #define PETSC_LIB_DIR "/home/zlwei/soft/mercurial/petsc-dev/arch-linux2-c-debug/lib" #define PETSC_USE_SOCKET_VIEWER 1 #define PETSC__POSIX_C_SOURCE_200112L 1 #define PETSC_HAVE_SOWING 1 #define PETSC_SLSUFFIX "" #define PETSC_FUNCTION_NAME_CXX __FUNCT__ #define PETSC_HAVE_ATOLL 1 #define PETSC_HAVE_DOUBLE_ALIGN_MALLOC 1 #define PETSC_UNUSED __attribute((unused)) #define PETSC_FUNCTION_NAME_C __func__ #define PETSC_HAVE_C2HTML 1 #define PETSC_HAVE_VALGRIND 1 #define PETSC_USE_SINGLE_LIBRARY 1 #define PETSC_HAVE_BUILTIN_EXPECT 1 #define PETSC_DIR_SEPARATOR '/' #define PETSC_PATH_SEPARATOR ':' #define PETSC__BSD_SOURCE 1 #define PETSC_HAVE_XMMINTRIN_H 1 #define PETSC_PREFETCH_HINT_NTA _MM_HINT_NTA #define PETSC_Prefetch(a,b,c) _mm_prefetch((const char*)(a),(c)) #define PETSC_HAVE_BLASLAPACK 1 #define PETSC_HAVE_STRING_H 1 #define PETSC_HAVE_SYS_TYPES_H 1 #define PETSC_HAVE_ENDIAN_H 1 #define PETSC_HAVE_SYS_PROCFS_H 1 #define PETSC_HAVE_DLFCN_H 1 #define PETSC_HAVE_SCHED_H 1 #define PETSC_HAVE_STDINT_H 1 #define PETSC_HAVE_LINUX_KERNEL_H 1 #define PETSC_HAVE_TIME_H 1 #define PETSC_HAVE_MATH_H 1 #define PETSC_TIME_WITH_SYS_TIME 1 #define PETSC_HAVE_SYS_PARAM_H 1 #define PETSC_HAVE_SYS_SOCKET_H 1 #define PETSC_HAVE_UNISTD_H 1 #define PETSC_HAVE_STDLIB_H 1 #define PETSC_HAVE_SYS_WAIT_H 1 #define PETSC_HAVE_LIMITS_H 1 #define PETSC_HAVE_SYS_UTSNAME_H 1 #define PETSC_HAVE_NETINET_IN_H 1 #define PETSC_HAVE_FENV_H 1 #define PETSC_HAVE_PTHREAD_H 1 #define PETSC_HAVE_FLOAT_H 1 #define PETSC_HAVE_SEARCH_H 1 #define PETSC_HAVE_SYS_RESOURCE_H 1 #define PETSC_HAVE_SYS_TIMES_H 1 #define PETSC_HAVE_NETDB_H 1 #define PETSC_HAVE_MALLOC_H 1 #define PETSC_HAVE_PWD_H 1 #define PETSC_HAVE_FCNTL_H 1 #define PETSC_HAVE_STRINGS_H 1 #define PETSC_HAVE_MEMORY_H 1 #define PETSC_HAVE_SYS_SYSINFO_H 1 #define PETSC_HAVE_SYS_TIME_H 1 #define PETSC_C_STATIC_INLINE static inline #define PETSC_C_RESTRICT __restrict__ #define PETSC_USING_F90 1 #define PETSC_HAVE_FORTRAN_UNDERSCORE 1 #define PETSC_HAVE_LIBDL 1 #define PETSC_HAVE_LIBM 1 #define PETSC_HAVE_LIBPTHREAD 1 #define PETSC_HAVE_LIBFLAPACK 1 #define PETSC_HAVE_ERF 1 #define PETSC_HAVE_LIBFBLAS 1 #define PETSC_HAVE_LIBRT 1 #define PETSC_ARCH "arch-linux2-c-debug" #define PETSC_VERSION_DATE_HG "Fri Sep 23 14:46:14 2011 -0700" #define PETSC_VERSION_BS_HG "e9fd775ab2bf270a9204f7cbc33603292ac5b1d8" #define PETSC_VERSION_HG "85e6055943e0711fccdec2d08caeba48971d3d55" #define PETSC_DIR "/home/zlwei/soft/mercurial/petsc-dev" #define PETSC_VERSION_BS_DATE_HG "Fri Sep 16 17:33:47 2011 +0200" #define HAVE_GZIP 1 #define PETSC_CLANGUAGE_C 1 #define PETSC_USE_EXTERN_CXX #define PETSC_USE_ERRORCHECKING 1 #define PETSC_MISSING_DREAL 1 #define PETSC_SIZEOF_MPI_COMM 4 #define PETSC_BITS_PER_BYTE 8 #define PETSC_SIZEOF_MPI_FINT 4 #define PETSC_SIZEOF_VOID_P 8 #define PETSC_RETSIGTYPE void #define PETSC_SIZEOF_LONG 8 #define PETSC_USE_FORTRANKIND 1 #define PETSC_SIZEOF_SIZE_T 8 #define PETSC_SIZEOF_CHAR 1 #define PETSC_SIZEOF_DOUBLE 8 #define PETSC_SIZEOF_FLOAT 4 #define PETSC_HAVE_C99_COMPLEX 1 #define PETSC_SIZEOF_INT 4 #define PETSC_SIZEOF_LONG_LONG 8 #define PETSC_SIZEOF_SHORT 2 #define PETSC_HAVE_STRCASECMP 1 #define PETSC_HAVE_POPEN 1 #define PETSC_HAVE_SIGSET 1 #define PETSC_HAVE_GETWD 1 #define PETSC_HAVE_VSNPRINTF 1 #define PETSC_HAVE_TIMES 1 #define PETSC_HAVE_DLSYM 1 #define PETSC_HAVE_SNPRINTF 1 #define PETSC_HAVE_GETPWUID 1 #define PETSC_HAVE_GETHOSTBYNAME 1 #define PETSC_HAVE_SLEEP 1 #define PETSC_HAVE_DLERROR 1 #define PETSC_HAVE_FORK 1 #define PETSC_HAVE_RAND 1 #define PETSC_HAVE_GETTIMEOFDAY 1 #define PETSC_HAVE_DLCLOSE 1 #define PETSC_HAVE_UNAME 1 #define PETSC_HAVE_GETHOSTNAME 1 #define PETSC_HAVE_MKSTEMP 1 #define PETSC_HAVE_SIGACTION 1 #define PETSC_HAVE_DRAND48 1 #define PETSC_HAVE_NANOSLEEP 1 #define PETSC_HAVE_VA_COPY 1 #define PETSC_HAVE_CLOCK 1 #define PETSC_HAVE_ACCESS 1 #define PETSC_HAVE_SIGNAL 1 #define PETSC_HAVE_USLEEP 1 #define PETSC_HAVE_GETRUSAGE 1 #define PETSC_HAVE_VFPRINTF 1 #define PETSC_HAVE_MEMALIGN 1 #define PETSC_HAVE_GETDOMAINNAME 1 #define PETSC_HAVE_TIME 1 #define PETSC_HAVE_LSEEK 1 #define PETSC_HAVE_SOCKET 1 #define PETSC_HAVE_SYSINFO 1 #define PETSC_HAVE_READLINK 1 #define PETSC_HAVE_REALPATH 1 #define PETSC_HAVE_DLOPEN 1 #define PETSC_HAVE_MEMMOVE 1 #define PETSC_HAVE__GFORTRAN_IARGC 1 #define PETSC_HAVE_GETCWD 1 #define PETSC_HAVE_VPRINTF 1 #define PETSC_HAVE_BZERO 1 #define PETSC_HAVE_GETPAGESIZE 1 #define PETSC_USE_SCALAR_REAL 1 #define PETSC_HAVE_ISINF 1 #define PETSC_HAVE_ISNAN 1 #define PETSC_USE_REAL_DOUBLE 1 #define PETSC_HAVE_MPI_COMM_C2F 1 #define PETSC_HAVE_MPI_LONG_DOUBLE 1 #define PETSC_HAVE_MPI_COMM_F2C 1 #define PETSC_HAVE_MPI_FINT 1 #define PETSC_HAVE_MPI_F90MODULE 1 #define PETSC_HAVE_MPI_FINALIZED 1 #define PETSC_HAVE_MPI_COMM_SPAWN 1 #define PETSC_HAVE_MPI_WIN_CREATE 1 #define PETSC_HAVE_MPI_EXSCAN 1 #define PETSC_HAVE_MPIIO 1 #define PETSC_HAVE_MPI_C_DOUBLE_COMPLEX 1 #define PETSC_HAVE_MPI_ALLTOALLW 1 #define PETSC_HAVE_MPI_IN_PLACE 1 #define PETSC_USE_INFO 1 #define PETSC_PETSC_USE_BACKWARD_LOOP 1 #define PETSC_Alignx(a,b) #define PETSC_USE_DEBUG 1 #define PETSC_USE_LOG 1 #define PETSC_IS_COLOR_VALUE_TYPE short #define PETSC_USE_CTABLE 1 #define PETSC_LEVEL1_DCACHE_LINESIZE 64 #define PETSC_LEVEL1_DCACHE_SIZE 32768 #define PETSC_LEVEL1_DCACHE_ASSOC 8 #define PETSC_MEMALIGN 16 #define PETSC_USE_PROC_FOR_SIZE 1 #define PETSC_HAVE_FORTRAN_GET_COMMAND_ARGUMENT 1 #define PETSC_HAVE_GFORTRAN_IARGC 1 #define PETSC_USE_GDB_DEBUGGER 1 #define PETSC_HAVE_SHARED_LIBRARIES 1 #define PETSC_HAVE_SCHED_CPU_SET_T 1 #define PETSC_HAVE_PTHREAD_BARRIER_T 1 #define PETSC_BLASLAPACK_UNDERSCORE 1 ----------------------------------------- Using C/C++ compile: /home/zlwei/soft/mercurial/petsc-dev/arch-linux2-c-debug/bin/mpicc -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 -I/home/zlwei/soft/mercurial/petsc-dev/include -I/home/zlwei/soft/mercurial/petsc-dev/arch-linux2-c-debug/include -D__INSDIR__=./ Using Fortran compile: /home/zlwei/soft/mercurial/petsc-dev/arch-linux2-c-debug/bin/mpif90 -c -Wall -Wno-unused-variable -g -I/home/zlwei/soft/mercurial/petsc-dev/include -I/home/zlwei/soft/mercurial/petsc-dev/arch-linux2-c-debug/include ----------------------------------------- Using C/C++ linker: /home/zlwei/soft/mercurial/petsc-dev/arch-linux2-c-debug/bin/mpicc Using C/C++ flags: -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 Using Fortran linker: /home/zlwei/soft/mercurial/petsc-dev/arch-linux2-c-debug/bin/mpif90 Using Fortran flags: -Wall -Wno-unused-variable -g ----------------------------------------- Using libraries: -L/home/zlwei/soft/mercurial/petsc-dev/arch-linux2-c-debug/lib -lpetsc -lpthread -Wl,-rpath,/home/zlwei/soft/mercurial/petsc-dev/arch-linux2-c-debug/lib -lflapack -lfblas -lm -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -ldl -lmpich -lopa -lmpl -lrt -lpthread -lgcc_s -lmpichf90 -lgfortran -lm -lm -ldl -lmpich -lopa -lmpl -lrt -lpthread -lgcc_s -ldl ------------------------------------------ Using mpiexec: /home/zlwei/soft/mercurial/petsc-dev/arch-linux2-c-debug/bin/mpiexec ========================================== /bin/rm -f -rf /home/zlwei/soft/mercurial/petsc-dev/arch-linux2-c-debug/lib/libpetsc*.* /bin/rm -f -f /home/zlwei/soft/mercurial/petsc-dev/arch-linux2-c-debug/include/petsc*.mod BEGINNING TO COMPILE LIBRARIES IN ALL DIRECTORIES ========================================= libfast in: /home/zlwei/soft/mercurial/petsc-dev/src libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/comm libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/impls libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/impls/socket libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/impls/socket/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/impls/ascii libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/impls/ascii/ftn-auto filevf.c:3:33: error: private/fortranimpl.h: No such file or directory filevf.c:67: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerasciisettab_? filevf.c:71: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerasciiaddtab_? filevf.c:75: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerasciisubtracttab_? filevf.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerasciipushtab_? filevf.c:83: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerasciipoptab_? filevf.c:87: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerasciiusetabs_? /usr/bin/ar: filevf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/impls/ascii/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/impls/binary libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/impls/binary/ftn-auto binvf.c:3:33: error: private/fortranimpl.h: No such file or directory binvf.c:67: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerbinaryskipinfo_? binvf.c:71: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerbinarysetskipoptions_? binvf.c:75: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerbinarygetskipoptions_? binvf.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerbinarysetskipheader_? binvf.c:83: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerbinarygetskipheader_? binvf.c:87: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerbinarysetmpiio_? /usr/bin/ar: binvf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/impls/binary/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/impls/binary/f90-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/impls/string libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/impls/string/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/impls/draw libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/impls/draw/ftn-auto drawvf.c:3:33: error: private/fortranimpl.h: No such file or directory drawvf.c:67: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerdrawclear_? drawvf.c:71: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerdrawgetpause_? drawvf.c:75: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerdrawsetpause_? drawvf.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerdrawsethold_? drawvf.c:83: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerdrawgethold_? drawvf.c:87: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerdrawsetbounds_? /usr/bin/ar: drawvf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/impls/draw/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/impls/vu libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/impls/vtk libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/impls/vtk/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/examples libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/examples/tutorials libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/examples/tests libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/interface libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/interface/ftn-auto viewf.c:3:33: error: private/fortranimpl.h: No such file or directory viewf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerdestroy_? viewf.c:50: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewersetup_? viewregf.c:3:33: error: private/fortranimpl.h: No such file or directory viewregf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewercreate_? flushf.c:3:33: error: private/fortranimpl.h: No such file or directory flushf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerflush_? duplf.c:3:33: error: private/fortranimpl.h: No such file or directory duplf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewergetsingleton_? duplf.c:61: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerrestoresingleton_? duplf.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewergetsubcomm_? duplf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscviewerrestoresubcomm_? /usr/bin/ar: viewf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/viewer/interface/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/draw libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/draw/interface drawreg.c: In function ?PetscDrawSetFromOptions?: drawreg.c:255: warning: unused variable ?movie? drawreg.c:254: warning: unused variable ?filename? drawreg.c:250: warning: unused variable ?save? libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/draw/interface/ftn-auto drectf.c:3:33: error: private/fortranimpl.h: No such file or directory drectf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawrectangle_? drectf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawsave_? dmousef.c:3:33: error: private/fortranimpl.h: No such file or directory dmousef.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawgetmousebutton_? dmousef.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawsynchronizedgetmousebutton_? dellipsef.c:3:33: error: private/fortranimpl.h: No such file or directory dellipsef.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawellipse_? dcoorf.c:3:33: error: private/fortranimpl.h: No such file or directory dcoorf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawsetcoordinates_? dtrif.c:3:33: error: private/fortranimpl.h: No such file or directory dtrif.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawtriangle_? dtrif.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawscalepopup_? dtrif.c:61: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawtensorcontourpatch_? dpointsf.c:3:33: error: private/fortranimpl.h: No such file or directory dpointsf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawpointsetsize_? dlinegwf.c:3:33: error: private/fortranimpl.h: No such file or directory dlinegwf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlinegetwidth_? dflushf.c:3:33: error: private/fortranimpl.h: No such file or directory dflushf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawflush_? dpausef.c:3:33: error: private/fortranimpl.h: No such file or directory dpausef.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawpause_? dsclearf.c:3:33: error: private/fortranimpl.h: No such file or directory dsclearf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawsynchronizedclear_? dbufff.c:3:33: error: private/fortranimpl.h: No such file or directory dbufff.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawisnull_? dbufff.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawsetdoublebuffer_? dgpausef.c:3:33: error: private/fortranimpl.h: No such file or directory dgpausef.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawgetpause_? dsflushf.c:3:33: error: private/fortranimpl.h: No such file or directory dsflushf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawsynchronizedflush_? dtextsf.c:3:33: error: private/fortranimpl.h: No such file or directory dtextsf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawstringsetsize_? dsetpausef.c:3:33: error: private/fortranimpl.h: No such file or directory dsetpausef.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawsetpause_? dgcoorf.c:3:33: error: private/fortranimpl.h: No such file or directory dgcoorf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawgetcoordinates_? dviewpf.c:3:33: error: private/fortranimpl.h: No such file or directory dviewpf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawsetviewport_? dviewpf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawsplitviewport_? dlinewf.c:3:33: error: private/fortranimpl.h: No such file or directory dlinewf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlinesetwidth_? drawf.c:3:33: error: private/fortranimpl.h: No such file or directory drawf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawresizewindow_? drawf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawcheckresizedwindow_? drawf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawdestroy_? drawf.c:73: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawgetpopup_? drawf.c:77: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawsetdisplay_? dtextgsf.c:3:33: error: private/fortranimpl.h: No such file or directory dtextgsf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawstringgetsize_? dclearf.c:3:33: error: private/fortranimpl.h: No such file or directory dclearf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawclear_? dclearf.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawbop_? dclearf.c:60: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdraweop_? dpointf.c:3:33: error: private/fortranimpl.h: No such file or directory dpointf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawpoint_? dlinef.c:3:33: error: private/fortranimpl.h: No such file or directory dlinef.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawline_? dlinef.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawarrow_? /usr/bin/ar: drectf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/draw/interface/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/draw/impls libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/draw/examples libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/draw/examples/tests libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/draw/examples/tutorials libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/draw/utils libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/draw/utils/ftn-auto lgcf.c:3:33: error: private/fortranimpl.h: No such file or directory lgcf.c:91: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlggetaxis_? lgcf.c:95: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlggetdraw_? lgcf.c:99: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlgspdraw_? lgcf.c:104: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlgcreate_? lgcf.c:108: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlgsetcolors_? lgcf.c:112: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlgsetdimension_? lgcf.c:116: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlgreset_? lgcf.c:120: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlgdestroy_? lgcf.c:123: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlgindicatedatapoints_? lgcf.c:127: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlgdraw_? lgcf.c:131: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlgprint_? lgf.c:3:33: error: private/fortranimpl.h: No such file or directory lgf.c:46: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlgaddpoint_? lgf.c:50: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawlgsetlimits_? histsf.c:3:33: error: private/fortranimpl.h: No such file or directory histsf.c:82: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawhgsetnumberbins_? histsf.c:86: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawhgreset_? histsf.c:90: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawhgaddvalue_? histsf.c:94: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawhgdraw_? histsf.c:98: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawhgprint_? histsf.c:102: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawhgsetcolor_? histsf.c:106: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawhgsetlimits_? histsf.c:110: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawhgcalcstats_? histsf.c:114: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawhgintegerbins_? axisf.c:3:33: error: private/fortranimpl.h: No such file or directory axisf.c:41: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawaxissetlimits_? dscatterf.c:3:33: error: private/fortranimpl.h: No such file or directory dscatterf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawspsetdimension_? dscatterf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawspreset_? dscatterf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawspaddpoint_? dscatterf.c:74: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawspdraw_? dscatterf.c:78: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawspsetlimits_? axiscf.c:3:33: error: private/fortranimpl.h: No such file or directory axiscf.c:61: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawaxiscreate_? axiscf.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawaxisdestroy_? axiscf.c:68: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawaxissetcolors_? axiscf.c:72: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawaxissetholdlimits_? axiscf.c:76: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdrawaxisdraw_? /usr/bin/ar: lgcf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/draw/utils/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/error libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/error/examples libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/error/examples/tests libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/error/ftn-auto errf.c:3:33: error: private/fortranimpl.h: No such file or directory errf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscpoperrorhandler_? adebugf.c:3:33: error: private/fortranimpl.h: No such file or directory adebugf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsetdefaultdebugger_? adebugf.c:50: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscattachdebugger_? fpf.c:3:33: error: private/fortranimpl.h: No such file or directory fpf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsetfptrap_? signalf.c:3:33: error: private/fortranimpl.h: No such file or directory signalf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdefaultsignalhandler_? signalf.c:50: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscpopsignalhandler_? /usr/bin/ar: errf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/error/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/dll libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/dll/ftn-auto regf.c:3:33: error: private/fortranimpl.h: No such file or directory regf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscflistdestroy_? regf.c:60: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscflistview_? regf.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscflistget_? regf.c:69: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscflistduplicate_? /usr/bin/ar: regf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/fileio libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/fileio/ftn-auto mpiuopenf.c:3:33: error: private/fortranimpl.h: No such file or directory mpiuopenf.c:41: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscfclose_? mprintf.c:3:33: error: private/fortranimpl.h: No such file or directory mprintf.c:41: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsynchronizedflush_? sysiof.c:3:33: error: private/fortranimpl.h: No such file or directory sysiof.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscbinaryread_? sysiof.c:59: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscbinarywrite_? sysiof.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscbinaryclose_? sysiof.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscbinaryseek_? /usr/bin/ar: mpiuopenf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/fileio/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/memory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/memory/ftn-auto memf.c:3:33: error: private/fortranimpl.h: No such file or directory memf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscmemorygetcurrentusage_? memf.c:50: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscmemorygetmaximumusage_? /usr/bin/ar: memf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/memory/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/objects libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/objects/ftn-auto gcommf.c:3:33: error: private/fortranimpl.h: No such file or directory gcommf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscobjectgettablevel_? gcommf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscobjectincrementtablevel_? optionsf.c:3:33: error: private/fortranimpl.h: No such file or directory optionsf.c:67: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscoptionsvalidkey_? optionsf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscoptionsprefixpush_? optionsf.c:73: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscoptionsprefixpop_? optionsf.c:76: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscoptionsleft_? optionsf.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscoptionssetfromoptions_? optionsf.c:82: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscoptionsmonitorcancel_? tagmf.c:3:33: error: private/fortranimpl.h: No such file or directory tagmf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsccommgetnewtag_? destroyf.c:3:33: error: private/fortranimpl.h: No such file or directory destroyf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscobjectdestroy_? ptypef.c:3:33: error: private/fortranimpl.h: No such file or directory ptypef.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscdatatypegetsize_? inheritf.c:3:33: error: private/fortranimpl.h: No such file or directory inheritf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscobjectreference_? inheritf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscobjectgetreference_? inheritf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscobjectdereference_? inheritf.c:74: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscobjectsetfromoptions_? inheritf.c:78: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscobjectsetup_? pinitf.c:3:33: error: private/fortranimpl.h: No such file or directory pinitf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscinitialized_? pinitf.c:50: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscfinalized_? /usr/bin/ar: gcommf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/objects/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/time libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/time/ftn-auto cputimef.c:3:33: error: private/fortranimpl.h: No such file or directory cputimef.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscgetcputime_? ptimef.c:3:33: error: private/fortranimpl.h: No such file or directory ptimef.c:41: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscgettime_? /usr/bin/ar: cputimef.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/utils libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/utils/ftn-auto sortdf.c:3:33: error: private/fortranimpl.h: No such file or directory sortdf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsortreal_? sortdf.c:55: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsortsplit_? sortdf.c:58: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsortsplitreal_? mpiuf.c:3:33: error: private/fortranimpl.h: No such file or directory mpiuf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsequentialphasebegin_? mpiuf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsequentialphaseend_? sortif.c:3:33: error: private/fortranimpl.h: No such file or directory sortif.c:67: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsortint_? sortif.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsortremovedupsint_? sortif.c:73: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsortintwitharray_? sortif.c:76: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsortmpiintwitharray_? sortif.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsortintwithscalararray_? sortif.c:82: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscprocesstree_? psplitf.c:3:33: error: private/fortranimpl.h: No such file or directory psplitf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsplitownershipblock_? psplitf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsplitownership_? memcf.c:3:33: error: private/fortranimpl.h: No such file or directory memcf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscmemcmp_? memcf.c:50: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscmemmove_? psleepf.c:3:33: error: private/fortranimpl.h: No such file or directory psleepf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsleep_? sortipf.c:3:33: error: private/fortranimpl.h: No such file or directory sortipf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsortintwithpermutation_? sortipf.c:50: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscsortrealwithpermutation_? /usr/bin/ar: sortdf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/utils/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/plog libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/plog/utils libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/plog/ftn-auto plogf.c:3:33: error: private/fortranimpl.h: No such file or directory plogf.c:103: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogtracebegin_? plogf.c:107: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogactions_? plogf.c:110: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogobjects_? plogf.c:113: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogstagesetactive_? plogf.c:116: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogstagegetactive_? plogf.c:119: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogstagesetvisible_? plogf.c:122: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogstagegetvisible_? plogf.c:125: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogeventactivate_? plogf.c:128: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogeventdeactivate_? plogf.c:131: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogeventsetactiveall_? plogf.c:134: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogeventactivateclass_? plogf.c:137: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogeventdeactivateclass_? plogf.c:140: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petsclogviewpython_? /usr/bin/ar: plogf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/plog/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/random libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/random/interface libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/random/interface/ftn-auto randomf.c:3:33: error: private/fortranimpl.h: No such file or directory randomf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscrandomgetvalue_? randomf.c:61: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscrandomgetvaluereal_? randomf.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscrandomgetinterval_? randomf.c:69: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscrandomsetinterval_? randomcf.c:3:33: error: private/fortranimpl.h: No such file or directory randomcf.c:72: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscrandomdestroy_? randomcf.c:75: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscrandomgetseed_? randomcf.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscrandomsetseed_? randomcf.c:83: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscrandomsetfromoptions_? randomcf.c:87: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscrandomviewfromoptions_? randomcf.c:92: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscrandomcreate_? randomcf.c:96: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscrandomseed_? /usr/bin/ar: randomf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/random/interface/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/random/examples libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/random/examples/tutorials libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/random/impls libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/random/impls/rand libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/random/impls/rand48 libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/bag libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/bag/ftn-auto bagf.c:3:33: error: private/fortranimpl.h: No such file or directory bagf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscbagcreate_? /usr/bin/ar: bagf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/bag/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/bag/f90-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/examples libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/examples/tests libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/examples/tutorials libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/verbose libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/verbose/ftn-auto verboseinfof.c:3:33: error: private/fortranimpl.h: No such file or directory verboseinfof.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscinfodeactivateclass_? verboseinfof.c:50: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?petscinfoactivateclass_? /usr/bin/ar: verboseinfof.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/verbose/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/fsrc libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/shell libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/shell/interface libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/f90-src libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/f90-src/fsrc libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/f90-mod libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/python libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/python/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/totalview libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/sf libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/sf/examples libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/sf/examples/tutorials libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/threadcomm libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/threadcomm/interface libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/threadcomm/impls libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/threadcomm/impls/nothread libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/threadcomm/examples libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/threadcomm/examples/tutorials libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/sys/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec/utils libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec/utils/ftn-auto vpscatf.c:3:33: error: private/fortranimpl.h: No such file or directory vpscatf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecscattercreatelocal_? combf.c:3:33: error: private/fortranimpl.h: No such file or directory combf.c:87: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecdotbegin_? combf.c:92: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecdotend_? combf.c:97: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vectdotbegin_? combf.c:102: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vectdotend_? combf.c:107: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecnormbegin_? combf.c:111: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecnormend_? combf.c:115: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecmdotbegin_? combf.c:119: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecmdotend_? combf.c:123: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecmtdotbegin_? combf.c:127: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecmtdotend_? vecmpitoseqf.c:3:33: error: private/fortranimpl.h: No such file or directory vecmpitoseqf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecscattercreatetoall_? vecmpitoseqf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecscattercreatetozero_? cmeshf.c:3:33: error: private/fortranimpl.h: No such file or directory cmeshf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?veccontourscale_? vinvf.c:3:33: error: private/fortranimpl.h: No such file or directory vinvf.c:147: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstrideset_? vinvf.c:151: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstridescale_? vinvf.c:155: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstridenorm_? vinvf.c:159: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstridemax_? vinvf.c:163: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstridemin_? vinvf.c:167: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstridescaleall_? vinvf.c:171: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstridenormall_? vinvf.c:175: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstridemaxall_? vinvf.c:179: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstrideminall_? vinvf.c:183: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstridegatherall_? vinvf.c:187: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstridescatterall_? vinvf.c:191: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstridegather_? vinvf.c:196: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstridescatter_? vinvf.c:201: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecexp_? vinvf.c:205: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?veclog_? vinvf.c:209: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsqrtabs_? vinvf.c:213: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecdotnorm2_? vinvf.c:218: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsum_? vinvf.c:222: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecshift_? vinvf.c:226: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecabs_? vinvf.c:230: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecpermute_? vinvf.c:235: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecequal_? vscatf.c:3:33: error: private/fortranimpl.h: No such file or directory vscatf.c:63: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecscattergetmerged_? vscatf.c:67: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecscatterbegin_? vscatf.c:73: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecscatterend_? vscatf.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecscattercopy_? vscatf.c:83: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecscatterview_? /usr/bin/ar: vpscatf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec/utils/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec/interface libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec/interface/ftn-auto veccreatef.c:3:33: error: private/fortranimpl.h: No such file or directory veccreatef.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?veccreate_? vectorf.c:3:33: error: private/fortranimpl.h: No such file or directory vectorf.c:197: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstashgetinfo_? vectorf.c:201: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetlocaltoglobalmapping_? vectorf.c:206: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetlocaltoglobalmappingblock_? vectorf.c:211: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecgetlocaltoglobalmapping_? vectorf.c:215: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecgetlocaltoglobalmappingblock_? vectorf.c:219: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecassemblybegin_? vectorf.c:223: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecassemblyend_? vectorf.c:227: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecpointwisemax_? vectorf.c:233: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecpointwisemin_? vectorf.c:239: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecpointwisemaxabs_? vectorf.c:245: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecpointwisedivide_? vectorf.c:251: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecduplicate_? vectorf.c:255: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecdestroy_? vectorf.c:258: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecviewfromoptions_? vectorf.c:262: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecgetsize_? vectorf.c:266: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecgetlocalsize_? vectorf.c:270: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetoption_? vectorf.c:274: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecresetarray_? vectorf.c:278: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecreciprocal_? vectorf.c:282: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstashsetinitialsize_? vectorf.c:286: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecconjugate_? vectorf.c:290: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecpointwisemult_? vectorf.c:296: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetrandom_? vectorf.c:301: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?veczeroentries_? vectorf.c:305: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetfromoptions_? vectorf.c:309: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetsizes_? vectorf.c:313: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetblocksize_? vectorf.c:317: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecgetblocksize_? vectorf.c:321: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetup_? vectorf.c:325: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?veccopy_? vectorf.c:330: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecswap_? vectorf.c:335: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecstashview_? rvectorf.c:3:33: error: private/fortranimpl.h: No such file or directory rvectorf.c:162: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecmaxpointwisedivide_? rvectorf.c:167: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecdot_? rvectorf.c:172: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecnorm_? rvectorf.c:176: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecnormavailable_? rvectorf.c:180: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecnormalize_? rvectorf.c:184: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecmin_? rvectorf.c:188: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vectdot_? rvectorf.c:193: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecscale_? rvectorf.c:197: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecset_? rvectorf.c:201: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecaxpy_? rvectorf.c:206: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecaxpby_? rvectorf.c:211: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecaxpbypcz_? rvectorf.c:217: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecaypx_? rvectorf.c:222: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecwaxpy_? rvectorf.c:228: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetvalues_? rvectorf.c:232: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecgetvalues_? rvectorf.c:236: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetvaluesblocked_? rvectorf.c:240: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetvalueslocal_? rvectorf.c:244: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecsetvaluesblockedlocal_? rvectorf.c:248: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecmtdot_? rvectorf.c:252: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecmdot_? rvectorf.c:256: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecmaxpy_? rvectorf.c:260: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecgetsubvector_? rvectorf.c:265: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecrestoresubvector_? rvectorf.c:270: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecplacearray_? /usr/bin/ar: veccreatef.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec/interface/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec/interface/f90-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec/impls libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec/impls/seq libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec/impls/seq/ftn-auto vseqcrf.c:3:33: error: private/fortranimpl.h: No such file or directory vseqcrf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?veccreateseq_? /usr/bin/ar: vseqcrf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec/impls/seq/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec/impls/seq/f90-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec/impls/mpi libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec/impls/mpi/ftn-auto pbvecf.c:3:33: error: private/fortranimpl.h: No such file or directory pbvecf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?veccreateghost_? pbvecf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?veccreateghostblock_? commonmpvecf.c:3:33: error: private/fortranimpl.h: No such file or directory commonmpvecf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecghostgetlocalform_? commonmpvecf.c:61: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecghostrestorelocalform_? commonmpvecf.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecghostupdatebegin_? commonmpvecf.c:69: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?vecghostupdateend_? vmpicrf.c:3:33: error: private/fortranimpl.h: No such file or directory vmpicrf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?veccreatempi_? /usr/bin/ar: pbvecf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec/impls/mpi/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec/impls/shared libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec/impls/shared/ftn-auto shvecf.c:3:33: error: private/fortranimpl.h: No such file or directory shvecf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?veccreateshared_? /usr/bin/ar: shvecf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec/impls/nest libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec/impls/nest/ftn-auto vecnestf.c:3:33: error: private/fortranimpl.h: No such file or directory vecnestf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?veccreatenest_? /usr/bin/ar: vecnestf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec/examples libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec/examples/tests libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/vec/examples/tutorials libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/is libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/is/interface libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/is/interface/ftn-auto isregf.c:3:33: error: private/fortranimpl.h: No such file or directory isregf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?iscreate_? indexf.c:3:33: error: private/fortranimpl.h: No such file or directory indexf.c:132: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isidentity_? indexf.c:136: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?issetidentity_? indexf.c:140: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?iscontiguouslocal_? indexf.c:144: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?ispermutation_? indexf.c:148: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?issetpermutation_? indexf.c:152: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isdestroy_? indexf.c:155: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isinvertpermutation_? indexf.c:159: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isgetsize_? indexf.c:163: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isgetlocalsize_? indexf.c:167: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isgetnonlocalis_? indexf.c:171: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isrestorenonlocalis_? indexf.c:175: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?issort_? indexf.c:179: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?istogeneral_? indexf.c:183: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?issorted_? indexf.c:187: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isduplicate_? indexf.c:191: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?iscopy_? indexf.c:196: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isoncomm_? indexf.c:201: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?issetblocksize_? indexf.c:205: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isgetblocksize_? /usr/bin/ar: isregf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/is/interface/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/is/interface/f90-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/is/impls libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/is/impls/general libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/is/impls/general/ftn-auto generalf.c:3:33: error: private/fortranimpl.h: No such file or directory generalf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?iscreategeneral_? generalf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isgeneralsetindices_? /usr/bin/ar: generalf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/is/impls/stride libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/is/impls/stride/ftn-auto stridef.c:3:33: error: private/fortranimpl.h: No such file or directory stridef.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isstridegetinfo_? stridef.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isstridesetstride_? stridef.c:60: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?iscreatestride_? /usr/bin/ar: stridef.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/is/impls/block libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/is/impls/block/ftn-auto blockf.c:3:33: error: private/fortranimpl.h: No such file or directory blockf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isblocksetindices_? blockf.c:61: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?iscreateblock_? blockf.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isblockgetlocalsize_? blockf.c:69: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isblockgetsize_? /usr/bin/ar: blockf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/is/impls/block/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/is/impls/f90-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/is/examples libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/is/examples/tests libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/is/examples/tutorials libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/is/utils libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/is/utils/ftn-auto isdifff.c:3:33: error: private/fortranimpl.h: No such file or directory isdifff.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isdifference_? isdifff.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?issum_? isdifff.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isexpand_? isltogf.c:3:33: error: private/fortranimpl.h: No such file or directory isltogf.c:73: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?islocaltoglobalmappingcreateis_? isltogf.c:77: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?islocaltoglobalmappingcreate_? isltogf.c:81: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?islocaltoglobalmappingblock_? isltogf.c:85: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?islocaltoglobalmappingunblock_? isltogf.c:89: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?islocaltoglobalmappingdestroy_? isltogf.c:92: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?islocaltoglobalmappingapplyis_? isltogf.c:97: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isglobaltolocalmappingapply_? iscompf.c:3:33: error: private/fortranimpl.h: No such file or directory iscompf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isequal_? iscoloringf.c:3:33: error: private/fortranimpl.h: No such file or directory iscoloringf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?iscoloringdestroy_? iscoloringf.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?ispartitioningtonumbering_? iscoloringf.c:69: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?ispartitioningcount_? iscoloringf.c:73: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?isallgather_? iscoloringf.c:77: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?iscomplement_? /usr/bin/ar: isdifff.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/is/utils/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/is/utils/f90-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/pf libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/pf/interface libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/pf/interface/ftn-auto pff.c:3:33: error: private/fortranimpl.h: No such file or directory pff.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pfapplyvec_? pff.c:63: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pfapply_? pff.c:67: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pfview_? pff.c:72: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pfsetfromoptions_? /usr/bin/ar: pff.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/pf/impls libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/pf/impls/constant libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/pf/impls/string libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/pf/examples libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/pf/examples/tutorials libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/f90-mod libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/vec/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/interface libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/interface/ftn-auto matrixf.c:3:33: error: private/fortranimpl.h: No such file or directory matrixf.c:547: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetdiagonalblock_? matrixf.c:551: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgettrace_? matrixf.c:555: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matrealpart_? matrixf.c:559: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matimaginarypart_? matrixf.c:563: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmissingdiagonal_? matrixf.c:567: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matconjugate_? matrixf.c:571: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetrowuppertriangular_? matrixf.c:575: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matrestorerowuppertriangular_? matrixf.c:579: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetup_? matrixf.c:583: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matscalesystem_? matrixf.c:589: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matunscalesystem_? matrixf.c:595: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matusescaledform_? matrixf.c:599: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matdestroy_? matrixf.c:602: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetvalues_? matrixf.c:606: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetvaluesrowlocal_? matrixf.c:610: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetvaluesrow_? matrixf.c:614: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetvaluesstencil_? matrixf.c:618: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetstencil_? matrixf.c:622: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetvaluesblocked_? matrixf.c:626: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetvalues_? matrixf.c:630: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetvaluesbatch_? matrixf.c:634: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetlocaltoglobalmapping_? matrixf.c:640: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetlocaltoglobalmappingblock_? matrixf.c:646: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetlocaltoglobalmapping_? matrixf.c:650: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetlocaltoglobalmappingblock_? matrixf.c:654: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetvalueslocal_? matrixf.c:658: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetvaluesblockedlocal_? matrixf.c:662: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmultdiagonalblock_? matrixf.c:668: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmult_? matrixf.c:674: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmulttranspose_? matrixf.c:680: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmulthermitiantranspose_? matrixf.c:686: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmultadd_? matrixf.c:693: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmulttransposeadd_? matrixf.c:700: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmulthermitiantransposeadd_? matrixf.c:707: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmultconstrained_? matrixf.c:713: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmulttransposeconstrained_? matrixf.c:719: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsolve_? matrixf.c:725: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmatsolve_? matrixf.c:731: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matforwardsolve_? matrixf.c:737: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matbackwardsolve_? matrixf.c:743: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsolveadd_? matrixf.c:750: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsolvetranspose_? matrixf.c:756: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsolvetransposeadd_? matrixf.c:763: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsor_? matrixf.c:769: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcopy_? matrixf.c:774: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matduplicate_? matrixf.c:778: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetdiagonal_? matrixf.c:783: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetrowmin_? matrixf.c:788: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetrowminabs_? matrixf.c:793: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetrowmax_? matrixf.c:798: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetrowmaxabs_? matrixf.c:803: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetrowsum_? matrixf.c:808: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?mattranspose_? matrixf.c:812: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matistranspose_? matrixf.c:817: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?mathermitiantranspose_? matrixf.c:821: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matishermitiantranspose_? matrixf.c:826: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matpermute_? matrixf.c:832: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matequal_? matrixf.c:837: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matdiagonalscale_? matrixf.c:843: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matscale_? matrixf.c:847: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matnorm_? matrixf.c:851: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matassemblybegin_? matrixf.c:855: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matassembled_? matrixf.c:859: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matassemblyend_? matrixf.c:863: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetoption_? matrixf.c:867: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matzeroentries_? matrixf.c:871: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetsize_? matrixf.c:875: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetlocalsize_? matrixf.c:879: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetownershiprangecolumn_? matrixf.c:883: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetownershiprange_? matrixf.c:887: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matincreaseoverlap_? matrixf.c:891: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetblocksize_? matrixf.c:895: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetblocksize_? matrixf.c:899: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetunfactored_? matrixf.c:903: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetsubmatrix_? matrixf.c:909: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matstashsetinitialsize_? matrixf.c:913: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matinterpolateadd_? matrixf.c:920: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matinterpolate_? matrixf.c:926: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matrestrict_? matrixf.c:932: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetnullspace_? matrixf.c:937: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetvaluesadic_? matrixf.c:941: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetcoloring_? matrixf.c:946: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetvaluesadifor_? matrixf.c:950: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matdiagonalscalelocal_? matrixf.c:955: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetinertia_? matrixf.c:959: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matissymmetric_? matrixf.c:963: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matishermitian_? matrixf.c:967: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matissymmetricknown_? matrixf.c:971: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matishermitianknown_? matrixf.c:975: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matisstructurallysymmetric_? matrixf.c:979: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matstashgetinfo_? matrixf.c:983: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matptap_? matrixf.c:988: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matptapnumeric_? matrixf.c:994: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matptapsymbolic_? matrixf.c:999: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmatmult_? matrixf.c:1004: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmatmultsymbolic_? matrixf.c:1009: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmatmultnumeric_? matrixf.c:1015: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmatmulttranspose_? matrixf.c:1020: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetlocalsubmatrix_? matrixf.c:1026: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matrestorelocalsubmatrix_? matrixf.c:1032: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matfindzerodiagonals_? matrixf.c:1036: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matinvertblockdiagonal_? mhasf.c:3:33: error: private/fortranimpl.h: No such file or directory mhasf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?mathasoperation_? matnullf.c:3:33: error: private/fortranimpl.h: No such file or directory matnullf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matnullspacecreate_? matnullf.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matnullspacedestroy_? matnullf.c:59: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matnullspacetest_? /usr/bin/ar: matrixf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/interface/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/interface/f90-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/dense libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/dense/seq libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/dense/seq/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/dense/mpi libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/dense/mpi/ftn-auto mpidensef.c:3:33: error: private/fortranimpl.h: No such file or directory mpidensef.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matdensegetlocalmatrix_? /usr/bin/ar: mpidensef.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/dense/mpi/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/aij libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/aij/seq libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/aij/seq/csrperm libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/aij/seq/crl libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/aij/seq/bas libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/aij/seq/ftn-auto aijf.c:3:33: error: private/fortranimpl.h: No such file or directory aijf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matseqaijsetcolumnindices_? aijf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matstorevalues_? aijf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matretrievevalues_? aijf.c:74: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matseqaijsetpreallocationcsr_? aijf.c:78: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreateseqaijwitharrays_? /usr/bin/ar: aijf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/aij/seq/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/aij/mpi libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/aij/mpi/csrperm libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/aij/mpi/crl libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/aij/mpi/ftn-auto mpiaijf.c:3:33: error: private/fortranimpl.h: No such file or directory mpiaijf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmpiaijsetpreallocationcsr_? mpiaijf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatempiaijwitharrays_? mpiaijf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmerge_? mpiaijf.c:75: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmpiaijgetlocalmat_? mpiaijf.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatempiaijwithsplitarrays_? /usr/bin/ar: mpiaijf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/aij/mpi/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/shell libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/shell/ftn-auto shellf.c:3:33: error: private/fortranimpl.h: No such file or directory shellf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matshellsetcontext_? /usr/bin/ar: shellf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/shell/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/baij libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/baij/seq libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/baij/seq/bstream libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/baij/seq/ftn-auto baijf.c:3:33: error: private/fortranimpl.h: No such file or directory baijf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matseqbaijsetcolumnindices_? baijf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreateseqbaijwitharrays_? /usr/bin/ar: baijf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/baij/seq/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/baij/mpi libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/baij/mpi/bstream libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/baij/mpi/ftn-auto mpibaijf.c:3:33: error: private/fortranimpl.h: No such file or directory mpibaijf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmpibaijsethashtablefactor_? mpibaijf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatempibaijwitharrays_? /usr/bin/ar: mpibaijf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/baij/mpi/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/adj libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/adj/mpi libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/adj/mpi/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/maij libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/is libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/is/ftn-auto matisf.c:3:33: error: private/fortranimpl.h: No such file or directory matisf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matisgetlocalmat_? matisf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreateis_? /usr/bin/ar: matisf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/sbaij libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/sbaij/seq libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/sbaij/seq/sbstream libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/sbaij/seq/ftn-auto sbaijf.c:3:33: error: private/fortranimpl.h: No such file or directory sbaijf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matseqsbaijsetcolumnindices_? sbaijf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreateseqsbaijwitharrays_? /usr/bin/ar: sbaijf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/sbaij/seq/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/sbaij/mpi libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/sbaij/mpi/sbstream libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/sbaij/mpi/ftn-auto mpisbaijf.c:3:33: error: private/fortranimpl.h: No such file or directory mpisbaijf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatempisbaijwitharrays_? /usr/bin/ar: mpisbaijf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/sbaij/mpi/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/normal libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/normal/ftn-auto normmf.c:3:33: error: private/fortranimpl.h: No such file or directory normmf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatenormal_? /usr/bin/ar: normmf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/lrc libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/lrc/ftn-auto lrcf.c:3:33: error: private/fortranimpl.h: No such file or directory lrcf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatelrc_? /usr/bin/ar: lrcf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/scatter libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/scatter/ftn-auto mscatterf.c:3:33: error: private/fortranimpl.h: No such file or directory mscatterf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matscattergetvecscatter_? mscatterf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matscattersetvecscatter_? /usr/bin/ar: mscatterf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/blockmat libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/blockmat/seq libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/composite libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/composite/ftn-auto mcompositef.c:3:33: error: private/fortranimpl.h: No such file or directory mcompositef.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcompositeaddmat_? /usr/bin/ar: mcompositef.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/mffd libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/mffd/ftn-auto mffddeff.c:3:33: error: private/fortranimpl.h: No such file or directory mffddeff.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmffddssetumin_? wpf.c:3:33: error: private/fortranimpl.h: No such file or directory wpf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmffdwpsetcomputenormu_? mffdf.c:3:33: error: private/fortranimpl.h: No such file or directory mffdf.c:82: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatemffd_? mffdf.c:86: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmffdgeth_? mffdf.c:90: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmffdsetperiod_? mffdf.c:94: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmffdsetfunctionerror_? mffdf.c:98: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmffdaddnullspace_? mffdf.c:103: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmffdsethhistory_? mffdf.c:107: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmffdresethhistory_? mffdf.c:111: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmffdsetbase_? mffdf.c:117: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmffdcheckpositivity_? /usr/bin/ar: mffddeff.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/mffd/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/transpose libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/transpose/ftn-auto transmf.c:3:33: error: private/fortranimpl.h: No such file or directory transmf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatetranspose_? /usr/bin/ar: transmf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/python libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/python/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/submat libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/submat/ftn-auto submatf.c:3:33: error: private/fortranimpl.h: No such file or directory submatf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatesubmatrix_? submatf.c:53: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsubmatrixupdate_? /usr/bin/ar: submatf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/localref libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/localref/ftn-auto mlocalreff.c:3:33: error: private/fortranimpl.h: No such file or directory mlocalreff.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatelocalref_? /usr/bin/ar: mlocalreff.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/nest libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/nest/ftn-auto matnestf.c:3:33: error: private/fortranimpl.h: No such file or directory matnestf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matnestsetsubmats_? matnestf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatenest_? /usr/bin/ar: matnestf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/fft libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/fft/ftn-auto fftf.c:3:33: error: private/fortranimpl.h: No such file or directory fftf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatefft_? /usr/bin/ar: fftf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/impls/ij libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/examples libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/examples/tests libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/examples/tutorials libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/utils libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/utils/ftn-auto zerodiagf.c:3:33: error: private/fortranimpl.h: No such file or directory zerodiagf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matreorderfornonzerodiagonal_? gcreatef.c:3:33: error: private/fortranimpl.h: No such file or directory gcreatef.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreate_? gcreatef.c:61: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetsizes_? gcreatef.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetfromoptions_? gcreatef.c:69: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetuppreallocation_? multequalf.c:3:33: error: private/fortranimpl.h: No such file or directory multequalf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmultequal_? multequalf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmultaddequal_? multequalf.c:67: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmulttransposeequal_? multequalf.c:72: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matmulttransposeaddequal_? axpyf.c:3:33: error: private/fortranimpl.h: No such file or directory axpyf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?mataxpy_? axpyf.c:67: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matshift_? axpyf.c:71: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matdiagonalset_? axpyf.c:76: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?mataypx_? axpyf.c:81: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcomputeexplicitoperator_? getcolvf.c:3:33: error: private/fortranimpl.h: No such file or directory getcolvf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetcolumnvector_? getcolvf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetcolumnnorms_? /usr/bin/ar: zerodiagf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/utils/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/matfd libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/matfd/ftn-auto fdmatrixf.c:3:33: error: private/fortranimpl.h: No such file or directory fdmatrixf.c:67: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matfdcoloringsetparameters_? fdmatrixf.c:71: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matfdcoloringsetfromoptions_? fdmatrixf.c:75: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matfdcoloringcreate_? fdmatrixf.c:80: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matfdcoloringdestroy_? fdmatrixf.c:83: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matfdcoloringapply_? fdmatrixf.c:89: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matfdcoloringapplyts_? /usr/bin/ar: fdmatrixf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/matfd/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/partition libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/partition/impls libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/partition/ftn-auto partitionf.c:3:33: error: private/fortranimpl.h: No such file or directory partitionf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matpartitioningapply_? partitionf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matpartitioningsetadjacency_? partitionf.c:71: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matpartitioningdestroy_? partitionf.c:74: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matpartitioningcreate_? partitionf.c:78: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matpartitioningsetfromoptions_? /usr/bin/ar: partitionf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/partition/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/coarsen libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/coarsen/impls libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/coarsen/impls/mis libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/coarsen/impls/hem libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/order libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/order/ftn-auto sorderf.c:3:33: error: private/fortranimpl.h: No such file or directory sorderf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matorderingregisterdestroy_? /usr/bin/ar: sorderf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/order/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/color libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/color/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/f90-mod libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/mat/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/ao libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/ao/interface libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/ao/interface/ftn-auto aof.c:3:33: error: private/fortranimpl.h: No such file or directory aof.c:77: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?aopetsctoapplicationis_? aof.c:82: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?aoapplicationtopetscis_? aof.c:87: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?aopetsctoapplication_? aof.c:91: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?aoapplicationtopetsc_? aof.c:95: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?aopetsctoapplicationpermuteint_? aof.c:99: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?aoapplicationtopetscpermuteint_? aof.c:103: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?aopetsctoapplicationpermutereal_? aof.c:107: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?aoapplicationtopetscpermutereal_? /usr/bin/ar: aof.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/ao/interface/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/ao/impls libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/ao/impls/basic libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/ao/impls/basic/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/ao/impls/mapping libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/ao/impls/mapping/ftn-auto aomappingf.c:3:33: error: private/fortranimpl.h: No such file or directory aomappingf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?aomappinghaspetscindex_? /usr/bin/ar: aomappingf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/ao/impls/mapping/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/ao/impls/memscalable libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/ao/examples libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/ao/examples/tests libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/ao/examples/tutorials libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/da libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/da/utils libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/da/ftn-auto dacreatef.c:3:33: error: private/fortranimpl.h: No such file or directory dacreatef.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdacreate_? dainterpf.c:3:33: error: private/fortranimpl.h: No such file or directory dainterpf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmgetinterpolationscale_? dagtonaf.c:3:33: error: private/fortranimpl.h: No such file or directory dagtonaf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdaglobaltonaturalallcreate_? dagtonaf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdanaturalalltoglobalcreate_? dagetarrayf.c:3:33: error: private/fortranimpl.h: No such file or directory dagetarrayf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdavecrestorearray_? dagetarrayf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdavecrestorearraydof_? dagtolf.c:3:33: error: private/fortranimpl.h: No such file or directory dagtolf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdaglobaltonaturalbegin_? dagtolf.c:63: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdaglobaltonaturalend_? dagtolf.c:69: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdanaturaltoglobalbegin_? dagtolf.c:75: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdanaturaltoglobalend_? daltolf.c:3:33: error: private/fortranimpl.h: No such file or directory daltolf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdalocaltolocalbegin_? daltolf.c:53: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdalocaltolocalend_? fddaf.c:3:33: error: private/fortranimpl.h: No such file or directory fddaf.c:48: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetblockfills_? fddaf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matsetdm_? gr1f.c:3:33: error: private/fortranimpl.h: No such file or directory gr1f.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetuniformcoordinates_? daindexf.c:3:33: error: private/fortranimpl.h: No such file or directory daindexf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdagetao_? dadistf.c:3:33: error: private/fortranimpl.h: No such file or directory dadistf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdacreatenaturalvector_? da2f.c:3:33: error: private/fortranimpl.h: No such file or directory da2f.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdaformfunction_? da2f.c:68: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdaformfunction1_? da2f.c:74: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdaformfunctioni1_? da2f.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdaformfunctionib1_? da2f.c:84: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdacomputejacobian1_? daghostf.c:3:33: error: private/fortranimpl.h: No such file or directory daghostf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdagetghostcorners_? dalocalf.c:3:33: error: private/fortranimpl.h: No such file or directory dalocalf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmgetlocalvector_? dalocalf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmrestorelocalvector_? dalocalf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmgetglobalvector_? dalocalf.c:74: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmclearglobalvectors_? dalocalf.c:78: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmrestoreglobalvector_? daf.c:3:33: error: private/fortranimpl.h: No such file or directory daf.c:92: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetdim_? daf.c:96: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetsizes_? daf.c:100: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetnumprocs_? daf.c:104: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetboundarytype_? daf.c:108: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetdof_? daf.c:112: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetstenciltype_? daf.c:116: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetstencilwidth_? daf.c:120: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetownershipranges_? daf.c:124: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetinterpolationtype_? daf.c:128: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdagetinterpolationtype_? daf.c:133: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetrefinementfactor_? dacornf.c:3:33: error: private/fortranimpl.h: No such file or directory dacornf.c:82: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetcoordinates_? dacornf.c:87: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdasetghostedcoordinates_? dacornf.c:92: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdagetcoordinates_? dacornf.c:96: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdagetcoordinateda_? dacornf.c:100: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdagetghostedcoordinates_? dacornf.c:104: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdagetcorners_? dacornf.c:108: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdagetlocalboundingbox_? dacornf.c:112: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdagetboundingbox_? dacornf.c:116: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdagetreducedda_? /usr/bin/ar: dacreatef.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/da/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/da/f90-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/adda libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/adda/examples libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/adda/examples/tests libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/adda/ftn-auto addaf.c:3:33: error: private/fortranimpl.h: No such file or directory addaf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmaddagetmatrixns_? addaf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmaddasetrefinement_? addaf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmaddagetcorners_? addaf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmaddagetghostcorners_? /usr/bin/ar: addaf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/sliced libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/composite libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/composite/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/composite/f90-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/redundant libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/complex libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/complex/examples libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/complex/examples/tests libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/complex/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/complex/f90-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/shell libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/patch libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/patch/examples libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/impls/patch/examples/tests libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/f90-mod libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/interface libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/interface/ftn-auto dmf.c:3:33: error: private/fortranimpl.h: No such file or directory dmf.c:197: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmcreate_? dmf.c:201: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmdestroy_? dmf.c:204: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmsetup_? dmf.c:208: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmsetfromoptions_? dmf.c:212: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmcreateglobalvector_? dmf.c:216: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmcreatelocalvector_? dmf.c:220: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmgetlocaltoglobalmapping_? dmf.c:224: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmgetlocaltoglobalmappingblock_? dmf.c:228: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmgetblocksize_? dmf.c:232: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmgetinterpolation_? dmf.c:237: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmgetinjection_? dmf.c:242: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmsetmatrixpreallocateonly_? dmf.c:246: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmrefine_? dmf.c:251: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmgetrefinelevel_? dmf.c:255: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmglobaltolocalbegin_? dmf.c:261: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmglobaltolocalend_? dmf.c:267: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmlocaltoglobalbegin_? dmf.c:273: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmlocaltoglobalend_? dmf.c:279: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmcomputejacobiandefault_? dmf.c:286: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmcoarsen_? dmf.c:291: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmgetaggregates_? dmf.c:296: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmsetapplicationcontext_? dmf.c:300: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmgetapplicationcontext_? dmf.c:304: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmsetinitialguess_? dmf.c:308: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmsetfunction_? dmf.c:312: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmsetjacobian_? dmf.c:316: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmcomputeinitialguess_? dmf.c:321: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmhasinitialguess_? dmf.c:325: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmhasfunction_? dmf.c:329: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmhasjacobian_? dmf.c:333: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmcomputefunction_? dmf.c:339: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dmcomputejacobian_? /usr/bin/ar: dmf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/interface/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/examples libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/examples/tests libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/dm/examples/tutorials libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/interface libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/interface/ftn-auto pcsetf.c:3:33: error: private/fortranimpl.h: No such file or directory pcsetf.c:67: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcregisterdestroy_? pcsetf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsetfromoptions_? pcsetf.c:74: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsetdm_? pcsetf.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcgetdm_? pcsetf.c:83: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsetapplicationcontext_? pcsetf.c:87: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcgetapplicationcontext_? preconf.c:3:33: error: private/fortranimpl.h: No such file or directory preconf.c:157: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcreset_? preconf.c:161: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcdestroy_? preconf.c:164: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsetdiagonalscale_? preconf.c:169: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcdiagonalscaleleft_? preconf.c:175: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcdiagonalscaleright_? preconf.c:181: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pccreate_? preconf.c:185: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcapply_? preconf.c:191: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcapplysymmetricleft_? preconf.c:197: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcapplysymmetricright_? preconf.c:203: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcapplytranspose_? preconf.c:209: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcapplytransposeexists_? preconf.c:213: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcapplybaorab_? preconf.c:220: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcapplybaorabtranspose_? preconf.c:227: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcapplyrichardsonexists_? preconf.c:231: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcapplyrichardson_? preconf.c:239: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsetup_? preconf.c:243: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsetuponblocks_? preconf.c:247: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsetoperators_? preconf.c:253: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorgetmatrix_? preconf.c:257: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcpresolve_? preconf.c:262: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcpostsolve_? preconf.c:267: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsetinitialguessnonzero_? preconf.c:271: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pccomputeexplicitoperator_? preconf.c:275: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsetcoordinates_? /usr/bin/ar: pcsetf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/interface/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/jacobi libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/jacobi/ftn-auto jacobif.c:3:33: error: private/fortranimpl.h: No such file or directory jacobif.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcjacobisetuseabs_? jacobif.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcjacobisetuserowmax_? jacobif.c:60: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcjacobisetuserowsum_? /usr/bin/ar: jacobif.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/none libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/sor libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/sor/ftn-auto sorf.c:3:33: error: private/fortranimpl.h: No such file or directory sorf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsorsetsymmetric_? sorf.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsorsetomega_? sorf.c:60: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcsorsetiterations_? /usr/bin/ar: sorf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/shell libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/shell/ftn-auto shellpcf.c:3:33: error: private/fortranimpl.h: No such file or directory shellpcf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcshellsetcontext_? /usr/bin/ar: shellpcf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/shell/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/bjacobi libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/bjacobi/ftn-auto bjacobif.c:3:33: error: private/fortranimpl.h: No such file or directory bjacobif.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcbjacobisetusetruelocal_? bjacobif.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcbjacobisettotalblocks_? bjacobif.c:60: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcbjacobisetlocalblocks_? /usr/bin/ar: bjacobif.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/bjacobi/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/mg libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/mg/ftn-auto mgfuncf.c:3:33: error: private/fortranimpl.h: No such file or directory mgfuncf.c:93: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmggetcoarsesolve_? mgfuncf.c:97: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsetinterpolation_? mgfuncf.c:102: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsetrestriction_? mgfuncf.c:107: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsetrscale_? mgfuncf.c:112: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmggetsmoother_? mgfuncf.c:116: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmggetsmootherup_? mgfuncf.c:120: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmggetsmootherdown_? mgfuncf.c:124: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsetcyclesonlevel_? mgfuncf.c:128: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsetrhs_? mgfuncf.c:133: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsetx_? mgfuncf.c:138: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsetr_? mgf.c:3:33: error: private/fortranimpl.h: No such file or directory mgf.c:77: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmggetlevels_? mgf.c:81: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsettype_? mgf.c:85: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsetcycletype_? mgf.c:89: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgmultiplicativesetcycles_? mgf.c:93: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsetgalerkin_? mgf.c:97: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmggetgalerkin_? mgf.c:101: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsetnumbersmoothdown_? mgf.c:105: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcmgsetnumbersmoothup_? /usr/bin/ar: mgfuncf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/mg/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/eisens libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/eisens/ftn-auto eisenf.c:3:33: error: private/fortranimpl.h: No such file or directory eisenf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pceisenstatsetomega_? eisenf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pceisenstatnodiagonalscaling_? /usr/bin/ar: eisenf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/asm libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/asm/ftn-auto asmf.c:3:33: error: private/fortranimpl.h: No such file or directory asmf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcasmsetoverlap_? asmf.c:61: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcasmsettype_? asmf.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcasmsetsortindices_? asmf.c:69: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcasmcreatesubdomains2d_? /usr/bin/ar: asmf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/asm/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/ksp libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/ksp/ftn-auto pckspf.c:3:33: error: private/fortranimpl.h: No such file or directory pckspf.c:48: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pckspsetusetrue_? pckspf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pckspgetksp_? /usr/bin/ar: pckspf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/composite libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/composite/ftn-auto compositef.c:3:33: error: private/fortranimpl.h: No such file or directory compositef.c:58: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pccompositesettype_? compositef.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pccompositespecialsetalpha_? compositef.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pccompositegetpc_? compositef.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pccompositesetusetrue_? /usr/bin/ar: compositef.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/composite/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/redundant libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/redundant/ftn-auto redundantf.c:3:33: error: private/fortranimpl.h: No such file or directory redundantf.c:58: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcredundantsetnumber_? redundantf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcredundantsetscatter_? redundantf.c:68: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcredundantgetksp_? redundantf.c:72: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcredundantgetoperators_? /usr/bin/ar: redundantf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/is libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/is/nn libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/pbjacobi libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/mat libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/tfs libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/fieldsplit libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/fieldsplit/ftn-auto fieldsplitf.c:3:33: error: private/fortranimpl.h: No such file or directory fieldsplitf.c:68: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfieldsplitsetfields_? fieldsplitf.c:72: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfieldsplitsetis_? fieldsplitf.c:77: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfieldsplitgetis_? fieldsplitf.c:81: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfieldsplitsetblocksize_? fieldsplitf.c:85: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfieldsplitschurprecondition_? fieldsplitf.c:90: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfieldsplitsettype_? /usr/bin/ar: fieldsplitf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/fieldsplit/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/factor libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/factor/lu libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/factor/ilu libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/factor/icc libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/factor/cholesky libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/factor/cholesky/ftn-auto choleskyf.c:3:33: error: private/fortranimpl.h: No such file or directory choleskyf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetreuseordering_? /usr/bin/ar: choleskyf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/factor/ftn-auto factorf.c:3:33: error: private/fortranimpl.h: No such file or directory factorf.c:97: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetupmatsolverpackage_? factorf.c:101: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetzeropivot_? factorf.c:105: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetshifttype_? factorf.c:109: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetshiftamount_? factorf.c:113: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetlevels_? factorf.c:117: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetallowdiagonalfill_? factorf.c:121: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorreorderfornonzerodiagonal_? factorf.c:125: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetfill_? factorf.c:129: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetuseinplace_? factorf.c:133: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetcolumnpivot_? factorf.c:137: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetpivotinblocks_? factorf.c:141: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcfactorsetreusefill_? /usr/bin/ar: factorf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/factor/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/galerkin libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/galerkin/ftn-auto galerkinf.c:3:33: error: private/fortranimpl.h: No such file or directory galerkinf.c:53: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcgalerkinsetrestriction_? galerkinf.c:58: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcgalerkinsetinterpolation_? galerkinf.c:63: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcgalerkingetksp_? /usr/bin/ar: galerkinf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/openmp libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/asa libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/cp libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/wb libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/wb/ftn-auto wbf.c:3:33: error: private/fortranimpl.h: No such file or directory wbf.c:43: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcexoticsettype_? /usr/bin/ar: wbf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/python libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/python/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/lsc libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/redistribute libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/redistribute/ftn-auto redistributef.c:3:33: error: private/fortranimpl.h: No such file or directory redistributef.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcredistributegetksp_? /usr/bin/ar: redistributef.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/gasm libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/gasm/ftn-auto gasmf.c:3:33: error: private/fortranimpl.h: No such file or directory gasmf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcgasmsetoverlap_? gasmf.c:61: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcgasmsettype_? gasmf.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcgasmsetsortindices_? gasmf.c:69: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?pcgasmcreatesubdomains2d_? /usr/bin/ar: gasmf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/svd libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/impls/gamg libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/examples libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/examples/tests libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/pc/examples/tutorials libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/interface libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/interface/ftn-auto itcreatef.c:3:33: error: private/fortranimpl.h: No such file or directory itcreatef.c:92: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetnormtype_? itcreatef.c:96: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetchecknormiteration_? itcreatef.c:100: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetlagnorm_? itcreatef.c:104: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetsupportednorm_? itcreatef.c:108: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetnormtype_? itcreatef.c:113: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetoperators_? itcreatef.c:119: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetoperators_? itcreatef.c:123: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspcreate_? itcreatef.c:127: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspregisterdestroy_? itcreatef.c:130: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetnullspace_? itcreatef.c:135: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetnullspace_? eigef.c:3:33: error: private/fortranimpl.h: No such file or directory eigef.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspcomputeexplicitoperator_? eigef.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspcomputeeigenvaluesexplicitly_? iterativf.c:3:33: error: private/fortranimpl.h: No such file or directory iterativf.c:87: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetresidualnorm_? iterativf.c:91: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetiterationnumber_? iterativf.c:95: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspdefaultconvergedsetuirnorm_? iterativf.c:99: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspdefaultconvergedsetumirnorm_? iterativf.c:103: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetconvergedreason_? iterativf.c:107: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetdm_? iterativf.c:112: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetdmactive_? iterativf.c:116: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetdm_? iterativf.c:120: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetapplicationcontext_? iterativf.c:124: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetapplicationcontext_? xmonf.c:3:33: error: private/fortranimpl.h: No such file or directory xmonf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspmonitorlgdestroy_? xmonf.c:50: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspmonitorlgrangedestroy_? itfuncf.c:3:33: error: private/fortranimpl.h: No such file or directory itfuncf.c:202: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspcomputeextremesingularvalues_? itfuncf.c:206: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspcomputeeigenvalues_? itfuncf.c:210: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetuponblocks_? itfuncf.c:214: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetup_? itfuncf.c:218: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsolve_? itfuncf.c:225: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsolvetranspose_? itfuncf.c:231: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspreset_? itfuncf.c:235: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspdestroy_? itfuncf.c:238: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetpcside_? itfuncf.c:242: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetpcside_? itfuncf.c:247: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgettolerances_? itfuncf.c:251: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsettolerances_? itfuncf.c:255: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetinitialguessnonzero_? itfuncf.c:259: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetinitialguessnonzero_? itfuncf.c:263: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspseterrorifnotconverged_? itfuncf.c:267: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgeterrorifnotconverged_? itfuncf.c:271: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetinitialguessknoll_? itfuncf.c:275: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetinitialguessknoll_? itfuncf.c:279: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetcomputesingularvalues_? itfuncf.c:283: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetcomputesingularvalues_? itfuncf.c:287: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetcomputeeigenvalues_? itfuncf.c:291: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetcomputeeigenvalues_? itfuncf.c:295: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetrhs_? itfuncf.c:299: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetsolution_? itfuncf.c:303: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetpc_? itfuncf.c:308: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetpc_? itfuncf.c:312: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspmonitor_? itfuncf.c:316: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspmonitorcancel_? itfuncf.c:320: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetresidualhistory_? itfuncf.c:324: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetdiagonalscale_? itfuncf.c:328: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetdiagonalscale_? itfuncf.c:332: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetdiagonalscalefix_? itfuncf.c:336: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgetdiagonalscalefix_? itclf.c:3:33: error: private/fortranimpl.h: No such file or directory itclf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspsetfromoptions_? itresf.c:3:33: error: private/fortranimpl.h: No such file or directory itresf.c:48: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspinitialresidual_? itresf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspunwindpreconditioner_? /usr/bin/ar: itcreatef.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/interface/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/interface/f90-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/cr libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/bcgs libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/bcgs/fbcgs libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/bcgs/fbcgsr libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/bcgsl libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/bcgsl/ftn-auto bcgslf.c:3:33: error: private/fortranimpl.h: No such file or directory bcgslf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspbcgslsetxres_? bcgslf.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspbcgslsetpol_? bcgslf.c:60: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspbcgslsetell_? /usr/bin/ar: bcgslf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/cg libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/cg/cgne libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/cg/gltr libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/cg/gltr/ftn-auto gltrf.c:3:33: error: private/fortranimpl.h: No such file or directory gltrf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgltrsetradius_? gltrf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgltrgetnormd_? gltrf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgltrgetobjfcn_? gltrf.c:74: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgltrgetmineig_? gltrf.c:78: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgltrgetlambda_? /usr/bin/ar: gltrf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/cg/nash libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/cg/nash/ftn-auto nashf.c:3:33: error: private/fortranimpl.h: No such file or directory nashf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspnashsetradius_? nashf.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspnashgetnormd_? nashf.c:60: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspnashgetobjfcn_? /usr/bin/ar: nashf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/cg/stcg libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/cg/stcg/ftn-auto stcgf.c:3:33: error: private/fortranimpl.h: No such file or directory stcgf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspstcgsetradius_? stcgf.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspstcggetnormd_? stcgf.c:60: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspstcggetobjfcn_? /usr/bin/ar: stcgf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/cg/ftn-auto cgtypef.c:3:33: error: private/fortranimpl.h: No such file or directory cgtypef.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspcgsettype_? cgtypef.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspcgusesinglereduction_? /usr/bin/ar: cgtypef.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/cgs libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/gmres libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/gmres/lgmres libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/gmres/fgmres libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/gmres/fgmres/ftn-auto modpcff.c:3:33: error: private/fortranimpl.h: No such file or directory modpcff.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspfgmresmodifypcnochange_? modpcff.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspfgmresmodifypcksp_? /usr/bin/ar: modpcff.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/gmres/fgmres/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/gmres/dgmres libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/gmres/pgmres libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/gmres/ftn-auto gmresf.c:3:33: error: private/fortranimpl.h: No such file or directory gmresf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgmressetcgsrefinementtype_? gmresf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgmresgetcgsrefinementtype_? gmresf.c:71: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgmressetrestart_? gmresf.c:75: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgmresgetrestart_? gmresf.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgmressethaptol_? gmpref.c:3:33: error: private/fortranimpl.h: No such file or directory gmpref.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspgmressetpreallocatevectors_? /usr/bin/ar: gmresf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/cheby libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/cheby/ftn-auto chebyf.c:3:33: error: private/fortranimpl.h: No such file or directory chebyf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspchebychevseteigenvalues_? chebyf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspchebychevsetestimateeigenvalues_? /usr/bin/ar: chebyf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/rich libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/rich/ftn-auto richscalef.c:3:33: error: private/fortranimpl.h: No such file or directory richscalef.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?ksprichardsonsetscale_? richscalef.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?ksprichardsonsetselfscale_? /usr/bin/ar: richscalef.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/lsqr libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/preonly libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/tcqmr libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/tfqmr libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/qcg libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/qcg/ftn-auto qcgf.c:3:33: error: private/fortranimpl.h: No such file or directory qcgf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspqcgsettrustregionradius_? qcgf.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspqcggettrialstepnorm_? qcgf.c:60: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?kspqcggetquadratic_? /usr/bin/ar: qcgf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/bicg libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/minres libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/symmlq libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/lcd libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/ibcgs libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/python libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/python/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/gcr libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/impls/specest libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/examples libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/examples/tests libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/examples/tutorials makefile:7: *** missing separator. Stop. libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/utils libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/ksp/utils/ftn-auto schurmf.c:3:33: error: private/fortranimpl.h: No such file or directory schurmf.c:58: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreateschurcomplement_? schurmf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matschurcomplementgetksp_? schurmf.c:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matschurcomplementupdate_? schurmf.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matgetschurcomplement_? /usr/bin/ar: schurmf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ksp/f90-mod libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/interface libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/interface/noise libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/interface/ftn-auto snesf.c:3:33: error: private/fortranimpl.h: No such file or directory snesf.c:277: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesseterrorifnotconverged_? snesf.c:281: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgeterrorifnotconverged_? snesf.c:285: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetfunctiondomainerror_? snesf.c:289: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetfromoptions_? snesf.c:293: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetcomputeapplicationcontext_? snesf.c:297: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetapplicationcontext_? snesf.c:301: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetapplicationcontext_? snesf.c:305: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetiterationnumber_? snesf.c:309: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetfunctionnorm_? snesf.c:313: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetnonlinearstepfailures_? snesf.c:317: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetmaxnonlinearstepfailures_? snesf.c:321: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetmaxnonlinearstepfailures_? snesf.c:325: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetnumberfunctionevals_? snesf.c:329: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetlinearsolvefailures_? snesf.c:333: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetmaxlinearsolvefailures_? snesf.c:337: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetmaxlinearsolvefailures_? snesf.c:341: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetlinearsolveiterations_? snesf.c:345: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetksp_? snesf.c:349: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetksp_? snesf.c:354: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snescreate_? snesf.c:358: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snescomputefunction_? snesf.c:364: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snescomputejacobian_? snesf.c:369: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetup_? snesf.c:373: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesreset_? snesf.c:377: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesdestroy_? snesf.c:380: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetlagpreconditioner_? snesf.c:384: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetgridsequence_? snesf.c:388: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetlagpreconditioner_? snesf.c:392: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetlagjacobian_? snesf.c:396: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetlagjacobian_? snesf.c:400: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessettolerances_? snesf.c:404: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgettolerances_? snesf.c:408: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessettrustregiontolerance_? snesf.c:412: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesmonitor_? snesf.c:416: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetconvergedreason_? snesf.c:420: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetconvergencehistory_? snesf.c:424: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesdefaultupdate_? snesf.c:428: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesregisterdestroy_? snesf.c:431: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetsolution_? snesf.c:435: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetsolutionupdate_? snesf.c:439: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?sneskspsetuseew_? snesf.c:443: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?sneskspgetuseew_? snesf.c:447: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?sneskspsetparametersew_? snesf.c:452: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?sneskspgetparametersew_? snesf.c:457: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetdm_? snesf.c:462: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetdm_? snesf.c:466: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snessetpc_? snesf.c:471: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesgetpc_? snesutf.c:3:33: error: private/fortranimpl.h: No such file or directory snesutf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesdefaultgetwork_? /usr/bin/ar: snesf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/interface/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/interface/f90-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/mf libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/mf/ftn-auto snesmfjf.c:3:33: error: private/fortranimpl.h: No such file or directory snesmfjf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?matcreatesnesmf_? /usr/bin/ar: snesmfjf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls/ksponly libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls/ls libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls/ls/ftn-auto lsparamsf.c:3:33: error: private/fortranimpl.h: No such file or directory lsparamsf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?sneslinesearchsetparams_? /usr/bin/ar: lsparamsf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls/tr libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls/test libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls/richardson libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls/python libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls/python/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls/vi libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls/vi/ss libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls/vi/rs libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls/vi/ftn-auto vif.c:3:33: error: private/fortranimpl.h: No such file or directory vif.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesvisetvariablebounds_? /usr/bin/ar: vif.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls/ngmres libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls/qn libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls/shell libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls/shell/ftn-auto snesshellf.c:3:33: error: private/fortranimpl.h: No such file or directory snesshellf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snesshellsetcontext_? /usr/bin/ar: snesshellf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls/shell/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls/ncg libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls/fas libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls/gs libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls/ms libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/impls/nasm libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/examples libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/examples/tests libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/examples/tutorials libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/examples/tutorials/ex10d libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/utils libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/f90-mod libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/linesearch libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/linesearch/interface libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/linesearch/interface/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/linesearch/impls libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/linesearch/impls/basic libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/linesearch/impls/l2 libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/linesearch/impls/cp libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/linesearch/impls/shell libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/linesearch/impls/shell/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/snes/linesearch/impls/bt libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/interface libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/interface/ftn-auto tsf.c:3:33: error: private/fortranimpl.h: No such file or directory tsf.c:237: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssetfromoptions_? tsf.c:241: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tscomputerhsjacobian_? tsf.c:246: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tscomputerhsfunction_? tsf.c:252: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tscomputeifunction_? tsf.c:259: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tscomputeijacobian_? tsf.c:265: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssetapplicationcontext_? tsf.c:269: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgetapplicationcontext_? tsf.c:273: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgettimestepnumber_? tsf.c:277: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssetinitialtimestep_? tsf.c:281: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssettimestep_? tsf.c:285: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssetexactfinaltime_? tsf.c:289: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgettimestep_? tsf.c:293: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgetsolution_? tsf.c:297: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssetproblemtype_? tsf.c:301: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssetup_? tsf.c:305: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsreset_? tsf.c:309: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsdestroy_? tsf.c:312: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgetsnes_? tsf.c:316: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgetksp_? tsf.c:320: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgetduration_? tsf.c:324: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssetduration_? tsf.c:328: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssetsolution_? tsf.c:333: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsprestep_? tsf.c:337: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tspoststep_? tsf.c:341: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsmonitordefault_? tsf.c:346: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssetretainstages_? tsf.c:350: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsinterpolate_? tsf.c:355: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsstep_? tsf.c:359: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssolve_? tsf.c:364: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsmonitor_? tsf.c:369: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgettime_? tsf.c:373: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssettime_? tsf.c:377: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssetdm_? tsf.c:382: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgetdm_? tsf.c:386: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snestsformfunction_? tsf.c:392: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?snestsformjacobian_? tsf.c:397: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgetconvergedreason_? tsf.c:402: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgetnonlinearsolveiterations_? tsf.c:406: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsgetlinearsolveiterations_? tsf.c:410: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsvisetvariablebounds_? /usr/bin/ar: tsf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/interface/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/impls libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/impls/explicit libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/impls/explicit/euler libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/impls/explicit/rk libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/impls/explicit/rk/ftn-auto rkf.c:3:33: error: private/fortranimpl.h: No such file or directory rkf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsrksettolerance_? /usr/bin/ar: rkf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/impls/explicit/ssp libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/impls/explicit/ssp/ftn-auto sspf.c:3:33: error: private/fortranimpl.h: No such file or directory sspf.c:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssspsetnumstages_? sspf.c:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tssspgetnumstages_? /usr/bin/ar: sspf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/impls/explicit/ssp/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/impls/implicit libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/impls/implicit/theta libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/impls/implicit/theta/ftn-auto thetaf.c:3:33: error: private/fortranimpl.h: No such file or directory thetaf.c:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsthetagettheta_? thetaf.c:61: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsthetasettheta_? thetaf.c:65: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsthetagetendpoint_? thetaf.c:69: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsthetasetendpoint_? /usr/bin/ar: thetaf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/impls/implicit/alpha libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/impls/implicit/alpha/ftn-auto alphaf.c:3:33: error: private/fortranimpl.h: No such file or directory alphaf.c:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsalphasetradius_? alphaf.c:56: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsalphasetparams_? alphaf.c:60: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tsalphagetparams_? /usr/bin/ar: alphaf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/impls/implicit/gl libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/impls/pseudo libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/impls/pseudo/ftn-auto posindepf.c:3:33: error: private/fortranimpl.h: No such file or directory posindepf.c:62: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tspseudocomputetimestep_? posindepf.c:66: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tspseudoverifytimestep_? posindepf.c:71: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tspseudosettimestepincrement_? posindepf.c:75: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tspseudosetmaxtimestep_? posindepf.c:79: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?tspseudoincrementdtfrominitialdt_? /usr/bin/ar: posindepf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/impls/python libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/impls/python/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/impls/arkimex libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/impls/arkimex/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/impls/rosw libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/impls/rosw/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/examples libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/examples/tests libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/examples/tutorials libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/examples/tutorials/phasefield libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/examples/tutorials/advection-diffusion-reaction libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/f90-mod libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/characteristic libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/characteristic/interface libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/characteristic/interface/ftn-auto characteristicf.c:3:33: error: private/fortranimpl.h: No such file or directory characteristicf.c:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?characteristicsetup_? /usr/bin/ar: characteristicf.o: No such file or directory libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/characteristic/impls libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/characteristic/impls/da libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/characteristic/examples libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/characteristic/examples/tutorials libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/adapt libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/adapt/interface libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/adapt/impls libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/adapt/impls/basic libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/adapt/impls/cfl libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/adapt/impls/none libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/ts/utils libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/contrib libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/contrib/fun3d libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/contrib/fun3d/comp libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/contrib/fun3d/incomp libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/benchmarks libfast in: /home/zlwei/soft/mercurial/petsc-dev/src/docs libfast in: /home/zlwei/soft/mercurial/petsc-dev/include libfast in: /home/zlwei/soft/mercurial/petsc-dev/include/finclude libfast in: /home/zlwei/soft/mercurial/petsc-dev/include/finclude/ftn-auto libfast in: /home/zlwei/soft/mercurial/petsc-dev/include/finclude/ftn-custom libfast in: /home/zlwei/soft/mercurial/petsc-dev/include/petsc-private libfast in: /home/zlwei/soft/mercurial/petsc-dev/include/sieve libfast in: /home/zlwei/soft/mercurial/petsc-dev/tutorials Completed building libraries ========================================= ******************************************************************** Error during compile, check arch-linux2-c-debug/conf/make.log Send it and arch-linux2-c-debug/conf/configure.log to petsc-maint at mcs.anl.gov ******************************************************************** From bsmith at mcs.anl.gov Thu Nov 8 12:58:34 2012 From: bsmith at mcs.anl.gov (Barry Smith) Date: Thu, 8 Nov 2012 12:58:34 -0600 Subject: [petsc-users] Conjugate transpose for rectangular complex matrices In-Reply-To: References: Message-ID: We need the entire error message and stack frames to see what happened. Cut and paste all the output and send it to petsc-maint at mcs.anl.gov On Nov 8, 2012, at 11:55 AM, Ganesh Hegde wrote: > Hi, > I have been using the MatHermitianTranspose method to get the conjugate transpose for complex square matrices. > To optimize code, I needed to make my matrix rectangular. > Doing so and using the same function call gave me the following error with code 60: > 'Nonconforming object sizes' > I then decided to do this in two steps - get the conjugate of the rectangular complex matrix and then call MatTranspose. > The error still persists. Can you suggest any alternatives to this problem? > Regards, > -- > Ganesh > From als88 at cam.ac.uk Thu Nov 8 13:00:50 2012 From: als88 at cam.ac.uk (A.L. Siahaan) Date: 08 Nov 2012 19:00:50 +0000 Subject: [petsc-users] problem in configuring petsc-dev Message-ID: Hi, I have used Petsc-3.2 and Petsc-3.3 before. Now I am trying to configure Petsc-dev with this simple configure line : ./configure --with-mpi-f90=/usr/bin/mpif90 PETSC_ARCH=linux-gnu-c-debug I got an error : ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Cannot determine Fortran module include flag ******************************************************************************* Even when I set (in the configure line) "--with-mpi-f90-include" and "--with-mpi-f90-lib" to the exact location, the same error occurs. I attach here the configure.log file. Regards, Antony -------------- next part -------------- A non-text attachment was scrubbed... Name: configure Type: application/octet-stream Size: 339 bytes Desc: configure URL: From balay at mcs.anl.gov Thu Nov 8 13:03:37 2012 From: balay at mcs.anl.gov (Satish Balay) Date: Thu, 8 Nov 2012 13:03:37 -0600 (CST) Subject: [petsc-users] Fwd: error messages while updating petsc-dev In-Reply-To: <509BF986.7080801@gmail.com> References: <509BF8B8.6090104@gmail.com> <509BF986.7080801@gmail.com> Message-ID: On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: > Dear folks, > I came across an error while making a code: > makefile:7: *** missing separator. Stop. > This happens after I was tying to update the petsc-dev with some error > message; the configure.log, error.log and make.log are attached. I've already > sent it to petsc-maint list. Is this makefile error related to the fail > update? >>>>>>>> This is a Mercurial clone Defined "VERSION_HG" to ""85e6055943e0711fccdec2d08caeba48971d3d55"" Defined "VERSION_DATE_HG" to ""Fri Sep 23 14:46:14 2011 -0700"" Defined "VERSION_BS_HG" to ""e9fd775ab2bf270a9204f7cbc33603292ac5b1d8"" Defined "VERSION_BS_DATE_HG" to ""Fri Sep 16 17:33:47 2011 +0200"" <<<<< You don't have the latest petsc-dev. Can you pull the latest petsc-dev and retry? Satish From zhenglun.wei at gmail.com Thu Nov 8 13:20:28 2012 From: zhenglun.wei at gmail.com (Zhenglun (Alan) Wei) Date: Thu, 08 Nov 2012 13:20:28 -0600 Subject: [petsc-users] Fwd: error messages while updating petsc-dev In-Reply-To: References: <509BF8B8.6090104@gmail.com> <509BF986.7080801@gmail.com> Message-ID: <509C05FC.9070601@gmail.com> Thanks for your reply, Dr. Balay. However, I do not know how to get the latest version of petsc-dev except following http://www.mcs.anl.gov/petsc/developers/index.html |cd petsc-dev|| hg pull -u ||./$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py ||make Those are all what I did. Should I do something else? thanks, Alan | > On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: > >> Dear folks, >> I came across an error while making a code: >> makefile:7: *** missing separator. Stop. >> This happens after I was tying to update the petsc-dev with some error >> message; the configure.log, error.log and make.log are attached. I've already >> sent it to petsc-maint list. Is this makefile error related to the fail >> update? > This is a Mercurial clone > Defined "VERSION_HG" to ""85e6055943e0711fccdec2d08caeba48971d3d55"" > Defined "VERSION_DATE_HG" to ""Fri Sep 23 14:46:14 2011 -0700"" > Defined "VERSION_BS_HG" to ""e9fd775ab2bf270a9204f7cbc33603292ac5b1d8"" > Defined "VERSION_BS_DATE_HG" to ""Fri Sep 16 17:33:47 2011 +0200"" > <<<<< > > You don't have the latest petsc-dev. Can you pull the latest petsc-dev and retry? > > Satish -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Thu Nov 8 13:33:06 2012 From: balay at mcs.anl.gov (Satish Balay) Date: Thu, 8 Nov 2012 13:33:06 -0600 (CST) Subject: [petsc-users] Fwd: error messages while updating petsc-dev In-Reply-To: <509C05FC.9070601@gmail.com> References: <509BF8B8.6090104@gmail.com> <509BF986.7080801@gmail.com> <509C05FC.9070601@gmail.com> Message-ID: please copy/paste the output of the following commands hg parent hg tip hg status hg pull hg update hg status cd config/BuildSystem hg parent hg tip hg status hg pull hg update hg status Satish On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: > Thanks for your reply, Dr. Balay. > However, I do not know how to get the latest version of petsc-dev except > following http://www.mcs.anl.gov/petsc/developers/index.html > |cd petsc-dev|| > hg pull -u > ||./$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py > ||make > > Those are all what I did. Should I do something else? > > thanks, > Alan > | > > On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: > > > > > Dear folks, > > > I came across an error while making a code: > > > makefile:7: *** missing separator. Stop. > > > This happens after I was tying to update the petsc-dev with some > > > error > > > message; the configure.log, error.log and make.log are attached. I've > > > already > > > sent it to petsc-maint list. Is this makefile error related to the fail > > > update? > > This is a Mercurial clone > > Defined "VERSION_HG" to > > ""85e6055943e0711fccdec2d08caeba48971d3d55"" > > Defined "VERSION_DATE_HG" to ""Fri Sep 23 14:46:14 2011 -0700"" > > Defined "VERSION_BS_HG" to > > ""e9fd775ab2bf270a9204f7cbc33603292ac5b1d8"" > > Defined "VERSION_BS_DATE_HG" to ""Fri Sep 16 17:33:47 2011 +0200"" > > <<<<< > > > > You don't have the latest petsc-dev. Can you pull the latest petsc-dev and > > retry? > > > > Satish > > From zhenglun.wei at gmail.com Thu Nov 8 13:52:28 2012 From: zhenglun.wei at gmail.com (Zhenglun (Alan) Wei) Date: Thu, 08 Nov 2012 13:52:28 -0600 Subject: [petsc-users] Fwd: error messages while updating petsc-dev In-Reply-To: References: <509BF8B8.6090104@gmail.com> <509BF986.7080801@gmail.com> <509C05FC.9070601@gmail.com> Message-ID: <509C0D7C.6070302@gmail.com> *_hg parent_* changeset: 24846:6e281c3f1f72 tag: tip user: Matthew G Knepley date: Thu Nov 08 11:41:01 2012 -0500 summary: Manual: Added part of a section on DMComplex _*hg tip*_ changeset: 24846:6e281c3f1f72 tag: tip user: Matthew G Knepley date: Thu Nov 08 11:41:01 2012 -0500 summary: Manual: Added part of a section on DMComplex _*hg status*_ M src/ksp/ksp/examples/tutorials/ex10.c M src/ksp/ksp/examples/tutorials/ex11f.F M src/ksp/ksp/examples/tutorials/ex13f90.F M src/ksp/ksp/examples/tutorials/ex14f.F M src/ksp/ksp/examples/tutorials/ex15f.F M src/ksp/ksp/examples/tutorials/ex1f.F M src/ksp/ksp/examples/tutorials/ex21f.F M src/ksp/ksp/examples/tutorials/ex27.c M src/ksp/ksp/examples/tutorials/ex29.c M src/ksp/ksp/examples/tutorials/ex2f.F M src/ksp/ksp/examples/tutorials/ex3.c M src/ksp/ksp/examples/tutorials/ex43-solCx.h M src/ksp/ksp/examples/tutorials/ex43.c M src/ksp/ksp/examples/tutorials/ex44f.F90 M src/ksp/ksp/examples/tutorials/ex45.c M src/ksp/ksp/examples/tutorials/ex49.c M src/ksp/ksp/examples/tutorials/ex50.c M src/ksp/ksp/examples/tutorials/ex52.c M src/ksp/ksp/examples/tutorials/makefile M src/ksp/ksp/examples/tutorials/output/ex10_24.out M src/ksp/ksp/examples/tutorials/output/ex10_25.out M src/ksp/ksp/examples/tutorials/output/ex22_1.out M src/ksp/ksp/examples/tutorials/output/ex43_1.out M src/ksp/ksp/examples/tutorials/output/ex4_1.out A src/ksp/ksp/examples/tutorials/ex22.c A src/ksp/ksp/examples/tutorials/ex47.c ! src/ksp/ksp/examples/tutorials/data/elem_2d_pln_strn_v_25.txt ! src/ksp/ksp/examples/tutorials/data/elem_2d_therm.txt ! src/ksp/ksp/examples/tutorials/data/elem_3d_elast_v_25.txt ! src/ksp/ksp/examples/tutorials/ex42-mgfs.opts ! src/ksp/ksp/examples/tutorials/ex42-mgfs2.opts ! src/ksp/ksp/examples/tutorials/output/ex4_0.out ! src/ksp/ksp/examples/tutorials/output/ex4_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/AlanRun ? src/ksp/ksp/examples/AlanTutorials20120409/Rank0Coord.xyz ? src/ksp/ksp/examples/AlanTutorials20120409/Rank0plt3d.q ? src/ksp/ksp/examples/AlanTutorials20120409/data/elem_2d_pln_strn_v_25.txt ? src/ksp/ksp/examples/AlanTutorials20120409/data/elem_2d_therm.txt ? src/ksp/ksp/examples/AlanTutorials20120409/data/elem_3d_elast_v_25.txt ? src/ksp/ksp/examples/AlanTutorials20120409/data/ex33bc.data ? src/ksp/ksp/examples/AlanTutorials20120409/ex1.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex10.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex11.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex11f.F ? src/ksp/ksp/examples/AlanTutorials20120409/ex12.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex13.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex13f90.F ? src/ksp/ksp/examples/AlanTutorials20120409/ex14f.F ? src/ksp/ksp/examples/AlanTutorials20120409/ex15.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex15f.F ? src/ksp/ksp/examples/AlanTutorials20120409/ex16.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex1f.F ? src/ksp/ksp/examples/AlanTutorials20120409/ex2.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex20options ? src/ksp/ksp/examples/AlanTutorials20120409/ex21f.F ? src/ksp/ksp/examples/AlanTutorials20120409/ex22.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex22f.F ? src/ksp/ksp/examples/AlanTutorials20120409/ex23.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex25.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex27.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex28.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex29.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex2f.F ? src/ksp/ksp/examples/AlanTutorials20120409/ex3.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex30.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex31.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex32.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex34.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex35.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex37.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex38.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex39.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex4.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex40.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex41.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex41.m ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-fsschur.opts ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgfs.opts ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgfs2.opts ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgschur.opts ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgschur_nestedfs.opts ? src/ksp/ksp/examples/AlanTutorials20120409/ex42.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex43-solCx.h ? src/ksp/ksp/examples/AlanTutorials20120409/ex43.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex44f.F90 ? src/ksp/ksp/examples/AlanTutorials20120409/ex45.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex46.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex47.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex49.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex5.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex50.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex51.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex52.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex53.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex54.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex55.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex56.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex6f.F ? src/ksp/ksp/examples/AlanTutorials20120409/ex7.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex8.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex8g.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex9.c ? src/ksp/ksp/examples/AlanTutorials20120409/makefile ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_10.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_11.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_12.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_13.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_14.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_15.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_16.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_17.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_18.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_22.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_23.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_24.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_25.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_3.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_4.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_5.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_6.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_7.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_8.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_9.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_ILU.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_cg_singlereduction.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mpicrl.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mpicsrperm.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mumps.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mumps_redundant.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_seqcrl.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_seqcsrperm.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_umfpack.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex11_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex11f_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_3.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex13_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex13f90_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex14_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex14_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex15_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex15f_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex16_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex18_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_3.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1f_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex20_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex20_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex21f_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex22_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex23_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex23_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex25_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex26_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex29_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex29_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_3.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_4.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_5.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_6.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_7.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi_3.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_chebyest_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_chebyest_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_specest_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_specest_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_umfpack.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2f_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex30_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex32_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex38_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex39_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex40_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex42_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex43_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex45_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex45_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_3.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_0.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex52_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex53.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex54_0.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex54_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex55_0.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex55_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex56_0.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_3.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_4.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_5.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_plapack.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex6f_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex7_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_3.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex9_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/AlanRun ? src/ksp/ksp/examples/AlanTutorials20120410/data/ex33bc.data ? src/ksp/ksp/examples/AlanTutorials20120410/ex1.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex10.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex11.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex11f.F ? src/ksp/ksp/examples/AlanTutorials20120410/ex12.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex13.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex13f90.F ? src/ksp/ksp/examples/AlanTutorials20120410/ex14f.F ? src/ksp/ksp/examples/AlanTutorials20120410/ex15.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex15f.F ? src/ksp/ksp/examples/AlanTutorials20120410/ex16.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex1f.F ? src/ksp/ksp/examples/AlanTutorials20120410/ex2.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex20options ? src/ksp/ksp/examples/AlanTutorials20120410/ex21f.F ? src/ksp/ksp/examples/AlanTutorials20120410/ex22.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex22f.F ? src/ksp/ksp/examples/AlanTutorials20120410/ex23.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex25.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex27.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex28.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex29.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex2f.F ? src/ksp/ksp/examples/AlanTutorials20120410/ex3.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex30.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex31.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex32.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex34.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex38.c ? 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src/ksp/ksp/examples/AlanTutorials20120409/ex5.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex50.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex51.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex52.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex53.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex54.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex55.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex56.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex6f.F ? src/ksp/ksp/examples/AlanTutorials20120409/ex7.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex8.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex8g.c ? src/ksp/ksp/examples/AlanTutorials20120409/ex9.c ? src/ksp/ksp/examples/AlanTutorials20120409/makefile ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_10.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_11.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_12.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_13.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_14.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_15.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_16.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_17.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_18.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_22.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_23.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_24.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_25.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_3.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_4.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_5.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_6.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_7.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_8.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_9.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_ILU.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_cg_singlereduction.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mpicrl.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mpicsrperm.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mumps.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mumps_redundant.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_seqcrl.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_seqcsrperm.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_umfpack.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex11_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex11f_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_3.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex13_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex13f90_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex14_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex14_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex15_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex15f_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex16_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex18_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_3.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1f_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex20_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex20_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex21f_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex22_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex23_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex23_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex25_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex26_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex29_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex29_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_3.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_4.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_5.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_6.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_7.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi_3.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_chebyest_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_chebyest_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_specest_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_specest_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_umfpack.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2f_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex30_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex32_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex38_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex39_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex40_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex42_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex43_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex45_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex45_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_3.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_0.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex52_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex53.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex54_0.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex54_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex55_0.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex55_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex56_0.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_3.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_4.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_5.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_plapack.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex6f_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex7_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_1.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_2.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_3.out ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex9_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/AlanRun ? src/ksp/ksp/examples/AlanTutorials20120410/data/ex33bc.data ? src/ksp/ksp/examples/AlanTutorials20120410/ex1.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex10.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex11.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex11f.F ? src/ksp/ksp/examples/AlanTutorials20120410/ex12.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex13.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex13f90.F ? src/ksp/ksp/examples/AlanTutorials20120410/ex14f.F ? src/ksp/ksp/examples/AlanTutorials20120410/ex15.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex15f.F ? src/ksp/ksp/examples/AlanTutorials20120410/ex16.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex1f.F ? src/ksp/ksp/examples/AlanTutorials20120410/ex2.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex20options ? src/ksp/ksp/examples/AlanTutorials20120410/ex21f.F ? src/ksp/ksp/examples/AlanTutorials20120410/ex22.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex22f.F ? src/ksp/ksp/examples/AlanTutorials20120410/ex23.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex25.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex27.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex28.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex29.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex2f.F ? src/ksp/ksp/examples/AlanTutorials20120410/ex3.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex30.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex31.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex32.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex34.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex38.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex39.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex4.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex40.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex41.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex41.m ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-fsschur.opts ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-mgschur.opts ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-mgschur_nestedfs.opts ? src/ksp/ksp/examples/AlanTutorials20120410/ex42.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex43-solCx.h ? src/ksp/ksp/examples/AlanTutorials20120410/ex43.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex44f.F90 ? src/ksp/ksp/examples/AlanTutorials20120410/ex45.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex45f.F ? src/ksp/ksp/examples/AlanTutorials20120410/ex46.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex47.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex49.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex5.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex50.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex51.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex52.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex53.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex54.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex54f.F ? src/ksp/ksp/examples/AlanTutorials20120410/ex55.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex56.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex57f.F ? src/ksp/ksp/examples/AlanTutorials20120410/ex58.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex6f.F ? src/ksp/ksp/examples/AlanTutorials20120410/ex7.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex8.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex8g.c ? src/ksp/ksp/examples/AlanTutorials20120410/ex9.c ? src/ksp/ksp/examples/AlanTutorials20120410/makefile ? src/ksp/ksp/examples/AlanTutorials20120410/out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_10.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_11.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_12.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_13.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_14.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_15.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_16.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_17.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_18.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_2.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_22.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_23.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_24.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_25.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_3.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_4.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_5.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_6.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_7.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_8.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_9.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_ILU.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_cg_singlereduction.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mpicrl.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mpicsrperm.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mumps.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mumps_redundant.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_seqcrl.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_seqcsrperm.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_umfpack.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex11_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex11f_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_2.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_3.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex13_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex13f90_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex14_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex14_2.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex15_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex15f_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex16_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex18_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1_2.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1_3.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1f_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex20_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex20_2.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex21f_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex22_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex23_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex23_2.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex25_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex25_2.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex26_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex28_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex29_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex29_2.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_2.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_3.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_4.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_5.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_6.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_7.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_bjacobi.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_bjacobi_2.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_bjacobi_3.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_specest_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_specest_2.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_umfpack.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2f_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex30_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex32_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex34_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex38_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex39_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex40_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex42_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex43_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex43_3.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45_2.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45f_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex49_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex49_2.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex49_3.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex4_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex50.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex50_2.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex52_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex53.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_0.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_2.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54f.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex55_0.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex55_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex56_0.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex58.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_2.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_3.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_4.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_5.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_plapack.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex6f_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex7_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_1.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_2.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_3.out ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex9_1.out _*cd config/BuildSystem hg parent*_ changeset: 2878:3d4bb7478b00 tag: tip user: Barry Smith date: Wed Nov 07 20:34:01 2012 -0600 summary: added support for --with-PACKAGENAME-pkg-config[=pathtosearch] _*hg tip*_ changeset: 2878:3d4bb7478b00 tag: tip user: Barry Smith date: Wed Nov 07 20:34:01 2012 -0600 summary: added support for --with-PACKAGENAME-pkg-config[=pathtosearch] _*hg status*_ no output _*hg pull*_ pulling from http://petsc.cs.iit.edu/petsc/BuildSystem searching for changes no changes found _*hg update*_ 0 files updated, 0 files merged, 0 files removed, 0 files unresolved _*hg status *_no output > please copy/paste the output of the following commands > > > hg parent > hg tip > hg status > hg pull > hg update > hg status > cd config/BuildSystem > hg parent > hg tip > hg status > hg pull > hg update > hg status > > Satish > > On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: > >> Thanks for your reply, Dr. Balay. >> However, I do not know how to get the latest version of petsc-dev except >> following http://www.mcs.anl.gov/petsc/developers/index.html >> |cd petsc-dev|| >> hg pull -u >> ||./$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py >> ||make >> >> Those are all what I did. Should I do something else? >> >> thanks, >> Alan >> | >>> On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: >>> >>>> Dear folks, >>>> I came across an error while making a code: >>>> makefile:7: *** missing separator. Stop. >>>> This happens after I was tying to update the petsc-dev with some >>>> error >>>> message; the configure.log, error.log and make.log are attached. I've >>>> already >>>> sent it to petsc-maint list. Is this makefile error related to the fail >>>> update? >>> This is a Mercurial clone >>> Defined "VERSION_HG" to >>> ""85e6055943e0711fccdec2d08caeba48971d3d55"" >>> Defined "VERSION_DATE_HG" to ""Fri Sep 23 14:46:14 2011 -0700"" >>> Defined "VERSION_BS_HG" to >>> ""e9fd775ab2bf270a9204f7cbc33603292ac5b1d8"" >>> Defined "VERSION_BS_DATE_HG" to ""Fri Sep 16 17:33:47 2011 +0200"" >>> <<<<< >>> >>> You don't have the latest petsc-dev. Can you pull the latest petsc-dev and >>> retry? >>> >>> Satish >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From als88 at cam.ac.uk Thu Nov 8 13:54:50 2012 From: als88 at cam.ac.uk (A.L. Siahaan) Date: 08 Nov 2012 19:54:50 +0000 Subject: [petsc-users] Fwd: error messages while updating petsc-dev In-Reply-To: References: <509BF8B8.6090104@gmail.com> <509BF986.7080801@gmail.com> <509C05FC.9070601@gmail.com> Message-ID: Hi, These are the outputs : antony at gnw20pc1:~/code/petsc-dev$ hg parent changeset: 24846:6e281c3f1f72 tag: tip user: Matthew G Knepley date: Thu Nov 08 11:41:01 2012 -0500 summary: Manual: Added part of a section on DMComplex antony at gnw20pc1:~/code/petsc-dev$ hg tip changeset: 24846:6e281c3f1f72 tag: tip user: Matthew G Knepley date: Thu Nov 08 11:41:01 2012 -0500 summary: Manual: Added part of a section on DMComplex antony at gnw20pc1:~/code/petsc-dev$ hg status ? configtest.mod0 antony at gnw20pc1:~/code/petsc-dev$ hg pull pulling from http://petsc.cs.iit.edu/petsc/petsc-dev searching for changes no changes found pulling from http://petsc.cs.iit.edu/petsc/BuildSystem searching for changes no changes found antony at gnw20pc1:~/code/petsc-dev$ hg update 0 files updated, 0 files merged, 0 files removed, 0 files unresolved antony at gnw20pc1:~/code/petsc-dev$ hg status ? configtest.mod0 antony at gnw20pc1:~/code/petsc-dev$ cd config/BuildSystem/ antony at gnw20pc1:~/code/petsc-dev/config/BuildSystem$ hg parent changeset: 2878:3d4bb7478b00 tag: tip user: Barry Smith date: Wed Nov 07 20:34:01 2012 -0600 summary: added support for --with-PACKAGENAME-pkg-config[=pathtosearch] antony at gnw20pc1:~/code/petsc-dev/config/BuildSystem$ hg tip changeset: 2878:3d4bb7478b00 tag: tip user: Barry Smith date: Wed Nov 07 20:34:01 2012 -0600 summary: added support for --with-PACKAGENAME-pkg-config[=pathtosearch] antony at gnw20pc1:~/code/petsc-dev/config/BuildSystem$ hg status antony at gnw20pc1:~/code/petsc-dev/config/BuildSystem$ hg pull pulling from http://petsc.cs.iit.edu/petsc/BuildSystem searching for changes no changes found antony at gnw20pc1:~/code/petsc-dev/config/BuildSystem$ hg update 0 files updated, 0 files merged, 0 files removed, 0 files unresolved antony at gnw20pc1:~/code/petsc-dev/config/BuildSystem$ hg status antony at gnw20pc1:~/code/petsc-dev/config/BuildSystem$ Regards, Antony On Nov 8 2012, Satish Balay wrote: >please copy/paste the output of the following commands > > >hg parent >hg tip >hg status >hg pull >hg update >hg status >cd config/BuildSystem >hg parent >hg tip >hg status >hg pull >hg update >hg status > >Satish > >On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: > >> Thanks for your reply, Dr. Balay. >> However, I do not know how to get the latest version of petsc-dev >> except following http://www.mcs.anl.gov/petsc/developers/index.html >> |cd petsc-dev|| >> hg pull -u >> ||./$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py >> ||make >> >> Those are all what I did. Should I do something else? >> >> thanks, >> Alan >> | >> > On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: >> > >> > > Dear folks, >> > > I came across an error while making a code: >> > > makefile:7: *** missing separator. Stop. >> > > This happens after I was tying to update the petsc-dev with >> > > some error message; the configure.log, error.log and make.log are >> > > attached. I've already sent it to petsc-maint list. Is this makefile >> > > error related to the fail update? >> > This is a Mercurial clone >> > Defined "VERSION_HG" to >> > ""85e6055943e0711fccdec2d08caeba48971d3d55"" >> > Defined "VERSION_DATE_HG" to ""Fri Sep 23 14:46:14 2011 >> > -0700"" >> > Defined "VERSION_BS_HG" to >> > ""e9fd775ab2bf270a9204f7cbc33603292ac5b1d8"" >> > Defined "VERSION_BS_DATE_HG" to ""Fri Sep 16 17:33:47 2011 >> > +0200"" <<<<< >> > >> > You don't have the latest petsc-dev. Can you pull the latest >> > petsc-dev and retry? >> > >> > Satish >> >> > > From balay at mcs.anl.gov Thu Nov 8 13:55:50 2012 From: balay at mcs.anl.gov (Satish Balay) Date: Thu, 8 Nov 2012 13:55:50 -0600 (CST) Subject: [petsc-users] Fwd: error messages while updating petsc-dev In-Reply-To: <509C0D7C.6070302@gmail.com> References: <509BF8B8.6090104@gmail.com> <509BF986.7080801@gmail.com> <509C05FC.9070601@gmail.com> <509C0D7C.6070302@gmail.com> Message-ID: ok. Can you rerun configure now [or run ./$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py] and then 'make'. If you still have issues - send the new logs to petsc-maint. Satish On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: > *_hg parent_* > changeset: 24846:6e281c3f1f72 > tag: tip > user: Matthew G Knepley > date: Thu Nov 08 11:41:01 2012 -0500 > summary: Manual: Added part of a section on DMComplex > > _*hg tip*_ > changeset: 24846:6e281c3f1f72 > tag: tip > user: Matthew G Knepley > date: Thu Nov 08 11:41:01 2012 -0500 > summary: Manual: Added part of a section on DMComplex > > > _*hg status*_ > M src/ksp/ksp/examples/tutorials/ex10.c > M src/ksp/ksp/examples/tutorials/ex11f.F > M src/ksp/ksp/examples/tutorials/ex13f90.F > M src/ksp/ksp/examples/tutorials/ex14f.F > M src/ksp/ksp/examples/tutorials/ex15f.F > M src/ksp/ksp/examples/tutorials/ex1f.F > M src/ksp/ksp/examples/tutorials/ex21f.F > M src/ksp/ksp/examples/tutorials/ex27.c > M src/ksp/ksp/examples/tutorials/ex29.c > M src/ksp/ksp/examples/tutorials/ex2f.F > M src/ksp/ksp/examples/tutorials/ex3.c > M src/ksp/ksp/examples/tutorials/ex43-solCx.h > M src/ksp/ksp/examples/tutorials/ex43.c > M src/ksp/ksp/examples/tutorials/ex44f.F90 > M src/ksp/ksp/examples/tutorials/ex45.c > M src/ksp/ksp/examples/tutorials/ex49.c > M src/ksp/ksp/examples/tutorials/ex50.c > M src/ksp/ksp/examples/tutorials/ex52.c > M src/ksp/ksp/examples/tutorials/makefile > M src/ksp/ksp/examples/tutorials/output/ex10_24.out > M src/ksp/ksp/examples/tutorials/output/ex10_25.out > M src/ksp/ksp/examples/tutorials/output/ex22_1.out > M src/ksp/ksp/examples/tutorials/output/ex43_1.out > M src/ksp/ksp/examples/tutorials/output/ex4_1.out > A src/ksp/ksp/examples/tutorials/ex22.c > A src/ksp/ksp/examples/tutorials/ex47.c > ! src/ksp/ksp/examples/tutorials/data/elem_2d_pln_strn_v_25.txt > ! src/ksp/ksp/examples/tutorials/data/elem_2d_therm.txt > ! src/ksp/ksp/examples/tutorials/data/elem_3d_elast_v_25.txt > ! src/ksp/ksp/examples/tutorials/ex42-mgfs.opts > ! src/ksp/ksp/examples/tutorials/ex42-mgfs2.opts > ! src/ksp/ksp/examples/tutorials/output/ex4_0.out > ! src/ksp/ksp/examples/tutorials/output/ex4_2.out > ? src/ksp/ksp/examples/AlanTutorials20120409/AlanRun > ? src/ksp/ksp/examples/AlanTutorials20120409/Rank0Coord.xyz > ? src/ksp/ksp/examples/AlanTutorials20120409/Rank0plt3d.q > ? src/ksp/ksp/examples/AlanTutorials20120409/data/elem_2d_pln_strn_v_25.txt > ? src/ksp/ksp/examples/AlanTutorials20120409/data/elem_2d_therm.txt > ? src/ksp/ksp/examples/AlanTutorials20120409/data/elem_3d_elast_v_25.txt > ? src/ksp/ksp/examples/AlanTutorials20120409/data/ex33bc.data > ? src/ksp/ksp/examples/AlanTutorials20120409/ex1.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex10.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex11.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex11f.F > ? src/ksp/ksp/examples/AlanTutorials20120409/ex12.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex13.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex13f90.F > ? src/ksp/ksp/examples/AlanTutorials20120409/ex14f.F > ? src/ksp/ksp/examples/AlanTutorials20120409/ex15.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex15f.F > ? src/ksp/ksp/examples/AlanTutorials20120409/ex16.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex1f.F > ? src/ksp/ksp/examples/AlanTutorials20120409/ex2.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex20options > ? src/ksp/ksp/examples/AlanTutorials20120409/ex21f.F > ? src/ksp/ksp/examples/AlanTutorials20120409/ex22.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex22f.F > ? src/ksp/ksp/examples/AlanTutorials20120409/ex23.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex25.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex27.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex28.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex29.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex2f.F > ? src/ksp/ksp/examples/AlanTutorials20120409/ex3.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex30.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex31.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex32.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex34.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex35.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex37.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex38.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex39.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex4.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex40.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex41.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex41.m > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-fsschur.opts > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgfs.opts > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgfs2.opts > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgschur.opts > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgschur_nestedfs.opts > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex43-solCx.h > ? src/ksp/ksp/examples/AlanTutorials20120409/ex43.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex44f.F90 > ? src/ksp/ksp/examples/AlanTutorials20120409/ex45.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex46.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex47.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex49.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex5.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex50.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex51.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex52.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex53.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex54.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex55.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex56.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex6f.F > ? src/ksp/ksp/examples/AlanTutorials20120409/ex7.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex8.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex8g.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex9.c > ? src/ksp/ksp/examples/AlanTutorials20120409/makefile > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_10.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_11.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_12.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_13.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_14.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_15.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_16.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_17.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_18.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_2.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_22.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_23.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_24.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_25.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_3.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_4.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_5.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_6.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_7.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_8.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_9.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_ILU.out > ? > src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_cg_singlereduction.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mpicrl.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mpicsrperm.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mumps.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mumps_redundant.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_seqcrl.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_seqcsrperm.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_umfpack.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex11_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex11f_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_2.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_3.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex13_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex13f90_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex14_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex14_2.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex15_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex15f_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex16_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex18_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_2.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_3.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1f_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex20_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex20_2.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex21f_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex22_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex23_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex23_2.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex25_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex26_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex29_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex29_2.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_2.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_3.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_4.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_5.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_6.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_7.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi.out > ? 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src/ksp/ksp/examples/AlanTutorials20120410/ex8g.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex9.c > ? src/ksp/ksp/examples/AlanTutorials20120410/makefile > ? src/ksp/ksp/examples/AlanTutorials20120410/out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_10.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_11.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_12.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_13.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_14.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_15.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_16.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_17.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_18.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_2.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_22.out > ? 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src/ksp/ksp/examples/AlanTutorials20120410/output/ex4_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex50.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex50_2.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex52_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex53.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_0.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_2.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54f.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex55_0.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex55_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex56_0.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex58.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_2.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_3.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_4.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_5.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_plapack.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex6f_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex7_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_2.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_3.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex9_1.out > > > *_hg pull_* > pulling from http://petsc.cs.iit.edu/petsc/petsc-dev > searching for changes > no changes found > > > _*hg update*_ > 0 files updated, 0 files merged, 0 files removed, 0 files unresolved > > _*hg status > *_M src/ksp/ksp/examples/tutorials/ex10.c > M src/ksp/ksp/examples/tutorials/ex11f.F > M src/ksp/ksp/examples/tutorials/ex13f90.F > M src/ksp/ksp/examples/tutorials/ex14f.F > M src/ksp/ksp/examples/tutorials/ex15f.F > M src/ksp/ksp/examples/tutorials/ex1f.F > M src/ksp/ksp/examples/tutorials/ex21f.F > M src/ksp/ksp/examples/tutorials/ex27.c > M src/ksp/ksp/examples/tutorials/ex29.c > M src/ksp/ksp/examples/tutorials/ex2f.F > M src/ksp/ksp/examples/tutorials/ex3.c > M src/ksp/ksp/examples/tutorials/ex43-solCx.h > M src/ksp/ksp/examples/tutorials/ex43.c > M src/ksp/ksp/examples/tutorials/ex44f.F90 > M src/ksp/ksp/examples/tutorials/ex45.c > M src/ksp/ksp/examples/tutorials/ex49.c > M src/ksp/ksp/examples/tutorials/ex50.c > M src/ksp/ksp/examples/tutorials/ex52.c > M src/ksp/ksp/examples/tutorials/makefile > M src/ksp/ksp/examples/tutorials/output/ex10_24.out > M src/ksp/ksp/examples/tutorials/output/ex10_25.out > M src/ksp/ksp/examples/tutorials/output/ex22_1.out > M src/ksp/ksp/examples/tutorials/output/ex43_1.out > M src/ksp/ksp/examples/tutorials/output/ex4_1.out > A src/ksp/ksp/examples/tutorials/ex22.c > A src/ksp/ksp/examples/tutorials/ex47.c > ! src/ksp/ksp/examples/tutorials/data/elem_2d_pln_strn_v_25.txt > ! src/ksp/ksp/examples/tutorials/data/elem_2d_therm.txt > ! src/ksp/ksp/examples/tutorials/data/elem_3d_elast_v_25.txt > ! src/ksp/ksp/examples/tutorials/ex42-mgfs.opts > ! src/ksp/ksp/examples/tutorials/ex42-mgfs2.opts > ! src/ksp/ksp/examples/tutorials/output/ex4_0.out > ! src/ksp/ksp/examples/tutorials/output/ex4_2.out > ? src/ksp/ksp/examples/AlanTutorials20120409/AlanRun > ? src/ksp/ksp/examples/AlanTutorials20120409/Rank0Coord.xyz > ? src/ksp/ksp/examples/AlanTutorials20120409/Rank0plt3d.q > ? src/ksp/ksp/examples/AlanTutorials20120409/data/elem_2d_pln_strn_v_25.txt > ? src/ksp/ksp/examples/AlanTutorials20120409/data/elem_2d_therm.txt > ? src/ksp/ksp/examples/AlanTutorials20120409/data/elem_3d_elast_v_25.txt > ? src/ksp/ksp/examples/AlanTutorials20120409/data/ex33bc.data > ? src/ksp/ksp/examples/AlanTutorials20120409/ex1.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex10.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex11.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex11f.F > ? src/ksp/ksp/examples/AlanTutorials20120409/ex12.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex13.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex13f90.F > ? src/ksp/ksp/examples/AlanTutorials20120409/ex14f.F > ? src/ksp/ksp/examples/AlanTutorials20120409/ex15.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex15f.F > ? src/ksp/ksp/examples/AlanTutorials20120409/ex16.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex1f.F > ? src/ksp/ksp/examples/AlanTutorials20120409/ex2.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex20options > ? src/ksp/ksp/examples/AlanTutorials20120409/ex21f.F > ? src/ksp/ksp/examples/AlanTutorials20120409/ex22.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex22f.F > ? src/ksp/ksp/examples/AlanTutorials20120409/ex23.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex25.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex27.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex28.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex29.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex2f.F > ? src/ksp/ksp/examples/AlanTutorials20120409/ex3.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex30.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex31.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex32.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex34.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex35.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex37.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex38.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex39.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex4.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex40.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex41.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex41.m > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-fsschur.opts > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgfs.opts > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgfs2.opts > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgschur.opts > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgschur_nestedfs.opts > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex43-solCx.h > ? src/ksp/ksp/examples/AlanTutorials20120409/ex43.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex44f.F90 > ? src/ksp/ksp/examples/AlanTutorials20120409/ex45.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex46.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex47.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex49.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex5.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex50.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex51.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex52.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex53.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex54.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex55.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex56.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex6f.F > ? src/ksp/ksp/examples/AlanTutorials20120409/ex7.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex8.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex8g.c > ? src/ksp/ksp/examples/AlanTutorials20120409/ex9.c > ? src/ksp/ksp/examples/AlanTutorials20120409/makefile > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_10.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_11.out > ? 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src/ksp/ksp/examples/AlanTutorials20120409/output/ex45_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex45_2.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_2.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_3.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_0.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_2.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex52_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex53.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex54_0.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex54_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex55_0.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex55_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex56_0.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_2.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_3.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_4.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_5.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_plapack.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex6f_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex7_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_1.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_2.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_3.out > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex9_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/AlanRun > ? src/ksp/ksp/examples/AlanTutorials20120410/data/ex33bc.data > ? src/ksp/ksp/examples/AlanTutorials20120410/ex1.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex10.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex11.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex11f.F > ? src/ksp/ksp/examples/AlanTutorials20120410/ex12.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex13.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex13f90.F > ? src/ksp/ksp/examples/AlanTutorials20120410/ex14f.F > ? src/ksp/ksp/examples/AlanTutorials20120410/ex15.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex15f.F > ? src/ksp/ksp/examples/AlanTutorials20120410/ex16.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex1f.F > ? src/ksp/ksp/examples/AlanTutorials20120410/ex2.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex20options > ? src/ksp/ksp/examples/AlanTutorials20120410/ex21f.F > ? src/ksp/ksp/examples/AlanTutorials20120410/ex22.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex22f.F > ? src/ksp/ksp/examples/AlanTutorials20120410/ex23.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex25.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex27.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex28.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex29.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex2f.F > ? src/ksp/ksp/examples/AlanTutorials20120410/ex3.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex30.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex31.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex32.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex34.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex38.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex39.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex4.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex40.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex41.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex41.m > ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-fsschur.opts > ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-mgschur.opts > ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-mgschur_nestedfs.opts > ? src/ksp/ksp/examples/AlanTutorials20120410/ex42.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex43-solCx.h > ? src/ksp/ksp/examples/AlanTutorials20120410/ex43.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex44f.F90 > ? src/ksp/ksp/examples/AlanTutorials20120410/ex45.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex45f.F > ? src/ksp/ksp/examples/AlanTutorials20120410/ex46.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex47.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex49.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex5.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex50.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex51.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex52.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex53.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex54.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex54f.F > ? src/ksp/ksp/examples/AlanTutorials20120410/ex55.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex56.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex57f.F > ? src/ksp/ksp/examples/AlanTutorials20120410/ex58.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex6f.F > ? src/ksp/ksp/examples/AlanTutorials20120410/ex7.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex8.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex8g.c > ? src/ksp/ksp/examples/AlanTutorials20120410/ex9.c > ? src/ksp/ksp/examples/AlanTutorials20120410/makefile > ? src/ksp/ksp/examples/AlanTutorials20120410/out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_10.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_11.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_12.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_13.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_14.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_15.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_16.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_17.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_18.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_2.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_22.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_23.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_24.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_25.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_3.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_4.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_5.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_6.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_7.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_8.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_9.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_ILU.out > ? > src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_cg_singlereduction.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mpicrl.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mpicsrperm.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mumps.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mumps_redundant.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_seqcrl.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_seqcsrperm.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_umfpack.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex11_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex11f_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_2.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_3.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex13_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex13f90_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex14_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex14_2.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex15_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex15f_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex16_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex18_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1_2.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1_3.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1f_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex20_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex20_2.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex21f_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex22_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex23_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex23_2.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex25_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex25_2.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex26_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex28_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex29_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex29_2.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_2.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_3.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_4.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_5.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_6.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_7.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_bjacobi.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_bjacobi_2.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_bjacobi_3.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_specest_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_specest_2.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_umfpack.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2f_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex30_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex32_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex34_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex38_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex39_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex40_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex42_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex43_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex43_3.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45_2.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45f_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex49_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex49_2.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex49_3.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex4_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex50.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex50_2.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex52_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex53.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_0.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_2.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54f.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex55_0.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex55_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex56_0.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex58.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_2.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_3.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_4.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_5.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_plapack.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex6f_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex7_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_1.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_2.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_3.out > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex9_1.out > > _*cd config/BuildSystem > hg parent*_ > changeset: 2878:3d4bb7478b00 > tag: tip > user: Barry Smith > date: Wed Nov 07 20:34:01 2012 -0600 > summary: added support for --with-PACKAGENAME-pkg-config[=pathtosearch] > > _*hg tip*_ > changeset: 2878:3d4bb7478b00 > tag: tip > user: Barry Smith > date: Wed Nov 07 20:34:01 2012 -0600 > summary: added support for --with-PACKAGENAME-pkg-config[=pathtosearch] > > > _*hg status*_ > no output > > _*hg pull*_ > pulling from http://petsc.cs.iit.edu/petsc/BuildSystem > searching for changes > no changes found > > _*hg update*_ > 0 files updated, 0 files merged, 0 files removed, 0 files unresolved > > _*hg status > *_no output > > > > > > please copy/paste the output of the following commands > > > > > > hg parent > > hg tip > > hg status > > hg pull > > hg update > > hg status > > cd config/BuildSystem > > hg parent > > hg tip > > hg status > > hg pull > > hg update > > hg status > > > > Satish > > > > On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: > > > > > Thanks for your reply, Dr. Balay. > > > However, I do not know how to get the latest version of petsc-dev > > > except > > > following http://www.mcs.anl.gov/petsc/developers/index.html > > > |cd petsc-dev|| > > > hg pull -u > > > ||./$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py > > > ||make > > > > > > Those are all what I did. Should I do something else? > > > > > > thanks, > > > Alan > > > | > > > > On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: > > > > > > > > > Dear folks, > > > > > I came across an error while making a code: > > > > > makefile:7: *** missing separator. Stop. > > > > > This happens after I was tying to update the petsc-dev with some > > > > > error > > > > > message; the configure.log, error.log and make.log are attached. I've > > > > > already > > > > > sent it to petsc-maint list. Is this makefile error related to the > > > > > fail > > > > > update? > > > > This is a Mercurial clone > > > > Defined "VERSION_HG" to > > > > ""85e6055943e0711fccdec2d08caeba48971d3d55"" > > > > Defined "VERSION_DATE_HG" to ""Fri Sep 23 14:46:14 2011 > > > > -0700"" > > > > Defined "VERSION_BS_HG" to > > > > ""e9fd775ab2bf270a9204f7cbc33603292ac5b1d8"" > > > > Defined "VERSION_BS_DATE_HG" to ""Fri Sep 16 17:33:47 2011 > > > > +0200"" > > > > <<<<< > > > > > > > > You don't have the latest petsc-dev. Can you pull the latest petsc-dev > > > > and > > > > retry? > > > > > > > > Satish > > > > > From zhenglun.wei at gmail.com Thu Nov 8 13:57:45 2012 From: zhenglun.wei at gmail.com (Zhenglun (Alan) Wei) Date: Thu, 08 Nov 2012 13:57:45 -0600 Subject: [petsc-users] Fwd: error messages while updating petsc-dev In-Reply-To: References: <509BF8B8.6090104@gmail.com> <509BF986.7080801@gmail.com> <509C05FC.9070601@gmail.com> <509C0D7C.6070302@gmail.com> Message-ID: <509C0EB9.2040804@gmail.com> Yes, it has some problem when I run ./$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py and similar problem when I do 'make' I will send the log file to petsc-maint in 10 mins. thanks, Alan > ok. Can you rerun configure now [or run > ./$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py] and then 'make'. If you > still have issues - send the new logs to petsc-maint. > > Satish > > On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: > >> *_hg parent_* >> changeset: 24846:6e281c3f1f72 >> tag: tip >> user: Matthew G Knepley >> date: Thu Nov 08 11:41:01 2012 -0500 >> summary: Manual: Added part of a section on DMComplex >> >> _*hg tip*_ >> changeset: 24846:6e281c3f1f72 >> tag: tip >> user: Matthew G Knepley >> date: Thu Nov 08 11:41:01 2012 -0500 >> summary: Manual: Added part of a section on DMComplex >> >> >> _*hg status*_ >> M src/ksp/ksp/examples/tutorials/ex10.c >> M src/ksp/ksp/examples/tutorials/ex11f.F >> M src/ksp/ksp/examples/tutorials/ex13f90.F >> M src/ksp/ksp/examples/tutorials/ex14f.F >> M src/ksp/ksp/examples/tutorials/ex15f.F >> M src/ksp/ksp/examples/tutorials/ex1f.F >> M src/ksp/ksp/examples/tutorials/ex21f.F >> M src/ksp/ksp/examples/tutorials/ex27.c >> M src/ksp/ksp/examples/tutorials/ex29.c >> M src/ksp/ksp/examples/tutorials/ex2f.F >> M src/ksp/ksp/examples/tutorials/ex3.c >> M src/ksp/ksp/examples/tutorials/ex43-solCx.h >> M src/ksp/ksp/examples/tutorials/ex43.c >> M src/ksp/ksp/examples/tutorials/ex44f.F90 >> M src/ksp/ksp/examples/tutorials/ex45.c >> M src/ksp/ksp/examples/tutorials/ex49.c >> M src/ksp/ksp/examples/tutorials/ex50.c >> M src/ksp/ksp/examples/tutorials/ex52.c >> M src/ksp/ksp/examples/tutorials/makefile >> M src/ksp/ksp/examples/tutorials/output/ex10_24.out >> M src/ksp/ksp/examples/tutorials/output/ex10_25.out >> M src/ksp/ksp/examples/tutorials/output/ex22_1.out >> M src/ksp/ksp/examples/tutorials/output/ex43_1.out >> M src/ksp/ksp/examples/tutorials/output/ex4_1.out >> A src/ksp/ksp/examples/tutorials/ex22.c >> A src/ksp/ksp/examples/tutorials/ex47.c >> ! src/ksp/ksp/examples/tutorials/data/elem_2d_pln_strn_v_25.txt >> ! src/ksp/ksp/examples/tutorials/data/elem_2d_therm.txt >> ! src/ksp/ksp/examples/tutorials/data/elem_3d_elast_v_25.txt >> ! src/ksp/ksp/examples/tutorials/ex42-mgfs.opts >> ! src/ksp/ksp/examples/tutorials/ex42-mgfs2.opts >> ! src/ksp/ksp/examples/tutorials/output/ex4_0.out >> ! src/ksp/ksp/examples/tutorials/output/ex4_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/AlanRun >> ? src/ksp/ksp/examples/AlanTutorials20120409/Rank0Coord.xyz >> ? src/ksp/ksp/examples/AlanTutorials20120409/Rank0plt3d.q >> ? src/ksp/ksp/examples/AlanTutorials20120409/data/elem_2d_pln_strn_v_25.txt >> ? src/ksp/ksp/examples/AlanTutorials20120409/data/elem_2d_therm.txt >> ? src/ksp/ksp/examples/AlanTutorials20120409/data/elem_3d_elast_v_25.txt >> ? src/ksp/ksp/examples/AlanTutorials20120409/data/ex33bc.data >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex1.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex10.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex11.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex11f.F >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex12.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex13.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex13f90.F >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex14f.F >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex15.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex15f.F >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex16.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex1f.F >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex2.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex20options >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex21f.F >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex22.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex22f.F >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex23.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex25.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex27.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex28.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex29.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex2f.F >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex3.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex30.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex31.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex32.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex34.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex35.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex37.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex38.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex39.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex4.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex40.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex41.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex41.m >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-fsschur.opts >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgfs.opts >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgfs2.opts >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgschur.opts >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgschur_nestedfs.opts >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex42.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex43-solCx.h >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex43.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex44f.F90 >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex45.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex46.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex47.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex49.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex5.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex50.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex51.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex52.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex53.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex54.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex55.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex56.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex6f.F >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex7.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex8.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex8g.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/ex9.c >> ? src/ksp/ksp/examples/AlanTutorials20120409/makefile >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_10.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_11.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_12.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_13.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_14.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_15.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_16.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_17.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_18.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_22.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_23.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_24.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_25.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_4.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_5.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_6.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_7.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_8.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_9.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_ILU.out >> ? >> src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_cg_singlereduction.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mpicrl.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mpicsrperm.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mumps.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mumps_redundant.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_seqcrl.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_seqcsrperm.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_umfpack.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex11_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex11f_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex13_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex13f90_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex14_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex14_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex15_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex15f_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex16_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex18_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1f_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex20_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex20_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex21f_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex22_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex23_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex23_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex25_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex26_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex29_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex29_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_4.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_5.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_6.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_7.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_chebyest_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_chebyest_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_specest_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_specest_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_umfpack.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2f_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex30_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex32_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex38_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex39_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex40_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex42_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex43_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex45_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex45_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_0.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex52_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex53.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex54_0.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex54_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex55_0.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex55_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex56_0.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_4.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_5.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_plapack.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex6f_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex7_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex9_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/AlanRun >> ? src/ksp/ksp/examples/AlanTutorials20120410/data/ex33bc.data >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex1.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex10.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex11.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex11f.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex12.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex13.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex13f90.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex14f.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex15.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex15f.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex16.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex1f.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex2.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex20options >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex21f.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex22.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex22f.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex23.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex25.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex27.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex28.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex29.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex2f.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex3.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex30.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex31.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex32.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex34.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex38.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex39.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex4.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex40.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex41.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex41.m >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-fsschur.opts >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-mgschur.opts >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-mgschur_nestedfs.opts >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex42.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex43-solCx.h >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex43.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex44f.F90 >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex45.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex45f.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex46.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex47.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex49.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex5.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex50.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex51.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex52.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex53.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex54.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex54f.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex55.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex56.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex57f.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex58.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex6f.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex7.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex8.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex8g.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex9.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/makefile >> ? src/ksp/ksp/examples/AlanTutorials20120410/out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_10.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_11.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_12.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_13.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_14.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_15.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_16.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_17.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_18.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_22.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_23.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_24.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_25.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_4.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_5.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_6.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_7.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_8.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_9.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_ILU.out >> ? >> src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_cg_singlereduction.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mpicrl.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mpicsrperm.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mumps.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mumps_redundant.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_seqcrl.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_seqcsrperm.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_umfpack.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex11_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex11f_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex13_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex13f90_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex14_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex14_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex15_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex15f_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex16_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex18_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1f_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex20_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex20_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex21f_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex22_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex23_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex23_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex25_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex25_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex26_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex28_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex29_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex29_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_4.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_5.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_6.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_7.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_bjacobi.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_bjacobi_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_bjacobi_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_specest_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_specest_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_umfpack.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2f_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex30_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex32_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex34_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex38_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex39_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex40_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex42_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex43_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex43_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45_2.out >> ? 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src/ksp/ksp/examples/AlanTutorials20120409/output/ex56_0.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_4.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_5.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_plapack.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex6f_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex7_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex9_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/AlanRun >> ? src/ksp/ksp/examples/AlanTutorials20120410/data/ex33bc.data >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex1.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex10.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex11.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex11f.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex12.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex13.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex13f90.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex14f.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex15.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex15f.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex16.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex1f.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex2.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex20options >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex21f.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex22.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex22f.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex23.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex25.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex27.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex28.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex29.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex2f.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex3.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex30.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex31.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex32.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex34.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex38.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex39.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex4.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex40.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex41.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex41.m >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-fsschur.opts >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-mgschur.opts >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-mgschur_nestedfs.opts >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex42.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex43-solCx.h >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex43.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex44f.F90 >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex45.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex45f.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex46.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex47.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex49.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex5.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex50.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex51.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex52.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex53.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex54.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex54f.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex55.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex56.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex57f.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex58.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex6f.F >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex7.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex8.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex8g.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/ex9.c >> ? src/ksp/ksp/examples/AlanTutorials20120410/makefile >> ? src/ksp/ksp/examples/AlanTutorials20120410/out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_10.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_11.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_12.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_13.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_14.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_15.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_16.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_17.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_18.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_22.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_23.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_24.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_25.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_4.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_5.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_6.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_7.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_8.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_9.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_ILU.out >> ? >> src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_cg_singlereduction.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mpicrl.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mpicsrperm.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mumps.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mumps_redundant.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_seqcrl.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_seqcsrperm.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_umfpack.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex11_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex11f_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex13_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex13f90_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex14_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex14_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex15_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex15f_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex16_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex18_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1f_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex20_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex20_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex21f_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex22_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex23_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex23_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex25_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex25_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex26_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex28_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex29_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex29_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_4.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_5.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_6.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_7.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_bjacobi.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_bjacobi_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_bjacobi_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_specest_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_specest_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_umfpack.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2f_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex30_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex32_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex34_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex38_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex39_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex40_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex42_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex43_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex43_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45f_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex49_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex49_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex49_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex4_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex50.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex50_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex52_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex53.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_0.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54f.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex55_0.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex55_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex56_0.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex58.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_4.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_5.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_plapack.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex6f_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex7_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_1.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_2.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_3.out >> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex9_1.out >> >> _*cd config/BuildSystem >> hg parent*_ >> changeset: 2878:3d4bb7478b00 >> tag: tip >> user: Barry Smith >> date: Wed Nov 07 20:34:01 2012 -0600 >> summary: added support for --with-PACKAGENAME-pkg-config[=pathtosearch] >> >> _*hg tip*_ >> changeset: 2878:3d4bb7478b00 >> tag: tip >> user: Barry Smith >> date: Wed Nov 07 20:34:01 2012 -0600 >> summary: added support for --with-PACKAGENAME-pkg-config[=pathtosearch] >> >> >> _*hg status*_ >> no output >> >> _*hg pull*_ >> pulling from http://petsc.cs.iit.edu/petsc/BuildSystem >> searching for changes >> no changes found >> >> _*hg update*_ >> 0 files updated, 0 files merged, 0 files removed, 0 files unresolved >> >> _*hg status >> *_no output >> >> >> >> >>> please copy/paste the output of the following commands >>> >>> >>> hg parent >>> hg tip >>> hg status >>> hg pull >>> hg update >>> hg status >>> cd config/BuildSystem >>> hg parent >>> hg tip >>> hg status >>> hg pull >>> hg update >>> hg status >>> >>> Satish >>> >>> On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: >>> >>>> Thanks for your reply, Dr. Balay. >>>> However, I do not know how to get the latest version of petsc-dev >>>> except >>>> following http://www.mcs.anl.gov/petsc/developers/index.html >>>> |cd petsc-dev|| >>>> hg pull -u >>>> ||./$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py >>>> ||make >>>> >>>> Those are all what I did. Should I do something else? >>>> >>>> thanks, >>>> Alan >>>> | >>>>> On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: >>>>> >>>>>> Dear folks, >>>>>> I came across an error while making a code: >>>>>> makefile:7: *** missing separator. Stop. >>>>>> This happens after I was tying to update the petsc-dev with some >>>>>> error >>>>>> message; the configure.log, error.log and make.log are attached. I've >>>>>> already >>>>>> sent it to petsc-maint list. Is this makefile error related to the >>>>>> fail >>>>>> update? >>>>> This is a Mercurial clone >>>>> Defined "VERSION_HG" to >>>>> ""85e6055943e0711fccdec2d08caeba48971d3d55"" >>>>> Defined "VERSION_DATE_HG" to ""Fri Sep 23 14:46:14 2011 >>>>> -0700"" >>>>> Defined "VERSION_BS_HG" to >>>>> ""e9fd775ab2bf270a9204f7cbc33603292ac5b1d8"" >>>>> Defined "VERSION_BS_DATE_HG" to ""Fri Sep 16 17:33:47 2011 >>>>> +0200"" >>>>> <<<<< >>>>> >>>>> You don't have the latest petsc-dev. Can you pull the latest petsc-dev >>>>> and >>>>> retry? >>>>> >>>>> Satish >> From balay at mcs.anl.gov Thu Nov 8 14:02:31 2012 From: balay at mcs.anl.gov (Satish Balay) Date: Thu, 8 Nov 2012 14:02:31 -0600 (CST) Subject: [petsc-users] Fwd: error messages while updating petsc-dev In-Reply-To: <509C0EB9.2040804@gmail.com> References: <509BF8B8.6090104@gmail.com> <509BF986.7080801@gmail.com> <509C05FC.9070601@gmail.com> <509C0D7C.6070302@gmail.com> <509C0EB9.2040804@gmail.com> Message-ID: save './$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py' rm -rf externalpackages PETSC_ARCH and retry [configure/make] - and then send us the logs. Satish On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: > Yes, it has some problem when I run > > ./$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py > > and similar problem when I do 'make' > > I will send the log file to petsc-maint in 10 mins. > > thanks, > Alan > > > ok. Can you rerun configure now [or run > > ./$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py] and then 'make'. If you > > still have issues - send the new logs to petsc-maint. > > > > Satish > > > > On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: > > > > > *_hg parent_* > > > changeset: 24846:6e281c3f1f72 > > > tag: tip > > > user: Matthew G Knepley > > > date: Thu Nov 08 11:41:01 2012 -0500 > > > summary: Manual: Added part of a section on DMComplex > > > > > > _*hg tip*_ > > > changeset: 24846:6e281c3f1f72 > > > tag: tip > > > user: Matthew G Knepley > > > date: Thu Nov 08 11:41:01 2012 -0500 > > > summary: Manual: Added part of a section on DMComplex > > > > > > > > > _*hg status*_ > > > M src/ksp/ksp/examples/tutorials/ex10.c > > > M src/ksp/ksp/examples/tutorials/ex11f.F > > > M src/ksp/ksp/examples/tutorials/ex13f90.F > > > M src/ksp/ksp/examples/tutorials/ex14f.F > > > M src/ksp/ksp/examples/tutorials/ex15f.F > > > M src/ksp/ksp/examples/tutorials/ex1f.F > > > M src/ksp/ksp/examples/tutorials/ex21f.F > > > M src/ksp/ksp/examples/tutorials/ex27.c > > > M src/ksp/ksp/examples/tutorials/ex29.c > > > M src/ksp/ksp/examples/tutorials/ex2f.F > > > M src/ksp/ksp/examples/tutorials/ex3.c > > > M src/ksp/ksp/examples/tutorials/ex43-solCx.h > > > M src/ksp/ksp/examples/tutorials/ex43.c > > > M src/ksp/ksp/examples/tutorials/ex44f.F90 > > > M src/ksp/ksp/examples/tutorials/ex45.c > > > M src/ksp/ksp/examples/tutorials/ex49.c > > > M src/ksp/ksp/examples/tutorials/ex50.c > > > M src/ksp/ksp/examples/tutorials/ex52.c > > > M src/ksp/ksp/examples/tutorials/makefile > > > M src/ksp/ksp/examples/tutorials/output/ex10_24.out > > > M src/ksp/ksp/examples/tutorials/output/ex10_25.out > > > M src/ksp/ksp/examples/tutorials/output/ex22_1.out > > > M src/ksp/ksp/examples/tutorials/output/ex43_1.out > > > M src/ksp/ksp/examples/tutorials/output/ex4_1.out > > > A src/ksp/ksp/examples/tutorials/ex22.c > > > A src/ksp/ksp/examples/tutorials/ex47.c > > > ! src/ksp/ksp/examples/tutorials/data/elem_2d_pln_strn_v_25.txt > > > ! src/ksp/ksp/examples/tutorials/data/elem_2d_therm.txt > > > ! src/ksp/ksp/examples/tutorials/data/elem_3d_elast_v_25.txt > > > ! src/ksp/ksp/examples/tutorials/ex42-mgfs.opts > > > ! src/ksp/ksp/examples/tutorials/ex42-mgfs2.opts > > > ! src/ksp/ksp/examples/tutorials/output/ex4_0.out > > > ! src/ksp/ksp/examples/tutorials/output/ex4_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/AlanRun > > > ? src/ksp/ksp/examples/AlanTutorials20120409/Rank0Coord.xyz > > > ? src/ksp/ksp/examples/AlanTutorials20120409/Rank0plt3d.q > > > ? > > > src/ksp/ksp/examples/AlanTutorials20120409/data/elem_2d_pln_strn_v_25.txt > > > ? src/ksp/ksp/examples/AlanTutorials20120409/data/elem_2d_therm.txt > > > ? src/ksp/ksp/examples/AlanTutorials20120409/data/elem_3d_elast_v_25.txt > > > ? src/ksp/ksp/examples/AlanTutorials20120409/data/ex33bc.data > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex1.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex10.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex11.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex11f.F > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex12.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex13.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex13f90.F > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex14f.F > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex15.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex15f.F > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex16.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex1f.F > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex2.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex20options > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex21f.F > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex22.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex22f.F > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex23.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex25.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex27.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex28.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex29.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex2f.F > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex3.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex30.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex31.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex32.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex34.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex35.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex37.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex38.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex39.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex4.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex40.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex41.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex41.m > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-fsschur.opts > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgfs.opts > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgfs2.opts > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgschur.opts > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgschur_nestedfs.opts > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex43-solCx.h > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex43.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex44f.F90 > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex45.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex46.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex47.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex49.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex5.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex50.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex51.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex52.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex53.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex54.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex55.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex56.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex6f.F > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex7.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex8.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex8g.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex9.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/makefile > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_10.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_11.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_12.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_13.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_14.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_15.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_16.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_17.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_18.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_22.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_23.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_24.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_25.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_3.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_4.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_5.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_6.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_7.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_8.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_9.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_ILU.out > > > ? > > > src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_cg_singlereduction.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mpicrl.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mpicsrperm.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mumps.out > > > ? > > > src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mumps_redundant.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_seqcrl.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_seqcsrperm.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_umfpack.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex11_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex11f_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_3.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex13_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex13f90_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex14_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex14_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex15_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex15f_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex16_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex18_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_3.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1f_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex20_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex20_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex21f_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex22_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex23_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex23_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex25_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex26_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex29_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex29_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_3.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_4.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_5.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_6.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_7.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi_3.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_chebyest_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_chebyest_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_specest_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_specest_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_umfpack.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2f_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex30_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex32_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex38_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex39_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex40_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex42_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex43_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex45_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex45_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_3.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_0.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex52_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex53.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex54_0.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex54_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex55_0.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex55_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex56_0.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_3.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_4.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_5.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_plapack.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex6f_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex7_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_3.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex9_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/AlanRun > > > ? src/ksp/ksp/examples/AlanTutorials20120410/data/ex33bc.data > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex1.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex10.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex11.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex11f.F > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex12.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex13.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex13f90.F > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex14f.F > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex15.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex15f.F > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex16.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex1f.F > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex2.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex20options > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex21f.F > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex22.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex22f.F > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex23.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex25.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex27.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex28.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex29.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex2f.F > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex3.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex30.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex31.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex32.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex34.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex38.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex39.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex4.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex40.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex41.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex41.m > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-fsschur.opts > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-mgschur.opts > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-mgschur_nestedfs.opts > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex42.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex43-solCx.h > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex43.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex44f.F90 > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex45.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex45f.F > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex46.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex47.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex49.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex5.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex50.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex51.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex52.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex53.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex54.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex54f.F > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex55.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex56.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex57f.F > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex58.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex6f.F > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex7.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex8.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex8g.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex9.c > > > ? src/ksp/ksp/examples/AlanTutorials20120410/makefile > > > ? src/ksp/ksp/examples/AlanTutorials20120410/out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_10.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_11.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_12.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_13.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_14.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_15.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_16.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_17.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_18.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_22.out > > > ? 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src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mumps.out > > > ? > > > src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mumps_redundant.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_seqcrl.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_seqcsrperm.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_umfpack.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex11_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex11f_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_3.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex13_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex13f90_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex14_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex14_2.out > > > ? 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src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_specest_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_specest_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_umfpack.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2f_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex30_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex32_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex34_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex38_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex39_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex40_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex42_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex43_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex43_3.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45_2.out > > > ? 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src/ksp/ksp/examples/AlanTutorials20120410/output/ex56_0.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex58.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_3.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_4.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_5.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_plapack.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex6f_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex7_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_3.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex9_1.out > > > > > > > > > *_hg pull_* > > > pulling from http://petsc.cs.iit.edu/petsc/petsc-dev > > > searching for changes > > > no changes found > > > > > > > > > _*hg update*_ > > > 0 files updated, 0 files merged, 0 files removed, 0 files unresolved > > > > > > _*hg status > > > *_M src/ksp/ksp/examples/tutorials/ex10.c > > > M src/ksp/ksp/examples/tutorials/ex11f.F > > > M src/ksp/ksp/examples/tutorials/ex13f90.F > > > M src/ksp/ksp/examples/tutorials/ex14f.F > > > M src/ksp/ksp/examples/tutorials/ex15f.F > > > M src/ksp/ksp/examples/tutorials/ex1f.F > > > M src/ksp/ksp/examples/tutorials/ex21f.F > > > M src/ksp/ksp/examples/tutorials/ex27.c > > > M src/ksp/ksp/examples/tutorials/ex29.c > > > M src/ksp/ksp/examples/tutorials/ex2f.F > > > M src/ksp/ksp/examples/tutorials/ex3.c > > > M src/ksp/ksp/examples/tutorials/ex43-solCx.h > > > M src/ksp/ksp/examples/tutorials/ex43.c > > > M src/ksp/ksp/examples/tutorials/ex44f.F90 > > > M src/ksp/ksp/examples/tutorials/ex45.c > > > M src/ksp/ksp/examples/tutorials/ex49.c > > > M src/ksp/ksp/examples/tutorials/ex50.c > > > M src/ksp/ksp/examples/tutorials/ex52.c > > > M src/ksp/ksp/examples/tutorials/makefile > > > M src/ksp/ksp/examples/tutorials/output/ex10_24.out > > > M src/ksp/ksp/examples/tutorials/output/ex10_25.out > > > M src/ksp/ksp/examples/tutorials/output/ex22_1.out > > > M src/ksp/ksp/examples/tutorials/output/ex43_1.out > > > M src/ksp/ksp/examples/tutorials/output/ex4_1.out > > > A src/ksp/ksp/examples/tutorials/ex22.c > > > A src/ksp/ksp/examples/tutorials/ex47.c > > > ! src/ksp/ksp/examples/tutorials/data/elem_2d_pln_strn_v_25.txt > > > ! src/ksp/ksp/examples/tutorials/data/elem_2d_therm.txt > > > ! src/ksp/ksp/examples/tutorials/data/elem_3d_elast_v_25.txt > > > ! src/ksp/ksp/examples/tutorials/ex42-mgfs.opts > > > ! src/ksp/ksp/examples/tutorials/ex42-mgfs2.opts > > > ! src/ksp/ksp/examples/tutorials/output/ex4_0.out > > > ! src/ksp/ksp/examples/tutorials/output/ex4_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120409/AlanRun > > > ? src/ksp/ksp/examples/AlanTutorials20120409/Rank0Coord.xyz > > > ? src/ksp/ksp/examples/AlanTutorials20120409/Rank0plt3d.q > > > ? > > > src/ksp/ksp/examples/AlanTutorials20120409/data/elem_2d_pln_strn_v_25.txt > > > ? src/ksp/ksp/examples/AlanTutorials20120409/data/elem_2d_therm.txt > > > ? src/ksp/ksp/examples/AlanTutorials20120409/data/elem_3d_elast_v_25.txt > > > ? src/ksp/ksp/examples/AlanTutorials20120409/data/ex33bc.data > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex1.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex10.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex11.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex11f.F > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex12.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex13.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex13f90.F > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex14f.F > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex15.c > > > ? 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src/ksp/ksp/examples/AlanTutorials20120409/ex34.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex35.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex37.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex38.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex39.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex4.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex40.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex41.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex41.m > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-fsschur.opts > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgfs.opts > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgfs2.opts > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgschur.opts > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgschur_nestedfs.opts > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex43-solCx.h > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex43.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex44f.F90 > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex45.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex46.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex47.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex49.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex5.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex50.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex51.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex52.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex53.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex54.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex55.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex56.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex6f.F > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex7.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex8.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex8g.c > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex9.c > > > ? 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src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_specest_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_specest_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_umfpack.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2f_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex30_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex32_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex34_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex38_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex39_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex40_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex42_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex43_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex43_3.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45f_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex49_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex49_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex49_3.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex4_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex50.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex50_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex52_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex53.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_0.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54f.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex55_0.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex55_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex56_0.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex58.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_3.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_4.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_5.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_plapack.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex6f_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex7_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_1.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_2.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_3.out > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex9_1.out > > > > > > _*cd config/BuildSystem > > > hg parent*_ > > > changeset: 2878:3d4bb7478b00 > > > tag: tip > > > user: Barry Smith > > > date: Wed Nov 07 20:34:01 2012 -0600 > > > summary: added support for > > > --with-PACKAGENAME-pkg-config[=pathtosearch] > > > > > > _*hg tip*_ > > > changeset: 2878:3d4bb7478b00 > > > tag: tip > > > user: Barry Smith > > > date: Wed Nov 07 20:34:01 2012 -0600 > > > summary: added support for > > > --with-PACKAGENAME-pkg-config[=pathtosearch] > > > > > > > > > _*hg status*_ > > > no output > > > > > > _*hg pull*_ > > > pulling from http://petsc.cs.iit.edu/petsc/BuildSystem > > > searching for changes > > > no changes found > > > > > > _*hg update*_ > > > 0 files updated, 0 files merged, 0 files removed, 0 files unresolved > > > > > > _*hg status > > > *_no output > > > > > > > > > > > > > > > > please copy/paste the output of the following commands > > > > > > > > > > > > hg parent > > > > hg tip > > > > hg status > > > > hg pull > > > > hg update > > > > hg status > > > > cd config/BuildSystem > > > > hg parent > > > > hg tip > > > > hg status > > > > hg pull > > > > hg update > > > > hg status > > > > > > > > Satish > > > > > > > > On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: > > > > > > > > > Thanks for your reply, Dr. Balay. > > > > > However, I do not know how to get the latest version of > > > > > petsc-dev > > > > > except > > > > > following http://www.mcs.anl.gov/petsc/developers/index.html > > > > > |cd petsc-dev|| > > > > > hg pull -u > > > > > ||./$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py > > > > > ||make > > > > > > > > > > Those are all what I did. Should I do something else? > > > > > > > > > > thanks, > > > > > Alan > > > > > | > > > > > > On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: > > > > > > > > > > > > > Dear folks, > > > > > > > I came across an error while making a code: > > > > > > > makefile:7: *** missing separator. Stop. > > > > > > > This happens after I was tying to update the petsc-dev with > > > > > > > some > > > > > > > error > > > > > > > message; the configure.log, error.log and make.log are attached. > > > > > > > I've > > > > > > > already > > > > > > > sent it to petsc-maint list. Is this makefile error related to the > > > > > > > fail > > > > > > > update? > > > > > > This is a Mercurial clone > > > > > > Defined "VERSION_HG" to > > > > > > ""85e6055943e0711fccdec2d08caeba48971d3d55"" > > > > > > Defined "VERSION_DATE_HG" to ""Fri Sep 23 14:46:14 2011 > > > > > > -0700"" > > > > > > Defined "VERSION_BS_HG" to > > > > > > ""e9fd775ab2bf270a9204f7cbc33603292ac5b1d8"" > > > > > > Defined "VERSION_BS_DATE_HG" to ""Fri Sep 16 17:33:47 > > > > > > 2011 > > > > > > +0200"" > > > > > > <<<<< > > > > > > > > > > > > You don't have the latest petsc-dev. Can you pull the latest > > > > > > petsc-dev > > > > > > and > > > > > > retry? > > > > > > > > > > > > Satish > > > > > From balay at mcs.anl.gov Thu Nov 8 14:02:52 2012 From: balay at mcs.anl.gov (Satish Balay) Date: Thu, 8 Nov 2012 14:02:52 -0600 (CST) Subject: [petsc-users] Fwd: error messages while updating petsc-dev In-Reply-To: References: <509BF8B8.6090104@gmail.com> <509BF986.7080801@gmail.com> <509C05FC.9070601@gmail.com> Message-ID: Antony, perhaps you are replying to the wrong e-mail thread. satish On Thu, 8 Nov 2012, A.L. Siahaan wrote: > Hi, > These are the outputs : > > antony at gnw20pc1:~/code/petsc-dev$ hg parent > changeset: 24846:6e281c3f1f72 > tag: tip > user: Matthew G Knepley > date: Thu Nov 08 11:41:01 2012 -0500 > summary: Manual: Added part of a section on DMComplex > > antony at gnw20pc1:~/code/petsc-dev$ hg tip > changeset: 24846:6e281c3f1f72 > tag: tip > user: Matthew G Knepley > date: Thu Nov 08 11:41:01 2012 -0500 > summary: Manual: Added part of a section on DMComplex > > antony at gnw20pc1:~/code/petsc-dev$ hg status > ? configtest.mod0 > antony at gnw20pc1:~/code/petsc-dev$ hg pull > pulling from http://petsc.cs.iit.edu/petsc/petsc-dev > searching for changes > no changes found > pulling from http://petsc.cs.iit.edu/petsc/BuildSystem > searching for changes > no changes found > antony at gnw20pc1:~/code/petsc-dev$ hg update > 0 files updated, 0 files merged, 0 files removed, 0 files unresolved > antony at gnw20pc1:~/code/petsc-dev$ hg status > ? configtest.mod0 > antony at gnw20pc1:~/code/petsc-dev$ cd config/BuildSystem/ > antony at gnw20pc1:~/code/petsc-dev/config/BuildSystem$ hg parent > changeset: 2878:3d4bb7478b00 > tag: tip > user: Barry Smith > date: Wed Nov 07 20:34:01 2012 -0600 > summary: added support for --with-PACKAGENAME-pkg-config[=pathtosearch] > > antony at gnw20pc1:~/code/petsc-dev/config/BuildSystem$ hg tip > changeset: 2878:3d4bb7478b00 > tag: tip > user: Barry Smith > date: Wed Nov 07 20:34:01 2012 -0600 > summary: added support for --with-PACKAGENAME-pkg-config[=pathtosearch] > > antony at gnw20pc1:~/code/petsc-dev/config/BuildSystem$ hg status > antony at gnw20pc1:~/code/petsc-dev/config/BuildSystem$ hg pull > pulling from http://petsc.cs.iit.edu/petsc/BuildSystem > searching for changes > no changes found > antony at gnw20pc1:~/code/petsc-dev/config/BuildSystem$ hg update > 0 files updated, 0 files merged, 0 files removed, 0 files unresolved > antony at gnw20pc1:~/code/petsc-dev/config/BuildSystem$ hg status > antony at gnw20pc1:~/code/petsc-dev/config/BuildSystem$ > > Regards, > Antony > > On Nov 8 2012, Satish Balay wrote: > > > please copy/paste the output of the following commands > > > > > > hg parent > > hg tip > > hg status > > hg pull > > hg update > > hg status > > cd config/BuildSystem > > hg parent > > hg tip > > hg status > > hg pull > > hg update > > hg status > > > > Satish > > > > On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: > > > > > Thanks for your reply, Dr. Balay. > > > However, I do not know how to get the latest version of petsc-dev > > > except following http://www.mcs.anl.gov/petsc/developers/index.html > > > |cd petsc-dev|| > > > hg pull -u > > > ||./$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py > > > ||make > > > > > > Those are all what I did. Should I do something else? > > > > > > thanks, > > > Alan > > > | > > > > On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: > > > > > > Dear folks, > > > > > I came across an error while making a code: > > > > > makefile:7: *** missing separator. Stop. > > > > > This happens after I was tying to update the petsc-dev with > > > > > some error message; the configure.log, error.log and make.log are > > > > > attached. I've already sent it to petsc-maint list. Is this makefile > > > > > error related to the fail update? > > > > This is a Mercurial clone > > > > Defined "VERSION_HG" to > > > > ""85e6055943e0711fccdec2d08caeba48971d3d55"" > > > > Defined "VERSION_DATE_HG" to ""Fri Sep 23 14:46:14 2011 > > > > -0700"" > > > > Defined "VERSION_BS_HG" to > > > > ""e9fd775ab2bf270a9204f7cbc33603292ac5b1d8"" > > > > Defined "VERSION_BS_DATE_HG" to ""Fri Sep 16 17:33:47 2011 > > > > +0200"" <<<<< > > > > > You don't have the latest petsc-dev. Can you pull the latest > > > > petsc-dev and retry? > > > > > Satish > > > > > > > > > > > From als88 at cam.ac.uk Thu Nov 8 14:11:44 2012 From: als88 at cam.ac.uk (A.L. Siahaan) Date: 08 Nov 2012 20:11:44 +0000 Subject: [petsc-users] Fwd: error messages while updating petsc-dev In-Reply-To: References: <509BF8B8.6090104@gmail.com> <509BF986.7080801@gmail.com> <509C05FC.9070601@gmail.com> Message-ID: Sorry...I thought the previous email was replied to me. It has similar subject. Antony On Nov 8 2012, Satish Balay wrote: >Antony, > >perhaps you are replying to the wrong e-mail thread. > >satish > >On Thu, 8 Nov 2012, A.L. Siahaan wrote: > >> Hi, >> These are the outputs : >> >> antony at gnw20pc1:~/code/petsc-dev$ hg parent >> changeset: 24846:6e281c3f1f72 >> tag: tip >> user: Matthew G Knepley >> date: Thu Nov 08 11:41:01 2012 -0500 >> summary: Manual: Added part of a section on DMComplex >> >> antony at gnw20pc1:~/code/petsc-dev$ hg tip >> changeset: 24846:6e281c3f1f72 >> tag: tip >> user: Matthew G Knepley >> date: Thu Nov 08 11:41:01 2012 -0500 >> summary: Manual: Added part of a section on DMComplex >> >> antony at gnw20pc1:~/code/petsc-dev$ hg status ? configtest.mod0 >> antony at gnw20pc1:~/code/petsc-dev$ hg pull pulling from >> http://petsc.cs.iit.edu/petsc/petsc-dev searching for changes no changes >> found pulling from http://petsc.cs.iit.edu/petsc/BuildSystem searching >> for changes no changes found antony at gnw20pc1:~/code/petsc-dev$ hg update >> 0 files updated, 0 files merged, 0 files removed, 0 files unresolved >> antony at gnw20pc1:~/code/petsc-dev$ hg status ? configtest.mod0 >> antony at gnw20pc1:~/code/petsc-dev$ cd config/BuildSystem/ >> antony at gnw20pc1:~/code/petsc-dev/config/BuildSystem$ hg parent >> changeset: 2878:3d4bb7478b00 tag: tip user: Barry Smith >> date: Wed Nov 07 20:34:01 2012 -0600 summary: added >> support for --with-PACKAGENAME-pkg-config[=pathtosearch] >> >> antony at gnw20pc1:~/code/petsc-dev/config/BuildSystem$ hg tip changeset: >> 2878:3d4bb7478b00 tag: tip user: Barry Smith date: >> Wed Nov 07 20:34:01 2012 -0600 summary: added support for >> --with-PACKAGENAME-pkg-config[=pathtosearch] >> >> antony at gnw20pc1:~/code/petsc-dev/config/BuildSystem$ hg status >> antony at gnw20pc1:~/code/petsc-dev/config/BuildSystem$ hg pull >> pulling from http://petsc.cs.iit.edu/petsc/BuildSystem >> searching for changes >> no changes found >> antony at gnw20pc1:~/code/petsc-dev/config/BuildSystem$ hg update >> 0 files updated, 0 files merged, 0 files removed, 0 files unresolved >> antony at gnw20pc1:~/code/petsc-dev/config/BuildSystem$ hg status >> antony at gnw20pc1:~/code/petsc-dev/config/BuildSystem$ >> >> Regards, >> Antony >> >> On Nov 8 2012, Satish Balay wrote: >> >> > please copy/paste the output of the following commands >> > >> > >> > hg parent >> > hg tip >> > hg status >> > hg pull >> > hg update >> > hg status >> > cd config/BuildSystem >> > hg parent >> > hg tip >> > hg status >> > hg pull >> > hg update >> > hg status >> > >> > Satish >> > >> > On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: >> > >> > > Thanks for your reply, Dr. Balay. >> > > However, I do not know how to get the latest version of >> > > petsc-dev except following >> > > http://www.mcs.anl.gov/petsc/developers/index.html >> > > |cd petsc-dev|| >> > > hg pull -u >> > > ||./$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py >> > > ||make >> > > >> > > Those are all what I did. Should I do something else? >> > > >> > > thanks, >> > > Alan >> > > | >> > > > On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: >> > > > > > Dear folks, >> > > > > I came across an error while making a code: >> > > > > makefile:7: *** missing separator. Stop. >> > > > > This happens after I was tying to update the petsc-dev >> > > > > with > > >> > > some error message; the configure.log, error.log and make.log are > >> > > > attached. I've already sent it to petsc-maint list. Is this >> > > makefile > > error related to the fail update? >> > > > This is a Mercurial clone >> > > > Defined "VERSION_HG" to >> > > > ""85e6055943e0711fccdec2d08caeba48971d3d55"" >> > > > Defined "VERSION_DATE_HG" to ""Fri Sep 23 14:46:14 2011 > >> > > -0700"" >> > > > Defined "VERSION_BS_HG" to >> > > > ""e9fd775ab2bf270a9204f7cbc33603292ac5b1d8"" >> > > > Defined "VERSION_BS_DATE_HG" to ""Fri Sep 16 17:33:47 >> > > > 2011 > >> > > +0200"" <<<<< >> > > > > You don't have the latest petsc-dev. Can you pull the latest > >> > > petsc-dev and retry? >> > > > > Satish >> > > >> > > >> > >> > >> > > From zhenglun.wei at gmail.com Thu Nov 8 14:40:44 2012 From: zhenglun.wei at gmail.com (Zhenglun (Alan) Wei) Date: Thu, 08 Nov 2012 14:40:44 -0600 Subject: [petsc-users] Fwd: error messages while updating petsc-dev In-Reply-To: References: <509BF8B8.6090104@gmail.com> <509BF986.7080801@gmail.com> <509C05FC.9070601@gmail.com> <509C0D7C.6070302@gmail.com> <509C0EB9.2040804@gmail.com> Message-ID: <509C18CC.7010400@gmail.com> Dear Satish, It is amazing that it works. However, I still have the problem when I was trying to 'make ex45' in /src/ksp/ksp/example/tutorial saying: makefile:7: *** missing separator. Stop. thanks, Alan > save './$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py' > > rm -rf externalpackages PETSC_ARCH > > and retry [configure/make] - and then send us the logs. > > Satish > > On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: > >> Yes, it has some problem when I run >> >> ./$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py >> >> and similar problem when I do 'make' >> >> I will send the log file to petsc-maint in 10 mins. >> >> thanks, >> Alan >> >>> ok. Can you rerun configure now [or run >>> ./$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py] and then 'make'. If you >>> still have issues - send the new logs to petsc-maint. >>> >>> Satish >>> >>> On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: >>> >>>> *_hg parent_* >>>> changeset: 24846:6e281c3f1f72 >>>> tag: tip >>>> user: Matthew G Knepley >>>> date: Thu Nov 08 11:41:01 2012 -0500 >>>> summary: Manual: Added part of a section on DMComplex >>>> >>>> _*hg tip*_ >>>> changeset: 24846:6e281c3f1f72 >>>> tag: tip >>>> user: Matthew G Knepley >>>> date: Thu Nov 08 11:41:01 2012 -0500 >>>> summary: Manual: Added part of a section on DMComplex >>>> >>>> >>>> _*hg status*_ >>>> M src/ksp/ksp/examples/tutorials/ex10.c >>>> M src/ksp/ksp/examples/tutorials/ex11f.F >>>> M src/ksp/ksp/examples/tutorials/ex13f90.F >>>> M src/ksp/ksp/examples/tutorials/ex14f.F >>>> M src/ksp/ksp/examples/tutorials/ex15f.F >>>> M src/ksp/ksp/examples/tutorials/ex1f.F >>>> M src/ksp/ksp/examples/tutorials/ex21f.F >>>> M src/ksp/ksp/examples/tutorials/ex27.c >>>> M src/ksp/ksp/examples/tutorials/ex29.c >>>> M src/ksp/ksp/examples/tutorials/ex2f.F >>>> M src/ksp/ksp/examples/tutorials/ex3.c >>>> M src/ksp/ksp/examples/tutorials/ex43-solCx.h >>>> M src/ksp/ksp/examples/tutorials/ex43.c >>>> M src/ksp/ksp/examples/tutorials/ex44f.F90 >>>> M src/ksp/ksp/examples/tutorials/ex45.c >>>> M src/ksp/ksp/examples/tutorials/ex49.c >>>> M src/ksp/ksp/examples/tutorials/ex50.c >>>> M src/ksp/ksp/examples/tutorials/ex52.c >>>> M src/ksp/ksp/examples/tutorials/makefile >>>> M src/ksp/ksp/examples/tutorials/output/ex10_24.out >>>> M src/ksp/ksp/examples/tutorials/output/ex10_25.out >>>> M src/ksp/ksp/examples/tutorials/output/ex22_1.out >>>> M src/ksp/ksp/examples/tutorials/output/ex43_1.out >>>> M src/ksp/ksp/examples/tutorials/output/ex4_1.out >>>> A src/ksp/ksp/examples/tutorials/ex22.c >>>> A src/ksp/ksp/examples/tutorials/ex47.c >>>> ! src/ksp/ksp/examples/tutorials/data/elem_2d_pln_strn_v_25.txt >>>> ! src/ksp/ksp/examples/tutorials/data/elem_2d_therm.txt >>>> ! src/ksp/ksp/examples/tutorials/data/elem_3d_elast_v_25.txt >>>> ! src/ksp/ksp/examples/tutorials/ex42-mgfs.opts >>>> ! src/ksp/ksp/examples/tutorials/ex42-mgfs2.opts >>>> ! src/ksp/ksp/examples/tutorials/output/ex4_0.out >>>> ! src/ksp/ksp/examples/tutorials/output/ex4_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/AlanRun >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/Rank0Coord.xyz >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/Rank0plt3d.q >>>> ? >>>> src/ksp/ksp/examples/AlanTutorials20120409/data/elem_2d_pln_strn_v_25.txt >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/data/elem_2d_therm.txt >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/data/elem_3d_elast_v_25.txt >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/data/ex33bc.data >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex1.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex10.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex11.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex11f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex12.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex13.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex13f90.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex14f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex15.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex15f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex16.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex1f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex2.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex20options >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex21f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex22.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex22f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex23.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex25.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex27.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex28.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex29.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex2f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex3.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex30.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex31.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex32.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex34.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex35.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex37.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex38.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex39.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex4.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex40.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex41.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex41.m >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-fsschur.opts >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgfs.opts >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgfs2.opts >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgschur.opts >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgschur_nestedfs.opts >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex42.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex43-solCx.h >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex43.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex44f.F90 >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex45.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex46.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex47.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex49.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex5.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex50.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex51.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex52.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex53.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex54.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex55.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex56.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex6f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex7.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex8.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex8g.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex9.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/makefile >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_10.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_11.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_12.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_13.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_14.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_15.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_16.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_17.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_18.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_22.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_23.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_24.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_25.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_4.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_5.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_6.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_7.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_8.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_9.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_ILU.out >>>> ? >>>> src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_cg_singlereduction.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mpicrl.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mpicsrperm.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mumps.out >>>> ? >>>> src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mumps_redundant.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_seqcrl.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_seqcsrperm.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_umfpack.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex11_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex11f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex13_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex13f90_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex14_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex14_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex15_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex15f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex16_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex18_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex20_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex20_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex21f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex22_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex23_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex23_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex25_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex26_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex29_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex29_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_4.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_5.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_6.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_7.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_chebyest_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_chebyest_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_specest_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_specest_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_umfpack.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex30_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex32_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex38_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex39_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex40_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex42_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex43_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex45_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex45_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_0.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex52_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex53.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex54_0.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex54_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex55_0.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex55_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex56_0.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_4.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_5.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_plapack.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex6f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex7_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex9_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/AlanRun >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/data/ex33bc.data >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex1.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex10.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex11.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex11f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex12.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex13.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex13f90.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex14f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex15.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex15f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex16.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex1f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex2.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex20options >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex21f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex22.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex22f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex23.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex25.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex27.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex28.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex29.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex2f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex3.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex30.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex31.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex32.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex34.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex38.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex39.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex4.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex40.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex41.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex41.m >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-fsschur.opts >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-mgschur.opts >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-mgschur_nestedfs.opts >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex42.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex43-solCx.h >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex43.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex44f.F90 >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex45.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex45f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex46.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex47.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex49.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex5.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex50.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex51.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex52.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex53.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex54.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex54f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex55.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex56.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex57f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex58.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex6f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex7.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex8.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex8g.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex9.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/makefile >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_10.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_11.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_12.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_13.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_14.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_15.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_16.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_17.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_18.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_22.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_23.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_24.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_25.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_4.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_5.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_6.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_7.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_8.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_9.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_ILU.out >>>> ? >>>> src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_cg_singlereduction.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mpicrl.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mpicsrperm.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mumps.out >>>> ? >>>> src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mumps_redundant.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_seqcrl.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_seqcsrperm.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_umfpack.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex11_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex11f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex13_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex13f90_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex14_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex14_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex15_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex15f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex16_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex18_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex20_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex20_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex21f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex22_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex23_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex23_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex25_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex25_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex26_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex28_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex29_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex29_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_4.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_5.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_6.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_7.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_bjacobi.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_bjacobi_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_bjacobi_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_specest_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_specest_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_umfpack.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex30_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex32_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex34_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex38_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex39_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex40_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex42_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex43_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex43_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex49_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex49_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex49_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex4_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex50.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex50_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex52_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex53.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_0.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54f.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex55_0.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex55_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex56_0.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex58.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_4.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_5.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_plapack.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex6f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex7_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex9_1.out >>>> >>>> >>>> *_hg pull_* >>>> pulling from http://petsc.cs.iit.edu/petsc/petsc-dev >>>> searching for changes >>>> no changes found >>>> >>>> >>>> _*hg update*_ >>>> 0 files updated, 0 files merged, 0 files removed, 0 files unresolved >>>> >>>> _*hg status >>>> *_M src/ksp/ksp/examples/tutorials/ex10.c >>>> M src/ksp/ksp/examples/tutorials/ex11f.F >>>> M src/ksp/ksp/examples/tutorials/ex13f90.F >>>> M src/ksp/ksp/examples/tutorials/ex14f.F >>>> M src/ksp/ksp/examples/tutorials/ex15f.F >>>> M src/ksp/ksp/examples/tutorials/ex1f.F >>>> M src/ksp/ksp/examples/tutorials/ex21f.F >>>> M src/ksp/ksp/examples/tutorials/ex27.c >>>> M src/ksp/ksp/examples/tutorials/ex29.c >>>> M src/ksp/ksp/examples/tutorials/ex2f.F >>>> M src/ksp/ksp/examples/tutorials/ex3.c >>>> M src/ksp/ksp/examples/tutorials/ex43-solCx.h >>>> M src/ksp/ksp/examples/tutorials/ex43.c >>>> M src/ksp/ksp/examples/tutorials/ex44f.F90 >>>> M src/ksp/ksp/examples/tutorials/ex45.c >>>> M src/ksp/ksp/examples/tutorials/ex49.c >>>> M src/ksp/ksp/examples/tutorials/ex50.c >>>> M src/ksp/ksp/examples/tutorials/ex52.c >>>> M src/ksp/ksp/examples/tutorials/makefile >>>> M src/ksp/ksp/examples/tutorials/output/ex10_24.out >>>> M src/ksp/ksp/examples/tutorials/output/ex10_25.out >>>> M src/ksp/ksp/examples/tutorials/output/ex22_1.out >>>> M src/ksp/ksp/examples/tutorials/output/ex43_1.out >>>> M src/ksp/ksp/examples/tutorials/output/ex4_1.out >>>> A src/ksp/ksp/examples/tutorials/ex22.c >>>> A src/ksp/ksp/examples/tutorials/ex47.c >>>> ! src/ksp/ksp/examples/tutorials/data/elem_2d_pln_strn_v_25.txt >>>> ! src/ksp/ksp/examples/tutorials/data/elem_2d_therm.txt >>>> ! src/ksp/ksp/examples/tutorials/data/elem_3d_elast_v_25.txt >>>> ! src/ksp/ksp/examples/tutorials/ex42-mgfs.opts >>>> ! src/ksp/ksp/examples/tutorials/ex42-mgfs2.opts >>>> ! src/ksp/ksp/examples/tutorials/output/ex4_0.out >>>> ! src/ksp/ksp/examples/tutorials/output/ex4_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/AlanRun >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/Rank0Coord.xyz >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/Rank0plt3d.q >>>> ? >>>> src/ksp/ksp/examples/AlanTutorials20120409/data/elem_2d_pln_strn_v_25.txt >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/data/elem_2d_therm.txt >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/data/elem_3d_elast_v_25.txt >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/data/ex33bc.data >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex1.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex10.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex11.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex11f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex12.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex13.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex13f90.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex14f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex15.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex15f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex16.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex1f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex2.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex20options >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex21f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex22.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex22f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex23.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex25.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex27.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex28.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex29.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex2f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex3.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex30.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex31.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex32.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex34.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex35.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex37.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex38.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex39.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex4.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex40.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex41.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex41.m >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-fsschur.opts >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgfs.opts >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgfs2.opts >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgschur.opts >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgschur_nestedfs.opts >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex42.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex43-solCx.h >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex43.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex44f.F90 >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex45.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex46.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex47.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex49.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex5.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex50.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex51.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex52.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex53.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex54.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex55.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex56.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex6f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex7.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex8.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex8g.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/ex9.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/makefile >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_10.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_11.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_12.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_13.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_14.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_15.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_16.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_17.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_18.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_22.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_23.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_24.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_25.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_4.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_5.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_6.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_7.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_8.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_9.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_ILU.out >>>> ? >>>> src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_cg_singlereduction.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mpicrl.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mpicsrperm.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mumps.out >>>> ? >>>> src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mumps_redundant.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_seqcrl.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_seqcsrperm.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_umfpack.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex11_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex11f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex13_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex13f90_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex14_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex14_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex15_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex15f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex16_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex18_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex20_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex20_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex21f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex22_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex23_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex23_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex25_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex26_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex29_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex29_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_4.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_5.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_6.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_7.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_chebyest_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_chebyest_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_specest_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_specest_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_umfpack.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex30_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex32_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex38_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex39_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex40_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex42_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex43_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex45_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex45_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_0.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex52_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex53.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex54_0.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex54_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex55_0.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex55_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex56_0.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_4.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_5.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_plapack.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex6f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex7_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex9_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/AlanRun >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/data/ex33bc.data >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex1.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex10.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex11.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex11f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex12.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex13.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex13f90.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex14f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex15.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex15f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex16.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex1f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex2.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex20options >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex21f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex22.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex22f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex23.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex25.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex27.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex28.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex29.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex2f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex3.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex30.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex31.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex32.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex34.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex38.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex39.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex4.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex40.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex41.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex41.m >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-fsschur.opts >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-mgschur.opts >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-mgschur_nestedfs.opts >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex42.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex43-solCx.h >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex43.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex44f.F90 >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex45.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex45f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex46.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex47.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex49.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex5.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex50.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex51.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex52.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex53.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex54.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex54f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex55.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex56.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex57f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex58.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex6f.F >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex7.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex8.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex8g.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/ex9.c >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/makefile >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_10.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_11.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_12.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_13.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_14.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_15.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_16.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_17.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_18.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_22.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_23.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_24.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_25.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_4.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_5.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_6.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_7.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_8.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_9.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_ILU.out >>>> ? >>>> src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_cg_singlereduction.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mpicrl.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mpicsrperm.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mumps.out >>>> ? >>>> src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mumps_redundant.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_seqcrl.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_seqcsrperm.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_umfpack.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex11_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex11f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex13_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex13f90_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex14_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex14_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex15_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex15f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex16_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex18_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex20_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex20_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex21f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex22_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex23_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex23_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex25_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex25_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex26_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex28_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex29_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex29_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_4.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_5.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_6.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_7.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_bjacobi.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_bjacobi_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_bjacobi_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_specest_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_specest_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_umfpack.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex30_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex32_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex34_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex38_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex39_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex40_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex42_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex43_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex43_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex49_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex49_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex49_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex4_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex50.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex50_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex52_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex53.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_0.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54f.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex55_0.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex55_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex56_0.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex58.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_4.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_5.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_plapack.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex6f_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex7_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_1.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_2.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_3.out >>>> ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex9_1.out >>>> >>>> _*cd config/BuildSystem >>>> hg parent*_ >>>> changeset: 2878:3d4bb7478b00 >>>> tag: tip >>>> user: Barry Smith >>>> date: Wed Nov 07 20:34:01 2012 -0600 >>>> summary: added support for >>>> --with-PACKAGENAME-pkg-config[=pathtosearch] >>>> >>>> _*hg tip*_ >>>> changeset: 2878:3d4bb7478b00 >>>> tag: tip >>>> user: Barry Smith >>>> date: Wed Nov 07 20:34:01 2012 -0600 >>>> summary: added support for >>>> --with-PACKAGENAME-pkg-config[=pathtosearch] >>>> >>>> >>>> _*hg status*_ >>>> no output >>>> >>>> _*hg pull*_ >>>> pulling from http://petsc.cs.iit.edu/petsc/BuildSystem >>>> searching for changes >>>> no changes found >>>> >>>> _*hg update*_ >>>> 0 files updated, 0 files merged, 0 files removed, 0 files unresolved >>>> >>>> _*hg status >>>> *_no output >>>> >>>> >>>> >>>> >>>>> please copy/paste the output of the following commands >>>>> >>>>> >>>>> hg parent >>>>> hg tip >>>>> hg status >>>>> hg pull >>>>> hg update >>>>> hg status >>>>> cd config/BuildSystem >>>>> hg parent >>>>> hg tip >>>>> hg status >>>>> hg pull >>>>> hg update >>>>> hg status >>>>> >>>>> Satish >>>>> >>>>> On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: >>>>> >>>>>> Thanks for your reply, Dr. Balay. >>>>>> However, I do not know how to get the latest version of >>>>>> petsc-dev >>>>>> except >>>>>> following http://www.mcs.anl.gov/petsc/developers/index.html >>>>>> |cd petsc-dev|| >>>>>> hg pull -u >>>>>> ||./$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py >>>>>> ||make >>>>>> >>>>>> Those are all what I did. Should I do something else? >>>>>> >>>>>> thanks, >>>>>> Alan >>>>>> | >>>>>>> On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: >>>>>>> >>>>>>>> Dear folks, >>>>>>>> I came across an error while making a code: >>>>>>>> makefile:7: *** missing separator. Stop. >>>>>>>> This happens after I was tying to update the petsc-dev with >>>>>>>> some >>>>>>>> error >>>>>>>> message; the configure.log, error.log and make.log are attached. >>>>>>>> I've >>>>>>>> already >>>>>>>> sent it to petsc-maint list. Is this makefile error related to the >>>>>>>> fail >>>>>>>> update? >>>>>>> This is a Mercurial clone >>>>>>> Defined "VERSION_HG" to >>>>>>> ""85e6055943e0711fccdec2d08caeba48971d3d55"" >>>>>>> Defined "VERSION_DATE_HG" to ""Fri Sep 23 14:46:14 2011 >>>>>>> -0700"" >>>>>>> Defined "VERSION_BS_HG" to >>>>>>> ""e9fd775ab2bf270a9204f7cbc33603292ac5b1d8"" >>>>>>> Defined "VERSION_BS_DATE_HG" to ""Fri Sep 16 17:33:47 >>>>>>> 2011 >>>>>>> +0200"" >>>>>>> <<<<< >>>>>>> >>>>>>> You don't have the latest petsc-dev. Can you pull the latest >>>>>>> petsc-dev >>>>>>> and >>>>>>> retry? >>>>>>> >>>>>>> Satish >> From balay at mcs.anl.gov Thu Nov 8 14:43:29 2012 From: balay at mcs.anl.gov (Satish Balay) Date: Thu, 8 Nov 2012 14:43:29 -0600 (CST) Subject: [petsc-users] Fwd: error messages while updating petsc-dev In-Reply-To: <509C18CC.7010400@gmail.com> References: <509BF8B8.6090104@gmail.com> <509BF986.7080801@gmail.com> <509C05FC.9070601@gmail.com> <509C0D7C.6070302@gmail.com> <509C0EB9.2040804@gmail.com> <509C18CC.7010400@gmail.com> Message-ID: > > > > > M src/ksp/ksp/examples/tutorials/makefile You have modified the makefile [perhaps with bad syntax]. So look at the line number pointed by the error message - and fix it Or 'hg revert src/ksp/ksp/examples/tutorials/makefile' to get rid of your changes. Satish. On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: > Dear Satish, > It is amazing that it works. However, I still have the problem when I was > trying to 'make ex45' in /src/ksp/ksp/example/tutorial saying: > makefile:7: *** missing separator. Stop. > > thanks, > Alan > > save './$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py' > > > > rm -rf externalpackages PETSC_ARCH > > > > and retry [configure/make] - and then send us the logs. > > > > Satish > > > > On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: > > > > > Yes, it has some problem when I run > > > > > > ./$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py > > > > > > and similar problem when I do 'make' > > > > > > I will send the log file to petsc-maint in 10 mins. > > > > > > thanks, > > > Alan > > > > > > > ok. Can you rerun configure now [or run > > > > ./$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py] and then 'make'. If you > > > > still have issues - send the new logs to petsc-maint. > > > > > > > > Satish > > > > > > > > On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: > > > > > > > > > *_hg parent_* > > > > > changeset: 24846:6e281c3f1f72 > > > > > tag: tip > > > > > user: Matthew G Knepley > > > > > date: Thu Nov 08 11:41:01 2012 -0500 > > > > > summary: Manual: Added part of a section on DMComplex > > > > > > > > > > _*hg tip*_ > > > > > changeset: 24846:6e281c3f1f72 > > > > > tag: tip > > > > > user: Matthew G Knepley > > > > > date: Thu Nov 08 11:41:01 2012 -0500 > > > > > summary: Manual: Added part of a section on DMComplex > > > > > > > > > > > > > > > _*hg status*_ > > > > > M src/ksp/ksp/examples/tutorials/ex10.c > > > > > M src/ksp/ksp/examples/tutorials/ex11f.F > > > > > M src/ksp/ksp/examples/tutorials/ex13f90.F > > > > > M src/ksp/ksp/examples/tutorials/ex14f.F > > > > > M src/ksp/ksp/examples/tutorials/ex15f.F > > > > > M src/ksp/ksp/examples/tutorials/ex1f.F > > > > > M src/ksp/ksp/examples/tutorials/ex21f.F > > > > > M src/ksp/ksp/examples/tutorials/ex27.c > > > > > M src/ksp/ksp/examples/tutorials/ex29.c > > > > > M src/ksp/ksp/examples/tutorials/ex2f.F > > > > > M src/ksp/ksp/examples/tutorials/ex3.c > > > > > M src/ksp/ksp/examples/tutorials/ex43-solCx.h > > > > > M src/ksp/ksp/examples/tutorials/ex43.c > > > > > M src/ksp/ksp/examples/tutorials/ex44f.F90 > > > > > M src/ksp/ksp/examples/tutorials/ex45.c > > > > > M src/ksp/ksp/examples/tutorials/ex49.c > > > > > M src/ksp/ksp/examples/tutorials/ex50.c > > > > > M src/ksp/ksp/examples/tutorials/ex52.c > > > > > M src/ksp/ksp/examples/tutorials/makefile > > > > > M src/ksp/ksp/examples/tutorials/output/ex10_24.out > > > > > M src/ksp/ksp/examples/tutorials/output/ex10_25.out > > > > > M src/ksp/ksp/examples/tutorials/output/ex22_1.out > > > > > M src/ksp/ksp/examples/tutorials/output/ex43_1.out > > > > > M src/ksp/ksp/examples/tutorials/output/ex4_1.out > > > > > A src/ksp/ksp/examples/tutorials/ex22.c > > > > > A src/ksp/ksp/examples/tutorials/ex47.c > > > > > ! src/ksp/ksp/examples/tutorials/data/elem_2d_pln_strn_v_25.txt > > > > > ! src/ksp/ksp/examples/tutorials/data/elem_2d_therm.txt > > > > > ! src/ksp/ksp/examples/tutorials/data/elem_3d_elast_v_25.txt > > > > > ! src/ksp/ksp/examples/tutorials/ex42-mgfs.opts > > > > > ! src/ksp/ksp/examples/tutorials/ex42-mgfs2.opts > > > > > ! src/ksp/ksp/examples/tutorials/output/ex4_0.out > > > > > ! src/ksp/ksp/examples/tutorials/output/ex4_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/AlanRun > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/Rank0Coord.xyz > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/Rank0plt3d.q > > > > > ? > > > > > src/ksp/ksp/examples/AlanTutorials20120409/data/elem_2d_pln_strn_v_25.txt > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/data/elem_2d_therm.txt > > > > > ? > > > > > src/ksp/ksp/examples/AlanTutorials20120409/data/elem_3d_elast_v_25.txt > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/data/ex33bc.data > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex1.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex10.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex11.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex11f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex12.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex13.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex13f90.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex14f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex15.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex15f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex16.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex1f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex2.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex20options > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex21f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex22.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex22f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex23.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex25.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex27.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex28.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex29.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex2f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex3.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex30.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex31.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex32.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex34.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex35.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex37.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex38.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex39.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex4.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex40.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex41.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex41.m > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-fsschur.opts > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgfs.opts > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgfs2.opts > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgschur.opts > > > > > ? > > > > > src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgschur_nestedfs.opts > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex43-solCx.h > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex43.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex44f.F90 > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex45.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex46.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex47.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex49.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex5.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex50.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex51.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex52.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex53.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex54.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex55.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex56.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex6f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex7.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex8.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex8g.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex9.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/makefile > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_10.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_11.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_12.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_13.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_14.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_15.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_16.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_17.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_18.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_22.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_23.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_24.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_25.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_4.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_5.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_6.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_7.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_8.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_9.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_ILU.out > > > > > ? > > > > > src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_cg_singlereduction.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mpicrl.out > > > > > ? > > > > > src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mpicsrperm.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mumps.out > > > > > ? > > > > > src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mumps_redundant.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_seqcrl.out > > > > > ? > > > > > src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_seqcsrperm.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_umfpack.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex11_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex11f_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex13_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex13f90_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex14_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex14_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex15_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex15f_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex16_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex18_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1f_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex20_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex20_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex21f_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex22_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex23_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex23_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex25_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex26_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex29_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex29_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_4.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_5.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_6.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_7.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_chebyest_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_chebyest_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_specest_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_specest_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_umfpack.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2f_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex30_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex32_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex38_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex39_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex40_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex42_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex43_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex45_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex45_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_0.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex52_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex53.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex54_0.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex54_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex55_0.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex55_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex56_0.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_4.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_5.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex5_plapack.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex6f_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex7_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex9_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/AlanRun > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/data/ex33bc.data > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex1.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex10.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex11.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex11f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex12.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex13.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex13f90.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex14f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex15.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex15f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex16.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex1f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex2.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex20options > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex21f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex22.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex22f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex23.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex25.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex27.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex28.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex29.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex2f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex3.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex30.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex31.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex32.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex34.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex38.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex39.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex4.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex40.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex41.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex41.m > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-fsschur.opts > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-mgschur.opts > > > > > ? > > > > > src/ksp/ksp/examples/AlanTutorials20120410/ex42-mgschur_nestedfs.opts > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex42.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex43-solCx.h > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex43.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex44f.F90 > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex45.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex45f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex46.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex47.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex49.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex5.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex50.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex51.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex52.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex53.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex54.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex54f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex55.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex56.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex57f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex58.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex6f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex7.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex8.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex8g.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex9.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/makefile > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_10.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_11.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_12.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_13.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_14.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_15.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_16.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_17.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_18.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_22.out > > > > > ? 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src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mumps.out > > > > > ? > > > > > src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mumps_redundant.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_seqcrl.out > > > > > ? > > > > > src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_seqcsrperm.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_umfpack.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex11_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex11f_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex13_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex13f90_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex14_1.out > > > > > ? 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src/ksp/ksp/examples/AlanTutorials20120410/output/ex7_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex9_1.out > > > > > > > > > > > > > > > *_hg pull_* > > > > > pulling from http://petsc.cs.iit.edu/petsc/petsc-dev > > > > > searching for changes > > > > > no changes found > > > > > > > > > > > > > > > _*hg update*_ > > > > > 0 files updated, 0 files merged, 0 files removed, 0 files unresolved > > > > > > > > > > _*hg status > > > > > *_M src/ksp/ksp/examples/tutorials/ex10.c > > > > > M src/ksp/ksp/examples/tutorials/ex11f.F > > > > > M src/ksp/ksp/examples/tutorials/ex13f90.F > > > > > M src/ksp/ksp/examples/tutorials/ex14f.F > > > > > M src/ksp/ksp/examples/tutorials/ex15f.F > > > > > M src/ksp/ksp/examples/tutorials/ex1f.F > > > > > M src/ksp/ksp/examples/tutorials/ex21f.F > > > > > M src/ksp/ksp/examples/tutorials/ex27.c > > > > > M src/ksp/ksp/examples/tutorials/ex29.c > > > > > M src/ksp/ksp/examples/tutorials/ex2f.F > > > > > M src/ksp/ksp/examples/tutorials/ex3.c > > > > > M src/ksp/ksp/examples/tutorials/ex43-solCx.h > > > > > M src/ksp/ksp/examples/tutorials/ex43.c > > > > > M src/ksp/ksp/examples/tutorials/ex44f.F90 > > > > > M src/ksp/ksp/examples/tutorials/ex45.c > > > > > M src/ksp/ksp/examples/tutorials/ex49.c > > > > > M src/ksp/ksp/examples/tutorials/ex50.c > > > > > M src/ksp/ksp/examples/tutorials/ex52.c > > > > > M src/ksp/ksp/examples/tutorials/makefile > > > > > M src/ksp/ksp/examples/tutorials/output/ex10_24.out > > > > > M src/ksp/ksp/examples/tutorials/output/ex10_25.out > > > > > M src/ksp/ksp/examples/tutorials/output/ex22_1.out > > > > > M src/ksp/ksp/examples/tutorials/output/ex43_1.out > > > > > M src/ksp/ksp/examples/tutorials/output/ex4_1.out > > > > > A src/ksp/ksp/examples/tutorials/ex22.c > > > > > A src/ksp/ksp/examples/tutorials/ex47.c > > > > > ! src/ksp/ksp/examples/tutorials/data/elem_2d_pln_strn_v_25.txt > > > > > ! src/ksp/ksp/examples/tutorials/data/elem_2d_therm.txt > > > > > ! src/ksp/ksp/examples/tutorials/data/elem_3d_elast_v_25.txt > > > > > ! src/ksp/ksp/examples/tutorials/ex42-mgfs.opts > > > > > ! src/ksp/ksp/examples/tutorials/ex42-mgfs2.opts > > > > > ! src/ksp/ksp/examples/tutorials/output/ex4_0.out > > > > > ! src/ksp/ksp/examples/tutorials/output/ex4_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/AlanRun > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/Rank0Coord.xyz > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/Rank0plt3d.q > > > > > ? > > > > > src/ksp/ksp/examples/AlanTutorials20120409/data/elem_2d_pln_strn_v_25.txt > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/data/elem_2d_therm.txt > > > > > ? > > > > > src/ksp/ksp/examples/AlanTutorials20120409/data/elem_3d_elast_v_25.txt > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/data/ex33bc.data > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex1.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex10.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex11.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex11f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex12.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex13.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex13f90.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex14f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex15.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex15f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex16.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex1f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex2.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex20options > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex21f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex22.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex22f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex23.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex25.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex27.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex28.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex29.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex2f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex3.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex30.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex31.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex32.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex34.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex35.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex37.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex38.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex39.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex4.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex40.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex41.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex41.m > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-fsschur.opts > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgfs.opts > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgfs2.opts > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgschur.opts > > > > > ? > > > > > src/ksp/ksp/examples/AlanTutorials20120409/ex42-mgschur_nestedfs.opts > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex42.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex43-solCx.h > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex43.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex44f.F90 > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex45.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex46.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex47.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex49.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex5.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex50.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex51.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex52.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex53.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex54.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex55.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex56.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex6f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex7.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex8.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex8g.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/ex9.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/makefile > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_10.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_11.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_12.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_13.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_14.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_15.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_16.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_17.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_18.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_22.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_23.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_24.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_25.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_4.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_5.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_6.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_7.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_8.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_9.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_ILU.out > > > > > ? > > > > > src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_cg_singlereduction.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mpicrl.out > > > > > ? > > > > > src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mpicsrperm.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mumps.out > > > > > ? > > > > > src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_mumps_redundant.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_seqcrl.out > > > > > ? > > > > > src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_seqcsrperm.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex10_umfpack.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex11_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex11f_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex12_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex13_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex13f90_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex14_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex14_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex15_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex15f_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex16_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex18_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex1f_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex20_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex20_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex21f_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex22_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex23_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex23_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex25_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex26_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex29_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex29_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_4.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_5.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_6.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_7.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_bjacobi_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_chebyest_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_chebyest_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_specest_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_specest_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2_umfpack.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex2f_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex30_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex32_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex38_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex39_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex40_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex42_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex43_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex45_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex45_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex49_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_0.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex4_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex52_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex53.out > > > > > ? 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src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex8g_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120409/output/ex9_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/AlanRun > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/data/ex33bc.data > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex1.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex10.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex11.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex11f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex12.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex13.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex13f90.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex14f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex15.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex15f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex16.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex1f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex2.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex20options > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex21f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex22.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex22f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex23.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex25.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex27.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex28.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex29.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex2f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex3.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex30.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex31.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex32.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex34.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex38.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex39.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex4.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex40.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex41.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex41.m > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-fsschur.opts > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex42-mgschur.opts > > > > > ? > > > > > src/ksp/ksp/examples/AlanTutorials20120410/ex42-mgschur_nestedfs.opts > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex42.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex43-solCx.h > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex43.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex44f.F90 > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex45.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex45f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex46.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex47.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex49.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex5.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex50.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex51.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex52.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex53.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex54.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex54f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex55.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex56.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex57f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex58.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex6f.F > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex7.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex8.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex8g.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/ex9.c > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/makefile > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_10.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_11.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_12.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_13.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_14.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_15.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_16.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_17.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_18.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_22.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_23.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_24.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_25.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_4.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_5.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_6.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_7.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_8.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_9.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_ILU.out > > > > > ? > > > > > src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_cg_singlereduction.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mpicrl.out > > > > > ? > > > > > src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mpicsrperm.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mumps.out > > > > > ? > > > > > src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_mumps_redundant.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_seqcrl.out > > > > > ? > > > > > src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_seqcsrperm.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex10_umfpack.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex11_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex11f_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex12_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex13_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex13f90_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex14_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex14_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex15_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex15f_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex16_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex18_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex1f_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex20_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex20_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex21f_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex22_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex23_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex23_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex25_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex25_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex26_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex28_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex29_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex29_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_4.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_5.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_6.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_7.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_bjacobi.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_bjacobi_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_bjacobi_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_specest_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_specest_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2_umfpack.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex2f_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex30_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex32_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex34_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex38_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex39_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex40_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex42_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex43_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex43_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex45f_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex49_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex49_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex49_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex4_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex50.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex50_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex52_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex53.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_0.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex54f.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex55_0.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex55_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex56_0.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex58.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_4.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_5.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex5_plapack.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex6f_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex7_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_1.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_2.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex8g_3.out > > > > > ? src/ksp/ksp/examples/AlanTutorials20120410/output/ex9_1.out > > > > > > > > > > _*cd config/BuildSystem > > > > > hg parent*_ > > > > > changeset: 2878:3d4bb7478b00 > > > > > tag: tip > > > > > user: Barry Smith > > > > > date: Wed Nov 07 20:34:01 2012 -0600 > > > > > summary: added support for > > > > > --with-PACKAGENAME-pkg-config[=pathtosearch] > > > > > > > > > > _*hg tip*_ > > > > > changeset: 2878:3d4bb7478b00 > > > > > tag: tip > > > > > user: Barry Smith > > > > > date: Wed Nov 07 20:34:01 2012 -0600 > > > > > summary: added support for > > > > > --with-PACKAGENAME-pkg-config[=pathtosearch] > > > > > > > > > > > > > > > _*hg status*_ > > > > > no output > > > > > > > > > > _*hg pull*_ > > > > > pulling from http://petsc.cs.iit.edu/petsc/BuildSystem > > > > > searching for changes > > > > > no changes found > > > > > > > > > > _*hg update*_ > > > > > 0 files updated, 0 files merged, 0 files removed, 0 files unresolved > > > > > > > > > > _*hg status > > > > > *_no output > > > > > > > > > > > > > > > > > > > > > > > > > > please copy/paste the output of the following commands > > > > > > > > > > > > > > > > > > hg parent > > > > > > hg tip > > > > > > hg status > > > > > > hg pull > > > > > > hg update > > > > > > hg status > > > > > > cd config/BuildSystem > > > > > > hg parent > > > > > > hg tip > > > > > > hg status > > > > > > hg pull > > > > > > hg update > > > > > > hg status > > > > > > > > > > > > Satish > > > > > > > > > > > > On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: > > > > > > > > > > > > > Thanks for your reply, Dr. Balay. > > > > > > > However, I do not know how to get the latest version of > > > > > > > petsc-dev > > > > > > > except > > > > > > > following http://www.mcs.anl.gov/petsc/developers/index.html > > > > > > > |cd petsc-dev|| > > > > > > > hg pull -u > > > > > > > ||./$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py > > > > > > > ||make > > > > > > > > > > > > > > Those are all what I did. Should I do something else? > > > > > > > > > > > > > > thanks, > > > > > > > Alan > > > > > > > | > > > > > > > > On Thu, 8 Nov 2012, Zhenglun (Alan) Wei wrote: > > > > > > > > > > > > > > > > > Dear folks, > > > > > > > > > I came across an error while making a code: > > > > > > > > > makefile:7: *** missing separator. Stop. > > > > > > > > > This happens after I was tying to update the petsc-dev > > > > > > > > > with > > > > > > > > > some > > > > > > > > > error > > > > > > > > > message; the configure.log, error.log and make.log are > > > > > > > > > attached. > > > > > > > > > I've > > > > > > > > > already > > > > > > > > > sent it to petsc-maint list. Is this makefile error related to > > > > > > > > > the > > > > > > > > > fail > > > > > > > > > update? > > > > > > > > This is a Mercurial clone > > > > > > > > Defined "VERSION_HG" to > > > > > > > > ""85e6055943e0711fccdec2d08caeba48971d3d55"" > > > > > > > > Defined "VERSION_DATE_HG" to ""Fri Sep 23 14:46:14 > > > > > > > > 2011 > > > > > > > > -0700"" > > > > > > > > Defined "VERSION_BS_HG" to > > > > > > > > ""e9fd775ab2bf270a9204f7cbc33603292ac5b1d8"" > > > > > > > > Defined "VERSION_BS_DATE_HG" to ""Fri Sep 16 > > > > > > > > 17:33:47 > > > > > > > > 2011 > > > > > > > > +0200"" > > > > > > > > <<<<< > > > > > > > > > > > > > > > > You don't have the latest petsc-dev. Can you pull the latest > > > > > > > > petsc-dev > > > > > > > > and > > > > > > > > retry? > > > > > > > > > > > > > > > > Satish > > > > > From zhenglun.wei at gmail.com Thu Nov 8 14:49:05 2012 From: zhenglun.wei at gmail.com (Zhenglun (Alan) Wei) Date: Thu, 08 Nov 2012 14:49:05 -0600 Subject: [petsc-users] A Question about Boundary Condition Message-ID: <509C1AC1.8090803@gmail.com> Dear all, I hope you're having a nice day. I'm working on the /src/ksp/ksp/example/tutorial/ex45.c right now and came across a problem with the boundary condition. It calls 'DMDACreate3d' in order to generate a structured mesh. However, it adopts 'DMDA_BOUNARY_NONE' for the ghost point along x, y, z direction. I wonder how does this work for the Neumann BC? What does the solver do when it calculate those points adjacent to the boundary point. I support it should have one layer ghost point in order to implement the Newmann BC. BTW, if I want to use the periodic BC in this case, should I just change 'DMDA_BOUNDARY_NONE' to 'DMDA_BONDARY_PERIODIC' in the direction that the periodic BC is applied? thanks, Alan From als88 at cam.ac.uk Thu Nov 8 14:54:37 2012 From: als88 at cam.ac.uk (A.L. Siahaan) Date: 08 Nov 2012 20:54:37 +0000 Subject: [petsc-users] MatSetNearNullSpace() or PCSetCoordinate for GAMG ? In-Reply-To: References: Message-ID: Referring to the following thread about setting nullspace and coordinate for GAMG : http://lists.mcs.anl.gov/pipermail/petsc-users/2012-April/012790.html Is there any difference of memory requirement (to set nullspace) between MatSetNearNullSpace() and PCSetCoordinate ? For PCSetCoordinate, is the order of x-y-z coordinate in thevector [0.x, 0.y, 0.z, 1.x, ..., N-1.z] with respect to the ordering of solution vector [0.u_x, 0.u_y, 0.u_z, 1.u_z, ..., N-1.u_z] ? I tried to use PCSetCoordinate for GAMG, but then I get an error : ============================================================ [0]PETSC ERROR: Floating point exception! [0]PETSC ERROR: Infinite or not-a-number generated in mdot, entry 0! ======================================================== I am wondering if it is due to the ordering of coordinate. Regards, Antony From mark.adams at columbia.edu Thu Nov 8 16:34:46 2012 From: mark.adams at columbia.edu (Mark F. Adams) Date: Thu, 8 Nov 2012 17:34:46 -0500 Subject: [petsc-users] MatSetNearNullSpace() or PCSetCoordinate for GAMG ? In-Reply-To: References: Message-ID: <70C34DB8-F083-42A3-92A2-B671B7F94278@columbia.edu> On Nov 8, 2012, at 3:54 PM, A.L. Siahaan wrote: > Referring to the following thread about setting nullspace and coordinate for GAMG : http://lists.mcs.anl.gov/pipermail/petsc-users/2012-April/012790.html > > Is there any difference of memory requirement (to set nullspace) between MatSetNearNullSpace() and PCSetCoordinate ? No, you can delete the data that your provide and the semantics of GAMG are exactly the same. > > For PCSetCoordinate, is the order of x-y-z coordinate in thevector [0.x, 0.y, 0.z, 1.x, ..., N-1.z] with respect to the ordering of solution vector [0.u_x, 0.u_y, 0.u_z, 1.u_z, ..., N-1.u_z] ? This seems obvious, maybe I'm missing something. > > I tried to use PCSetCoordinate for GAMG, but then I get an error : > ============================================================ > [0]PETSC ERROR: Floating point exception! > [0]PETSC ERROR: Infinite or not-a-number generated in mdot, entry 0! > ======================================================== > > I am wondering if it is due to the ordering of coordinate. > I doubt it. Try commenting out your setCoordinates line and see if that helps. > Regards, > Antony > > From knepley at gmail.com Thu Nov 8 17:09:50 2012 From: knepley at gmail.com (Matthew Knepley) Date: Thu, 8 Nov 2012 18:09:50 -0500 Subject: [petsc-users] A Question about Boundary Condition In-Reply-To: <509C1AC1.8090803@gmail.com> References: <509C1AC1.8090803@gmail.com> Message-ID: On Thu, Nov 8, 2012 at 3:49 PM, Zhenglun (Alan) Wei wrote: > Dear all, > I hope you're having a nice day. > I'm working on the /src/ksp/ksp/example/tutorial/ex45.c right now and > came across a problem with the boundary condition. > It calls 'DMDACreate3d' in order to generate a structured mesh. However, > it adopts 'DMDA_BOUNARY_NONE' for the ghost point along x, y, z > direction. I wonder how does this work for the Neumann BC? What does the > solver do when it calculate those points adjacent to the boundary point. > I support it should have one layer ghost point in order to implement the > Newmann BC. It does it by hand, shortening the solve domain accordingly. > BTW, if I want to use the periodic BC in this case, should I just change > 'DMDA_BOUNDARY_NONE' to 'DMDA_BONDARY_PERIODIC' in the direction that > the periodic BC is applied? Yes, it you want periodic, use BOUNDARY_PERIODIC. Matt > thanks, > Alan -- 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 From ghegde at purdue.edu Thu Nov 8 19:36:59 2012 From: ghegde at purdue.edu (Ganesh Hegde) Date: Thu, 8 Nov 2012 20:36:59 -0500 Subject: [petsc-users] Conjugate transpose for rectangular complex matrices In-Reply-To: References: Message-ID: It looks like I was doing the transpose in place using MAT_REUSE_MATRIX because of which it was giving the nonconformality error. It seems to have been resolved now. Thanks anyway. On Thu, Nov 8, 2012 at 1:58 PM, Barry Smith wrote: > > We need the entire error message and stack frames to see what happened. > Cut and paste all the output and send it to petsc-maint at mcs.anl.gov > > On Nov 8, 2012, at 11:55 AM, Ganesh Hegde wrote: > > > Hi, > > I have been using the MatHermitianTranspose method to get the conjugate > transpose for complex square matrices. > > To optimize code, I needed to make my matrix rectangular. > > Doing so and using the same function call gave me the following error > with code 60: > > 'Nonconforming object sizes' > > I then decided to do this in two steps - get the conjugate of the > rectangular complex matrix and then call MatTranspose. > > The error still persists. Can you suggest any alternatives to this > problem? > > Regards, > > -- > > Ganesh > > > > -- Ganesh -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghegde at purdue.edu Thu Nov 8 21:10:09 2012 From: ghegde at purdue.edu (Ganesh Hegde) Date: Thu, 8 Nov 2012 22:10:09 -0500 Subject: [petsc-users] improving efficiency of matrix multiplication by calling BLAS directly Message-ID: I have an application where I am multiplying several large, complex PETSc matrices (that could be sparse) with each other. This happens often enough during program execution that I am interested in looking for optimal solutions to this. The usual algorithm followed is initializing a PETSc matrix with the required dimensionality and specifying the sparsity pattern. They're then multiplied with each other. So my questions are as follows: 1) Could specifying a matrix as full instead of sparse improve speed by reducing overhead involved in processing sparse matrices? 2) If not, should BLAS routines be called directly from the code instead of PETSc calling them, to improve performance? Regards, -- Ganesh -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Thu Nov 8 22:28:49 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Thu, 8 Nov 2012 22:28:49 -0600 Subject: [petsc-users] improving efficiency of matrix multiplication by calling BLAS directly In-Reply-To: References: Message-ID: Only if your matrices are *not sparse*, by which we main that more than, say, 20% of the entries are nonzero. On Thu, Nov 8, 2012 at 9:10 PM, Ganesh Hegde wrote: > I have an application where I am multiplying several large, complex PETSc > matrices (that could be sparse) with each other. > This happens often enough during program execution that I am interested in > looking for optimal solutions to this. > The usual algorithm followed is initializing a PETSc matrix with the > required dimensionality and specifying the sparsity pattern. > They're then multiplied with each other. > So my questions are as follows: > 1) Could specifying a matrix as full instead of sparse improve speed by > reducing overhead involved in processing sparse matrices? > 2) If not, should BLAS routines be called directly from the code instead > of PETSc calling them, to improve performance? > Regards, > -- > Ganesh > > -------------- next part -------------- An HTML attachment was scrubbed... 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This email was intended for Matt Funk. Learn why this is included: http://www.linkedin.com/e/-r9oj6w-h9bca8zv-3a/plh/http%3A%2F%2Fhelp%2Elinkedin%2Ecom%2Fapp%2Fanswers%2Fdetail%2Fa_id%2F4788/-GXI/?hs=false&tok=3Fj0jm5t96YRs1 (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA. -------------- next part -------------- An HTML attachment was scrubbed... URL: From w_ang_temp at 163.com Fri Nov 9 09:05:01 2012 From: w_ang_temp at 163.com (w_ang_temp) Date: Fri, 9 Nov 2012 23:05:01 +0800 (CST) Subject: [petsc-users] How to use multigrid? In-Reply-To: References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> Message-ID: <60857783.ad35.13ae5b3e01f.Coremail.w_ang_temp@163.com> Hello,Jed Sorry again for the interruption. As you said, if I want to use Algebraic multigrid, I can just use '-pc_type gamg -pc_gamg_agg_nsmooths 1' in the command line. I think there are many other -pc_gamg_XXX parameters. How can I find all the -pc_gamg_XXX? Besides, I want to know more about AMG. Are there any details from PETSc, like manual, documentaion, FAQ, etc? Also, from the above post, I want to know that if AMG can not be used in 3.2 by command line option, because now I have to use 3.3 for using AMG. I just donot want to change my version 3.2 now. I am major in Civil Engineering and not good at math and programming. So please forgive my weakness. Thanks. Jim >At 2012-10-28 21:17:00,"Jed Brown" wrote: >Algebraic multigrid can be used directly, -pc_type gamg -pc_gamg_agg_nsmooths 1. Geometric either required that you use the PCMG interface to set >interpolation (and provide a coarse operator for non-Galerkin) or use a DM that provides coarsening capability. >What kind of problem are you solving? >>On Oct 28, 2012 6:09 AM, "w_ang_temp" wrote: >>Hello, >> I want to use the multigrid as a preconditioner. The introduction about it in the manual is little. >>So are there some typical examples or details about multigrid? Is it used just like other preconditioners >>like jacobi, sor, which can be simply used in the cammand line options? >> Thanks. > > Jim -------------- next part -------------- An HTML attachment was scrubbed... URL: From mark.adams at columbia.edu Fri Nov 9 09:15:34 2012 From: mark.adams at columbia.edu (Mark F. Adams) Date: Fri, 9 Nov 2012 10:15:34 -0500 Subject: [petsc-users] How to use multigrid? In-Reply-To: <60857783.ad35.13ae5b3e01f.Coremail.w_ang_temp@163.com> References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <60857783.ad35.13ae5b3e01f.Coremail.w_ang_temp@163.com> Message-ID: On Nov 9, 2012, at 10:05 AM, w_ang_temp wrote: > Hello,Jed > > Sorry again for the interruption. > > As you said, if I want to use Algebraic multigrid, I can just use '-pc_type gamg > -pc_gamg_agg_nsmooths 1' in the command line. I think there are many other -pc_gamg_XXX > parameters. How can I find all the -pc_gamg_XXX? -help > > Besides, I want to know more about AMG. Are there any details from PETSc, like manual, > documentaion, FAQ, etc? I would recommend the book "Multigrid" by Trottenberg, et al, and the classic "Multigrid Tutorial" is good to look at also. > Also, from the above post, I want to know that if AMG can not be used in 3.2 by command > line option, because now I have to use 3.3 for using AMG. I just donot want to change my > version 3.2 now. You can use 3.2 if you like (free country) but this code was developed a lot between 3.2 and 3.3. I forget what was in 3.2 exactly. If you have a straight forward problem and 3.2 works then its is probably OK for your current purposes. > > I am major in Civil Engineering and not good at math and programming. So please > forgive my weakness. > Thanks. > Jim > > > > > > > >At 2012-10-28 21:17:00,"Jed Brown" wrote: > >Algebraic multigrid can be used directly, -pc_type gamg -pc_gamg_agg_nsmooths 1. Geometric either required that you use the PCMG interface to set >interpolation (and provide a coarse operator for non-Galerkin) or use a DM that provides coarsening capability. > > >What kind of problem are you solving? > > >>On Oct 28, 2012 6:09 AM, "w_ang_temp" wrote: > >>Hello, > >> I want to use the multigrid as a preconditioner. The introduction about it in the manual is little. > >>So are there some typical examples or details about multigrid? Is it used just like other preconditioners > >>like jacobi, sor, which can be simply used in the cammand line options? > >> Thanks. > > > Jim > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From w_ang_temp at 163.com Fri Nov 9 09:28:02 2012 From: w_ang_temp at 163.com (w_ang_temp) Date: Fri, 9 Nov 2012 23:28:02 +0800 (CST) Subject: [petsc-users] How to use multigrid? In-Reply-To: References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <60857783.ad35.13ae5b3e01f.Coremail.w_ang_temp@163.com> Message-ID: <3e728b.116ef.13ae5c8f1c5.Coremail.w_ang_temp@163.com> By the way, as a graduate student, I find that it is difficult to write a paper just using PETSc to deal with a large problem. Because it seems that there is no an innovative idea by just using the available things. It is also not easy to get something new based on the src of PETSc. Any suggestions? Thanks. Jim -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Fri Nov 9 09:38:00 2012 From: knepley at gmail.com (Matthew Knepley) Date: Fri, 9 Nov 2012 10:38:00 -0500 Subject: [petsc-users] How to use multigrid? In-Reply-To: <3e728b.116ef.13ae5c8f1c5.Coremail.w_ang_temp@163.com> References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <60857783.ad35.13ae5b3e01f.Coremail.w_ang_temp@163.com> <3e728b.116ef.13ae5c8f1c5.Coremail.w_ang_temp@163.com> Message-ID: On Fri, Nov 9, 2012 at 10:28 AM, w_ang_temp wrote: > By the way, as a graduate student, I find that it is difficult to write a > paper just using PETSc > to deal with a large problem. Because it seems that there is no an > innovative idea by just using > the available things. It is also not easy to get something new based on the > src of PETSc. You are supposed to be writing papers about your results. Matt > Any suggestions? > Thanks. > Jim > > -- 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 From jedbrown at mcs.anl.gov Fri Nov 9 09:44:45 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Fri, 9 Nov 2012 09:44:45 -0600 Subject: [petsc-users] How to use multigrid? In-Reply-To: <3e728b.116ef.13ae5c8f1c5.Coremail.w_ang_temp@163.com> References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <60857783.ad35.13ae5b3e01f.Coremail.w_ang_temp@163.com> <3e728b.116ef.13ae5c8f1c5.Coremail.w_ang_temp@163.com> Message-ID: On Fri, Nov 9, 2012 at 9:28 AM, w_ang_temp wrote: > By the way, as a graduate student, I find that it is difficult to write a > paper just using PETSc > to deal with a large problem. Because it seems that there is no an > innovative idea by just using > the available things. > Reimplementing an existing method is not new either. Now there are many papers that reimplement existing methods under a new name, without citing its existing use, and usually with less rigorous analysis than earlier work. This is caused either by stubborn ignorance or intentional deception. It's not science and only survives due to negligent reviewers. Creating genuinely new methods that solve meaningful problems and work better than existing methods is Hard. To start with, it's important to understand the capabilities and limitations of existing methods. Unless your intended research area is pretty focused, expect to read at least 1000 papers and write dozens of experimental codes. You might be able to rely on your advisor to accelerate this process, but advisors are not always right. > It is also not easy to get something new based on the src of PETSc. > If you work in an application area, focus on the modeling and method components specific to your problem. Build the special ingredients using PETSc and let the library do the rest of the work. Better understanding of methods will help you do this faster and in more powerful ways. -------------- next part -------------- An HTML attachment was scrubbed... URL: From w_ang_temp at 163.com Fri Nov 9 10:14:22 2012 From: w_ang_temp at 163.com (w_ang_temp) Date: Sat, 10 Nov 2012 00:14:22 +0800 (CST) Subject: [petsc-users] How to use multigrid? In-Reply-To: References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <60857783.ad35.13ae5b3e01f.Coremail.w_ang_temp@163.com> <3e728b.116ef.13ae5c8f1c5.Coremail.w_ang_temp@163.com> Message-ID: <2b3d9910.11cc5.13ae5f35da1.Coremail.w_ang_temp@163.com> Sincerely thank you for your advices. Thanks Matthew, too. I will try my best. Jim >On 2012-11-09 23:44:45?"Jed Brown" ??? >>On Fri, Nov 9, 2012 at 9:28 AM, w_ang_temp wrote: >>By the way, as a graduate student, I find that it is difficult to write a paper just using PETSc >>to deal with a large problem. Because it seems that there is no an innovative idea by just using >>the available things. >Reimplementing an existing method is not new either. Now there are many papers that reimplement existing methods under a new name, without citing its >existing use, and usually with less rigorous analysis than earlier work. This is caused either by stubborn ignorance or intentional deception. It's not science >and only survives due to negligent reviewers. >Creating genuinely new methods that solve meaningful problems and work better than existing methods is Hard. To start with, it's important to understand >the capabilities and limitations of existing methods. Unless your intended research area is pretty focused, expect to read at least 1000 papers and write >dozens of experimental codes. You might be able to rely on your advisor to accelerate this process, but advisors are not always right. >>It is also not easy to get something new based on the src of PETSc. >If you work in an application area, focus on the modeling and method components specific to your problem. Build the special ingredients using PETSc and >let the library do the rest of the work. Better understanding of methods will help you do this faster and in more powerful ways. -------------- next part -------------- An HTML attachment was scrubbed... URL: From als88 at cam.ac.uk Fri Nov 9 10:37:43 2012 From: als88 at cam.ac.uk (A.L. Siahaan) Date: 09 Nov 2012 16:37:43 +0000 Subject: [petsc-users] How to use multigrid? In-Reply-To: References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <60857783.ad35.13ae5b3e01f.Coremail.w_ang_temp@163.com> Message-ID: Is PCGAMG a combination of AMG and geometric multigrid ? Do we have to choose either pure AMG (when using -pc_type gamg -pc_gamg_agg_nsmooths 1) or pure geometric MG (type="geo") ? From my thread search in this mailing list about using PCGAMG, it is mostly advised to use pure AMG (-pc_type gamg -pc_gamg_agg_nsmooths 1). Of all algebraic multigrid implemented or interfaced in PETSc, i.e. BoomerAMG (PCHypre), ML(PCML), and PCGAMG("agg"), what is the order of the cost (memory) to set up the preconditioner (setting nullspace etc) ? Regards, Antony On Nov 9 2012, Mark F. Adams wrote: > >On Nov 9, 2012, at 10:05 AM, w_ang_temp wrote: > >> Hello,Jed >> >> Sorry again for the interruption. >> >> As you said, if I want to use Algebraic multigrid, I can just use >> '-pc_type gamg -pc_gamg_agg_nsmooths 1' in the command line. I think >> there are many other -pc_gamg_XXX parameters. How can I find all the >> -pc_gamg_XXX? > >-help > >> >> Besides, I want to know more about AMG. Are there any details from >> PETSc, like manual, documentaion, FAQ, etc? > > I would recommend the book "Multigrid" by Trottenberg, et al, and the > classic "Multigrid Tutorial" is good to look at also. > >> Also, from the above post, I want to know that if AMG can not be >> used in 3.2 by command line option, because now I have to use 3.3 for >> using AMG. I just donot want to change my version 3.2 now. > > You can use 3.2 if you like (free country) but this code was developed a > lot between 3.2 and 3.3. I forget what was in 3.2 exactly. If you have a > straight forward problem and 3.2 works then its is probably OK for your > current purposes. > >> >> I am major in Civil Engineering and not good at math and >> programming. So please forgive my weakness. >> Thanks. >> Jim >> >> >> >> >> >> >> > At 2012-10-28 21:17:00,"Jed Brown" wrote: >> > Algebraic multigrid can be used directly, -pc_type gamg >> > -pc_gamg_agg_nsmooths 1. Geometric either required that you use the >> > PCMG interface to set >interpolation (and provide a coarse operator >> > for non-Galerkin) or use a DM that provides coarsening capability. >> >> >What kind of problem are you solving? >> >> >>On Oct 28, 2012 6:09 AM, "w_ang_temp" wrote: >> >>Hello, >> >> I want to use the multigrid as a preconditioner. The introduction >> >> about it in the manual is little. >> >> So are there some typical examples or details about multigrid? Is it >> >> used just like other preconditioners like jacobi, sor, which can be >> >> simply used in the cammand line options? >> >> Thanks. >> > > >> > > Jim >> >> >> >> > > From mark.adams at columbia.edu Fri Nov 9 11:09:58 2012 From: mark.adams at columbia.edu (Mark F. Adams) Date: Fri, 9 Nov 2012 12:09:58 -0500 Subject: [petsc-users] How to use multigrid? In-Reply-To: References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <60857783.ad35.13ae5b3e01f.Coremail.w_ang_temp@163.com> Message-ID: <3481C4F4-67A8-4D25-9316-041933CD2632@columbia.edu> On Nov 9, 2012, at 11:37 AM, "A.L. Siahaan" wrote: > Is PCGAMG a combination of AMG and geometric multigrid ? Do we have to choose either pure AMG (when using -pc_type gamg -pc_gamg_agg_nsmooths 1) or pure geometric MG (type="geo") ? Thing of GAMG as an AMG solver. "geo" is an unstructured GMG method that is there as a reference implementation, to stress the framework a bit, but is not for real use. > From my thread search in this mailing list about using PCGAMG, it is mostly advised to use pure AMG (-pc_type gamg -pc_gamg_agg_nsmooths 1). Yes > > Of all algebraic multigrid implemented or interfaced in PETSc, i.e. BoomerAMG (PCHypre), ML(PCML), and PCGAMG("agg"), what is the order of the cost (memory) to set up the preconditioner (setting nullspace etc) ? Not a simple question. ML and GAMG use very similar algorithms and ML is implemented in a more "native" way than hypre (GAMG is completely native). GAMG/ML are probably better for elasticity, hypre is great for 2D low order discretizations of Laplacian, and it is a very hardened implementation. hypre is not native so there are some things that don't work as well. > > Regards, > Antony > > > > On Nov 9 2012, Mark F. Adams wrote: > >> >> On Nov 9, 2012, at 10:05 AM, w_ang_temp wrote: >> >>> Hello,Jed >>> Sorry again for the interruption. >>> As you said, if I want to use Algebraic multigrid, I can just use '-pc_type gamg -pc_gamg_agg_nsmooths 1' in the command line. I think there are many other -pc_gamg_XXX parameters. How can I find all the -pc_gamg_XXX? >> >> -help >> >>> Besides, I want to know more about AMG. Are there any details from PETSc, like manual, documentaion, FAQ, etc? >> >> I would recommend the book "Multigrid" by Trottenberg, et al, and the classic "Multigrid Tutorial" is good to look at also. >> >>> Also, from the above post, I want to know that if AMG can not be used in 3.2 by command line option, because now I have to use 3.3 for using AMG. I just donot want to change my version 3.2 now. >> >> You can use 3.2 if you like (free country) but this code was developed a lot between 3.2 and 3.3. I forget what was in 3.2 exactly. If you have a straight forward problem and 3.2 works then its is probably OK for your current purposes. >> >>> I am major in Civil Engineering and not good at math and programming. So please forgive my weakness. >>> Thanks. >>> Jim > At 2012-10-28 21:17:00,"Jed Brown" wrote: > Algebraic multigrid can be used directly, -pc_type gamg > -pc_gamg_agg_nsmooths 1. Geometric either required that you use the > PCMG interface to set >interpolation (and provide a coarse operator > for non-Galerkin) or use a DM that provides coarsening capability. >>> >What kind of problem are you solving? >>> >>On Oct 28, 2012 6:09 AM, "w_ang_temp" wrote: >>> >>Hello, >>> >> I want to use the multigrid as a preconditioner. The introduction >> about it in the manual is little. >>> >> So are there some typical examples or details about multigrid? Is it >> used just like other preconditioners like jacobi, sor, which can be >> simply used in the cammand line options? >>> >> Thanks. >>> > > > > Jim >> >> > From reubendb at utk.edu Fri Nov 9 11:20:06 2012 From: reubendb at utk.edu (Reuben D. Budiardja) Date: Fri, 9 Nov 2012 12:20:06 -0500 Subject: [petsc-users] Benchmarking different PETSc installations Message-ID: <2218518.1FPX9NMvZ3@prometheus> Hello, I would like to compare / benchmark several different PETSc installations on my system. The differences may be: different compilers or compiler flags, different libraries used by PETSc (e.g. BLAS&LAPACK, and any other packages used by PETSc that I included in the build like SuperLU_Dist, Metis/ParMetis, Hypre, etc). Some of these libraries were provided by different vendors and some we built ourselves and I'd like to compare the performances as used by PETSc. So I am wondering if there's any kind of general PETSc benchmarking code out there that can do this. The more thorough parts of PETSc that gets exersized by the benchmark code the better, but even if only parts are tested it'd be useful too. Also I'm more interested on the benchmark code that can run with larger number of processors (e.g. order of hundreds and thousands). I've tried Google search but that hasn't yielded much of anything. So any help in pointing me to the right direction is greatly appreciated. Thank you RDB From als88 at cam.ac.uk Fri Nov 9 11:26:11 2012 From: als88 at cam.ac.uk (A.L. Siahaan) Date: 09 Nov 2012 17:26:11 +0000 Subject: [petsc-users] How to use multigrid? In-Reply-To: <3481C4F4-67A8-4D25-9316-041933CD2632@columbia.edu> References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <60857783.ad35.13ae5b3e01f.Coremail.w_ang_temp@163.com> <3481C4F4-67A8-4D25-9316-041933CD2632@columbia.edu> Message-ID: Thank's a lot, Mark ! What does 'native' mean here ? That it is PETSc's built-in and not interface ? Antony On Nov 9 2012, Mark F. Adams wrote: >> Of all algebraic multigrid implemented or interfaced in PETSc, i.e. >> BoomerAMG (PCHypre), ML(PCML), and PCGAMG("agg"), what is the order of >> the cost (memory) to set up the preconditioner (setting nullspace etc) ? > > Not a simple question. ML and GAMG use very similar algorithms and ML is > implemented in a more "native" way than hypre (GAMG is completely > native). GAMG/ML are probably better for elasticity, hypre is great for > 2D low order discretizations of Laplacian, and it is a very hardened > implementation. hypre is not native so there are some things that don't > work as well. > >> >> Regards, >> Antony >> From thomas.witkowski at tu-dresden.de Fri Nov 9 11:37:40 2012 From: thomas.witkowski at tu-dresden.de (Thomas Witkowski) Date: Fri, 09 Nov 2012 18:37:40 +0100 Subject: [petsc-users] How to use multigrid? In-Reply-To: <3481C4F4-67A8-4D25-9316-041933CD2632@columbia.edu> References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <60857783.ad35.13ae5b3e01f.Coremail.w_ang_temp@163.com> <3481C4F4-67A8-4D25-9316-041933CD2632@columbia.edu> Message-ID: <509D3F64.3040708@tu-dresden.de> While we're at it, can some of you tell me some world about parallel scaling of algebraic multigrid methods? In most of my codes I use them to precondition some simple blocks, e.g. Laplace matrix. I'm pretty sure that parallel scaling of my solver is limited mostly by scaling of the AMG method which is used. What are the expectations, when going to 10^3 or 10^4 cores? Thomas Am 09.11.2012 18:09, schrieb Mark F. Adams: > On Nov 9, 2012, at 11:37 AM, "A.L. Siahaan" wrote: > >> Is PCGAMG a combination of AMG and geometric multigrid ? Do we have to choose either pure AMG (when using -pc_type gamg -pc_gamg_agg_nsmooths 1) or pure geometric MG (type="geo") ? > Thing of GAMG as an AMG solver. "geo" is an unstructured GMG method that is there as a reference implementation, to stress the framework a bit, but is not for real use. > >> From my thread search in this mailing list about using PCGAMG, it is mostly advised to use pure AMG (-pc_type gamg -pc_gamg_agg_nsmooths 1). > Yes > >> Of all algebraic multigrid implemented or interfaced in PETSc, i.e. BoomerAMG (PCHypre), ML(PCML), and PCGAMG("agg"), what is the order of the cost (memory) to set up the preconditioner (setting nullspace etc) ? > Not a simple question. ML and GAMG use very similar algorithms and ML is implemented in a more "native" way than hypre (GAMG is completely native). GAMG/ML are probably better for elasticity, hypre is great for 2D low order discretizations of Laplacian, and it is a very hardened implementation. hypre is not native so there are some things that don't work as well. > >> Regards, >> Antony >> >> >> >> On Nov 9 2012, Mark F. Adams wrote: >> >>> On Nov 9, 2012, at 10:05 AM, w_ang_temp wrote: >>> >>>> Hello,Jed >>>> Sorry again for the interruption. >>>> As you said, if I want to use Algebraic multigrid, I can just use '-pc_type gamg -pc_gamg_agg_nsmooths 1' in the command line. I think there are many other -pc_gamg_XXX parameters. How can I find all the -pc_gamg_XXX? >>> -help >>> >>>> Besides, I want to know more about AMG. Are there any details from PETSc, like manual, documentaion, FAQ, etc? >>> I would recommend the book "Multigrid" by Trottenberg, et al, and the classic "Multigrid Tutorial" is good to look at also. >>> >>>> Also, from the above post, I want to know that if AMG can not be used in 3.2 by command line option, because now I have to use 3.3 for using AMG. I just donot want to change my version 3.2 now. >>> You can use 3.2 if you like (free country) but this code was developed a lot between 3.2 and 3.3. I forget what was in 3.2 exactly. If you have a straight forward problem and 3.2 works then its is probably OK for your current purposes. >>> >>>> I am major in Civil Engineering and not good at math and programming. So please forgive my weakness. >>>> Thanks. >>>> Jim > At 2012-10-28 21:17:00,"Jed Brown" wrote: > Algebraic multigrid can be used directly, -pc_type gamg > -pc_gamg_agg_nsmooths 1. Geometric either required that you use the > PCMG interface to set >interpolation (and provide a coarse operator > for non-Galerkin) or use a DM that provides coarsening capability. >>>>> What kind of problem are you solving? >>>>>> On Oct 28, 2012 6:09 AM, "w_ang_temp" wrote: >>>>>> Hello, >>>>>> I want to use the multigrid as a preconditioner. The introduction >> about it in the manual is little. >>>>>> So are there some typical examples or details about multigrid? Is it >> used just like other preconditioners like jacobi, sor, which can be >> simply used in the cammand line options? >>>>>> Thanks. >>>>>> > > Jim >>> From jedbrown at mcs.anl.gov Fri Nov 9 11:40:23 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Fri, 9 Nov 2012 11:40:23 -0600 Subject: [petsc-users] How to use multigrid? In-Reply-To: <509D3F64.3040708@tu-dresden.de> References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <60857783.ad35.13ae5b3e01f.Coremail.w_ang_temp@163.com> <3481C4F4-67A8-4D25-9316-041933CD2632@columbia.edu> <509D3F64.3040708@tu-dresden.de> Message-ID: Don't speculate, send -log_summary and information about the problem and machine. Some setup operations degrade, but solves should scale pretty well. On Fri, Nov 9, 2012 at 11:37 AM, Thomas Witkowski < thomas.witkowski at tu-dresden.de> wrote: > While we're at it, can some of you tell me some world about parallel > scaling of algebraic multigrid methods? In most of my codes I use them to > precondition some simple blocks, e.g. Laplace matrix. I'm pretty sure that > parallel scaling of my solver is limited mostly by scaling of the AMG > method which is used. What are the expectations, when going to 10^3 or 10^4 > cores? -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.witkowski at tu-dresden.de Fri Nov 9 11:43:55 2012 From: thomas.witkowski at tu-dresden.de (Thomas Witkowski) Date: Fri, 09 Nov 2012 18:43:55 +0100 Subject: [petsc-users] How to use multigrid? In-Reply-To: References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <60857783.ad35.13ae5b3e01f.Coremail.w_ang_temp@163.com> <3481C4F4-67A8-4D25-9316-041933CD2632@columbia.edu> <509D3F64.3040708@tu-dresden.de> Message-ID: <509D40DB.207@tu-dresden.de> :) It was just a question whether is makes sense to run my solver in this range of number of cores, or whether AMG by itself will not scale here anymore. As my computational time is limited, I have to think carefully when using 10^4 cores. Thomas Am 09.11.2012 18:40, schrieb Jed Brown: > Don't speculate, send -log_summary and information about the problem > and machine. Some setup operations degrade, but solves should scale > pretty well. > > On Fri, Nov 9, 2012 at 11:37 AM, Thomas Witkowski > > wrote: > > While we're at it, can some of you tell me some world about > parallel scaling of algebraic multigrid methods? In most of my > codes I use them to precondition some simple blocks, e.g. Laplace > matrix. I'm pretty sure that parallel scaling of my solver is > limited mostly by scaling of the AMG method which is used. What > are the expectations, when going to 10^3 or 10^4 cores? > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Fri Nov 9 11:49:40 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Fri, 9 Nov 2012 11:49:40 -0600 Subject: [petsc-users] How to use multigrid? In-Reply-To: <509D40DB.207@tu-dresden.de> References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <60857783.ad35.13ae5b3e01f.Coremail.w_ang_temp@163.com> <3481C4F4-67A8-4D25-9316-041933CD2632@columbia.edu> <509D3F64.3040708@tu-dresden.de> <509D40DB.207@tu-dresden.de> Message-ID: On Fri, Nov 9, 2012 at 11:43 AM, Thomas Witkowski < thomas.witkowski at tu-dresden.de> wrote: > :) It was just a question whether is makes sense to run my solver in this > range of number of cores, or whether AMG by itself will not scale here > anymore. As my computational time is limited, I have to think carefully > when using 10^4 cores. Yes, but do a shorter run before a long production run if you need an accurate estimate of how long it will take and how much memory it will need. Depending on the architecture, you can extrapolate, but be sure to control for subdomain sizes. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mark.adams at columbia.edu Fri Nov 9 11:50:35 2012 From: mark.adams at columbia.edu (Mark F. Adams) Date: Fri, 9 Nov 2012 12:50:35 -0500 Subject: [petsc-users] How to use multigrid? In-Reply-To: References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <60857783.ad35.13ae5b3e01f.Coremail.w_ang_temp@163.com> <3481C4F4-67A8-4D25-9316-041933CD2632@columbia.edu> Message-ID: <73AD5015-8A1A-4492-8E72-00753A9652E4@columbia.edu> yes On Nov 9, 2012, at 12:26 PM, "A.L. Siahaan" wrote: > Thank's a lot, Mark ! What does 'native' mean here ? That it is PETSc's built-in and not interface ? > > Antony > > On Nov 9 2012, Mark F. Adams wrote: > >>> Of all algebraic multigrid implemented or interfaced in PETSc, i.e. BoomerAMG (PCHypre), ML(PCML), and PCGAMG("agg"), what is the order of the cost (memory) to set up the preconditioner (setting nullspace etc) ? >> >> Not a simple question. ML and GAMG use very similar algorithms and ML is implemented in a more "native" way than hypre (GAMG is completely native). GAMG/ML are probably better for elasticity, hypre is great for 2D low order discretizations of Laplacian, and it is a very hardened implementation. hypre is not native so there are some things that don't work as well. >> >>> Regards, >>> Antony > > From als88 at cam.ac.uk Fri Nov 9 12:13:11 2012 From: als88 at cam.ac.uk (A.L. Siahaan) Date: 09 Nov 2012 18:13:11 +0000 Subject: [petsc-users] How to use multigrid? In-Reply-To: <73AD5015-8A1A-4492-8E72-00753A9652E4@columbia.edu> References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <60857783.ad35.13ae5b3e01f.Coremail.w_ang_temp@163.com> <3481C4F4-67A8-4D25-9316-041933CD2632@columbia.edu> <73AD5015-8A1A-4492-8E72-00753A9652E4@columbia.edu> Message-ID: When you mentioned that ML is implemented in a more "native" way than Hypre, did you mean that PCML is not exactly a PETSc's interface to the Trilinos ML ? On Nov 9 2012, Mark F. Adams wrote: >yes >On Nov 9, 2012, at 12:26 PM, "A.L. Siahaan" wrote: > >> Thank's a lot, Mark ! What does 'native' mean here ? That it is PETSc's >> built-in and not interface ? >> >> Antony >> >> On Nov 9 2012, Mark F. Adams wrote: >> >>>> Of all algebraic multigrid implemented or interfaced in PETSc, i.e. >>>> BoomerAMG (PCHypre), ML(PCML), and PCGAMG("agg"), what is the order of >>>> the cost (memory) to set up the preconditioner (setting nullspace etc) >>>> ? >>> >>> Not a simple question. ML and GAMG use very similar algorithms and ML >>> is implemented in a more "native" way than hypre (GAMG is completely >>> native). GAMG/ML are probably better for elasticity, hypre is great for >>> 2D low order discretizations of Laplacian, and it is a very hardened >>> implementation. hypre is not native so there are some things that don't >>> work as well. >>> >>>> Regards, >>>> Antony >> >> > > From jedbrown at mcs.anl.gov Fri Nov 9 12:23:31 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Fri, 9 Nov 2012 12:23:31 -0600 Subject: [petsc-users] How to use multigrid? In-Reply-To: References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <60857783.ad35.13ae5b3e01f.Coremail.w_ang_temp@163.com> <3481C4F4-67A8-4D25-9316-041933CD2632@columbia.edu> <73AD5015-8A1A-4492-8E72-00753A9652E4@columbia.edu> Message-ID: On Fri, Nov 9, 2012 at 12:13 PM, A.L. Siahaan wrote: > When you mentioned that ML is implemented in a more "native" way than > Hypre, did you mean that PCML is not exactly a PETSc's interface to the > Trilinos ML ? ML exposes the mulitgrid hierarchy, allowing great smoother and coarse grid flexibility, monitoring, and even composition with other systems. In contrast, BoomerAMG is a "black box" so only those methods they specifically support are available. -------------- next part -------------- An HTML attachment was scrubbed... URL: From stali at geology.wisc.edu Fri Nov 9 12:38:38 2012 From: stali at geology.wisc.edu (Tabrez Ali) Date: Fri, 09 Nov 2012 12:38:38 -0600 Subject: [petsc-users] Benchmarking different PETSc installations In-Reply-To: <2218518.1FPX9NMvZ3@prometheus> References: <2218518.1FPX9NMvZ3@prometheus> Message-ID: <509D4DAE.5000208@geology.wisc.edu> You can start by benchmarking MatMult which I guess is one of the heavily used kernels native to PETSc. Based on few runs (attached), which I tried a while back, I am yet to see a large difference across different compilers (for MatMult). Also for some reason I was not able to use -fast with Intel and -O3 with Open64 compilers (PETSc's build system was complaining and I dont exactly remember why). T On 11/09/2012 11:20 AM, Reuben D. Budiardja wrote: > Hello, > > I would like to compare / benchmark several different PETSc installations on my > system. The differences may be: different compilers or compiler flags, different > libraries used by PETSc (e.g. BLAS&LAPACK, and any other packages used by > PETSc that I included in the build like SuperLU_Dist, Metis/ParMetis, Hypre, > etc). Some of these libraries were provided by different vendors and some we > built ourselves and I'd like to compare the performances as used by PETSc. > > So I am wondering if there's any kind of general PETSc benchmarking code out > there that can do this. The more thorough parts of PETSc that gets exersized > by the benchmark code the better, but even if only parts are tested it'd be > useful too. Also I'm more interested on the benchmark code that can run with > larger number of processors (e.g. order of hundreds and thousands). I've tried > Google search but that hasn't yielded much of anything. So any help in > pointing me to the right direction is greatly appreciated. > > Thank you > RDB -- No one trusts a model except the one who wrote it; Everyone trusts an observation except the one who made it - Harlow Shapley -------------- next part -------------- An HTML attachment was scrubbed... URL: From mark.adams at columbia.edu Fri Nov 9 12:40:45 2012 From: mark.adams at columbia.edu (Mark F. Adams) Date: Fri, 9 Nov 2012 13:40:45 -0500 Subject: [petsc-users] How to use multigrid? In-Reply-To: <509D40DB.207@tu-dresden.de> References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <60857783.ad35.13ae5b3e01f.Coremail.w_ang_temp@163.com> <3481C4F4-67A8-4D25-9316-041933CD2632@columbia.edu> <509D3F64.3040708@tu-dresden.de> <509D40DB.207@tu-dresden.de> Message-ID: <75AB4AC1-C846-4A78-B0B7-CC658E5DFC7A@columbia.edu> If your machine can "scale" a dot product then it can scale AMG. That said, implementing AMG to scale well takes work. GAMG should be able to go to 10^4 processes. We are working on some scaling problems in the setup code and I'm not too sure what and where GAMG will break as you scale up. I'd be curious to know. hypre should scale pretty well. On Nov 9, 2012, at 12:43 PM, Thomas Witkowski wrote: > :) It was just a question whether is makes sense to run my solver in this range of number of cores, or whether AMG by itself will not scale here anymore. As my computational time is limited, I have to think carefully when using 10^4 cores. > > Thomas > > > Am 09.11.2012 18:40, schrieb Jed Brown: >> Don't speculate, send -log_summary and information about the problem and machine. Some setup operations degrade, but solves should scale pretty well. >> >> On Fri, Nov 9, 2012 at 11:37 AM, Thomas Witkowski wrote: >> While we're at it, can some of you tell me some world about parallel scaling of algebraic multigrid methods? In most of my codes I use them to precondition some simple blocks, e.g. Laplace matrix. I'm pretty sure that parallel scaling of my solver is limited mostly by scaling of the AMG method which is used. What are the expectations, when going to 10^3 or 10^4 cores? >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Fri Nov 9 12:43:36 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Fri, 9 Nov 2012 12:43:36 -0600 Subject: [petsc-users] Benchmarking different PETSc installations In-Reply-To: <2218518.1FPX9NMvZ3@prometheus> References: <2218518.1FPX9NMvZ3@prometheus> Message-ID: Run examples that are representative of a workload you are interested in. src/snes/examples/tutorials/ex5.c is a simple problem that is easy to understand. Use a 3D problem if that's what you're interested in. Run with -log_summary to get detailed information. Read the user's manual section on profiling for more details. On Fri, Nov 9, 2012 at 11:20 AM, Reuben D. Budiardja wrote: > Hello, > > I would like to compare / benchmark several different PETSc installations > on my > system. The differences may be: different compilers or compiler flags, > different > libraries used by PETSc (e.g. BLAS&LAPACK, and any other packages used by > PETSc that I included in the build like SuperLU_Dist, Metis/ParMetis, > Hypre, > etc). Some of these libraries were provided by different vendors and some > we > built ourselves and I'd like to compare the performances as used by PETSc. > > So I am wondering if there's any kind of general PETSc benchmarking code > out > there that can do this. The more thorough parts of PETSc that gets > exersized > by the benchmark code the better, but even if only parts are tested it'd be > useful too. Also I'm more interested on the benchmark code that can run > with > larger number of processors (e.g. order of hundreds and thousands). I've > tried > Google search but that hasn't yielded much of anything. So any help in > pointing me to the right direction is greatly appreciated. > > Thank you > RDB > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Fri Nov 9 12:46:46 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Fri, 9 Nov 2012 12:46:46 -0600 Subject: [petsc-users] Benchmarking different PETSc installations In-Reply-To: References: <2218518.1FPX9NMvZ3@prometheus> Message-ID: MatMult is limited by memory bandwidth. Always analyze the data movement in your algorithm and compare the achieved "sustained memory bandwidth" to STREAM. MatMult will get a high fraction (often >80%) as long as the matrix ordering allows for reasonable cache reuse. Don't bother benchmarking with a bad ordering except to make the point that it's a bad thing to do. On Fri, Nov 9, 2012 at 12:43 PM, Jed Brown wrote: > Run examples that are representative of a workload you are interested in. > src/snes/examples/tutorials/ex5.c is a simple problem that is easy to > understand. Use a 3D problem if that's what you're interested in. Run with > -log_summary to get detailed information. Read the user's manual section on > profiling for more details. > > > On Fri, Nov 9, 2012 at 11:20 AM, Reuben D. Budiardja wrote: > >> Hello, >> >> I would like to compare / benchmark several different PETSc installations >> on my >> system. The differences may be: different compilers or compiler flags, >> different >> libraries used by PETSc (e.g. BLAS&LAPACK, and any other packages used by >> PETSc that I included in the build like SuperLU_Dist, Metis/ParMetis, >> Hypre, >> etc). Some of these libraries were provided by different vendors and some >> we >> built ourselves and I'd like to compare the performances as used by PETSc. >> >> So I am wondering if there's any kind of general PETSc benchmarking code >> out >> there that can do this. The more thorough parts of PETSc that gets >> exersized >> by the benchmark code the better, but even if only parts are tested it'd >> be >> useful too. Also I'm more interested on the benchmark code that can run >> with >> larger number of processors (e.g. order of hundreds and thousands). I've >> tried >> Google search but that hasn't yielded much of anything. So any help in >> pointing me to the right direction is greatly appreciated. >> >> Thank you >> RDB >> >> >> >> >> >> >> >> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Fri Nov 9 16:34:44 2012 From: bsmith at mcs.anl.gov (Barry Smith) Date: Fri, 9 Nov 2012 16:34:44 -0600 Subject: [petsc-users] How to use multigrid? In-Reply-To: <3e728b.116ef.13ae5c8f1c5.Coremail.w_ang_temp@163.com> References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <60857783.ad35.13ae5b3e01f.Coremail.w_ang_temp@163.com> <3e728b.116ef.13ae5c8f1c5.Coremail.w_ang_temp@163.com> Message-ID: <6538AF5F-D0CB-4ABD-ADB7-8CB08F1B9455@mcs.anl.gov> I remember a conversation in 1994 I had with Lennart Johnsson who led the development of the math libraries for the Thinking Machines (which were way ahead of their time). He recounted being told by various academic types that they would not be purchasing Thinking Machines but instead IBM Sps and Intel paragons because those other machines had no math libraries thus there was plenty of "research" the academic types could do on them that would be redundant (and hence unpublishable) on the Thinking Machines. So what you do depends on your research plans. 1) If you are in a scientific area (materials, engineering, ?. whatever) then you should use PETSc to do NEW simulations that other people have not done yet (and cannot do) with new or more detailed models etc. For example, if everyone in your community drops some "stuff" from their model because they "are too hard" to include you can include them in the model and then demonstrate they are important. Don't just run the standard models people have been running for decades do models that other people can only dream about. 2) If you are in mathematics/CS numerical analysis then you need to do innovative things that combine several capabilities in new ways. Barry On Nov 9, 2012, at 9:28 AM, w_ang_temp wrote: > By the way, as a graduate student, I find that it is difficult to write a paper just using PETSc > to deal with a large problem. Because it seems that there is no an innovative idea by just using > the available things. It is also not easy to get something new based on the src of PETSc. > Any suggestions? > Thanks. > Jim > > From bsmith at mcs.anl.gov Fri Nov 9 16:42:49 2012 From: bsmith at mcs.anl.gov (Barry Smith) Date: Fri, 9 Nov 2012 16:42:49 -0600 Subject: [petsc-users] Benchmarking different PETSc installations In-Reply-To: <2218518.1FPX9NMvZ3@prometheus> References: <2218518.1FPX9NMvZ3@prometheus> Message-ID: <82970D13-5A27-4B3D-A6D4-09437AE2924C@mcs.anl.gov> We don't really have a good application included with PETSc for this purpose, our examples are too simple, implemented just to demonstrate specific ideas. You might talk to Richard Mills who is at ORNL about using PFLOTRAN for this purpose. Barry On Nov 9, 2012, at 11:20 AM, Reuben D. Budiardja wrote: > Hello, > > I would like to compare / benchmark several different PETSc installations on my > system. The differences may be: different compilers or compiler flags, different > libraries used by PETSc (e.g. BLAS&LAPACK, and any other packages used by > PETSc that I included in the build like SuperLU_Dist, Metis/ParMetis, Hypre, > etc). Some of these libraries were provided by different vendors and some we > built ourselves and I'd like to compare the performances as used by PETSc. > > So I am wondering if there's any kind of general PETSc benchmarking code out > there that can do this. The more thorough parts of PETSc that gets exersized > by the benchmark code the better, but even if only parts are tested it'd be > useful too. Also I'm more interested on the benchmark code that can run with > larger number of processors (e.g. order of hundreds and thousands). I've tried > Google search but that hasn't yielded much of anything. So any help in > pointing me to the right direction is greatly appreciated. > > Thank you > RDB > > > > > > > > > From mark.adams at columbia.edu Fri Nov 9 17:59:50 2012 From: mark.adams at columbia.edu (Mark F. Adams) Date: Fri, 9 Nov 2012 18:59:50 -0500 Subject: [petsc-users] How to use multigrid? In-Reply-To: <6538AF5F-D0CB-4ABD-ADB7-8CB08F1B9455@mcs.anl.gov> References: <2dce573b.e609.13aa77d4c8e.Coremail.w_ang_temp@163.com> <60857783.ad35.13ae5b3e01f.Coremail.w_ang_temp@163.com> <3e728b.116ef.13ae5c8f1c5.Coremail.w_ang_temp@163.com> <6538AF5F-D0CB-4ABD-ADB7-8CB08F1B9455@mcs.anl.gov> Message-ID: <1018405A-9E53-4E28-BAFE-20C6E9053734@columbia.edu> I would just add a (3) or extend (2) by saying that PETSc provides an ideal language to develop new algorithms, and just use PETSc's parallel arithmetic and tools. Assuming your algorithm is not so different that it can not even use PETSc's tools. On Nov 9, 2012, at 5:34 PM, Barry Smith wrote: > > I remember a conversation in 1994 I had with Lennart Johnsson who led the development of the math libraries for the Thinking Machines (which were way ahead of their time). He recounted being told by various academic types that they would not be purchasing Thinking Machines but instead IBM Sps and Intel paragons because those other machines had no math libraries thus there was plenty of "research" the academic types could do on them that would be redundant (and hence unpublishable) on the Thinking Machines. > > So what you do depends on your research plans. > > 1) If you are in a scientific area (materials, engineering, ?. whatever) then you should use PETSc to do NEW simulations that other people have not done yet (and cannot do) with new or more detailed models etc. For example, if everyone in your community drops some "stuff" from their model because they "are too hard" to include you can include them in the model and then demonstrate they are important. Don't just run the standard models people have been running for decades do models that other people can only dream about. > > 2) If you are in mathematics/CS numerical analysis then you need to do innovative things that combine several capabilities in new ways. > > Barry > > > > On Nov 9, 2012, at 9:28 AM, w_ang_temp wrote: > >> By the way, as a graduate student, I find that it is difficult to write a paper just using PETSc >> to deal with a large problem. Because it seems that there is no an innovative idea by just using >> the available things. It is also not easy to get something new based on the src of PETSc. >> Any suggestions? >> Thanks. >> Jim >> >> > > From dominik at itis.ethz.ch Sat Nov 10 15:38:55 2012 From: dominik at itis.ethz.ch (Dominik Szczerba) Date: Sat, 10 Nov 2012 22:38:55 +0100 Subject: [petsc-users] Wrapping PetscFPrintf Message-ID: Hi, I need to have a wrapper to PetscFPrintf and PetscSynchronizedFPrintf. I am aware of the problems and tried following as described here: http://c-faq.com/varargs/handoff.html So I have: virtual bool VPrint(const char* format, va_list argp) = 0; virtual bool Print(const char* format, ...) = 0; implemented as: bool CXCoreReporting::VPrint(const char* format, va_list argp) { vfprintf(stderr, format, argp); return true; } bool CXCoreReporting::Print(const char* format, ...) { va_list argp; va_start(argp, format); VPrint(format, argp); va_end(argp); return true; } Now the problem is that it just does not work... I still get trash when calling e.g. Print("%d", i). Does anyone see a way out? Many thanks Dominik From jedbrown at mcs.anl.gov Sat Nov 10 18:25:42 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Sat, 10 Nov 2012 18:25:42 -0600 Subject: [petsc-users] Wrapping PetscFPrintf In-Reply-To: References: Message-ID: If you are getting garbage, run in valgrind and/or a debugger. Also make sure the int sizes are converted correctly as for a direct call to printf. On Sat, Nov 10, 2012 at 3:38 PM, Dominik Szczerba wrote: > Hi, > > I need to have a wrapper to PetscFPrintf and PetscSynchronizedFPrintf. > I am aware of the problems and tried following as described here: > > http://c-faq.com/varargs/handoff.html > > So I have: > > virtual bool VPrint(const char* format, va_list argp) = 0; > virtual bool Print(const char* format, ...) = 0; > > implemented as: > > bool CXCoreReporting::VPrint(const char* format, va_list argp) > { > vfprintf(stderr, format, argp); > return true; > } > > bool CXCoreReporting::Print(const char* format, ...) > { > va_list argp; > va_start(argp, format); > VPrint(format, argp); > va_end(argp); > return true; > } > > > Now the problem is that it just does not work... I still get trash > when calling e.g. Print("%d", i). > Does anyone see a way out? > > Many thanks > Dominik > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dominik at itis.ethz.ch Sun Nov 11 07:34:16 2012 From: dominik at itis.ethz.ch (Dominik Szczerba) Date: Sun, 11 Nov 2012 14:34:16 +0100 Subject: [petsc-users] Wrapping PetscFPrintf In-Reply-To: References: Message-ID: Thanks for the hint. Unfortunately, I do not see any related error messages in valgrind and the whole va_list machinery is a bit obfuscated. What I experimentally discovered, however, is that the problem goes away if the two functions are directly provided in the same source file in C-style. As soon as they go out to a class the problem occurs. But I found a very promising solution: PetscVFPrintf. It solves my problem for my own Print function. But I do not seem to find a corresponding function for synchronized printing (PetscFPrintf). Any clues how to use PetscVFPrintf for synchronized printing please? Dominik On Sun, Nov 11, 2012 at 1:25 AM, Jed Brown wrote: > If you are getting garbage, run in valgrind and/or a debugger. Also make > sure the int sizes are converted correctly as for a direct call to printf. > > > On Sat, Nov 10, 2012 at 3:38 PM, Dominik Szczerba > wrote: >> >> Hi, >> >> I need to have a wrapper to PetscFPrintf and PetscSynchronizedFPrintf. >> I am aware of the problems and tried following as described here: >> >> http://c-faq.com/varargs/handoff.html >> >> So I have: >> >> virtual bool VPrint(const char* format, va_list argp) = 0; >> virtual bool Print(const char* format, ...) = 0; >> >> implemented as: >> >> bool CXCoreReporting::VPrint(const char* format, va_list argp) >> { >> vfprintf(stderr, format, argp); >> return true; >> } >> >> bool CXCoreReporting::Print(const char* format, ...) >> { >> va_list argp; >> va_start(argp, format); >> VPrint(format, argp); >> va_end(argp); >> return true; >> } >> >> >> Now the problem is that it just does not work... I still get trash >> when calling e.g. Print("%d", i). >> Does anyone see a way out? >> >> Many thanks >> Dominik > > From jedbrown at mcs.anl.gov Sun Nov 11 08:35:55 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Sun, 11 Nov 2012 08:35:55 -0600 Subject: [petsc-users] Wrapping PetscFPrintf In-Reply-To: References: Message-ID: On Sun, Nov 11, 2012 at 7:34 AM, Dominik Szczerba wrote: > Unfortunately, I do not see any related error messages in valgrind and > the whole va_list machinery is a bit obfuscated. What I experimentally > discovered, however, is that the problem goes away if the two > functions are directly provided in the same source file in C-style. As > soon as they go out to a class the problem occurs. > They'll be okay as _static_ class functions. I wasn't aware that va_list doesn't work properly from a member function, but it does modify the calling sequence. It could be compiler-dependent. C++ is not my favorite language. > But I found a very promising solution: PetscVFPrintf. It solves my > problem for my own Print function. But I do not seem to find a > corresponding function for synchronized printing (PetscFPrintf). Any > clues how to use PetscVFPrintf for synchronized printing please? > PetscSynchronizedVFPrintf is missing, but should be added. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Sun Nov 11 09:18:56 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Sun, 11 Nov 2012 09:18:56 -0600 Subject: [petsc-users] Wrapping PetscFPrintf In-Reply-To: References: Message-ID: On Sun, Nov 11, 2012 at 8:35 AM, Jed Brown wrote: > But I found a very promising solution: PetscVFPrintf. It solves my >> problem for my own Print function. But I do not seem to find a >> corresponding function for synchronized printing (PetscFPrintf). Any >> clues how to use PetscVFPrintf for synchronized printing please? >> > > PetscSynchronizedVFPrintf is missing, but should be added. > There is actually an implementation issue. The current version dynamically sizes the local buffer by calling PetscVSNPrintf repeatedly, increasing the buffer size as necessary [1]. We cannot offer a PetscSynchronizedVFPrintf() without either (a) truncating sufficient long strings or (b) using vasprintf() which is a GNU extension. You can roll your own loop over va_start, vsnprintf(), va_end, resize-array-if-necessary and then call PetscSynchronizedPrintf(), or, if you can use the GNU extension, just use asprintf(). [1] The implementation is hideous, leaking memory quadratic in the input size for large data volume. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dominik at itis.ethz.ch Mon Nov 12 01:16:25 2012 From: dominik at itis.ethz.ch (Dominik Szczerba) Date: Mon, 12 Nov 2012 08:16:25 +0100 Subject: [petsc-users] Wrapping PetscFPrintf In-Reply-To: References: Message-ID: > They'll be okay as _static_ class functions. I wasn't aware that va_list doesn't work properly from a member function, but it does modify the calling sequence. Indeed. The problem was that the functions had to be virtual, so no static possible in C++. > It could be compiler-dependent. C++ is not my favorite language. I am really curious, what is your favorite language? > PetscSynchronizedVFPrintf is missing, but should be added. > (...) > There is actually an implementation issue. It is possible that I will have to resolve it (by contributing code), and therefore I may soon come back for some more pointers. Regards, Dominik From agrayver at gfz-potsdam.de Mon Nov 12 03:35:24 2012 From: agrayver at gfz-potsdam.de (Alexander Grayver) Date: Mon, 12 Nov 2012 10:35:24 +0100 Subject: [petsc-users] Does PETSc take advantage of symmetry in iterative solvers Message-ID: <50A0C2DC.8040904@gfz-potsdam.de> Hello, I remember similar question has been asked long time ago, but I can not find it. If I set MatSetOption(A,MAT_SYMMETRIC,PETSC_TRUE), does PETSc take this into account when doing MatMult or similar operations? As far as I can see it does not (I'm not sure I look at the right place though). Could it really save time in principle? -- Regards, Alexander From dominik at itis.ethz.ch Mon Nov 12 04:50:01 2012 From: dominik at itis.ethz.ch (Dominik Szczerba) Date: Mon, 12 Nov 2012 11:50:01 +0100 Subject: [petsc-users] Report progress to an external driver code Message-ID: Hi, I need to report progress (0-100%, which I compute myself) of my Petsc solver code to an external driver code that is controlling my solver. I had a look at the many Petsc logging functions and examples but I am still not sure which way to go. I tried PetscLogStage, but it does not seem to display any information during the execution, and I also do not see a way this information could be sent somewhere and accessed by e.g. registering a custom (static) function used to inform the downstream code what the solver is doing at the moment. The most trivial solution that I have found is to output a message like [STATUS 50%], which could be intercepted in the downstream code by overwriting PetscVFPrintf, but it sounds rather inelegant. I would be very glad to receive some pointers where to start looking. Regards, Dominik From jedbrown at mcs.anl.gov Mon Nov 12 06:40:03 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Mon, 12 Nov 2012 06:40:03 -0600 Subject: [petsc-users] Does PETSc take advantage of symmetry in iterative solvers In-Reply-To: <50A0C2DC.8040904@gfz-potsdam.de> References: <50A0C2DC.8040904@gfz-potsdam.de> Message-ID: On Mon, Nov 12, 2012 at 3:35 AM, Alexander Grayver wrote: > I remember similar question has been asked long time ago, but I can not > find it. > > If I set MatSetOption(A,MAT_SYMMETRIC,**PETSC_TRUE), does PETSc take this > into account when doing MatMult or similar operations? > The option does not change the format, but it does change some defaults (e.g., it makes ASM symmetric instead of using RASM). If you want to use a symmetric _format_, use MATSBAIJ. > As far as I can see it does not (I'm not sure I look at the right place > though). Could it really save time in principle? > Symmetric formats require more communication, but win on memory bandwidth. -------------- next part -------------- An HTML attachment was scrubbed... URL: From agrayver at gfz-potsdam.de Mon Nov 12 08:43:27 2012 From: agrayver at gfz-potsdam.de (Alexander Grayver) Date: Mon, 12 Nov 2012 15:43:27 +0100 Subject: [petsc-users] Does PETSc take advantage of symmetry in iterative solvers In-Reply-To: References: <50A0C2DC.8040904@gfz-potsdam.de> Message-ID: <50A10B0F.2040006@gfz-potsdam.de> On 12.11.2012 13:40, Jed Brown wrote: > The option does not change the format, but it does change some > defaults (e.g., it makes ASM symmetric instead of using RASM). If you > want to use a symmetric _format_, use MATSBAIJ. Jed, Thanks. Does it make sense that in fortran one has to call MatCreateMPISBAIJ? /EXTERN_C_BEGIN void PETSC_STDCALL matcreatempisbaij_(MPI_Comm *comm,PetscInt *bs,PetscInt *m,PetscInt *n,PetscInt *M,PetscInt *N, PetscInt *d_nz,PetscInt *d_nnz,PetscInt *o_nz,PetscInt *o_nnz,Mat *newmat,PetscErrorCode *ierr) { CHKFORTRANNULLINTEGER(d_nnz); CHKFORTRANNULLINTEGER(o_nnz); *ierr = MatCreateSBAIJ(MPI_Comm_f2c(*(MPI_Fint *)&*comm),*bs,*m,*n,*M,*N,*d_nz,d_nnz,*o_nz,o_nnz,newmat); } / -- Regards, Alexander -------------- next part -------------- An HTML attachment was scrubbed... URL: From rfk102 at arl.psu.edu Mon Nov 12 10:21:08 2012 From: rfk102 at arl.psu.edu (Rob Kunz) Date: Mon, 12 Nov 2012 16:21:08 +0000 Subject: [petsc-users] Parallel vs. single processor Message-ID: Hi: I have a pressure based CFD code using PETSC for nearly SPD pressure equation. PETSC default solver + preconditioner (GMRES+BJ for n-proc) is very reliable for me. However I have a very tough bearing problem with extremely high aspect ratio cells and the 1-processor run works fine (GMRES+ILU0), but for nproc>1 the code does not converge. Of course I can get the code to return identical 1-proc and 12-proc convergence histories if I choose a point preconditioner like Jacobi, but that kills the convergence of both. Any recommendations? Thanks Rob Kunz -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Mon Nov 12 10:31:27 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Mon, 12 Nov 2012 10:31:27 -0600 Subject: [petsc-users] Parallel vs. single processor In-Reply-To: References: Message-ID: Try (e.g., -pc_type gamg) and additive Schwarz. Also try using ASM as a smoother. On Mon, Nov 12, 2012 at 10:21 AM, Rob Kunz wrote: > Hi:**** > > I have a pressure based CFD code using PETSC for nearly SPD pressure > equation.**** > > PETSC default solver + preconditioner (GMRES+BJ for n-proc) is very > reliable for me.**** > > However I have a very tough bearing problem with extremely high aspect > ratio cells and the 1-processor run works fine (GMRES+ILU0), but for > nproc>1 the code does not converge.**** > > Of course I can get the code to return identical 1-proc and 12-proc > convergence histories if I choose a point preconditioner like Jacobi, but > that kills the convergence of both.**** > > Any recommendations?**** > > Thanks > Rob Kunz**** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Mon Nov 12 10:58:44 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Mon, 12 Nov 2012 10:58:44 -0600 Subject: [petsc-users] Does PETSc take advantage of symmetry in iterative solvers In-Reply-To: <50A10B0F.2040006@gfz-potsdam.de> References: <50A0C2DC.8040904@gfz-potsdam.de> <50A10B0F.2040006@gfz-potsdam.de> Message-ID: On Mon, Nov 12, 2012 at 8:43 AM, Alexander Grayver wrote: > Does it make sense that in fortran one has to call MatCreateMPISBAIJ? > No, this was missed in the rename. It's fixed here. https://bitbucket.org/petsc/petsc-dev/changeset/cfa58f9da86656f6ddf509089493a99a1d503d6f This should probably be back-ported to 3.3, though it will break an existing Fortran user that forgot to fix that call (or noticed the bug and didn't report it). The petsc.cs.iit.edu server is down right now and although we are migrating to bitbucket, we haven't decided how to manage the release repository there yet. https://bitbucket.org/petsc/petsc-dev/issue/22/backport-bug-fixes-to-33-once-release > > *EXTERN_C_BEGIN > void PETSC_STDCALL matcreatempisbaij_(MPI_Comm *comm,PetscInt *bs,PetscInt > *m,PetscInt *n,PetscInt *M,PetscInt *N, > PetscInt *d_nz,PetscInt *d_nnz,PetscInt *o_nz,PetscInt *o_nnz,Mat*newmat,PetscErrorCode *ierr) > { > CHKFORTRANNULLINTEGER(d_nnz); > CHKFORTRANNULLINTEGER(o_nnz); > *ierr = MatCreateSBAIJ(MPI_Comm_f2c(*(MPI_Fint > *)&*comm),*bs,*m,*n,*M,*N,*d_nz,d_nnz,*o_nz,o_nnz,newmat); > }* > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Mon Nov 12 11:14:48 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Mon, 12 Nov 2012 11:14:48 -0600 Subject: [petsc-users] FW: Parallel vs. single processor In-Reply-To: References: Message-ID: 1. Please reply to the list rather than me personally. 2. Upgrade to petsc-3.3 for GAMG. You can also use ML or BoomerAMG with older versions of PETSc. 3. Send full convergence output. 4. Lots of general tips here: http://scicomp.stackexchange.com/questions/513/why-is-my-iterative-linear-solver-not-converging On Mon, Nov 12, 2012 at 11:10 AM, Rob Kunz wrote: > Hi Jed:**** > > Thanks for your response.**** > > I am currently doing all PETSC call from C.**** > > Attached is the code snippet I am using based on ex54.c.html.**** > > I get an error that PCGAMG is undefined.**** > > Must I do something on the command line?**** > > Thanks**** > > Rob**** > > ** ** > > ** ** > > Robert F. Kunz**** > > Head, Computational Mechanics Division, Applied Research Laboratory**** > > Professor, Aerospace Engineering**** > > The Pennsylvania State University**** > > PO Box 30**** > > University Park, PA 16804**** > > rfk102 at arl.psu.edu**** > > 814-360-1901**** > > ** ** > > ** ** > > ** ** > > ** ** > > ** ** > > ** ** > > *From:* petsc-users-bounces at mcs.anl.gov [mailto: > petsc-users-bounces at mcs.anl.gov] *On Behalf Of *Jed Brown > *Sent:* Monday, November 12, 2012 11:31 AM > *To:* PETSc users list > *Subject:* Re: [petsc-users] Parallel vs. single processor**** > > ** ** > > Try (e.g., -pc_type gamg) and additive Schwarz. Also try using ASM as a > smoother.**** > > ** ** > > On Mon, Nov 12, 2012 at 10:21 AM, Rob Kunz wrote:**** > > Hi:**** > > I have a pressure based CFD code using PETSC for nearly SPD pressure > equation.**** > > PETSC default solver + preconditioner (GMRES+BJ for n-proc) is very > reliable for me.**** > > However I have a very tough bearing problem with extremely high aspect > ratio cells and the 1-processor run works fine (GMRES+ILU0), but for > nproc>1 the code does not converge.**** > > Of course I can get the code to return identical 1-proc and 12-proc > convergence histories if I choose a point preconditioner like Jacobi, but > that kills the convergence of both.**** > > Any recommendations?**** > > Thanks > Rob Kunz**** > > ** ** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Mon Nov 12 11:29:48 2012 From: bsmith at mcs.anl.gov (Barry Smith) Date: Mon, 12 Nov 2012 11:29:48 -0600 Subject: [petsc-users] Report progress to an external driver code In-Reply-To: References: Message-ID: <61D3B104-E047-44C4-9DE1-5B94DAD3C9B9@mcs.anl.gov> If you are calling KSP directly you can write a custom monitor and set it with KSPMonitorSet(), similarly with SNES write a custom monitor and set it with SNESMonitorSet() or both. These monitors can do anything you like, print to a GUI, communicate via a unix socket to another process, etc. Barry The logging stuff is really not intended for this purpose. On Nov 12, 2012, at 4:50 AM, Dominik Szczerba wrote: > Hi, > > I need to report progress (0-100%, which I compute myself) of my Petsc > solver code to an external driver code that is controlling my solver. > I had a look at the many Petsc logging functions and examples but I am > still not sure which way to go. I tried PetscLogStage, but it does not > seem to display any information during the execution, and I also do > not see a way this information could be sent somewhere and accessed by > e.g. registering a custom (static) function used to inform the > downstream code what the solver is doing at the moment. The most > trivial solution that I have found is to output a message like [STATUS > 50%], which could be intercepted in the downstream code by overwriting > PetscVFPrintf, but it sounds rather inelegant. I would be very glad to > receive some pointers where to start looking. > > Regards, > Dominik From jedbrown at mcs.anl.gov Mon Nov 12 11:41:16 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Mon, 12 Nov 2012 11:41:16 -0600 Subject: [petsc-users] Wrapping PetscFPrintf In-Reply-To: References: Message-ID: On Mon, Nov 12, 2012 at 1:16 AM, Dominik Szczerba wrote: > Indeed. The problem was that the functions had to be virtual, so no > static possible in C++. > Can you check whether the function calling va_start needs to be static/non-virtual (Print), or just the function that you pass a va_list to (your VPrint)? > > > It could be compiler-dependent. C++ is not my favorite language. > > I am really curious, what is your favorite language? > Heh, there are very interesting languages that are not terribly practical, at least for scientific computing. Haskell and Racket come to mind. Extremely expressive and extensible. There is a very new language called Julia that I think is a pleasure to work with, though I think it will have growing pains. Then there are the practical languages like C and Python. If I were to leave C for a systems language, I would not ask for object oriented features, I would ask for (1) a proper module system and (2) native multiple dispatch. > > > PetscSynchronizedVFPrintf is missing, but should be added. > > (...) > > There is actually an implementation issue. > > It is possible that I will have to resolve it (by contributing code), > and therefore I may soon come back for some more pointers. > The problem is that you _can't_ implement the V versions without vasprintf() or similar because you can't determine the required buffer size without exhausting the va_list. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bourdin at lsu.edu Mon Nov 12 11:47:40 2012 From: bourdin at lsu.edu (Blaise A Bourdin) Date: Mon, 12 Nov 2012 17:47:40 +0000 Subject: [petsc-users] Wrapping PetscFPrintf In-Reply-To: References: Message-ID: <6C4AE5741C2B874282F58DA136A2CCB82FB035@BY2PRD0611MB441.namprd06.prod.outlook.com> On Nov 12, 2012, at 11:41 AM, Jed Brown wrote: > If I were to leave C for a systems language, I would not ask for object oriented features, I would ask for (1) a proper module system and (2) native multiple dispatch. Do you mean that you are contemplating switching to fortran90? ;) Blaise -- Department of Mathematics and Center for Computation & Technology Louisiana State University, Baton Rouge, LA 70803, USA Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 http://www.math.lsu.edu/~bourdin From jedbrown at mcs.anl.gov Mon Nov 12 14:15:12 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Mon, 12 Nov 2012 14:15:12 -0600 Subject: [petsc-users] Wrapping PetscFPrintf In-Reply-To: <6C4AE5741C2B874282F58DA136A2CCB82FB035@BY2PRD0611MB441.namprd06.prod.outlook.com> References: <6C4AE5741C2B874282F58DA136A2CCB82FB035@BY2PRD0611MB441.namprd06.prod.outlook.com> Message-ID: On Mon, Nov 12, 2012 at 11:47 AM, Blaise A Bourdin wrote: > > If I were to leave C for a systems language, I would not ask for object > oriented features, I would ask for (1) a proper module system and (2) > native multiple dispatch. > Do you mean that you are contemplating switching to fortran90? ;) May I ask what part of that abomination you consider to be a proper module system? Note that compile-time overloading is completely different from multiple dispatch. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bourdin at lsu.edu Mon Nov 12 14:42:21 2012 From: bourdin at lsu.edu (Blaise A Bourdin) Date: Mon, 12 Nov 2012 20:42:21 +0000 Subject: [petsc-users] Wrapping PetscFPrintf In-Reply-To: References: <6C4AE5741C2B874282F58DA136A2CCB82FB035@BY2PRD0611MB441.namprd06.prod.outlook.com> Message-ID: <6C4AE5741C2B874282F58DA136A2CCB82FB6CC@BY2PRD0611MB441.namprd06.prod.outlook.com> On Nov 12, 2012, at 2:15 PM, Jed Brown > wrote: On Mon, Nov 12, 2012 at 11:47 AM, Blaise A Bourdin > wrote: > If I were to leave C for a systems language, I would not ask for object oriented features, I would ask for (1) a proper module system and (2) native multiple dispatch. Do you mean that you are contemplating switching to fortran90? ;) May I ask what part of that abomination you consider to be a proper module system? "abomination"? I was expecting something more creative. Note that compile-time overloading is completely different from multiple dispatch. Remember: we, fortran programers, don't understand the difference, so does it really matter? Just kiddin', Blaise -- Department of Mathematics and Center for Computation & Technology Louisiana State University, Baton Rouge, LA 70803, USA Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 http://www.math.lsu.edu/~bourdin -------------- next part -------------- An HTML attachment was scrubbed... URL: From dominik at itis.ethz.ch Tue Nov 13 06:21:14 2012 From: dominik at itis.ethz.ch (Dominik Szczerba) Date: Tue, 13 Nov 2012 13:21:14 +0100 Subject: [petsc-users] Report progress to an external driver code In-Reply-To: <61D3B104-E047-44C4-9DE1-5B94DAD3C9B9@mcs.anl.gov> References: <61D3B104-E047-44C4-9DE1-5B94DAD3C9B9@mcs.anl.gov> Message-ID: Thanks a lot for your suggestion. No I did not mean just KSP progress, but the overall progress from my solver. I have solved it now by offering a custom function pointer that the downstream user can provide. This function is then called several times during the computation and calculates the overall progress. Dominik On Mon, Nov 12, 2012 at 6:29 PM, Barry Smith wrote: > > If you are calling KSP directly you can write a custom monitor and set it with KSPMonitorSet(), similarly with SNES write a custom monitor and set it with SNESMonitorSet() or both. These monitors can do anything you like, print to a GUI, communicate via a unix socket to another process, etc. > > Barry > > The logging stuff is really not intended for this purpose. > > > > > On Nov 12, 2012, at 4:50 AM, Dominik Szczerba wrote: > >> Hi, >> >> I need to report progress (0-100%, which I compute myself) of my Petsc >> solver code to an external driver code that is controlling my solver. >> I had a look at the many Petsc logging functions and examples but I am >> still not sure which way to go. I tried PetscLogStage, but it does not >> seem to display any information during the execution, and I also do >> not see a way this information could be sent somewhere and accessed by >> e.g. registering a custom (static) function used to inform the >> downstream code what the solver is doing at the moment. The most >> trivial solution that I have found is to output a message like [STATUS >> 50%], which could be intercepted in the downstream code by overwriting >> PetscVFPrintf, but it sounds rather inelegant. I would be very glad to >> receive some pointers where to start looking. >> >> Regards, >> Dominik > From rfk102 at arl.psu.edu Tue Nov 13 07:16:00 2012 From: rfk102 at arl.psu.edu (Rob Kunz) Date: Tue, 13 Nov 2012 13:16:00 +0000 Subject: [petsc-users] Parallel vs. single processor In-Reply-To: References: Message-ID: I have successfully implemented the GAMG and I am getting convergence now as expected from a multigrid solver! Two issues: 1) Every iteration if the CFD solver the pressure equation takes more solution time. Iteration 1 the code executes at 5e-5 wall secs/cell*iteration. Iteration 1000 the code executes at 3e-4 wall secs/cell*iteration. Steady increase. Why does this happen? 2) I would like to see some documentation on how to control the GAMG, the online docs are too limited for my modest experience. Also there is only one example and that has very basic implementation. I am particularly interested in trying to get the solver to act only in the strong coefficient direction, with multiple cell agglomeration ? i.e., try and make the solver act like a block correction multigrid. Thanks Rob From: petsc-users-bounces at mcs.anl.gov [mailto:petsc-users-bounces at mcs.anl.gov] On Behalf Of Jed Brown Sent: Monday, November 12, 2012 11:31 AM To: PETSc users list Subject: Re: [petsc-users] Parallel vs. single processor Try (e.g., -pc_type gamg) and additive Schwarz. Also try using ASM as a smoother. On Mon, Nov 12, 2012 at 10:21 AM, Rob Kunz > wrote: Hi: I have a pressure based CFD code using PETSC for nearly SPD pressure equation. PETSC default solver + preconditioner (GMRES+BJ for n-proc) is very reliable for me. However I have a very tough bearing problem with extremely high aspect ratio cells and the 1-processor run works fine (GMRES+ILU0), but for nproc>1 the code does not converge. Of course I can get the code to return identical 1-proc and 12-proc convergence histories if I choose a point preconditioner like Jacobi, but that kills the convergence of both. Any recommendations? Thanks Rob Kunz -------------- next part -------------- An HTML attachment was scrubbed... URL: From paulhuaizhang at gmail.com Thu Nov 15 11:23:45 2012 From: paulhuaizhang at gmail.com (paul zhang) Date: Thu, 15 Nov 2012 12:23:45 -0500 Subject: [petsc-users] Some questions in PETSc installation. Message-ID: Hi there, Can I get some help to solve this issue? [hzh225 at dlxlogin2-2 petsc-3.1-p4]$ make PETSC_DIR=/home/hzh225/LIB_CFD/PETSC test Running test examples to verify correct installation Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI process See http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html -------------------------------------------------------------------------- WARNING: It appears that your OpenFabrics subsystem is configured to only allow registering part of your physical memory. This can cause MPI jobs to run with erratic performance, hang, and/or crash. This may be caused by your OpenFabrics vendor limiting the amount of physical memory that can be registered. You should investigate the relevant Linux kernel module parameters that control how much physical memory can be registered, and increase them to allow registering all physical memory on your machine. -- Huaibao (Paul) Zhang *Gas Surface Interactions Lab* Department of Mechanical Engineering University of Kentucky, Lexington, KY, 40506-0503* Office*: 216 Ralph G. Anderson Building *Web*:gsil.engineering.uky.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Thu Nov 15 11:29:01 2012 From: knepley at gmail.com (Matthew Knepley) Date: Thu, 15 Nov 2012 12:29:01 -0500 Subject: [petsc-users] Some questions in PETSc installation. In-Reply-To: References: Message-ID: On Thu, Nov 15, 2012 at 12:23 PM, paul zhang wrote: > Hi there, > Can I get some help to solve this issue? > > > [hzh225 at dlxlogin2-2 petsc-3.1-p4]$ make PETSC_DIR=/home/hzh225/LIB_CFD/PETSC > test > Running test examples to verify correct installation > Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI > process > See http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html > -------------------------------------------------------------------------- This is not our message. It comes from your MPI. Matt > WARNING: It appears that your OpenFabrics subsystem is configured to only > allow registering part of your physical memory. This can cause MPI jobs to > run with erratic performance, hang, and/or crash. > > This may be caused by your OpenFabrics vendor limiting the amount of > physical memory that can be registered. You should investigate the > relevant Linux kernel module parameters that control how much physical > memory can be registered, and increase them to allow registering all > physical memory on your machine. > > > > -- > Huaibao (Paul) Zhang > Gas Surface Interactions Lab > Department of Mechanical Engineering > University of Kentucky, > Lexington, > KY, 40506-0503 > Office: 216 Ralph G. Anderson Building > Web:gsil.engineering.uky.edu > -- 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 From paulhuaizhang at gmail.com Thu Nov 15 11:30:28 2012 From: paulhuaizhang at gmail.com (huaibao zhang) Date: Thu, 15 Nov 2012 12:30:28 -0500 Subject: [petsc-users] Some questions in PETSc installation. In-Reply-To: References: Message-ID: Thanks a lot for your help Matt. Paul -- Huaibao (Paul) Zhang Gas Surface Interactions Lab Department of Mechanical Engineering University of Kentucky, Lexington, KY, 40506-0503 Office: 216 Ralph G. Anderson Building Web:gsil.engineering.uky.edu On Nov 15, 2012, at 12:29 PM, Matthew Knepley wrote: > On Thu, Nov 15, 2012 at 12:23 PM, paul zhang wrote: >> Hi there, >> Can I get some help to solve this issue? >> >> >> [hzh225 at dlxlogin2-2 petsc-3.1-p4]$ make PETSC_DIR=/home/hzh225/LIB_CFD/PETSC >> test >> Running test examples to verify correct installation >> Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI >> process >> See http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html >> -------------------------------------------------------------------------- > > This is not our message. It comes from your MPI. > > Matt > >> WARNING: It appears that your OpenFabrics subsystem is configured to only >> allow registering part of your physical memory. This can cause MPI jobs to >> run with erratic performance, hang, and/or crash. >> >> This may be caused by your OpenFabrics vendor limiting the amount of >> physical memory that can be registered. You should investigate the >> relevant Linux kernel module parameters that control how much physical >> memory can be registered, and increase them to allow registering all >> physical memory on your machine. >> >> >> >> -- >> Huaibao (Paul) Zhang >> Gas Surface Interactions Lab >> Department of Mechanical Engineering >> University of Kentucky, >> Lexington, >> KY, 40506-0503 >> Office: 216 Ralph G. Anderson Building >> Web:gsil.engineering.uky.edu >> > > > > -- > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From paulhuaizhang at gmail.com Thu Nov 15 12:18:14 2012 From: paulhuaizhang at gmail.com (paul zhang) Date: Thu, 15 Nov 2012 13:18:14 -0500 Subject: [petsc-users] Some questions in PETSc installation. In-Reply-To: References: Message-ID: Hi Matt, Do you have some idea to install f2cblas and f2clapack to /usr/lib on my local Ubuntu? Since PETSc needs them. Thanks, Paul On Thu, Nov 15, 2012 at 12:30 PM, huaibao zhang wrote: > Thanks a lot for your help Matt. > Paul > > -- > Huaibao (Paul) Zhang > *Gas Surface Interactions Lab* > Department of Mechanical Engineering > University of Kentucky, > Lexington, KY, 40506-0503 > *Office*: 216 Ralph G. Anderson Building > *Web*:gsil.engineering.uky.edu > > On Nov 15, 2012, at 12:29 PM, Matthew Knepley wrote: > > On Thu, Nov 15, 2012 at 12:23 PM, paul zhang > wrote: > > Hi there, > Can I get some help to solve this issue? > > > [hzh225 at dlxlogin2-2 petsc-3.1-p4]$ make > PETSC_DIR=/home/hzh225/LIB_CFD/PETSC > test > Running test examples to verify correct installation > Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI > process > See > http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html > -------------------------------------------------------------------------- > > > This is not our message. It comes from your MPI. > > Matt > > WARNING: It appears that your OpenFabrics subsystem is configured to only > allow registering part of your physical memory. This can cause MPI jobs to > run with erratic performance, hang, and/or crash. > > This may be caused by your OpenFabrics vendor limiting the amount of > physical memory that can be registered. You should investigate the > relevant Linux kernel module parameters that control how much physical > memory can be registered, and increase them to allow registering all > physical memory on your machine. > > > > -- > Huaibao (Paul) Zhang > Gas Surface Interactions Lab > Department of Mechanical Engineering > University of Kentucky, > Lexington, > KY, 40506-0503 > Office: 216 Ralph G. Anderson Building > Web:gsil.engineering.uky.edu > > > > > -- > 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 > > > -- Huaibao (Paul) Zhang *Gas Surface Interactions Lab* Department of Mechanical Engineering University of Kentucky, Lexington, KY, 40506-0503* Office*: 216 Ralph G. Anderson Building *Web*:gsil.engineering.uky.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Thu Nov 15 12:50:39 2012 From: knepley at gmail.com (Matthew Knepley) Date: Thu, 15 Nov 2012 13:50:39 -0500 Subject: [petsc-users] Some questions in PETSc installation. In-Reply-To: References: Message-ID: On Thu, Nov 15, 2012 at 1:18 PM, paul zhang wrote: > Hi Matt, > > Do you have some idea to install f2cblas and f2clapack to /usr/lib on my > local Ubuntu? Since PETSc needs them. Just use --download-f-blas-lapack. Matt > Thanks, > Paul > > > On Thu, Nov 15, 2012 at 12:30 PM, huaibao zhang > wrote: >> >> Thanks a lot for your help Matt. >> Paul >> >> -- >> Huaibao (Paul) Zhang >> Gas Surface Interactions Lab >> Department of Mechanical Engineering >> University of Kentucky, >> Lexington, KY, 40506-0503 >> Office: 216 Ralph G. Anderson Building >> Web:gsil.engineering.uky.edu >> >> On Nov 15, 2012, at 12:29 PM, Matthew Knepley wrote: >> >> On Thu, Nov 15, 2012 at 12:23 PM, paul zhang >> wrote: >> >> Hi there, >> Can I get some help to solve this issue? >> >> >> [hzh225 at dlxlogin2-2 petsc-3.1-p4]$ make >> PETSC_DIR=/home/hzh225/LIB_CFD/PETSC >> test >> Running test examples to verify correct installation >> Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI >> process >> See >> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html >> -------------------------------------------------------------------------- >> >> >> This is not our message. It comes from your MPI. >> >> Matt >> >> WARNING: It appears that your OpenFabrics subsystem is configured to only >> allow registering part of your physical memory. This can cause MPI jobs >> to >> run with erratic performance, hang, and/or crash. >> >> This may be caused by your OpenFabrics vendor limiting the amount of >> physical memory that can be registered. You should investigate the >> relevant Linux kernel module parameters that control how much physical >> memory can be registered, and increase them to allow registering all >> physical memory on your machine. >> >> >> >> -- >> Huaibao (Paul) Zhang >> Gas Surface Interactions Lab >> Department of Mechanical Engineering >> University of Kentucky, >> Lexington, >> KY, 40506-0503 >> Office: 216 Ralph G. Anderson Building >> Web:gsil.engineering.uky.edu >> >> >> >> >> -- >> 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 >> >> > > > > -- > Huaibao (Paul) Zhang > Gas Surface Interactions Lab > Department of Mechanical Engineering > University of Kentucky, > Lexington, > KY, 40506-0503 > Office: 216 Ralph G. Anderson Building > Web:gsil.engineering.uky.edu > -- 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 From balay at mcs.anl.gov Thu Nov 15 12:57:14 2012 From: balay at mcs.anl.gov (Satish Balay) Date: Thu, 15 Nov 2012 12:57:14 -0600 (CST) Subject: [petsc-users] Some questions in PETSc installation. In-Reply-To: References: Message-ID: for one petsc-3.1 is pretty old. Suggest using petsc-3.3 And ubuntu provides blas/lapack which can be installed with: sudo apt-get install liblapack-dev Satish On Thu, 15 Nov 2012, Matthew Knepley wrote: > On Thu, Nov 15, 2012 at 1:18 PM, paul zhang wrote: > > Hi Matt, > > > > Do you have some idea to install f2cblas and f2clapack to /usr/lib on my > > local Ubuntu? Since PETSc needs them. > > Just use --download-f-blas-lapack. > > Matt > > > Thanks, > > Paul > > > > > > On Thu, Nov 15, 2012 at 12:30 PM, huaibao zhang > > wrote: > >> > >> Thanks a lot for your help Matt. > >> Paul > >> > >> -- > >> Huaibao (Paul) Zhang > >> Gas Surface Interactions Lab > >> Department of Mechanical Engineering > >> University of Kentucky, > >> Lexington, KY, 40506-0503 > >> Office: 216 Ralph G. Anderson Building > >> Web:gsil.engineering.uky.edu > >> > >> On Nov 15, 2012, at 12:29 PM, Matthew Knepley wrote: > >> > >> On Thu, Nov 15, 2012 at 12:23 PM, paul zhang > >> wrote: > >> > >> Hi there, > >> Can I get some help to solve this issue? > >> > >> > >> [hzh225 at dlxlogin2-2 petsc-3.1-p4]$ make > >> PETSC_DIR=/home/hzh225/LIB_CFD/PETSC > >> test > >> Running test examples to verify correct installation > >> Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI > >> process > >> See > >> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html > >> -------------------------------------------------------------------------- > >> > >> > >> This is not our message. It comes from your MPI. > >> > >> Matt > >> > >> WARNING: It appears that your OpenFabrics subsystem is configured to only > >> allow registering part of your physical memory. This can cause MPI jobs > >> to > >> run with erratic performance, hang, and/or crash. > >> > >> This may be caused by your OpenFabrics vendor limiting the amount of > >> physical memory that can be registered. You should investigate the > >> relevant Linux kernel module parameters that control how much physical > >> memory can be registered, and increase them to allow registering all > >> physical memory on your machine. > >> > >> > >> > >> -- > >> Huaibao (Paul) Zhang > >> Gas Surface Interactions Lab > >> Department of Mechanical Engineering > >> University of Kentucky, > >> Lexington, > >> KY, 40506-0503 > >> Office: 216 Ralph G. Anderson Building > >> Web:gsil.engineering.uky.edu > >> > >> > >> > >> > >> -- > >> 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 > >> > >> > > > > > > > > -- > > Huaibao (Paul) Zhang > > Gas Surface Interactions Lab > > Department of Mechanical Engineering > > University of Kentucky, > > Lexington, > > KY, 40506-0503 > > Office: 216 Ralph G. Anderson Building > > Web:gsil.engineering.uky.edu > > > > > > -- > 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 > From paulhuaizhang at gmail.com Thu Nov 15 15:41:13 2012 From: paulhuaizhang at gmail.com (huaibao zhang) Date: Thu, 15 Nov 2012 16:41:13 -0500 Subject: [petsc-users] Some questions in PETSc installation. In-Reply-To: References: Message-ID: Great. Thanks very much. Paul -- Huaibao (Paul) Zhang Gas Surface Interactions Lab Department of Mechanical Engineering University of Kentucky, Lexington, KY, 40506-0503 Office: 216 Ralph G. Anderson Building Web:gsil.engineering.uky.edu On Nov 15, 2012, at 1:50 PM, Matthew Knepley wrote: > On Thu, Nov 15, 2012 at 1:18 PM, paul zhang wrote: >> Hi Matt, >> >> Do you have some idea to install f2cblas and f2clapack to /usr/lib on my >> local Ubuntu? Since PETSc needs them. > > Just use --download-f-blas-lapack. > > Matt > >> Thanks, >> Paul >> >> >> On Thu, Nov 15, 2012 at 12:30 PM, huaibao zhang >> wrote: >>> >>> Thanks a lot for your help Matt. >>> Paul >>> >>> -- >>> Huaibao (Paul) Zhang >>> Gas Surface Interactions Lab >>> Department of Mechanical Engineering >>> University of Kentucky, >>> Lexington, KY, 40506-0503 >>> Office: 216 Ralph G. Anderson Building >>> Web:gsil.engineering.uky.edu >>> >>> On Nov 15, 2012, at 12:29 PM, Matthew Knepley wrote: >>> >>> On Thu, Nov 15, 2012 at 12:23 PM, paul zhang >>> wrote: >>> >>> Hi there, >>> Can I get some help to solve this issue? >>> >>> >>> [hzh225 at dlxlogin2-2 petsc-3.1-p4]$ make >>> PETSC_DIR=/home/hzh225/LIB_CFD/PETSC >>> test >>> Running test examples to verify correct installation >>> Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI >>> process >>> See >>> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html >>> -------------------------------------------------------------------------- >>> >>> >>> This is not our message. It comes from your MPI. >>> >>> Matt >>> >>> WARNING: It appears that your OpenFabrics subsystem is configured to only >>> allow registering part of your physical memory. This can cause MPI jobs >>> to >>> run with erratic performance, hang, and/or crash. >>> >>> This may be caused by your OpenFabrics vendor limiting the amount of >>> physical memory that can be registered. You should investigate the >>> relevant Linux kernel module parameters that control how much physical >>> memory can be registered, and increase them to allow registering all >>> physical memory on your machine. >>> >>> >>> >>> -- >>> Huaibao (Paul) Zhang >>> Gas Surface Interactions Lab >>> Department of Mechanical Engineering >>> University of Kentucky, >>> Lexington, >>> KY, 40506-0503 >>> Office: 216 Ralph G. Anderson Building >>> Web:gsil.engineering.uky.edu >>> >>> >>> >>> >>> -- >>> 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 >>> >>> >> >> >> >> -- >> Huaibao (Paul) Zhang >> Gas Surface Interactions Lab >> Department of Mechanical Engineering >> University of Kentucky, >> Lexington, >> KY, 40506-0503 >> Office: 216 Ralph G. Anderson Building >> Web:gsil.engineering.uky.edu >> > > > > -- > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From fande.kong at colorado.edu Thu Nov 15 16:41:20 2012 From: fande.kong at colorado.edu (Fande Kong) Date: Thu, 15 Nov 2012 15:41:20 -0700 Subject: [petsc-users] Which IDE you use to develop petsc application Message-ID: Hi all, In order to improve development the efficient of the petsc application development, which IDE are you using? Regards, -- Fande Kong Department of Computer Science University of Colorado at Boulder -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Thu Nov 15 16:49:23 2012 From: knepley at gmail.com (Matthew Knepley) Date: Thu, 15 Nov 2012 17:49:23 -0500 Subject: [petsc-users] Which IDE you use to develop petsc application In-Reply-To: References: Message-ID: On Thu, Nov 15, 2012 at 5:41 PM, Fande Kong wrote: > Hi all, > > In order to improve development the efficient of the petsc application > development, which IDE are you using? Emacs+gdb. Matt > Regards, > -- > Fande Kong > Department of Computer Science > University of Colorado at Boulder > > -- 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 From fd.kong at siat.ac.cn Thu Nov 15 16:52:25 2012 From: fd.kong at siat.ac.cn (Fande Kong) Date: Thu, 15 Nov 2012 15:52:25 -0700 Subject: [petsc-users] Which IDE you use to develop petsc application In-Reply-To: References: Message-ID: Got it. Thanks. On Thu, Nov 15, 2012 at 3:49 PM, Matthew Knepley wrote: > On Thu, Nov 15, 2012 at 5:41 PM, Fande Kong > wrote: > > Hi all, > > > > In order to improve development the efficient of the petsc application > > development, which IDE are you using? > > Emacs+gdb. > > Matt > > > Regards, > > -- > > Fande Kong > > Department of Computer Science > > University of Colorado at Boulder > > > > > > > > -- > 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 > > -- Fande Kong ShenZhen Institutes of Advanced Technology Chinese Academy of Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Thu Nov 15 17:35:53 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Thu, 15 Nov 2012 18:35:53 -0500 Subject: [petsc-users] Parallel vs. single processor In-Reply-To: References: Message-ID: On Tue, Nov 13, 2012 at 8:16 AM, Rob Kunz wrote: > I have successfully implemented the GAMG and I am getting convergence > now as expected from a multigrid solver!**** > > Two issues:**** > > **1) **Every iteration if the CFD solver the pressure equation takes > more solution time. Iteration 1 the code executes at 5e-5 wall > secs/cell*iteration. Iteration 1000 the code executes at 3e-4 wall > secs/cell*iteration. Steady increase. Why does this happen? > The most common cause is a memory leak. Maybe you are creating an object and not freeing it? Run a small model with -malloc_dump. > **** > > **2) **I would like to see some documentation on how to control the > GAMG, the online docs are too limited for my modest experience. Also there > is only one example and that has very basic implementation. I am > particularly interested in trying to get the solver to act only in the > strong coefficient direction, with multiple cell agglomeration ? i.e., try > and make the solver act like a block correction multigrid. > I'm afraid there aren't comprehensive docs at this time. If you are familiar with multigrid (see, e.g., Trottenberg's Multigrid book), the multigrid options should be easy to understand. You'll have to read about smoothed aggregation to interpret some of the -pc_gamg_* options. We are refactoring some of the components in GAMG (should not affect the high-level interface) and will write better documentation once that is complete. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Thu Nov 15 19:03:22 2012 From: bsmith at mcs.anl.gov (Barry Smith) Date: Thu, 15 Nov 2012 19:03:22 -0600 Subject: [petsc-users] Which IDE you use to develop petsc application In-Reply-To: References: Message-ID: Because we are developing PETSc as a library that must be portable to many users most people who develop the PETSc libraries do not use a IDE. For someone who is writing AN APPLICATION that uses PETSc (especially an application with guis) it makes sense to use an IDL to do that development. What you chose should depend on what machine you develop on and what your are experienced with or comfortable with. In the users manual we try to provide some information on using PETSc from a variety of IDEs. We are interested in collecting information on using PETSc from IDEs and improving our documentation. Barry On Nov 15, 2012, at 4:52 PM, Fande Kong wrote: > Got it. Thanks. > On Thu, Nov 15, 2012 at 3:49 PM, Matthew Knepley wrote: > On Thu, Nov 15, 2012 at 5:41 PM, Fande Kong wrote: > > Hi all, > > > > In order to improve development the efficient of the petsc application > > development, which IDE are you using? > > Emacs+gdb. > > Matt > > > Regards, > > -- > > Fande Kong > > Department of Computer Science > > University of Colorado at Boulder > > > > > > > > -- > 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 > > > > > -- > Fande Kong > ShenZhen Institutes of Advanced Technology > Chinese Academy of Sciences > From subramanya.g at gmail.com Fri Nov 16 00:04:30 2012 From: subramanya.g at gmail.com (Subramanya G) Date: Thu, 15 Nov 2012 22:04:30 -0800 Subject: [petsc-users] Is the mcs site down? Message-ID: Hi, I have been unable to get to the hg clone working and also been unable to download mpich from the mpich site. Is there a problem with the website ? Thanks. Subramanya G Sadasiva, Graduate Research Assistant, Hierarchical Design and Characterization Laboratory, School of Mechanical Engineering, Purdue University. "The art of structure is where to put the holes" Robert Le Ricolais, 1894-1977 -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Fri Nov 16 00:23:49 2012 From: balay at mcs.anl.gov (Satish Balay) Date: Fri, 16 Nov 2012 00:23:49 -0600 (CST) Subject: [petsc-users] Is the mcs site down? In-Reply-To: References: Message-ID: On Thu, 15 Nov 2012, Subramanya G wrote: > Hi, > I have been unable to get to the hg clone working and also been unable to > download mpich from the mpich site. Is there a problem with the website ? use hg clone https://bitbucket.org/petsc/petsc-dev cd petsc-dev/config hg clone https://bitbucket.org/petsc/buildsystem BuildSystem latest petsc-dev/buildsystem is updated to the current mpich download url. Satish > Thanks. > > Subramanya G Sadasiva, > > Graduate Research Assistant, > Hierarchical Design and Characterization Laboratory, > School of Mechanical Engineering, > Purdue University. > > "The art of structure is where to put the holes" > Robert Le Ricolais, 1894-1977 > From jedbrown at mcs.anl.gov Fri Nov 16 06:27:15 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Fri, 16 Nov 2012 07:27:15 -0500 Subject: [petsc-users] Is the mcs site down? In-Reply-To: References: Message-ID: MPICH moved to www.mpich.org On Fri, Nov 16, 2012 at 1:23 AM, Satish Balay wrote: > On Thu, 15 Nov 2012, Subramanya G wrote: > > > Hi, > > I have been unable to get to the hg clone working and also been unable to > > download mpich from the mpich site. Is there a problem with the website ? > > use > > hg clone https://bitbucket.org/petsc/petsc-dev > cd petsc-dev/config > hg clone https://bitbucket.org/petsc/buildsystem BuildSystem > > latest petsc-dev/buildsystem is updated to the current mpich download url. > > Satish > > > > Thanks. > > > > Subramanya G Sadasiva, > > > > Graduate Research Assistant, > > Hierarchical Design and Characterization Laboratory, > > School of Mechanical Engineering, > > Purdue University. > > > > "The art of structure is where to put the holes" > > Robert Le Ricolais, 1894-1977 > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mirzadeh at gmail.com Fri Nov 16 14:16:52 2012 From: mirzadeh at gmail.com (Mohammad Mirzadeh) Date: Fri, 16 Nov 2012 12:16:52 -0800 Subject: [petsc-users] Which IDE you use to develop petsc application In-Reply-To: References: Message-ID: I have successfully used Qt Creator with any C/C++ program I have developed regardless of what external package I'm linking against. It works for my projects with PETSc really nicely and you get all the benefits of auto-compeletion, refactoring, and function/class lookups. Plus, you can use the visual debugger which is just a front-end to gdb and works quite nicely whether you are debugging serial, MPI, or threaded codes. This strategy is perfect for local development where you later deploy the code to a remote cluster for running. If you want to directly edit codes on a remote cluster, you can mount the remote drive and just use the IDE as if you were editing local files. The debugger won't work in this case obviously (although there are supports for remote-debugging as well but I have not tried them out). Finally it has got front-ends to valgrind for both men-check and calgrind tools. There is a little bit of information in the manual on this, but do not hesitate to ask me questions if you were interested. On Thu, Nov 15, 2012 at 5:03 PM, Barry Smith wrote: > > Because we are developing PETSc as a library that must be portable to > many users most people who develop the PETSc libraries do not use a IDE. > > For someone who is writing AN APPLICATION that uses PETSc (especially > an application with guis) it makes sense to use an IDL to do that > development. What you chose should depend on what machine you develop on > and what your are experienced with or comfortable with. In the users manual > we try to provide some information on using PETSc from a variety of IDEs. > We are interested in collecting information on using PETSc from IDEs and > improving our documentation. > > > Barry > > > On Nov 15, 2012, at 4:52 PM, Fande Kong wrote: > > > Got it. Thanks. > > On Thu, Nov 15, 2012 at 3:49 PM, Matthew Knepley > wrote: > > On Thu, Nov 15, 2012 at 5:41 PM, Fande Kong > wrote: > > > Hi all, > > > > > > In order to improve development the efficient of the petsc application > > > development, which IDE are you using? > > > > Emacs+gdb. > > > > Matt > > > > > Regards, > > > -- > > > Fande Kong > > > Department of Computer Science > > > University of Colorado at Boulder > > > > > > > > > > > > > > -- > > 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 > > > > > > > > > > -- > > Fande Kong > > ShenZhen Institutes of Advanced Technology > > Chinese Academy of Sciences > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Fri Nov 16 14:21:39 2012 From: bsmith at mcs.anl.gov (Barry Smith) Date: Fri, 16 Nov 2012 14:21:39 -0600 Subject: [petsc-users] Which IDE you use to develop petsc application In-Reply-To: References: Message-ID: On Nov 16, 2012, at 2:16 PM, Mohammad Mirzadeh wrote: > I have successfully used Qt Creator with any C/C++ program I have developed regardless of what external package I'm linking against. It works for my projects with PETSc really nicely and you get all the benefits of auto-compeletion, refactoring, and function/class lookups. Plus, you can use the visual debugger which is just a front-end to gdb and works quite nicely whether you are debugging serial, MPI, or threaded codes. This is great and I'm really glad to hear it. I think that most PETSc users could benefit from working in a GUI development system and I'd like to hear more experiences so we can provide more documentation etc to help people with that. Barry > > This strategy is perfect for local development where you later deploy the code to a remote cluster for running. If you want to directly edit codes on a remote cluster, you can mount the remote drive and just use the IDE as if you were editing local files. The debugger won't work in this case obviously (although there are supports for remote-debugging as well but I have not tried them out). Finally it has got front-ends to valgrind for both men-check and calgrind tools. > > There is a little bit of information in the manual on this, but do not hesitate to ask me questions if you were interested. > > > On Thu, Nov 15, 2012 at 5:03 PM, Barry Smith wrote: > > Because we are developing PETSc as a library that must be portable to many users most people who develop the PETSc libraries do not use a IDE. > > For someone who is writing AN APPLICATION that uses PETSc (especially an application with guis) it makes sense to use an IDL to do that development. What you chose should depend on what machine you develop on and what your are experienced with or comfortable with. In the users manual we try to provide some information on using PETSc from a variety of IDEs. We are interested in collecting information on using PETSc from IDEs and improving our documentation. > > > Barry > > > On Nov 15, 2012, at 4:52 PM, Fande Kong wrote: > > > Got it. Thanks. > > On Thu, Nov 15, 2012 at 3:49 PM, Matthew Knepley wrote: > > On Thu, Nov 15, 2012 at 5:41 PM, Fande Kong wrote: > > > Hi all, > > > > > > In order to improve development the efficient of the petsc application > > > development, which IDE are you using? > > > > Emacs+gdb. > > > > Matt > > > > > Regards, > > > -- > > > Fande Kong > > > Department of Computer Science > > > University of Colorado at Boulder > > > > > > > > > > > > > > -- > > 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 > > > > > > > > > > -- > > Fande Kong > > ShenZhen Institutes of Advanced Technology > > Chinese Academy of Sciences > > > > From fd.kong at siat.ac.cn Fri Nov 16 18:35:55 2012 From: fd.kong at siat.ac.cn (Fande Kong) Date: Fri, 16 Nov 2012 17:35:55 -0700 Subject: [petsc-users] Which IDE you use to develop petsc application In-Reply-To: References: Message-ID: Thanks.It sounds very interesting. I always use Eclipse as my IDE for developing other applications (including java application, Android mobile application, web server and so on), but I don't know how to use it to develop Petsc application. I can't find any documents about how to do this. On Fri, Nov 16, 2012 at 1:16 PM, Mohammad Mirzadeh wrote: > I have successfully used Qt Creator with any C/C++ program I have > developed regardless of what external package I'm linking against. It works > for my projects with PETSc really nicely and you get all the benefits of > auto-compeletion, refactoring, and function/class lookups. Plus, you can > use the visual debugger which is just a front-end to gdb and works quite > nicely whether you are debugging serial, MPI, or threaded codes. > > This strategy is perfect for local development where you later deploy the > code to a remote cluster for running. If you want to directly edit codes on > a remote cluster, you can mount the remote drive and just use the IDE as if > you were editing local files. The debugger won't work in this case > obviously (although there are supports for remote-debugging as well but I > have not tried them out). Finally it has got front-ends to valgrind for > both men-check and calgrind tools. > > There is a little bit of information in the manual on this, but do not > hesitate to ask me questions if you were interested. > > > On Thu, Nov 15, 2012 at 5:03 PM, Barry Smith wrote: > >> >> Because we are developing PETSc as a library that must be portable to >> many users most people who develop the PETSc libraries do not use a IDE. >> >> For someone who is writing AN APPLICATION that uses PETSc (especially >> an application with guis) it makes sense to use an IDL to do that >> development. What you chose should depend on what machine you develop on >> and what your are experienced with or comfortable with. In the users manual >> we try to provide some information on using PETSc from a variety of IDEs. >> We are interested in collecting information on using PETSc from IDEs and >> improving our documentation. >> >> >> Barry >> >> >> On Nov 15, 2012, at 4:52 PM, Fande Kong wrote: >> >> > Got it. Thanks. >> > On Thu, Nov 15, 2012 at 3:49 PM, Matthew Knepley >> wrote: >> > On Thu, Nov 15, 2012 at 5:41 PM, Fande Kong >> wrote: >> > > Hi all, >> > > >> > > In order to improve development the efficient of the petsc application >> > > development, which IDE are you using? >> > >> > Emacs+gdb. >> > >> > Matt >> > >> > > Regards, >> > > -- >> > > Fande Kong >> > > Department of Computer Science >> > > University of Colorado at Boulder >> > > >> > > >> > >> > >> > >> > -- >> > 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 >> > >> > >> > >> > >> > -- >> > Fande Kong >> > ShenZhen Institutes of Advanced Technology >> > Chinese Academy of Sciences >> > >> >> > -- Fande Kong ShenZhen Institutes of Advanced Technology Chinese Academy of Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Fri Nov 16 19:59:04 2012 From: bsmith at mcs.anl.gov (Barry Smith) Date: Fri, 16 Nov 2012 19:59:04 -0600 Subject: [petsc-users] Which IDE you use to develop petsc application In-Reply-To: References: Message-ID: On Nov 16, 2012, at 6:35 PM, Fande Kong wrote: > Thanks.It sounds very interesting. I always use Eclipse as my IDE for developing other applications (including java application, Android mobile application, web server and so on), but I don't know how to use it to develop Petsc application. I can't find any documents about how to do this. In our users manual we have a small amount of information at http://www.mcs.anl.gov/petsc/petsc-current/docs/manual.pdf 13.10 Eclipse Users Any additional information you can provide to our users manual would be appreciated. Thanks Barry > > On Fri, Nov 16, 2012 at 1:16 PM, Mohammad Mirzadeh wrote: > I have successfully used Qt Creator with any C/C++ program I have developed regardless of what external package I'm linking against. It works for my projects with PETSc really nicely and you get all the benefits of auto-compeletion, refactoring, and function/class lookups. Plus, you can use the visual debugger which is just a front-end to gdb and works quite nicely whether you are debugging serial, MPI, or threaded codes. > > This strategy is perfect for local development where you later deploy the code to a remote cluster for running. If you want to directly edit codes on a remote cluster, you can mount the remote drive and just use the IDE as if you were editing local files. The debugger won't work in this case obviously (although there are supports for remote-debugging as well but I have not tried them out). Finally it has got front-ends to valgrind for both men-check and calgrind tools. > > There is a little bit of information in the manual on this, but do not hesitate to ask me questions if you were interested. > > > On Thu, Nov 15, 2012 at 5:03 PM, Barry Smith wrote: > > Because we are developing PETSc as a library that must be portable to many users most people who develop the PETSc libraries do not use a IDE. > > For someone who is writing AN APPLICATION that uses PETSc (especially an application with guis) it makes sense to use an IDL to do that development. What you chose should depend on what machine you develop on and what your are experienced with or comfortable with. In the users manual we try to provide some information on using PETSc from a variety of IDEs. We are interested in collecting information on using PETSc from IDEs and improving our documentation. > > > Barry > > > On Nov 15, 2012, at 4:52 PM, Fande Kong wrote: > > > Got it. Thanks. > > On Thu, Nov 15, 2012 at 3:49 PM, Matthew Knepley wrote: > > On Thu, Nov 15, 2012 at 5:41 PM, Fande Kong wrote: > > > Hi all, > > > > > > In order to improve development the efficient of the petsc application > > > development, which IDE are you using? > > > > Emacs+gdb. > > > > Matt > > > > > Regards, > > > -- > > > Fande Kong > > > Department of Computer Science > > > University of Colorado at Boulder > > > > > > > > > > > > > > -- > > 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 > > > > > > > > > > -- > > Fande Kong > > ShenZhen Institutes of Advanced Technology > > Chinese Academy of Sciences > > > > > > > > -- > Fande Kong > ShenZhen Institutes of Advanced Technology > Chinese Academy of Sciences > From popov at uni-mainz.de Sat Nov 17 04:08:01 2012 From: popov at uni-mainz.de (Anton Popov) Date: Sat, 17 Nov 2012 11:08:01 +0100 Subject: [petsc-users] Which IDE you use to develop petsc application In-Reply-To: References: Message-ID: <50A76201.8010607@uni-mainz.de> On 11/16/12 2:03 AM, Barry Smith wrote: > Because we are developing PETSc as a library that must be portable to many users most people who develop the PETSc libraries do not use a IDE. > > For someone who is writing AN APPLICATION that uses PETSc (especially an application with guis) it makes sense to use an IDL to do that development. What you chose should depend on what machine you develop on and what your are experienced with or comfortable with. In the users manual we try to provide some information on using PETSc from a variety of IDEs. We are interested in collecting information on using PETSc from IDEs and improving our documentation. I managed Eclipse PTP on Mac OS (probably the same on Linux). Provided that a debug (preferably valgrind-clean) version of MPICH2 library with MPD process manager can be installed, Eclipse Indigo can be easily configured for using PARALLEL SDM debugger with PETSc applications. If you're interested, I can send detailed configuration / setup instructions. Anton > > > Barry > > > On Nov 15, 2012, at 4:52 PM, Fande Kong wrote: > >> Got it. Thanks. >> On Thu, Nov 15, 2012 at 3:49 PM, Matthew Knepley wrote: >> On Thu, Nov 15, 2012 at 5:41 PM, Fande Kong wrote: >>> Hi all, >>> >>> In order to improve development the efficient of the petsc application >>> development, which IDE are you using? >> Emacs+gdb. >> >> Matt >> >>> Regards, >>> -- >>> Fande Kong >>> Department of Computer Science >>> University of Colorado at Boulder >>> >>> >> >> >> -- >> 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 >> >> >> >> >> -- >> Fande Kong >> ShenZhen Institutes of Advanced Technology >> Chinese Academy of Sciences >> From fuentesdt at gmail.com Sat Nov 17 09:50:38 2012 From: fuentesdt at gmail.com (David Fuentes) Date: Sat, 17 Nov 2012 09:50:38 -0600 Subject: [petsc-users] CPU utilization during GPU solver Message-ID: Hi, I'm using petsc 3.3p4 I'm trying to run a nonlinear SNES solver on GPU with gmres and jacobi PC using VECSEQCUSP and MATSEQAIJCUSP datatypes for the rhs and jacobian matrix respectively. When running top I still see significant CPU utilization (800-900 %CPU) during the solve ? possibly from some multithreaded operations ? Is this expected ? I was thinking that since I input everything into the solver as a CUSP datatype, all linear algebra operations would be on the GPU device from there and wasn't expecting to see such CPU utilization during the solve ? Do I probably have an error in my code somewhere ? Thanks, David -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Sat Nov 17 11:02:22 2012 From: knepley at gmail.com (Matthew Knepley) Date: Sat, 17 Nov 2012 12:02:22 -0500 Subject: [petsc-users] CPU utilization during GPU solver In-Reply-To: References: Message-ID: On Sat, Nov 17, 2012 at 10:50 AM, David Fuentes wrote: > Hi, > > I'm using petsc 3.3p4 > I'm trying to run a nonlinear SNES solver on GPU with gmres and jacobi PC > using VECSEQCUSP and MATSEQAIJCUSP datatypes for the rhs and jacobian matrix > respectively. > When running top I still see significant CPU utilization (800-900 %CPU) > during the solve ? possibly from some multithreaded operations ? > > Is this expected ? > I was thinking that since I input everything into the solver as a CUSP > datatype, all linear algebra operations would be on the GPU device from > there and wasn't expecting to see such CPU utilization during the solve ? > Do I probably have an error in my code somewhere ? We cannot answer performance questions without -log_summary Matt > Thanks, > David -- 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 From fuentesdt at gmail.com Sat Nov 17 13:41:35 2012 From: fuentesdt at gmail.com (David Fuentes) Date: Sat, 17 Nov 2012 13:41:35 -0600 Subject: [petsc-users] CPU utilization during GPU solver In-Reply-To: References: Message-ID: thanks Matt, My log summary is below. ************************************************************************************************************************ *** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r -fCourier9' to print this document *** ************************************************************************************************************************ ---------------------------------------------- PETSc Performance Summary: ---------------------------------------------- ./FocusUltraSoundModel on a gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg named SCRGP2 with 1 processor, by fuentes Sat Nov 17 13:35:06 2012 Using Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 CDT 2012 Max Max/Min Avg Total Time (sec): 3.164e+01 1.00000 3.164e+01 Objects: 4.100e+01 1.00000 4.100e+01 Flops: 2.561e+09 1.00000 2.561e+09 2.561e+09 Flops/sec: 8.097e+07 1.00000 8.097e+07 8.097e+07 Memory: 2.129e+08 1.00000 2.129e+08 MPI Messages: 0.000e+00 0.00000 0.000e+00 0.000e+00 MPI Message Lengths: 0.000e+00 0.00000 0.000e+00 0.000e+00 MPI Reductions: 4.230e+02 1.00000 Flop counting convention: 1 flop = 1 real number operation of type (multiply/divide/add/subtract) e.g., VecAXPY() for real vectors of length N --> 2N flops and VecAXPY() for complex vectors of length N --> 8N flops Summary of Stages: ----- Time ------ ----- Flops ----- --- Messages --- -- Message Lengths -- -- Reductions -- Avg %Total Avg %Total counts %Total Avg %Total counts %Total 0: Main Stage: 3.1636e+01 100.0% 2.5615e+09 100.0% 0.000e+00 0.0% 0.000e+00 0.0% 4.220e+02 99.8% ------------------------------------------------------------------------------------------------------------------------ See the 'Profiling' chapter of the users' manual for details on interpreting output. Phase summary info: Count: number of times phase was executed Time and Flops: Max - maximum over all processors Ratio - ratio of maximum to minimum over all processors Mess: number of messages sent Avg. len: average message length Reduct: number of global reductions Global: entire computation Stage: stages of a computation. Set stages with PetscLogStagePush() and PetscLogStagePop(). %T - percent time in this phase %f - percent flops in this phase %M - percent messages in this phase %L - percent message lengths in this phase %R - percent reductions in this phase Total Mflop/s: 10e-6 * (sum of flops over all processors)/(max time over all processors) ------------------------------------------------------------------------------------------------------------------------ ########################################################## # # # WARNING!!! # # # # This code was compiled with a debugging option, # # To get timing results run ./configure # # using --with-debugging=no, the performance will # # be generally two or three times faster. # # # ########################################################## Event Count Time (sec) Flops --- Global --- --- Stage --- Total Max Ratio Max Ratio Max Ratio Mess Avg len Reduct %T %f %M %L %R %T %f %M %L %R Mflop/s ------------------------------------------------------------------------------------------------------------------------ --- Event Stage 0: Main Stage ComputeFunction 52 1.0 3.9104e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 3.0e+00 1 0 0 0 1 1 0 0 0 1 0 VecDot 50 1.0 3.2072e-02 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 0.0e+00 0 4 0 0 0 0 4 0 0 0 3025 VecMDot 50 1.0 1.3100e-01 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 0.0e+00 0 4 0 0 0 0 4 0 0 0 741 VecNorm 200 1.0 9.7943e-02 1.0 3.88e+08 1.0 0.0e+00 0.0e+00 0.0e+00 0 15 0 0 0 0 15 0 0 0 3963 VecScale 100 1.0 1.3496e-01 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 0.0e+00 0 4 0 0 0 0 4 0 0 0 719 VecCopy 150 1.0 4.8405e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 VecSet 164 1.0 2.9707e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 VecAXPY 50 1.0 3.2194e-02 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 0.0e+00 0 4 0 0 0 0 4 0 0 0 3014 VecWAXPY 50 1.0 2.9040e-01 1.0 4.85e+07 1.0 0.0e+00 0.0e+00 0.0e+00 1 2 0 0 0 1 2 0 0 0 167 VecMAXPY 100 1.0 5.4555e-01 1.0 1.94e+08 1.0 0.0e+00 0.0e+00 0.0e+00 2 8 0 0 0 2 8 0 0 0 356 VecPointwiseMult 100 1.0 5.3003e-01 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 0.0e+00 2 4 0 0 0 2 4 0 0 0 183 VecScatterBegin 53 1.0 1.8660e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 VecReduceArith 101 1.0 6.9973e-02 1.0 1.96e+08 1.0 0.0e+00 0.0e+00 0.0e+00 0 8 0 0 0 0 8 0 0 0 2801 VecReduceComm 51 1.0 1.0252e-04 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecNormalize 100 1.0 1.8565e-01 1.0 2.91e+08 1.0 0.0e+00 0.0e+00 0.0e+00 1 11 0 0 0 1 11 0 0 0 1568 VecCUSPCopyTo 152 1.0 5.8016e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 VecCUSPCopyFrom 201 1.0 6.0029e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 MatMult 100 1.0 6.8465e-01 1.0 1.25e+09 1.0 0.0e+00 0.0e+00 0.0e+00 2 49 0 0 0 2 49 0 0 0 1825 MatAssemblyBegin 3 1.0 3.3379e-06 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 MatAssemblyEnd 3 1.0 2.7767e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 MatZeroEntries 1 1.0 2.0346e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 MatCUSPCopyTo 3 1.0 1.4056e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 SNESSolve 1 1.0 2.2094e+01 1.0 2.56e+09 1.0 0.0e+00 0.0e+00 3.7e+02 70100 0 0 88 70100 0 0 89 116 SNESFunctionEval 51 1.0 3.9031e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 SNESJacobianEval 50 1.0 1.3191e+00 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 4 0 0 0 0 4 0 0 0 0 0 SNESLineSearch 50 1.0 6.2922e+00 1.0 1.16e+09 1.0 0.0e+00 0.0e+00 5.0e+01 20 45 0 0 12 20 45 0 0 12 184 KSPGMRESOrthog 50 1.0 4.0436e-01 1.0 1.94e+08 1.0 0.0e+00 0.0e+00 5.0e+01 1 8 0 0 12 1 8 0 0 12 480 KSPSetUp 50 1.0 2.1935e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 1.5e+01 0 0 0 0 4 0 0 0 0 4 0 KSPSolve 50 1.0 1.3230e+01 1.0 1.40e+09 1.0 0.0e+00 0.0e+00 3.2e+02 42 55 0 0 75 42 55 0 0 75 106 PCSetUp 50 1.0 1.9897e+00 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 4.9e+01 6 0 0 0 12 6 0 0 0 12 0 PCApply 100 1.0 5.7457e-01 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 4.0e+00 2 4 0 0 1 2 4 0 0 1 169 ------------------------------------------------------------------------------------------------------------------------ Memory usage is given in bytes: Object Type Creations Destructions Memory Descendants' Mem. Reports information only for process 0. --- Event Stage 0: Main Stage Container 2 2 1096 0 Vector 16 16 108696592 0 Vector Scatter 2 2 1240 0 Matrix 1 1 96326824 0 Distributed Mesh 3 3 7775936 0 Bipartite Graph 6 6 4104 0 Index Set 5 5 3884908 0 IS L to G Mapping 1 1 3881760 0 SNES 1 1 1268 0 SNESLineSearch 1 1 840 0 Viewer 1 0 0 0 Krylov Solver 1 1 18288 0 Preconditioner 1 1 792 0 ======================================================================================================================== Average time to get PetscTime(): 9.53674e-08 #PETSc Option Table entries: -da_vec_type cusp -dm_mat_type seqaijcusp -ksp_monitor -log_summary -pc_type jacobi -snes_converged_reason -snes_monitor #End of PETSc Option Table entries Compiled without FORTRAN kernels Compiled with full precision matrices (default) sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 sizeof(PetscScalar) 8 sizeof(PetscInt) 4 Configure run at: Fri Nov 16 08:40:52 2012 Configure options: --with-clanguage=C++ --with-mpi-dir=/usr --with-shared-libraries --with-cuda-arch=sm_20 --CFLAGS=-O0 --CXXFLAGS=-O0 --CUDAFLAGS=-O0 --with-etags=1 --with-mpi4py=0 --with-blas-lapack-lib="[/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_rt.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_intel_thread.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_core.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libiomp5.so]" --download-blacs --download-superlu_dist --download-triangle --download-parmetis --download-metis --download-mumps --download-scalapack --with-cuda=1 --with-cusp=1 --with-thrust=1 --with-cuda-dir=/opt/apps/cuda/4.2//cuda --with-sieve=1 --download-exodusii=yes --download-netcdf --with-boost=1 --with-boost-dir=/usr --download-fiat=yes --download-generator --download-scientificpython --with-matlab=1 --with-matlab-engine=1 --with-matlab-dir=/opt/MATLAB/R2011a ----------------------------------------- Libraries compiled on Fri Nov 16 08:40:52 2012 on SCRGP2 Machine characteristics: Linux-2.6.32-41-server-x86_64-with-debian-squeeze-sid Using PETSc directory: /opt/apps/PETSC/petsc-3.3-p4 Using PETSc arch: gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg ----------------------------------------- Using C compiler: /usr/bin/mpicxx -O0 -g -fPIC ${COPTFLAGS} ${CFLAGS} Using Fortran compiler: /usr/bin/mpif90 -fPIC -Wall -Wno-unused-variable -g ${FOPTFLAGS} ${FFLAGS} ----------------------------------------- Using include paths: -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/include -I/opt/apps/PETSC/petsc-3.3-p4/include -I/opt/apps/PETSC/petsc-3.3-p4/include -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/include -I/opt/apps/cuda/4.2//cuda/include -I/opt/apps/PETSC/petsc-3.3-p4/include/sieve -I/opt/MATLAB/R2011a/extern/include -I/usr/include -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/cbind/include -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/forbind/include -I/usr/include/mpich2 ----------------------------------------- Using C linker: /usr/bin/mpicxx Using Fortran linker: /usr/bin/mpif90 Using libraries: -Wl,-rpath,/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib -L/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib -lpetsc -Wl,-rpath,/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib -L/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib -ltriangle -lX11 -lpthread -lsuperlu_dist_3.1 -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lparmetis -lmetis -lscalapack -lblacs -Wl,-rpath,/opt/apps/cuda/4.2//cuda/lib64 -L/opt/apps/cuda/4.2//cuda/lib64 -lcufft -lcublas -lcudart -lcusparse -Wl,-rpath,/opt/MATLAB/R2011a/sys/os/glnxa64:/opt/MATLAB/R2011a/bin/glnxa64:/opt/MATLAB/R2011a/extern/lib/glnxa64 -L/opt/MATLAB/R2011a/bin/glnxa64 -L/opt/MATLAB/R2011a/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc -Wl,-rpath,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib -L/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib -lmkl_rt -lmkl_intel_thread -lmkl_core -liomp5 -lexoIIv2for -lexodus -lnetcdf_c++ -lnetcdf -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.4.3 -L/usr/lib/gcc/x86_64-linux-gnu/4.4.3 -lmpichf90 -lgfortran -lm -lm -lmpichcxx -lstdc++ -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lpthread -lrt -lgcc_s -ldl ----------------------------------------- On Sat, Nov 17, 2012 at 11:02 AM, Matthew Knepley wrote: > On Sat, Nov 17, 2012 at 10:50 AM, David Fuentes > wrote: > > Hi, > > > > I'm using petsc 3.3p4 > > I'm trying to run a nonlinear SNES solver on GPU with gmres and jacobi PC > > using VECSEQCUSP and MATSEQAIJCUSP datatypes for the rhs and jacobian > matrix > > respectively. > > When running top I still see significant CPU utilization (800-900 %CPU) > > during the solve ? possibly from some multithreaded operations ? > > > > Is this expected ? > > I was thinking that since I input everything into the solver as a CUSP > > datatype, all linear algebra operations would be on the GPU device from > > there and wasn't expecting to see such CPU utilization during the solve ? > > Do I probably have an error in my code somewhere ? > > We cannot answer performance questions without -log_summary > > Matt > > > Thanks, > > David > > > > -- > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Sat Nov 17 13:49:51 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Sat, 17 Nov 2012 14:49:51 -0500 Subject: [petsc-users] CPU utilization during GPU solver In-Reply-To: References: Message-ID: Please read the large boxed message about debugging mode. (Replying from phone so can't make it 72 point blinking red, sorry.) On Nov 17, 2012 1:41 PM, "David Fuentes" wrote: > thanks Matt, > > My log summary is below. > > > ************************************************************************************************************************ > *** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r > -fCourier9' to print this document *** > > ************************************************************************************************************************ > > ---------------------------------------------- PETSc Performance Summary: > ---------------------------------------------- > > ./FocusUltraSoundModel on a gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg named > SCRGP2 with 1 processor, by fuentes Sat Nov 17 13:35:06 2012 > Using Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 CDT 2012 > > Max Max/Min Avg Total > Time (sec): 3.164e+01 1.00000 3.164e+01 > Objects: 4.100e+01 1.00000 4.100e+01 > Flops: 2.561e+09 1.00000 2.561e+09 2.561e+09 > Flops/sec: 8.097e+07 1.00000 8.097e+07 8.097e+07 > Memory: 2.129e+08 1.00000 2.129e+08 > MPI Messages: 0.000e+00 0.00000 0.000e+00 0.000e+00 > MPI Message Lengths: 0.000e+00 0.00000 0.000e+00 0.000e+00 > MPI Reductions: 4.230e+02 1.00000 > > Flop counting convention: 1 flop = 1 real number operation of type > (multiply/divide/add/subtract) > e.g., VecAXPY() for real vectors of length N > --> 2N flops > and VecAXPY() for complex vectors of length N > --> 8N flops > > Summary of Stages: ----- Time ------ ----- Flops ----- --- Messages > --- -- Message Lengths -- -- Reductions -- > Avg %Total Avg %Total counts > %Total Avg %Total counts %Total > 0: Main Stage: 3.1636e+01 100.0% 2.5615e+09 100.0% 0.000e+00 > 0.0% 0.000e+00 0.0% 4.220e+02 99.8% > > > ------------------------------------------------------------------------------------------------------------------------ > See the 'Profiling' chapter of the users' manual for details on > interpreting output. > Phase summary info: > Count: number of times phase was executed > Time and Flops: Max - maximum over all processors > Ratio - ratio of maximum to minimum over all processors > Mess: number of messages sent > Avg. len: average message length > Reduct: number of global reductions > Global: entire computation > Stage: stages of a computation. Set stages with PetscLogStagePush() and > PetscLogStagePop(). > %T - percent time in this phase %f - percent flops in this > phase > %M - percent messages in this phase %L - percent message lengths > in this phase > %R - percent reductions in this phase > Total Mflop/s: 10e-6 * (sum of flops over all processors)/(max time > over all processors) > > ------------------------------------------------------------------------------------------------------------------------ > > > ########################################################## > # # > # WARNING!!! # > # # > # This code was compiled with a debugging option, # > # To get timing results run ./configure # > # using --with-debugging=no, the performance will # > # be generally two or three times faster. # > # # > ########################################################## > > > Event Count Time (sec) Flops > --- Global --- --- Stage --- Total > Max Ratio Max Ratio Max Ratio Mess Avg len > Reduct %T %f %M %L %R %T %f %M %L %R Mflop/s > > ------------------------------------------------------------------------------------------------------------------------ > > --- Event Stage 0: Main Stage > > ComputeFunction 52 1.0 3.9104e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 3.0e+00 1 0 0 0 1 1 0 0 0 1 0 > VecDot 50 1.0 3.2072e-02 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 > 0.0e+00 0 4 0 0 0 0 4 0 0 0 3025 > VecMDot 50 1.0 1.3100e-01 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 > 0.0e+00 0 4 0 0 0 0 4 0 0 0 741 > VecNorm 200 1.0 9.7943e-02 1.0 3.88e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 0 15 0 0 0 0 15 0 0 0 3963 > VecScale 100 1.0 1.3496e-01 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 > 0.0e+00 0 4 0 0 0 0 4 0 0 0 719 > VecCopy 150 1.0 4.8405e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 > VecSet 164 1.0 2.9707e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 > VecAXPY 50 1.0 3.2194e-02 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 > 0.0e+00 0 4 0 0 0 0 4 0 0 0 3014 > VecWAXPY 50 1.0 2.9040e-01 1.0 4.85e+07 1.0 0.0e+00 0.0e+00 > 0.0e+00 1 2 0 0 0 1 2 0 0 0 167 > VecMAXPY 100 1.0 5.4555e-01 1.0 1.94e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 2 8 0 0 0 2 8 0 0 0 356 > VecPointwiseMult 100 1.0 5.3003e-01 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 > 0.0e+00 2 4 0 0 0 2 4 0 0 0 183 > VecScatterBegin 53 1.0 1.8660e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 > VecReduceArith 101 1.0 6.9973e-02 1.0 1.96e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 0 8 0 0 0 0 8 0 0 0 2801 > VecReduceComm 51 1.0 1.0252e-04 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > VecNormalize 100 1.0 1.8565e-01 1.0 2.91e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 1 11 0 0 0 1 11 0 0 0 1568 > VecCUSPCopyTo 152 1.0 5.8016e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 > VecCUSPCopyFrom 201 1.0 6.0029e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 > MatMult 100 1.0 6.8465e-01 1.0 1.25e+09 1.0 0.0e+00 0.0e+00 > 0.0e+00 2 49 0 0 0 2 49 0 0 0 1825 > MatAssemblyBegin 3 1.0 3.3379e-06 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatAssemblyEnd 3 1.0 2.7767e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 > MatZeroEntries 1 1.0 2.0346e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatCUSPCopyTo 3 1.0 1.4056e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > SNESSolve 1 1.0 2.2094e+01 1.0 2.56e+09 1.0 0.0e+00 0.0e+00 > 3.7e+02 70100 0 0 88 70100 0 0 89 116 > SNESFunctionEval 51 1.0 3.9031e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 > SNESJacobianEval 50 1.0 1.3191e+00 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 4 0 0 0 0 4 0 0 0 0 0 > SNESLineSearch 50 1.0 6.2922e+00 1.0 1.16e+09 1.0 0.0e+00 0.0e+00 > 5.0e+01 20 45 0 0 12 20 45 0 0 12 184 > KSPGMRESOrthog 50 1.0 4.0436e-01 1.0 1.94e+08 1.0 0.0e+00 0.0e+00 > 5.0e+01 1 8 0 0 12 1 8 0 0 12 480 > KSPSetUp 50 1.0 2.1935e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 1.5e+01 0 0 0 0 4 0 0 0 0 4 0 > KSPSolve 50 1.0 1.3230e+01 1.0 1.40e+09 1.0 0.0e+00 0.0e+00 > 3.2e+02 42 55 0 0 75 42 55 0 0 75 106 > PCSetUp 50 1.0 1.9897e+00 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 4.9e+01 6 0 0 0 12 6 0 0 0 12 0 > PCApply 100 1.0 5.7457e-01 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 > 4.0e+00 2 4 0 0 1 2 4 0 0 1 169 > > ------------------------------------------------------------------------------------------------------------------------ > > Memory usage is given in bytes: > > Object Type Creations Destructions Memory Descendants' Mem. > Reports information only for process 0. > > --- Event Stage 0: Main Stage > > Container 2 2 1096 0 > Vector 16 16 108696592 0 > Vector Scatter 2 2 1240 0 > Matrix 1 1 96326824 0 > Distributed Mesh 3 3 7775936 0 > Bipartite Graph 6 6 4104 0 > Index Set 5 5 3884908 0 > IS L to G Mapping 1 1 3881760 0 > SNES 1 1 1268 0 > SNESLineSearch 1 1 840 0 > Viewer 1 0 0 0 > Krylov Solver 1 1 18288 0 > Preconditioner 1 1 792 0 > > ======================================================================================================================== > Average time to get PetscTime(): 9.53674e-08 > #PETSc Option Table entries: > -da_vec_type cusp > -dm_mat_type seqaijcusp > -ksp_monitor > -log_summary > -pc_type jacobi > -snes_converged_reason > -snes_monitor > #End of PETSc Option Table entries > Compiled without FORTRAN kernels > Compiled with full precision matrices (default) > sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 > sizeof(PetscScalar) 8 sizeof(PetscInt) 4 > Configure run at: Fri Nov 16 08:40:52 2012 > Configure options: --with-clanguage=C++ --with-mpi-dir=/usr > --with-shared-libraries --with-cuda-arch=sm_20 --CFLAGS=-O0 --CXXFLAGS=-O0 > --CUDAFLAGS=-O0 --with-etags=1 --with-mpi4py=0 > --with-blas-lapack-lib="[/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_rt.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_intel_thread.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_core.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libiomp5.so]" > --download-blacs --download-superlu_dist --download-triangle > --download-parmetis --download-metis --download-mumps --download-scalapack > --with-cuda=1 --with-cusp=1 --with-thrust=1 > --with-cuda-dir=/opt/apps/cuda/4.2//cuda --with-sieve=1 > --download-exodusii=yes --download-netcdf --with-boost=1 > --with-boost-dir=/usr --download-fiat=yes --download-generator > --download-scientificpython --with-matlab=1 --with-matlab-engine=1 > --with-matlab-dir=/opt/MATLAB/R2011a > ----------------------------------------- > Libraries compiled on Fri Nov 16 08:40:52 2012 on SCRGP2 > Machine characteristics: > Linux-2.6.32-41-server-x86_64-with-debian-squeeze-sid > Using PETSc directory: /opt/apps/PETSC/petsc-3.3-p4 > Using PETSc arch: gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg > ----------------------------------------- > > Using C compiler: /usr/bin/mpicxx -O0 -g -fPIC ${COPTFLAGS} ${CFLAGS} > Using Fortran compiler: /usr/bin/mpif90 -fPIC -Wall -Wno-unused-variable > -g ${FOPTFLAGS} ${FFLAGS} > ----------------------------------------- > > Using include paths: > -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/include > -I/opt/apps/PETSC/petsc-3.3-p4/include > -I/opt/apps/PETSC/petsc-3.3-p4/include > -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/include > -I/opt/apps/cuda/4.2//cuda/include > -I/opt/apps/PETSC/petsc-3.3-p4/include/sieve > -I/opt/MATLAB/R2011a/extern/include -I/usr/include > -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/cbind/include > -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/forbind/include > -I/usr/include/mpich2 > ----------------------------------------- > > Using C linker: /usr/bin/mpicxx > Using Fortran linker: /usr/bin/mpif90 > Using libraries: > -Wl,-rpath,/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib > -L/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib > -lpetsc > -Wl,-rpath,/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib > -L/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib > -ltriangle -lX11 -lpthread -lsuperlu_dist_3.1 -lcmumps -ldmumps -lsmumps > -lzmumps -lmumps_common -lpord -lparmetis -lmetis -lscalapack -lblacs > -Wl,-rpath,/opt/apps/cuda/4.2//cuda/lib64 -L/opt/apps/cuda/4.2//cuda/lib64 > -lcufft -lcublas -lcudart -lcusparse > -Wl,-rpath,/opt/MATLAB/R2011a/sys/os/glnxa64:/opt/MATLAB/R2011a/bin/glnxa64:/opt/MATLAB/R2011a/extern/lib/glnxa64 > -L/opt/MATLAB/R2011a/bin/glnxa64 -L/opt/MATLAB/R2011a/extern/lib/glnxa64 > -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc > -Wl,-rpath,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib > -L/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib -lmkl_rt -lmkl_intel_thread > -lmkl_core -liomp5 -lexoIIv2for -lexodus -lnetcdf_c++ -lnetcdf > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.4.3 > -L/usr/lib/gcc/x86_64-linux-gnu/4.4.3 -lmpichf90 -lgfortran -lm -lm > -lmpichcxx -lstdc++ -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lpthread -lrt > -lgcc_s -ldl > ----------------------------------------- > > > > On Sat, Nov 17, 2012 at 11:02 AM, Matthew Knepley wrote: > >> On Sat, Nov 17, 2012 at 10:50 AM, David Fuentes >> wrote: >> > Hi, >> > >> > I'm using petsc 3.3p4 >> > I'm trying to run a nonlinear SNES solver on GPU with gmres and jacobi >> PC >> > using VECSEQCUSP and MATSEQAIJCUSP datatypes for the rhs and jacobian >> matrix >> > respectively. >> > When running top I still see significant CPU utilization (800-900 %CPU) >> > during the solve ? possibly from some multithreaded operations ? >> > >> > Is this expected ? >> > I was thinking that since I input everything into the solver as a CUSP >> > datatype, all linear algebra operations would be on the GPU device from >> > there and wasn't expecting to see such CPU utilization during the solve >> ? >> > Do I probably have an error in my code somewhere ? >> >> We cannot answer performance questions without -log_summary >> >> Matt >> >> > Thanks, >> > David >> >> >> >> -- >> 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 >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From fuentesdt at gmail.com Sat Nov 17 14:05:03 2012 From: fuentesdt at gmail.com (David Fuentes) Date: Sat, 17 Nov 2012 14:05:03 -0600 Subject: [petsc-users] CPU utilization during GPU solver In-Reply-To: References: Message-ID: Thanks Jed. I was trying to run it in dbg mode to verify if all significant parts of the solver were running on the GPU and not on the CPU by mistake. I cant pinpoint what part of the solver is running on the CPU. When I run top while running the solver there seems to be ~800% CPU utilization that I wasn't expecting. I cant tell if i'm slowing things down by transferring between CPU/GPU on accident? thanks again, df On Sat, Nov 17, 2012 at 1:49 PM, Jed Brown wrote: > Please read the large boxed message about debugging mode. > > (Replying from phone so can't make it 72 point blinking red, sorry.) > On Nov 17, 2012 1:41 PM, "David Fuentes" wrote: > >> thanks Matt, >> >> My log summary is below. >> >> >> ************************************************************************************************************************ >> *** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r >> -fCourier9' to print this document *** >> >> ************************************************************************************************************************ >> >> ---------------------------------------------- PETSc Performance Summary: >> ---------------------------------------------- >> >> ./FocusUltraSoundModel on a gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg named >> SCRGP2 with 1 processor, by fuentes Sat Nov 17 13:35:06 2012 >> Using Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 CDT 2012 >> >> Max Max/Min Avg Total >> Time (sec): 3.164e+01 1.00000 3.164e+01 >> Objects: 4.100e+01 1.00000 4.100e+01 >> Flops: 2.561e+09 1.00000 2.561e+09 2.561e+09 >> Flops/sec: 8.097e+07 1.00000 8.097e+07 8.097e+07 >> Memory: 2.129e+08 1.00000 2.129e+08 >> MPI Messages: 0.000e+00 0.00000 0.000e+00 0.000e+00 >> MPI Message Lengths: 0.000e+00 0.00000 0.000e+00 0.000e+00 >> MPI Reductions: 4.230e+02 1.00000 >> >> Flop counting convention: 1 flop = 1 real number operation of type >> (multiply/divide/add/subtract) >> e.g., VecAXPY() for real vectors of length N >> --> 2N flops >> and VecAXPY() for complex vectors of length N >> --> 8N flops >> >> Summary of Stages: ----- Time ------ ----- Flops ----- --- Messages >> --- -- Message Lengths -- -- Reductions -- >> Avg %Total Avg %Total counts >> %Total Avg %Total counts %Total >> 0: Main Stage: 3.1636e+01 100.0% 2.5615e+09 100.0% 0.000e+00 >> 0.0% 0.000e+00 0.0% 4.220e+02 99.8% >> >> >> ------------------------------------------------------------------------------------------------------------------------ >> See the 'Profiling' chapter of the users' manual for details on >> interpreting output. >> Phase summary info: >> Count: number of times phase was executed >> Time and Flops: Max - maximum over all processors >> Ratio - ratio of maximum to minimum over all processors >> Mess: number of messages sent >> Avg. len: average message length >> Reduct: number of global reductions >> Global: entire computation >> Stage: stages of a computation. Set stages with PetscLogStagePush() >> and PetscLogStagePop(). >> %T - percent time in this phase %f - percent flops in this >> phase >> %M - percent messages in this phase %L - percent message >> lengths in this phase >> %R - percent reductions in this phase >> Total Mflop/s: 10e-6 * (sum of flops over all processors)/(max time >> over all processors) >> >> ------------------------------------------------------------------------------------------------------------------------ >> >> >> ########################################################## >> # # >> # WARNING!!! # >> # # >> # This code was compiled with a debugging option, # >> # To get timing results run ./configure # >> # using --with-debugging=no, the performance will # >> # be generally two or three times faster. # >> # # >> ########################################################## >> >> >> Event Count Time (sec) Flops >> --- Global --- --- Stage --- Total >> Max Ratio Max Ratio Max Ratio Mess Avg len >> Reduct %T %f %M %L %R %T %f %M %L %R Mflop/s >> >> ------------------------------------------------------------------------------------------------------------------------ >> >> --- Event Stage 0: Main Stage >> >> ComputeFunction 52 1.0 3.9104e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 3.0e+00 1 0 0 0 1 1 0 0 0 1 0 >> VecDot 50 1.0 3.2072e-02 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 >> 0.0e+00 0 4 0 0 0 0 4 0 0 0 3025 >> VecMDot 50 1.0 1.3100e-01 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 >> 0.0e+00 0 4 0 0 0 0 4 0 0 0 741 >> VecNorm 200 1.0 9.7943e-02 1.0 3.88e+08 1.0 0.0e+00 0.0e+00 >> 0.0e+00 0 15 0 0 0 0 15 0 0 0 3963 >> VecScale 100 1.0 1.3496e-01 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 >> 0.0e+00 0 4 0 0 0 0 4 0 0 0 719 >> VecCopy 150 1.0 4.8405e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 >> VecSet 164 1.0 2.9707e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 >> VecAXPY 50 1.0 3.2194e-02 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 >> 0.0e+00 0 4 0 0 0 0 4 0 0 0 3014 >> VecWAXPY 50 1.0 2.9040e-01 1.0 4.85e+07 1.0 0.0e+00 0.0e+00 >> 0.0e+00 1 2 0 0 0 1 2 0 0 0 167 >> VecMAXPY 100 1.0 5.4555e-01 1.0 1.94e+08 1.0 0.0e+00 0.0e+00 >> 0.0e+00 2 8 0 0 0 2 8 0 0 0 356 >> VecPointwiseMult 100 1.0 5.3003e-01 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 >> 0.0e+00 2 4 0 0 0 2 4 0 0 0 183 >> VecScatterBegin 53 1.0 1.8660e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 >> VecReduceArith 101 1.0 6.9973e-02 1.0 1.96e+08 1.0 0.0e+00 0.0e+00 >> 0.0e+00 0 8 0 0 0 0 8 0 0 0 2801 >> VecReduceComm 51 1.0 1.0252e-04 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >> VecNormalize 100 1.0 1.8565e-01 1.0 2.91e+08 1.0 0.0e+00 0.0e+00 >> 0.0e+00 1 11 0 0 0 1 11 0 0 0 1568 >> VecCUSPCopyTo 152 1.0 5.8016e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 >> VecCUSPCopyFrom 201 1.0 6.0029e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 >> MatMult 100 1.0 6.8465e-01 1.0 1.25e+09 1.0 0.0e+00 0.0e+00 >> 0.0e+00 2 49 0 0 0 2 49 0 0 0 1825 >> MatAssemblyBegin 3 1.0 3.3379e-06 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >> MatAssemblyEnd 3 1.0 2.7767e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 >> MatZeroEntries 1 1.0 2.0346e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >> MatCUSPCopyTo 3 1.0 1.4056e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >> SNESSolve 1 1.0 2.2094e+01 1.0 2.56e+09 1.0 0.0e+00 0.0e+00 >> 3.7e+02 70100 0 0 88 70100 0 0 89 116 >> SNESFunctionEval 51 1.0 3.9031e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 >> SNESJacobianEval 50 1.0 1.3191e+00 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 4 0 0 0 0 4 0 0 0 0 0 >> SNESLineSearch 50 1.0 6.2922e+00 1.0 1.16e+09 1.0 0.0e+00 0.0e+00 >> 5.0e+01 20 45 0 0 12 20 45 0 0 12 184 >> KSPGMRESOrthog 50 1.0 4.0436e-01 1.0 1.94e+08 1.0 0.0e+00 0.0e+00 >> 5.0e+01 1 8 0 0 12 1 8 0 0 12 480 >> KSPSetUp 50 1.0 2.1935e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 1.5e+01 0 0 0 0 4 0 0 0 0 4 0 >> KSPSolve 50 1.0 1.3230e+01 1.0 1.40e+09 1.0 0.0e+00 0.0e+00 >> 3.2e+02 42 55 0 0 75 42 55 0 0 75 106 >> PCSetUp 50 1.0 1.9897e+00 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 4.9e+01 6 0 0 0 12 6 0 0 0 12 0 >> PCApply 100 1.0 5.7457e-01 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 >> 4.0e+00 2 4 0 0 1 2 4 0 0 1 169 >> >> ------------------------------------------------------------------------------------------------------------------------ >> >> Memory usage is given in bytes: >> >> Object Type Creations Destructions Memory Descendants' >> Mem. >> Reports information only for process 0. >> >> --- Event Stage 0: Main Stage >> >> Container 2 2 1096 0 >> Vector 16 16 108696592 0 >> Vector Scatter 2 2 1240 0 >> Matrix 1 1 96326824 0 >> Distributed Mesh 3 3 7775936 0 >> Bipartite Graph 6 6 4104 0 >> Index Set 5 5 3884908 0 >> IS L to G Mapping 1 1 3881760 0 >> SNES 1 1 1268 0 >> SNESLineSearch 1 1 840 0 >> Viewer 1 0 0 0 >> Krylov Solver 1 1 18288 0 >> Preconditioner 1 1 792 0 >> >> ======================================================================================================================== >> Average time to get PetscTime(): 9.53674e-08 >> #PETSc Option Table entries: >> -da_vec_type cusp >> -dm_mat_type seqaijcusp >> -ksp_monitor >> -log_summary >> -pc_type jacobi >> -snes_converged_reason >> -snes_monitor >> #End of PETSc Option Table entries >> Compiled without FORTRAN kernels >> Compiled with full precision matrices (default) >> sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 >> sizeof(PetscScalar) 8 sizeof(PetscInt) 4 >> Configure run at: Fri Nov 16 08:40:52 2012 >> Configure options: --with-clanguage=C++ --with-mpi-dir=/usr >> --with-shared-libraries --with-cuda-arch=sm_20 --CFLAGS=-O0 --CXXFLAGS=-O0 >> --CUDAFLAGS=-O0 --with-etags=1 --with-mpi4py=0 >> --with-blas-lapack-lib="[/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_rt.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_intel_thread.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_core.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libiomp5.so]" >> --download-blacs --download-superlu_dist --download-triangle >> --download-parmetis --download-metis --download-mumps --download-scalapack >> --with-cuda=1 --with-cusp=1 --with-thrust=1 >> --with-cuda-dir=/opt/apps/cuda/4.2//cuda --with-sieve=1 >> --download-exodusii=yes --download-netcdf --with-boost=1 >> --with-boost-dir=/usr --download-fiat=yes --download-generator >> --download-scientificpython --with-matlab=1 --with-matlab-engine=1 >> --with-matlab-dir=/opt/MATLAB/R2011a >> ----------------------------------------- >> Libraries compiled on Fri Nov 16 08:40:52 2012 on SCRGP2 >> Machine characteristics: >> Linux-2.6.32-41-server-x86_64-with-debian-squeeze-sid >> Using PETSc directory: /opt/apps/PETSC/petsc-3.3-p4 >> Using PETSc arch: gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg >> ----------------------------------------- >> >> Using C compiler: /usr/bin/mpicxx -O0 -g -fPIC ${COPTFLAGS} ${CFLAGS} >> Using Fortran compiler: /usr/bin/mpif90 -fPIC -Wall -Wno-unused-variable >> -g ${FOPTFLAGS} ${FFLAGS} >> ----------------------------------------- >> >> Using include paths: >> -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/include >> -I/opt/apps/PETSC/petsc-3.3-p4/include >> -I/opt/apps/PETSC/petsc-3.3-p4/include >> -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/include >> -I/opt/apps/cuda/4.2//cuda/include >> -I/opt/apps/PETSC/petsc-3.3-p4/include/sieve >> -I/opt/MATLAB/R2011a/extern/include -I/usr/include >> -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/cbind/include >> -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/forbind/include >> -I/usr/include/mpich2 >> ----------------------------------------- >> >> Using C linker: /usr/bin/mpicxx >> Using Fortran linker: /usr/bin/mpif90 >> Using libraries: >> -Wl,-rpath,/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib >> -L/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib >> -lpetsc >> -Wl,-rpath,/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib >> -L/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib >> -ltriangle -lX11 -lpthread -lsuperlu_dist_3.1 -lcmumps -ldmumps -lsmumps >> -lzmumps -lmumps_common -lpord -lparmetis -lmetis -lscalapack -lblacs >> -Wl,-rpath,/opt/apps/cuda/4.2//cuda/lib64 -L/opt/apps/cuda/4.2//cuda/lib64 >> -lcufft -lcublas -lcudart -lcusparse >> -Wl,-rpath,/opt/MATLAB/R2011a/sys/os/glnxa64:/opt/MATLAB/R2011a/bin/glnxa64:/opt/MATLAB/R2011a/extern/lib/glnxa64 >> -L/opt/MATLAB/R2011a/bin/glnxa64 -L/opt/MATLAB/R2011a/extern/lib/glnxa64 >> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >> -Wl,-rpath,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib >> -L/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib -lmkl_rt -lmkl_intel_thread >> -lmkl_core -liomp5 -lexoIIv2for -lexodus -lnetcdf_c++ -lnetcdf >> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.4.3 >> -L/usr/lib/gcc/x86_64-linux-gnu/4.4.3 -lmpichf90 -lgfortran -lm -lm >> -lmpichcxx -lstdc++ -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lpthread -lrt >> -lgcc_s -ldl >> ----------------------------------------- >> >> >> >> On Sat, Nov 17, 2012 at 11:02 AM, Matthew Knepley wrote: >> >>> On Sat, Nov 17, 2012 at 10:50 AM, David Fuentes >>> wrote: >>> > Hi, >>> > >>> > I'm using petsc 3.3p4 >>> > I'm trying to run a nonlinear SNES solver on GPU with gmres and jacobi >>> PC >>> > using VECSEQCUSP and MATSEQAIJCUSP datatypes for the rhs and jacobian >>> matrix >>> > respectively. >>> > When running top I still see significant CPU utilization (800-900 %CPU) >>> > during the solve ? possibly from some multithreaded operations ? >>> > >>> > Is this expected ? >>> > I was thinking that since I input everything into the solver as a CUSP >>> > datatype, all linear algebra operations would be on the GPU device from >>> > there and wasn't expecting to see such CPU utilization during the >>> solve ? >>> > Do I probably have an error in my code somewhere ? >>> >>> We cannot answer performance questions without -log_summary >>> >>> Matt >>> >>> > Thanks, >>> > David >>> >>> >>> >>> -- >>> 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 >>> >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From rupp at mcs.anl.gov Sat Nov 17 14:39:55 2012 From: rupp at mcs.anl.gov (Karl Rupp) Date: Sat, 17 Nov 2012 14:39:55 -0600 Subject: [petsc-users] CPU utilization during GPU solver In-Reply-To: References: Message-ID: <50A7F61B.1060308@mcs.anl.gov> Hi David, the cuda-runtime might spawn threads in addition to PETSc. How many GPUs do you have on your system? You might also want to compare with the CUDA examples. If they also run at ~800% CPU utilization, then it's definitely due to the CUDA runtime. Note that there might full CPU utilization even if all the operations were carried out on the GPU, because the CPU-threads are waiting in a synchronization loop for the GPU kernels to terminate. This is, of course, nothing specific to PETSc. Best regards, Karli On 11/17/2012 02:05 PM, David Fuentes wrote: > Thanks Jed. > I was trying to run it in dbg mode to verify if all significant parts of > the solver were running on the GPU and not on the CPU by mistake. > I cant pinpoint what part of the solver is running on the CPU. When I > run top while running the solver there seems to be ~800% CPU utilization > that I wasn't expecting. I cant tell if i'm slowing things down > by transferring between CPU/GPU on accident? > > thanks again, > df > > On Sat, Nov 17, 2012 at 1:49 PM, Jed Brown > wrote: > > Please read the large boxed message about debugging mode. > > (Replying from phone so can't make it 72 point blinking red, sorry.) > > On Nov 17, 2012 1:41 PM, "David Fuentes" > wrote: > > thanks Matt, > > My log summary is below. > > ************************************************************************************************************************ > *** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use > 'enscript -r -fCourier9' to print this document *** > ************************************************************************************************************************ > > ---------------------------------------------- PETSc Performance > Summary: ---------------------------------------------- > > ./FocusUltraSoundModel on a gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg > named SCRGP2 with 1 processor, by fuentes Sat Nov 17 13:35:06 2012 > Using Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 > CDT 2012 > > Max Max/Min Avg Total > Time (sec): 3.164e+01 1.00000 3.164e+01 > Objects: 4.100e+01 1.00000 4.100e+01 > Flops: 2.561e+09 1.00000 2.561e+09 2.561e+09 > Flops/sec: 8.097e+07 1.00000 8.097e+07 8.097e+07 > Memory: 2.129e+08 1.00000 2.129e+08 > MPI Messages: 0.000e+00 0.00000 0.000e+00 0.000e+00 > MPI Message Lengths: 0.000e+00 0.00000 0.000e+00 0.000e+00 > MPI Reductions: 4.230e+02 1.00000 > > Flop counting convention: 1 flop = 1 real number operation of > type (multiply/divide/add/subtract) > e.g., VecAXPY() for real vectors of > length N --> 2N flops > and VecAXPY() for complex vectors > of length N --> 8N flops > > Summary of Stages: ----- Time ------ ----- Flops ----- --- > Messages --- -- Message Lengths -- -- Reductions -- > Avg %Total Avg %Total > counts %Total Avg %Total counts %Total > 0: Main Stage: 3.1636e+01 100.0% 2.5615e+09 100.0% > 0.000e+00 0.0% 0.000e+00 0.0% 4.220e+02 99.8% > > ------------------------------------------------------------------------------------------------------------------------ > See the 'Profiling' chapter of the users' manual for details on > interpreting output. > Phase summary info: > Count: number of times phase was executed > Time and Flops: Max - maximum over all processors > Ratio - ratio of maximum to minimum over all > processors > Mess: number of messages sent > Avg. len: average message length > Reduct: number of global reductions > Global: entire computation > Stage: stages of a computation. Set stages with > PetscLogStagePush() and PetscLogStagePop(). > %T - percent time in this phase %f - percent > flops in this phase > %M - percent messages in this phase %L - percent > message lengths in this phase > %R - percent reductions in this phase > Total Mflop/s: 10e-6 * (sum of flops over all > processors)/(max time over all processors) > ------------------------------------------------------------------------------------------------------------------------ > > > ########################################################## > # # > # WARNING!!! # > # # > # This code was compiled with a debugging option, # > # To get timing results run ./configure # > # using --with-debugging=no, the performance will # > # be generally two or three times faster. # > # # > ########################################################## > > > Event Count Time (sec) Flops > --- Global --- --- Stage --- Total > Max Ratio Max Ratio Max Ratio Mess > Avg len Reduct %T %f %M %L %R %T %f %M %L %R Mflop/s > ------------------------------------------------------------------------------------------------------------------------ > > --- Event Stage 0: Main Stage > > ComputeFunction 52 1.0 3.9104e-01 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 3.0e+00 1 0 0 0 1 1 0 0 0 1 0 > VecDot 50 1.0 3.2072e-02 1.0 9.70e+07 1.0 0.0e+00 > 0.0e+00 0.0e+00 0 4 0 0 0 0 4 0 0 0 3025 > VecMDot 50 1.0 1.3100e-01 1.0 9.70e+07 1.0 0.0e+00 > 0.0e+00 0.0e+00 0 4 0 0 0 0 4 0 0 0 741 > VecNorm 200 1.0 9.7943e-02 1.0 3.88e+08 1.0 0.0e+00 > 0.0e+00 0.0e+00 0 15 0 0 0 0 15 0 0 0 3963 > VecScale 100 1.0 1.3496e-01 1.0 9.70e+07 1.0 0.0e+00 > 0.0e+00 0.0e+00 0 4 0 0 0 0 4 0 0 0 719 > VecCopy 150 1.0 4.8405e-01 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 > VecSet 164 1.0 2.9707e-01 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 > VecAXPY 50 1.0 3.2194e-02 1.0 9.70e+07 1.0 0.0e+00 > 0.0e+00 0.0e+00 0 4 0 0 0 0 4 0 0 0 3014 > VecWAXPY 50 1.0 2.9040e-01 1.0 4.85e+07 1.0 0.0e+00 > 0.0e+00 0.0e+00 1 2 0 0 0 1 2 0 0 0 167 > VecMAXPY 100 1.0 5.4555e-01 1.0 1.94e+08 1.0 0.0e+00 > 0.0e+00 0.0e+00 2 8 0 0 0 2 8 0 0 0 356 > VecPointwiseMult 100 1.0 5.3003e-01 1.0 9.70e+07 1.0 0.0e+00 > 0.0e+00 0.0e+00 2 4 0 0 0 2 4 0 0 0 183 > VecScatterBegin 53 1.0 1.8660e-01 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 > VecReduceArith 101 1.0 6.9973e-02 1.0 1.96e+08 1.0 0.0e+00 > 0.0e+00 0.0e+00 0 8 0 0 0 0 8 0 0 0 2801 > VecReduceComm 51 1.0 1.0252e-04 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > VecNormalize 100 1.0 1.8565e-01 1.0 2.91e+08 1.0 0.0e+00 > 0.0e+00 0.0e+00 1 11 0 0 0 1 11 0 0 0 1568 > VecCUSPCopyTo 152 1.0 5.8016e-01 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 > VecCUSPCopyFrom 201 1.0 6.0029e-01 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 > MatMult 100 1.0 6.8465e-01 1.0 1.25e+09 1.0 0.0e+00 > 0.0e+00 0.0e+00 2 49 0 0 0 2 49 0 0 0 1825 > MatAssemblyBegin 3 1.0 3.3379e-06 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatAssemblyEnd 3 1.0 2.7767e-01 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 > MatZeroEntries 1 1.0 2.0346e-02 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatCUSPCopyTo 3 1.0 1.4056e-01 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > SNESSolve 1 1.0 2.2094e+01 1.0 2.56e+09 1.0 0.0e+00 > 0.0e+00 3.7e+02 70100 0 0 88 70100 0 0 89 116 > SNESFunctionEval 51 1.0 3.9031e-01 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 > SNESJacobianEval 50 1.0 1.3191e+00 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 0.0e+00 4 0 0 0 0 4 0 0 0 0 0 > SNESLineSearch 50 1.0 6.2922e+00 1.0 1.16e+09 1.0 0.0e+00 > 0.0e+00 5.0e+01 20 45 0 0 12 20 45 0 0 12 184 > KSPGMRESOrthog 50 1.0 4.0436e-01 1.0 1.94e+08 1.0 0.0e+00 > 0.0e+00 5.0e+01 1 8 0 0 12 1 8 0 0 12 480 > KSPSetUp 50 1.0 2.1935e-02 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 1.5e+01 0 0 0 0 4 0 0 0 0 4 0 > KSPSolve 50 1.0 1.3230e+01 1.0 1.40e+09 1.0 0.0e+00 > 0.0e+00 3.2e+02 42 55 0 0 75 42 55 0 0 75 106 > PCSetUp 50 1.0 1.9897e+00 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 4.9e+01 6 0 0 0 12 6 0 0 0 12 0 > PCApply 100 1.0 5.7457e-01 1.0 9.70e+07 1.0 0.0e+00 > 0.0e+00 4.0e+00 2 4 0 0 1 2 4 0 0 1 169 > ------------------------------------------------------------------------------------------------------------------------ > > Memory usage is given in bytes: > > Object Type Creations Destructions Memory > Descendants' Mem. > Reports information only for process 0. > > --- Event Stage 0: Main Stage > > Container 2 2 1096 0 > Vector 16 16 108696592 > 0 > Vector Scatter 2 2 1240 0 > Matrix 1 1 96326824 0 > Distributed Mesh 3 3 7775936 0 > Bipartite Graph 6 6 4104 0 > Index Set 5 5 3884908 0 > IS L to G Mapping 1 1 3881760 0 > SNES 1 1 1268 0 > SNESLineSearch 1 1 840 0 > Viewer 1 0 0 0 > Krylov Solver 1 1 18288 0 > Preconditioner 1 1 792 0 > ======================================================================================================================== > Average time to get PetscTime(): 9.53674e-08 > #PETSc Option Table entries: > -da_vec_type cusp > -dm_mat_type seqaijcusp > -ksp_monitor > -log_summary > -pc_type jacobi > -snes_converged_reason > -snes_monitor > #End of PETSc Option Table entries > Compiled without FORTRAN kernels > Compiled with full precision matrices (default) > sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 > sizeof(PetscScalar) 8 sizeof(PetscInt) 4 > Configure run at: Fri Nov 16 08:40:52 2012 > Configure options: --with-clanguage=C++ --with-mpi-dir=/usr > --with-shared-libraries --with-cuda-arch=sm_20 --CFLAGS=-O0 > --CXXFLAGS=-O0 --CUDAFLAGS=-O0 --with-etags=1 --with-mpi4py=0 > --with-blas-lapack-lib="[/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_rt.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_intel_thread.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_core.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libiomp5.so]" > --download-blacs --download-superlu_dist --download-triangle > --download-parmetis --download-metis --download-mumps > --download-scalapack --with-cuda=1 --with-cusp=1 --with-thrust=1 > --with-cuda-dir=/opt/apps/cuda/4.2//cuda --with-sieve=1 > --download-exodusii=yes --download-netcdf --with-boost=1 > --with-boost-dir=/usr --download-fiat=yes --download-generator > --download-scientificpython --with-matlab=1 > --with-matlab-engine=1 --with-matlab-dir=/opt/MATLAB/R2011a > ----------------------------------------- > Libraries compiled on Fri Nov 16 08:40:52 2012 on SCRGP2 > Machine characteristics: > Linux-2.6.32-41-server-x86_64-with-debian-squeeze-sid > Using PETSc directory: /opt/apps/PETSC/petsc-3.3-p4 > Using PETSc arch: gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg > ----------------------------------------- > > Using C compiler: /usr/bin/mpicxx -O0 -g -fPIC ${COPTFLAGS} > ${CFLAGS} > Using Fortran compiler: /usr/bin/mpif90 -fPIC -Wall > -Wno-unused-variable -g ${FOPTFLAGS} ${FFLAGS} > ----------------------------------------- > > Using include paths: > -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/include > -I/opt/apps/PETSC/petsc-3.3-p4/include > -I/opt/apps/PETSC/petsc-3.3-p4/include > -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/include > -I/opt/apps/cuda/4.2//cuda/include > -I/opt/apps/PETSC/petsc-3.3-p4/include/sieve > -I/opt/MATLAB/R2011a/extern/include -I/usr/include > -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/cbind/include > -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/forbind/include > -I/usr/include/mpich2 > ----------------------------------------- > > Using C linker: /usr/bin/mpicxx > Using Fortran linker: /usr/bin/mpif90 > Using libraries: > -Wl,-rpath,/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib > -L/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib > -lpetsc > -Wl,-rpath,/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib > -L/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib > -ltriangle -lX11 -lpthread -lsuperlu_dist_3.1 -lcmumps -ldmumps > -lsmumps -lzmumps -lmumps_common -lpord -lparmetis -lmetis > -lscalapack -lblacs -Wl,-rpath,/opt/apps/cuda/4.2//cuda/lib64 > -L/opt/apps/cuda/4.2//cuda/lib64 -lcufft -lcublas -lcudart > -lcusparse > -Wl,-rpath,/opt/MATLAB/R2011a/sys/os/glnxa64:/opt/MATLAB/R2011a/bin/glnxa64:/opt/MATLAB/R2011a/extern/lib/glnxa64 > -L/opt/MATLAB/R2011a/bin/glnxa64 > -L/opt/MATLAB/R2011a/extern/lib/glnxa64 -leng -lmex -lmx -lmat > -lut -licudata -licui18n -licuuc > -Wl,-rpath,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib > -L/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib -lmkl_rt > -lmkl_intel_thread -lmkl_core -liomp5 -lexoIIv2for -lexodus > -lnetcdf_c++ -lnetcdf > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.4.3 > -L/usr/lib/gcc/x86_64-linux-gnu/4.4.3 -lmpichf90 -lgfortran -lm > -lm -lmpichcxx -lstdc++ -lmpichcxx -lstdc++ -ldl -lmpich -lopa > -lpthread -lrt -lgcc_s -ldl > ----------------------------------------- > > > > On Sat, Nov 17, 2012 at 11:02 AM, Matthew Knepley > > wrote: > > On Sat, Nov 17, 2012 at 10:50 AM, David Fuentes > > wrote: > > Hi, > > > > I'm using petsc 3.3p4 > > I'm trying to run a nonlinear SNES solver on GPU with > gmres and jacobi PC > > using VECSEQCUSP and MATSEQAIJCUSP datatypes for the rhs > and jacobian matrix > > respectively. > > When running top I still see significant CPU utilization > (800-900 %CPU) > > during the solve ? possibly from some multithreaded > operations ? > > > > Is this expected ? > > I was thinking that since I input everything into the > solver as a CUSP > > datatype, all linear algebra operations would be on the > GPU device from > > there and wasn't expecting to see such CPU utilization > during the solve ? > > Do I probably have an error in my code somewhere ? > > We cannot answer performance questions without -log_summary > > Matt > > > Thanks, > > David > > > > -- > 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 > > > From knepley at gmail.com Sat Nov 17 14:42:58 2012 From: knepley at gmail.com (Matthew Knepley) Date: Sat, 17 Nov 2012 15:42:58 -0500 Subject: [petsc-users] CPU utilization during GPU solver In-Reply-To: References: Message-ID: On Sat, Nov 17, 2012 at 3:05 PM, David Fuentes wrote: > Thanks Jed. > I was trying to run it in dbg mode to verify if all significant parts of the > solver were running on the GPU and not on the CPU by mistake. > I cant pinpoint what part of the solver is running on the CPU. When I run > top while running the solver there seems to be ~800% CPU utilization > that I wasn't expecting. I cant tell if i'm slowing things down by > transferring between CPU/GPU on accident? 1) I am not sure what you mean by 800%, but it is definitely legitimate to want to know where you are computing. 2) At least some computation is happening on the GPU. I can tell this from the Vec/MatCopyToGPU events. 3) Your flop rates are not great. The MatMult is about half what we get on the Tesla, but you could have another card without good support for double precision. The vector ops however are pretty bad. 4) It looks like half the flops are in MatMult, which is definitely on the card, and the others are in vector operations. Do you create any other vectors without the CUSP type? Matt > thanks again, > df > > On Sat, Nov 17, 2012 at 1:49 PM, Jed Brown wrote: >> >> Please read the large boxed message about debugging mode. >> >> (Replying from phone so can't make it 72 point blinking red, sorry.) >> >> On Nov 17, 2012 1:41 PM, "David Fuentes" wrote: >>> >>> thanks Matt, >>> >>> My log summary is below. >>> >>> >>> ************************************************************************************************************************ >>> *** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r >>> -fCourier9' to print this document *** >>> >>> ************************************************************************************************************************ >>> >>> ---------------------------------------------- PETSc Performance Summary: >>> ---------------------------------------------- >>> >>> ./FocusUltraSoundModel on a gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg named >>> SCRGP2 with 1 processor, by fuentes Sat Nov 17 13:35:06 2012 >>> Using Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 CDT 2012 >>> >>> Max Max/Min Avg Total >>> Time (sec): 3.164e+01 1.00000 3.164e+01 >>> Objects: 4.100e+01 1.00000 4.100e+01 >>> Flops: 2.561e+09 1.00000 2.561e+09 2.561e+09 >>> Flops/sec: 8.097e+07 1.00000 8.097e+07 8.097e+07 >>> Memory: 2.129e+08 1.00000 2.129e+08 >>> MPI Messages: 0.000e+00 0.00000 0.000e+00 0.000e+00 >>> MPI Message Lengths: 0.000e+00 0.00000 0.000e+00 0.000e+00 >>> MPI Reductions: 4.230e+02 1.00000 >>> >>> Flop counting convention: 1 flop = 1 real number operation of type >>> (multiply/divide/add/subtract) >>> e.g., VecAXPY() for real vectors of length N >>> --> 2N flops >>> and VecAXPY() for complex vectors of length N >>> --> 8N flops >>> >>> Summary of Stages: ----- Time ------ ----- Flops ----- --- Messages >>> --- -- Message Lengths -- -- Reductions -- >>> Avg %Total Avg %Total counts >>> %Total Avg %Total counts %Total >>> 0: Main Stage: 3.1636e+01 100.0% 2.5615e+09 100.0% 0.000e+00 >>> 0.0% 0.000e+00 0.0% 4.220e+02 99.8% >>> >>> >>> ------------------------------------------------------------------------------------------------------------------------ >>> See the 'Profiling' chapter of the users' manual for details on >>> interpreting output. >>> Phase summary info: >>> Count: number of times phase was executed >>> Time and Flops: Max - maximum over all processors >>> Ratio - ratio of maximum to minimum over all >>> processors >>> Mess: number of messages sent >>> Avg. len: average message length >>> Reduct: number of global reductions >>> Global: entire computation >>> Stage: stages of a computation. Set stages with PetscLogStagePush() >>> and PetscLogStagePop(). >>> %T - percent time in this phase %f - percent flops in this >>> phase >>> %M - percent messages in this phase %L - percent message >>> lengths in this phase >>> %R - percent reductions in this phase >>> Total Mflop/s: 10e-6 * (sum of flops over all processors)/(max time >>> over all processors) >>> >>> ------------------------------------------------------------------------------------------------------------------------ >>> >>> >>> ########################################################## >>> # # >>> # WARNING!!! # >>> # # >>> # This code was compiled with a debugging option, # >>> # To get timing results run ./configure # >>> # using --with-debugging=no, the performance will # >>> # be generally two or three times faster. # >>> # # >>> ########################################################## >>> >>> >>> Event Count Time (sec) Flops >>> --- Global --- --- Stage --- Total >>> Max Ratio Max Ratio Max Ratio Mess Avg len >>> Reduct %T %f %M %L %R %T %f %M %L %R Mflop/s >>> >>> ------------------------------------------------------------------------------------------------------------------------ >>> >>> --- Event Stage 0: Main Stage >>> >>> ComputeFunction 52 1.0 3.9104e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >>> 3.0e+00 1 0 0 0 1 1 0 0 0 1 0 >>> VecDot 50 1.0 3.2072e-02 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 >>> 0.0e+00 0 4 0 0 0 0 4 0 0 0 3025 >>> VecMDot 50 1.0 1.3100e-01 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 >>> 0.0e+00 0 4 0 0 0 0 4 0 0 0 741 >>> VecNorm 200 1.0 9.7943e-02 1.0 3.88e+08 1.0 0.0e+00 0.0e+00 >>> 0.0e+00 0 15 0 0 0 0 15 0 0 0 3963 >>> VecScale 100 1.0 1.3496e-01 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 >>> 0.0e+00 0 4 0 0 0 0 4 0 0 0 719 >>> VecCopy 150 1.0 4.8405e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >>> 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 >>> VecSet 164 1.0 2.9707e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >>> 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 >>> VecAXPY 50 1.0 3.2194e-02 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 >>> 0.0e+00 0 4 0 0 0 0 4 0 0 0 3014 >>> VecWAXPY 50 1.0 2.9040e-01 1.0 4.85e+07 1.0 0.0e+00 0.0e+00 >>> 0.0e+00 1 2 0 0 0 1 2 0 0 0 167 >>> VecMAXPY 100 1.0 5.4555e-01 1.0 1.94e+08 1.0 0.0e+00 0.0e+00 >>> 0.0e+00 2 8 0 0 0 2 8 0 0 0 356 >>> VecPointwiseMult 100 1.0 5.3003e-01 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 >>> 0.0e+00 2 4 0 0 0 2 4 0 0 0 183 >>> VecScatterBegin 53 1.0 1.8660e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >>> 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 >>> VecReduceArith 101 1.0 6.9973e-02 1.0 1.96e+08 1.0 0.0e+00 0.0e+00 >>> 0.0e+00 0 8 0 0 0 0 8 0 0 0 2801 >>> VecReduceComm 51 1.0 1.0252e-04 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >>> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >>> VecNormalize 100 1.0 1.8565e-01 1.0 2.91e+08 1.0 0.0e+00 0.0e+00 >>> 0.0e+00 1 11 0 0 0 1 11 0 0 0 1568 >>> VecCUSPCopyTo 152 1.0 5.8016e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >>> 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 >>> VecCUSPCopyFrom 201 1.0 6.0029e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >>> 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 >>> MatMult 100 1.0 6.8465e-01 1.0 1.25e+09 1.0 0.0e+00 0.0e+00 >>> 0.0e+00 2 49 0 0 0 2 49 0 0 0 1825 >>> MatAssemblyBegin 3 1.0 3.3379e-06 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >>> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >>> MatAssemblyEnd 3 1.0 2.7767e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >>> 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 >>> MatZeroEntries 1 1.0 2.0346e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >>> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >>> MatCUSPCopyTo 3 1.0 1.4056e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >>> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >>> SNESSolve 1 1.0 2.2094e+01 1.0 2.56e+09 1.0 0.0e+00 0.0e+00 >>> 3.7e+02 70100 0 0 88 70100 0 0 89 116 >>> SNESFunctionEval 51 1.0 3.9031e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >>> 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 >>> SNESJacobianEval 50 1.0 1.3191e+00 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >>> 0.0e+00 4 0 0 0 0 4 0 0 0 0 0 >>> SNESLineSearch 50 1.0 6.2922e+00 1.0 1.16e+09 1.0 0.0e+00 0.0e+00 >>> 5.0e+01 20 45 0 0 12 20 45 0 0 12 184 >>> KSPGMRESOrthog 50 1.0 4.0436e-01 1.0 1.94e+08 1.0 0.0e+00 0.0e+00 >>> 5.0e+01 1 8 0 0 12 1 8 0 0 12 480 >>> KSPSetUp 50 1.0 2.1935e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >>> 1.5e+01 0 0 0 0 4 0 0 0 0 4 0 >>> KSPSolve 50 1.0 1.3230e+01 1.0 1.40e+09 1.0 0.0e+00 0.0e+00 >>> 3.2e+02 42 55 0 0 75 42 55 0 0 75 106 >>> PCSetUp 50 1.0 1.9897e+00 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >>> 4.9e+01 6 0 0 0 12 6 0 0 0 12 0 >>> PCApply 100 1.0 5.7457e-01 1.0 9.70e+07 1.0 0.0e+00 0.0e+00 >>> 4.0e+00 2 4 0 0 1 2 4 0 0 1 169 >>> >>> ------------------------------------------------------------------------------------------------------------------------ >>> >>> Memory usage is given in bytes: >>> >>> Object Type Creations Destructions Memory Descendants' >>> Mem. >>> Reports information only for process 0. >>> >>> --- Event Stage 0: Main Stage >>> >>> Container 2 2 1096 0 >>> Vector 16 16 108696592 0 >>> Vector Scatter 2 2 1240 0 >>> Matrix 1 1 96326824 0 >>> Distributed Mesh 3 3 7775936 0 >>> Bipartite Graph 6 6 4104 0 >>> Index Set 5 5 3884908 0 >>> IS L to G Mapping 1 1 3881760 0 >>> SNES 1 1 1268 0 >>> SNESLineSearch 1 1 840 0 >>> Viewer 1 0 0 0 >>> Krylov Solver 1 1 18288 0 >>> Preconditioner 1 1 792 0 >>> >>> ======================================================================================================================== >>> Average time to get PetscTime(): 9.53674e-08 >>> #PETSc Option Table entries: >>> -da_vec_type cusp >>> -dm_mat_type seqaijcusp >>> -ksp_monitor >>> -log_summary >>> -pc_type jacobi >>> -snes_converged_reason >>> -snes_monitor >>> #End of PETSc Option Table entries >>> Compiled without FORTRAN kernels >>> Compiled with full precision matrices (default) >>> sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 >>> sizeof(PetscScalar) 8 sizeof(PetscInt) 4 >>> Configure run at: Fri Nov 16 08:40:52 2012 >>> Configure options: --with-clanguage=C++ --with-mpi-dir=/usr >>> --with-shared-libraries --with-cuda-arch=sm_20 --CFLAGS=-O0 --CXXFLAGS=-O0 >>> --CUDAFLAGS=-O0 --with-etags=1 --with-mpi4py=0 >>> --with-blas-lapack-lib="[/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_rt.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_intel_thread.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_core.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libiomp5.so]" >>> --download-blacs --download-superlu_dist --download-triangle >>> --download-parmetis --download-metis --download-mumps --download-scalapack >>> --with-cuda=1 --with-cusp=1 --with-thrust=1 >>> --with-cuda-dir=/opt/apps/cuda/4.2//cuda --with-sieve=1 >>> --download-exodusii=yes --download-netcdf --with-boost=1 >>> --with-boost-dir=/usr --download-fiat=yes --download-generator >>> --download-scientificpython --with-matlab=1 --with-matlab-engine=1 >>> --with-matlab-dir=/opt/MATLAB/R2011a >>> ----------------------------------------- >>> Libraries compiled on Fri Nov 16 08:40:52 2012 on SCRGP2 >>> Machine characteristics: >>> Linux-2.6.32-41-server-x86_64-with-debian-squeeze-sid >>> Using PETSc directory: /opt/apps/PETSC/petsc-3.3-p4 >>> Using PETSc arch: gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg >>> ----------------------------------------- >>> >>> Using C compiler: /usr/bin/mpicxx -O0 -g -fPIC ${COPTFLAGS} ${CFLAGS} >>> Using Fortran compiler: /usr/bin/mpif90 -fPIC -Wall -Wno-unused-variable >>> -g ${FOPTFLAGS} ${FFLAGS} >>> ----------------------------------------- >>> >>> Using include paths: >>> -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/include >>> -I/opt/apps/PETSC/petsc-3.3-p4/include >>> -I/opt/apps/PETSC/petsc-3.3-p4/include >>> -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/include >>> -I/opt/apps/cuda/4.2//cuda/include >>> -I/opt/apps/PETSC/petsc-3.3-p4/include/sieve >>> -I/opt/MATLAB/R2011a/extern/include -I/usr/include >>> -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/cbind/include >>> -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/forbind/include >>> -I/usr/include/mpich2 >>> ----------------------------------------- >>> >>> Using C linker: /usr/bin/mpicxx >>> Using Fortran linker: /usr/bin/mpif90 >>> Using libraries: >>> -Wl,-rpath,/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib >>> -L/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib >>> -lpetsc >>> -Wl,-rpath,/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib >>> -L/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib >>> -ltriangle -lX11 -lpthread -lsuperlu_dist_3.1 -lcmumps -ldmumps -lsmumps >>> -lzmumps -lmumps_common -lpord -lparmetis -lmetis -lscalapack -lblacs >>> -Wl,-rpath,/opt/apps/cuda/4.2//cuda/lib64 -L/opt/apps/cuda/4.2//cuda/lib64 >>> -lcufft -lcublas -lcudart -lcusparse >>> -Wl,-rpath,/opt/MATLAB/R2011a/sys/os/glnxa64:/opt/MATLAB/R2011a/bin/glnxa64:/opt/MATLAB/R2011a/extern/lib/glnxa64 >>> -L/opt/MATLAB/R2011a/bin/glnxa64 -L/opt/MATLAB/R2011a/extern/lib/glnxa64 >>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >>> -Wl,-rpath,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib >>> -L/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib -lmkl_rt -lmkl_intel_thread >>> -lmkl_core -liomp5 -lexoIIv2for -lexodus -lnetcdf_c++ -lnetcdf >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.4.3 >>> -L/usr/lib/gcc/x86_64-linux-gnu/4.4.3 -lmpichf90 -lgfortran -lm -lm >>> -lmpichcxx -lstdc++ -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lpthread -lrt >>> -lgcc_s -ldl >>> ----------------------------------------- >>> >>> >>> >>> On Sat, Nov 17, 2012 at 11:02 AM, Matthew Knepley >>> wrote: >>>> >>>> On Sat, Nov 17, 2012 at 10:50 AM, David Fuentes >>>> wrote: >>>> > Hi, >>>> > >>>> > I'm using petsc 3.3p4 >>>> > I'm trying to run a nonlinear SNES solver on GPU with gmres and jacobi >>>> > PC >>>> > using VECSEQCUSP and MATSEQAIJCUSP datatypes for the rhs and jacobian >>>> > matrix >>>> > respectively. >>>> > When running top I still see significant CPU utilization (800-900 >>>> > %CPU) >>>> > during the solve ? possibly from some multithreaded operations ? >>>> > >>>> > Is this expected ? >>>> > I was thinking that since I input everything into the solver as a CUSP >>>> > datatype, all linear algebra operations would be on the GPU device >>>> > from >>>> > there and wasn't expecting to see such CPU utilization during the >>>> > solve ? >>>> > Do I probably have an error in my code somewhere ? >>>> >>>> We cannot answer performance questions without -log_summary >>>> >>>> Matt >>>> >>>> > Thanks, >>>> > David >>>> >>>> >>>> >>>> -- >>>> 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 >>> >>> > -- 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 From fuentesdt at gmail.com Sat Nov 17 15:00:04 2012 From: fuentesdt at gmail.com (David Fuentes) Date: Sat, 17 Nov 2012 15:00:04 -0600 Subject: [petsc-users] CPU utilization during GPU solver In-Reply-To: References: Message-ID: Thanks Karl, Matt, I thought I created all vectors of CUSP type. I'll double check. I was trying to find vectors that I may have accidentally setup not with CUSP type through somehow interface with the SNES solver? I'll also double check w/ the cuda examples as Karl suggested. There are 6 Tesla M2070 on this box, but i'm only running on one of them. On Sat, Nov 17, 2012 at 2:42 PM, Matthew Knepley wrote: > On Sat, Nov 17, 2012 at 3:05 PM, David Fuentes > wrote: > > Thanks Jed. > > I was trying to run it in dbg mode to verify if all significant parts of > the > > solver were running on the GPU and not on the CPU by mistake. > > I cant pinpoint what part of the solver is running on the CPU. When I run > > top while running the solver there seems to be ~800% CPU utilization > > that I wasn't expecting. I cant tell if i'm slowing things down by > > transferring between CPU/GPU on accident? > > 1) I am not sure what you mean by 800%, but it is definitely > legitimate to want to know where you are computing. > > 2) At least some computation is happening on the GPU. I can tell this from > the > Vec/MatCopyToGPU events. > > 3) Your flop rates are not great. The MatMult is about half what we > get on the Tesla, but you > could have another card without good support for double precision. > The vector ops however > are pretty bad. > > 4) It looks like half the flops are in MatMult, which is definitely on > the card, and the others are in > vector operations. Do you create any other vectors without the CUSP > type? > > Matt > > > thanks again, > > df > > > > On Sat, Nov 17, 2012 at 1:49 PM, Jed Brown wrote: > >> > >> Please read the large boxed message about debugging mode. > >> > >> (Replying from phone so can't make it 72 point blinking red, sorry.) > >> > >> On Nov 17, 2012 1:41 PM, "David Fuentes" wrote: > >>> > >>> thanks Matt, > >>> > >>> My log summary is below. > >>> > >>> > >>> > ************************************************************************************************************************ > >>> *** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r > >>> -fCourier9' to print this document *** > >>> > >>> > ************************************************************************************************************************ > >>> > >>> ---------------------------------------------- PETSc Performance > Summary: > >>> ---------------------------------------------- > >>> > >>> ./FocusUltraSoundModel on a gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg named > >>> SCRGP2 with 1 processor, by fuentes Sat Nov 17 13:35:06 2012 > >>> Using Petsc Release Version 3.3.0, Patch 4, Fri Oct 26 10:46:51 CDT > 2012 > >>> > >>> Max Max/Min Avg Total > >>> Time (sec): 3.164e+01 1.00000 3.164e+01 > >>> Objects: 4.100e+01 1.00000 4.100e+01 > >>> Flops: 2.561e+09 1.00000 2.561e+09 2.561e+09 > >>> Flops/sec: 8.097e+07 1.00000 8.097e+07 8.097e+07 > >>> Memory: 2.129e+08 1.00000 2.129e+08 > >>> MPI Messages: 0.000e+00 0.00000 0.000e+00 0.000e+00 > >>> MPI Message Lengths: 0.000e+00 0.00000 0.000e+00 0.000e+00 > >>> MPI Reductions: 4.230e+02 1.00000 > >>> > >>> Flop counting convention: 1 flop = 1 real number operation of type > >>> (multiply/divide/add/subtract) > >>> e.g., VecAXPY() for real vectors of length > N > >>> --> 2N flops > >>> and VecAXPY() for complex vectors of > length N > >>> --> 8N flops > >>> > >>> Summary of Stages: ----- Time ------ ----- Flops ----- --- Messages > >>> --- -- Message Lengths -- -- Reductions -- > >>> Avg %Total Avg %Total counts > >>> %Total Avg %Total counts %Total > >>> 0: Main Stage: 3.1636e+01 100.0% 2.5615e+09 100.0% 0.000e+00 > >>> 0.0% 0.000e+00 0.0% 4.220e+02 99.8% > >>> > >>> > >>> > ------------------------------------------------------------------------------------------------------------------------ > >>> See the 'Profiling' chapter of the users' manual for details on > >>> interpreting output. > >>> Phase summary info: > >>> Count: number of times phase was executed > >>> Time and Flops: Max - maximum over all processors > >>> Ratio - ratio of maximum to minimum over all > >>> processors > >>> Mess: number of messages sent > >>> Avg. len: average message length > >>> Reduct: number of global reductions > >>> Global: entire computation > >>> Stage: stages of a computation. Set stages with PetscLogStagePush() > >>> and PetscLogStagePop(). > >>> %T - percent time in this phase %f - percent flops in > this > >>> phase > >>> %M - percent messages in this phase %L - percent message > >>> lengths in this phase > >>> %R - percent reductions in this phase > >>> Total Mflop/s: 10e-6 * (sum of flops over all processors)/(max time > >>> over all processors) > >>> > >>> > ------------------------------------------------------------------------------------------------------------------------ > >>> > >>> > >>> ########################################################## > >>> # # > >>> # WARNING!!! # > >>> # # > >>> # This code was compiled with a debugging option, # > >>> # To get timing results run ./configure # > >>> # using --with-debugging=no, the performance will # > >>> # be generally two or three times faster. # > >>> # # > >>> ########################################################## > >>> > >>> > >>> Event Count Time (sec) Flops > >>> --- Global --- --- Stage --- Total > >>> Max Ratio Max Ratio Max Ratio Mess Avg > len > >>> Reduct %T %f %M %L %R %T %f %M %L %R Mflop/s > >>> > >>> > ------------------------------------------------------------------------------------------------------------------------ > >>> > >>> --- Event Stage 0: Main Stage > >>> > >>> ComputeFunction 52 1.0 3.9104e-01 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 > >>> 3.0e+00 1 0 0 0 1 1 0 0 0 1 0 > >>> VecDot 50 1.0 3.2072e-02 1.0 9.70e+07 1.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 0 4 0 0 0 0 4 0 0 0 3025 > >>> VecMDot 50 1.0 1.3100e-01 1.0 9.70e+07 1.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 0 4 0 0 0 0 4 0 0 0 741 > >>> VecNorm 200 1.0 9.7943e-02 1.0 3.88e+08 1.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 0 15 0 0 0 0 15 0 0 0 3963 > >>> VecScale 100 1.0 1.3496e-01 1.0 9.70e+07 1.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 0 4 0 0 0 0 4 0 0 0 719 > >>> VecCopy 150 1.0 4.8405e-01 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 > >>> VecSet 164 1.0 2.9707e-01 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 > >>> VecAXPY 50 1.0 3.2194e-02 1.0 9.70e+07 1.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 0 4 0 0 0 0 4 0 0 0 3014 > >>> VecWAXPY 50 1.0 2.9040e-01 1.0 4.85e+07 1.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 1 2 0 0 0 1 2 0 0 0 167 > >>> VecMAXPY 100 1.0 5.4555e-01 1.0 1.94e+08 1.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 2 8 0 0 0 2 8 0 0 0 356 > >>> VecPointwiseMult 100 1.0 5.3003e-01 1.0 9.70e+07 1.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 2 4 0 0 0 2 4 0 0 0 183 > >>> VecScatterBegin 53 1.0 1.8660e-01 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 > >>> VecReduceArith 101 1.0 6.9973e-02 1.0 1.96e+08 1.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 0 8 0 0 0 0 8 0 0 0 2801 > >>> VecReduceComm 51 1.0 1.0252e-04 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > >>> VecNormalize 100 1.0 1.8565e-01 1.0 2.91e+08 1.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 1 11 0 0 0 1 11 0 0 0 1568 > >>> VecCUSPCopyTo 152 1.0 5.8016e-01 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 > >>> VecCUSPCopyFrom 201 1.0 6.0029e-01 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 > >>> MatMult 100 1.0 6.8465e-01 1.0 1.25e+09 1.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 2 49 0 0 0 2 49 0 0 0 1825 > >>> MatAssemblyBegin 3 1.0 3.3379e-06 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > >>> MatAssemblyEnd 3 1.0 2.7767e-01 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 > >>> MatZeroEntries 1 1.0 2.0346e-02 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > >>> MatCUSPCopyTo 3 1.0 1.4056e-01 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > >>> SNESSolve 1 1.0 2.2094e+01 1.0 2.56e+09 1.0 0.0e+00 > 0.0e+00 > >>> 3.7e+02 70100 0 0 88 70100 0 0 89 116 > >>> SNESFunctionEval 51 1.0 3.9031e-01 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 > >>> SNESJacobianEval 50 1.0 1.3191e+00 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 > >>> 0.0e+00 4 0 0 0 0 4 0 0 0 0 0 > >>> SNESLineSearch 50 1.0 6.2922e+00 1.0 1.16e+09 1.0 0.0e+00 > 0.0e+00 > >>> 5.0e+01 20 45 0 0 12 20 45 0 0 12 184 > >>> KSPGMRESOrthog 50 1.0 4.0436e-01 1.0 1.94e+08 1.0 0.0e+00 > 0.0e+00 > >>> 5.0e+01 1 8 0 0 12 1 8 0 0 12 480 > >>> KSPSetUp 50 1.0 2.1935e-02 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 > >>> 1.5e+01 0 0 0 0 4 0 0 0 0 4 0 > >>> KSPSolve 50 1.0 1.3230e+01 1.0 1.40e+09 1.0 0.0e+00 > 0.0e+00 > >>> 3.2e+02 42 55 0 0 75 42 55 0 0 75 106 > >>> PCSetUp 50 1.0 1.9897e+00 1.0 0.00e+00 0.0 0.0e+00 > 0.0e+00 > >>> 4.9e+01 6 0 0 0 12 6 0 0 0 12 0 > >>> PCApply 100 1.0 5.7457e-01 1.0 9.70e+07 1.0 0.0e+00 > 0.0e+00 > >>> 4.0e+00 2 4 0 0 1 2 4 0 0 1 169 > >>> > >>> > ------------------------------------------------------------------------------------------------------------------------ > >>> > >>> Memory usage is given in bytes: > >>> > >>> Object Type Creations Destructions Memory Descendants' > >>> Mem. > >>> Reports information only for process 0. > >>> > >>> --- Event Stage 0: Main Stage > >>> > >>> Container 2 2 1096 0 > >>> Vector 16 16 108696592 0 > >>> Vector Scatter 2 2 1240 0 > >>> Matrix 1 1 96326824 0 > >>> Distributed Mesh 3 3 7775936 0 > >>> Bipartite Graph 6 6 4104 0 > >>> Index Set 5 5 3884908 0 > >>> IS L to G Mapping 1 1 3881760 0 > >>> SNES 1 1 1268 0 > >>> SNESLineSearch 1 1 840 0 > >>> Viewer 1 0 0 0 > >>> Krylov Solver 1 1 18288 0 > >>> Preconditioner 1 1 792 0 > >>> > >>> > ======================================================================================================================== > >>> Average time to get PetscTime(): 9.53674e-08 > >>> #PETSc Option Table entries: > >>> -da_vec_type cusp > >>> -dm_mat_type seqaijcusp > >>> -ksp_monitor > >>> -log_summary > >>> -pc_type jacobi > >>> -snes_converged_reason > >>> -snes_monitor > >>> #End of PETSc Option Table entries > >>> Compiled without FORTRAN kernels > >>> Compiled with full precision matrices (default) > >>> sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 > >>> sizeof(PetscScalar) 8 sizeof(PetscInt) 4 > >>> Configure run at: Fri Nov 16 08:40:52 2012 > >>> Configure options: --with-clanguage=C++ --with-mpi-dir=/usr > >>> --with-shared-libraries --with-cuda-arch=sm_20 --CFLAGS=-O0 > --CXXFLAGS=-O0 > >>> --CUDAFLAGS=-O0 --with-etags=1 --with-mpi4py=0 > >>> > --with-blas-lapack-lib="[/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_rt.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_intel_thread.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libmkl_core.so,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib/libiomp5.so]" > >>> --download-blacs --download-superlu_dist --download-triangle > >>> --download-parmetis --download-metis --download-mumps > --download-scalapack > >>> --with-cuda=1 --with-cusp=1 --with-thrust=1 > >>> --with-cuda-dir=/opt/apps/cuda/4.2//cuda --with-sieve=1 > >>> --download-exodusii=yes --download-netcdf --with-boost=1 > >>> --with-boost-dir=/usr --download-fiat=yes --download-generator > >>> --download-scientificpython --with-matlab=1 --with-matlab-engine=1 > >>> --with-matlab-dir=/opt/MATLAB/R2011a > >>> ----------------------------------------- > >>> Libraries compiled on Fri Nov 16 08:40:52 2012 on SCRGP2 > >>> Machine characteristics: > >>> Linux-2.6.32-41-server-x86_64-with-debian-squeeze-sid > >>> Using PETSc directory: /opt/apps/PETSC/petsc-3.3-p4 > >>> Using PETSc arch: gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg > >>> ----------------------------------------- > >>> > >>> Using C compiler: /usr/bin/mpicxx -O0 -g -fPIC ${COPTFLAGS} > ${CFLAGS} > >>> Using Fortran compiler: /usr/bin/mpif90 -fPIC -Wall > -Wno-unused-variable > >>> -g ${FOPTFLAGS} ${FFLAGS} > >>> ----------------------------------------- > >>> > >>> Using include paths: > >>> > -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/include > >>> -I/opt/apps/PETSC/petsc-3.3-p4/include > >>> -I/opt/apps/PETSC/petsc-3.3-p4/include > >>> > -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/include > >>> -I/opt/apps/cuda/4.2//cuda/include > >>> -I/opt/apps/PETSC/petsc-3.3-p4/include/sieve > >>> -I/opt/MATLAB/R2011a/extern/include -I/usr/include > >>> > -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/cbind/include > >>> > -I/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/forbind/include > >>> -I/usr/include/mpich2 > >>> ----------------------------------------- > >>> > >>> Using C linker: /usr/bin/mpicxx > >>> Using Fortran linker: /usr/bin/mpif90 > >>> Using libraries: > >>> > -Wl,-rpath,/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib > >>> -L/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib > >>> -lpetsc > >>> > -Wl,-rpath,/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib > >>> -L/opt/apps/PETSC/petsc-3.3-p4/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib > >>> -ltriangle -lX11 -lpthread -lsuperlu_dist_3.1 -lcmumps -ldmumps > -lsmumps > >>> -lzmumps -lmumps_common -lpord -lparmetis -lmetis -lscalapack -lblacs > >>> -Wl,-rpath,/opt/apps/cuda/4.2//cuda/lib64 > -L/opt/apps/cuda/4.2//cuda/lib64 > >>> -lcufft -lcublas -lcudart -lcusparse > >>> > -Wl,-rpath,/opt/MATLAB/R2011a/sys/os/glnxa64:/opt/MATLAB/R2011a/bin/glnxa64:/opt/MATLAB/R2011a/extern/lib/glnxa64 > >>> -L/opt/MATLAB/R2011a/bin/glnxa64 > -L/opt/MATLAB/R2011a/extern/lib/glnxa64 > >>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc > >>> -Wl,-rpath,/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib > >>> -L/opt/apps/EPD/epd-7.3-1-rh5-x86_64/lib -lmkl_rt -lmkl_intel_thread > >>> -lmkl_core -liomp5 -lexoIIv2for -lexodus -lnetcdf_c++ -lnetcdf > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.4.3 > >>> -L/usr/lib/gcc/x86_64-linux-gnu/4.4.3 -lmpichf90 -lgfortran -lm -lm > >>> -lmpichcxx -lstdc++ -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lpthread > -lrt > >>> -lgcc_s -ldl > >>> ----------------------------------------- > >>> > >>> > >>> > >>> On Sat, Nov 17, 2012 at 11:02 AM, Matthew Knepley > >>> wrote: > >>>> > >>>> On Sat, Nov 17, 2012 at 10:50 AM, David Fuentes > >>>> wrote: > >>>> > Hi, > >>>> > > >>>> > I'm using petsc 3.3p4 > >>>> > I'm trying to run a nonlinear SNES solver on GPU with gmres and > jacobi > >>>> > PC > >>>> > using VECSEQCUSP and MATSEQAIJCUSP datatypes for the rhs and > jacobian > >>>> > matrix > >>>> > respectively. > >>>> > When running top I still see significant CPU utilization (800-900 > >>>> > %CPU) > >>>> > during the solve ? possibly from some multithreaded operations ? > >>>> > > >>>> > Is this expected ? > >>>> > I was thinking that since I input everything into the solver as a > CUSP > >>>> > datatype, all linear algebra operations would be on the GPU device > >>>> > from > >>>> > there and wasn't expecting to see such CPU utilization during the > >>>> > solve ? > >>>> > Do I probably have an error in my code somewhere ? > >>>> > >>>> We cannot answer performance questions without -log_summary > >>>> > >>>> Matt > >>>> > >>>> > Thanks, > >>>> > David > >>>> > >>>> > >>>> > >>>> -- > >>>> 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 > >>> > >>> > > > > > > -- > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From fd.kong at siat.ac.cn Sun Nov 18 09:43:39 2012 From: fd.kong at siat.ac.cn (Fande Kong) Date: Sun, 18 Nov 2012 08:43:39 -0700 Subject: [petsc-users] Which IDE you use to develop petsc application In-Reply-To: <50A76201.8010607@uni-mainz.de> References: <50A76201.8010607@uni-mainz.de> Message-ID: yeap, It sounds very interesting. Could you please give some instructions on how to use eclipse link both Petsc and MPI? On Sat, Nov 17, 2012 at 3:08 AM, Anton Popov wrote: > On 11/16/12 2:03 AM, Barry Smith wrote: > >> Because we are developing PETSc as a library that must be portable to >> many users most people who develop the PETSc libraries do not use a IDE. >> >> For someone who is writing AN APPLICATION that uses PETSc (especially >> an application with guis) it makes sense to use an IDL to do that >> development. What you chose should depend on what machine you develop on >> and what your are experienced with or comfortable with. In the users manual >> we try to provide some information on using PETSc from a variety of IDEs. >> We are interested in collecting information on using PETSc from IDEs and >> improving our documentation. >> > I managed Eclipse PTP on Mac OS (probably the same on Linux). Provided > that a debug (preferably valgrind-clean) version of MPICH2 library with MPD > process manager can be installed, Eclipse Indigo can be easily configured > for using PARALLEL SDM debugger with PETSc applications. > > If you're interested, I can send detailed configuration / setup > instructions. > > Anton > > >> >> Barry >> >> >> On Nov 15, 2012, at 4:52 PM, Fande Kong wrote: >> >> Got it. Thanks. >>> On Thu, Nov 15, 2012 at 3:49 PM, Matthew Knepley >>> wrote: >>> On Thu, Nov 15, 2012 at 5:41 PM, Fande Kong >>> wrote: >>> >>>> Hi all, >>>> >>>> In order to improve development the efficient of the petsc application >>>> development, which IDE are you using? >>>> >>> Emacs+gdb. >>> >>> Matt >>> >>> Regards, >>>> -- >>>> Fande Kong >>>> Department of Computer Science >>>> University of Colorado at Boulder >>>> >>>> >>>> >>> >>> -- >>> 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 >>> >>> >>> >>> >>> -- >>> Fande Kong >>> ShenZhen Institutes of Advanced Technology >>> Chinese Academy of Sciences >>> >>> > > -- Fande Kong ShenZhen Institutes of Advanced Technology Chinese Academy of Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From bourdin at lsu.edu Sun Nov 18 15:10:29 2012 From: bourdin at lsu.edu (Blaise A Bourdin) Date: Sun, 18 Nov 2012 21:10:29 +0000 Subject: [petsc-users] Questions about PetscObjectCompose and DM user context Message-ID: <6C4AE5741C2B874282F58DA136A2CCB8312A11@BY2PRD0611MB441.namprd06.prod.outlook.com> Hi, Following on last week's discussion with Jed on petsc-dev, I am looking a moving the DM's associated to parameters in a PDE from a user context to the DM associated with the solution field, using PetscObjectCompose. Let's imagine for a second that I want to solve the PDE -div (k(x) \cdot u(x) ) = f + Boundary conditions, where k(x) is a a vector-valued coefficient and u(x) is the field I am solving for. Assume that the DM for u is dmU and the one for K is dmK, and that they have been created. Once both DMs are created, I can stash dmK inside dmU, using PetscObjectCompose((PetscObject) dmU,"SomeName",(PetscObject) dmK); At this point, my understanding is that I can safely destroy dmK without causing a memory link, am I right? In my jacobian evaluation, I get a copy of dmK using PetscObjectQuery with the proper name: PetscObjectQuery((PetscObject) dmU,"SomeName",(PetscObject*) &dmK); Again, I _can_ safely call DMDestroy(&dmK) at the end of the jacobian. Can I simply let dmK fall out of scope? I assume that dmK gets automatically destroyed when dmU is destroyed, right? Finally, as far as I understand, I can either set the user context to the Jacobian function explicitly in the call to SNESSetJacobian or attach it to the DM using DMSetApplicationContext, or to the SNES using SNESSetApplicationContext. What would be the pros and cons of each technique? The same question would apply to DMCoarsenHookAdd. Regards, Blaise -- Department of Mathematics and Center for Computation & Technology Louisiana State University, Baton Rouge, LA 70803, USA Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 http://www.math.lsu.edu/~bourdin From thomas.witkowski at tu-dresden.de Mon Nov 19 01:29:43 2012 From: thomas.witkowski at tu-dresden.de (Thomas Witkowski) Date: Mon, 19 Nov 2012 08:29:43 +0100 Subject: [petsc-users] Creating PCFieldSplit Preconditioner in source code Message-ID: <50A9DFE7.9030407@tu-dresden.de> In the implementation of my Navier-Stokes solver, I initialize the PCFieldSplit preconditioner in my source code (thus not on the command line) in the following way: PCSetType(pc, PCFIELDSPLIT); PCFieldSplitSetType(pc, PC_COMPOSITE_SCHUR); PCFieldSplitSetSchurFactType(pc, PC_FIELDSPLIT_SCHUR_FACT_FULL); ... KSPSetUp(ksp); KSP *subKsp; PetscInt nSubKsp; PCFieldSplitGetSubKSP(pc, &nSubKsp, &subKsp); KSP kspVelocity = subKsp[0]; KSP kspSchur = subKsp[1]; ... And then kspVelocity and kspSchur are filled with appropriate options. The point is now, that to get the sub solver objects, I have to run KSPSetUp before. In this case, the sub solver objects are also initialized with some predefined options (block jacobi ILU), which I don't need and what takes some time and memory. Is there any other way to get the sub solver objects before and to initialize than the outer solver correctly with the inner solver I have specified? Thomas From knepley at gmail.com Mon Nov 19 02:41:26 2012 From: knepley at gmail.com (Matthew Knepley) Date: Mon, 19 Nov 2012 03:41:26 -0500 Subject: [petsc-users] Questions about PetscObjectCompose and DM user context In-Reply-To: <6C4AE5741C2B874282F58DA136A2CCB8312A11@BY2PRD0611MB441.namprd06.prod.outlook.com> References: <6C4AE5741C2B874282F58DA136A2CCB8312A11@BY2PRD0611MB441.namprd06.prod.outlook.com> Message-ID: On Sun, Nov 18, 2012 at 4:10 PM, Blaise A Bourdin wrote: > Hi, > > Following on last week's discussion with Jed on petsc-dev, I am looking a moving the DM's associated to parameters in a PDE from a user context to the DM associated with the solution field, using PetscObjectCompose. > Let's imagine for a second that I want to solve the PDE > -div (k(x) \cdot u(x) ) = f + Boundary conditions, > where k(x) is a a vector-valued coefficient and u(x) is the field I am solving for. > Assume that the DM for u is dmU and the one for K is dmK, and that they have been created. > Once both DMs are created, I can stash dmK inside dmU, using > PetscObjectCompose((PetscObject) dmU,"SomeName",(PetscObject) dmK); > At this point, my understanding is that I can safely destroy dmK without causing a memory link, am I right? Yes. > In my jacobian evaluation, I get a copy of dmK using PetscObjectQuery with the proper name: > PetscObjectQuery((PetscObject) dmU,"SomeName",(PetscObject*) &dmK); > Again, I _can_ safely call DMDestroy(&dmK) at the end of the jacobian. Can I simply let dmK fall out of scope? You do not destroy after a query. Just let it go out of scope. > I assume that dmK gets automatically destroyed when dmU is destroyed, right? Yes. > Finally, as far as I understand, I can either set the user context to the Jacobian function explicitly in the call to SNESSetJacobian or attach it to the DM using DMSetApplicationContext, or to the SNES using SNESSetApplicationContext. What would be the pros and cons of each technique? The same question would apply to DMCoarsenHookAdd. I have not figured out what is the best yet. We are still experimenting. I tend to favor setting the DM describing a solution with SNESSetDM(), which you can always get back. Now all vectors that come from DMs have it attached, so you can use VecGetDM(). Then if you need auxiliary data for the solve, I think SNESSetAppCtx() is right for that. Thanks, Matt > Regards, > > Blaise > -- > Department of Mathematics and Center for Computation & Technology > Louisiana State University, Baton Rouge, LA 70803, USA > Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 http://www.math.lsu.edu/~bourdin > > -- 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 From jedbrown at mcs.anl.gov Mon Nov 19 02:48:40 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Mon, 19 Nov 2012 03:48:40 -0500 Subject: [petsc-users] Creating PCFieldSplit Preconditioner in source code In-Reply-To: <50A9DFE7.9030407@tu-dresden.de> References: <50A9DFE7.9030407@tu-dresden.de> Message-ID: Unfortunately, options are currently the only way to avoid the initial setup. We could add a special setup routine to the PCFieldSplit interface that you could call, but there are lots of other PCs that you sometimes want to reconfigure after "partial setup". I've been unhappy with this for years, but have not found a general and maintainable way to support, and configuration via options is a better approach most of the time. On Mon, Nov 19, 2012 at 2:29 AM, Thomas Witkowski < thomas.witkowski at tu-dresden.de> wrote: > In the implementation of my Navier-Stokes solver, I initialize the > PCFieldSplit preconditioner in my source code (thus not on the command > line) in the following way: > > PCSetType(pc, PCFIELDSPLIT); > PCFieldSplitSetType(pc, PC_COMPOSITE_SCHUR); > PCFieldSplitSetSchurFactType(**pc, PC_FIELDSPLIT_SCHUR_FACT_FULL)**; > ... > KSPSetUp(ksp); > KSP *subKsp; > PetscInt nSubKsp; > PCFieldSplitGetSubKSP(pc, &nSubKsp, &subKsp); > KSP kspVelocity = subKsp[0]; > KSP kspSchur = subKsp[1]; > ... > > And then kspVelocity and kspSchur are filled with appropriate options. The > point is now, that to get the sub solver objects, I have to run KSPSetUp > before. In this case, the sub solver objects are also initialized with some > predefined options (block jacobi ILU), which I don't need and what takes > some time and memory. Is there any other way to get the sub solver objects > before and to initialize than the outer solver correctly with the inner > solver I have specified? > > > Thomas > -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.witkowski at tu-dresden.de Mon Nov 19 02:54:16 2012 From: thomas.witkowski at tu-dresden.de (Thomas Witkowski) Date: Mon, 19 Nov 2012 09:54:16 +0100 Subject: [petsc-users] Creating PCFieldSplit Preconditioner in source code In-Reply-To: References: <50A9DFE7.9030407@tu-dresden.de> Message-ID: <50A9F3B8.4030403@tu-dresden.de> Jed: To you think that I can write a work-around in just using PetscOptionsInsertString before KSPSetUp with some settings that I don't will use later but which would make KSPSetUp on the corresponding solver object cheap? Thomas Am 19.11.2012 09:48, schrieb Jed Brown: > Unfortunately, options are currently the only way to avoid the initial > setup. We could add a special setup routine to the PCFieldSplit > interface that you could call, but there are lots of other PCs that > you sometimes want to reconfigure after "partial setup". I've been > unhappy with this for years, but have not found a general and > maintainable way to support, and configuration via options is a better > approach most of the time. > > > On Mon, Nov 19, 2012 at 2:29 AM, Thomas Witkowski > > wrote: > > In the implementation of my Navier-Stokes solver, I initialize the > PCFieldSplit preconditioner in my source code (thus not on the > command line) in the following way: > > PCSetType(pc, PCFIELDSPLIT); > PCFieldSplitSetType(pc, PC_COMPOSITE_SCHUR); > PCFieldSplitSetSchurFactType(pc, PC_FIELDSPLIT_SCHUR_FACT_FULL); > ... > KSPSetUp(ksp); > KSP *subKsp; > PetscInt nSubKsp; > PCFieldSplitGetSubKSP(pc, &nSubKsp, &subKsp); > KSP kspVelocity = subKsp[0]; > KSP kspSchur = subKsp[1]; > ... > > And then kspVelocity and kspSchur are filled with appropriate > options. The point is now, that to get the sub solver objects, I > have to run KSPSetUp before. In this case, the sub solver objects > are also initialized with some predefined options (block jacobi > ILU), which I don't need and what takes some time and memory. Is > there any other way to get the sub solver objects before and to > initialize than the outer solver correctly with the inner solver I > have specified? > > > Thomas > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Mon Nov 19 02:58:34 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Mon, 19 Nov 2012 09:58:34 +0100 Subject: [petsc-users] Creating PCFieldSplit Preconditioner in source code In-Reply-To: <50A9F3B8.4030403@tu-dresden.de> References: <50A9DFE7.9030407@tu-dresden.de> <50A9F3B8.4030403@tu-dresden.de> Message-ID: Yes On Mon, Nov 19, 2012 at 9:54 AM, Thomas Witkowski < thomas.witkowski at tu-dresden.de> wrote: > Jed: To you think that I can write a work-around in just using > PetscOptionsInsertString before KSPSetUp with some settings that I don't > will use later but which would make KSPSetUp on the corresponding solver > object cheap? > > Thomas > > Am 19.11.2012 09:48, schrieb Jed Brown: > > Unfortunately, options are currently the only way to avoid the initial > setup. We could add a special setup routine to the PCFieldSplit interface > that you could call, but there are lots of other PCs that you sometimes > want to reconfigure after "partial setup". I've been unhappy with this for > years, but have not found a general and maintainable way to support, and > configuration via options is a better approach most of the time. > > > On Mon, Nov 19, 2012 at 2:29 AM, Thomas Witkowski < > thomas.witkowski at tu-dresden.de> wrote: > >> In the implementation of my Navier-Stokes solver, I initialize the >> PCFieldSplit preconditioner in my source code (thus not on the command >> line) in the following way: >> >> PCSetType(pc, PCFIELDSPLIT); >> PCFieldSplitSetType(pc, PC_COMPOSITE_SCHUR); >> PCFieldSplitSetSchurFactType(pc, PC_FIELDSPLIT_SCHUR_FACT_FULL); >> ... >> KSPSetUp(ksp); >> KSP *subKsp; >> PetscInt nSubKsp; >> PCFieldSplitGetSubKSP(pc, &nSubKsp, &subKsp); >> KSP kspVelocity = subKsp[0]; >> KSP kspSchur = subKsp[1]; >> ... >> >> And then kspVelocity and kspSchur are filled with appropriate options. >> The point is now, that to get the sub solver objects, I have to run >> KSPSetUp before. In this case, the sub solver objects are also initialized >> with some predefined options (block jacobi ILU), which I don't need and >> what takes some time and memory. Is there any other way to get the sub >> solver objects before and to initialize than the outer solver correctly >> with the inner solver I have specified? >> >> >> Thomas >> > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.witkowski at tu-dresden.de Mon Nov 19 04:26:48 2012 From: thomas.witkowski at tu-dresden.de (Thomas Witkowski) Date: Mon, 19 Nov 2012 11:26:48 +0100 Subject: [petsc-users] KSPSetUp does not scale Message-ID: <50AA0968.7050401@tu-dresden.de> I have some scaling problem in KSPSetUp, maybe some of you can help me to fix it. It takes 4.5 seconds on 64 cores, and 4.0 cores on 128 cores. The matrix has around 11 million rows and is not perfectly balanced, but the number of maximum rows per core in the 128 cases is exactly halfe of the number in the case when using 64 cores. Besides the scaling, why does the setup takes so long? I though that just some objects are created but no calculation is going on! The KSPView on the corresponding solver objects is as follows: KSP Object:(ns_) 64 MPI processes type: fgmres GMRES: restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative refinement GMRES: happy breakdown tolerance 1e-30 maximum iterations=100, initial guess is zero tolerances: relative=1e-06, absolute=1e-08, divergence=10000 right preconditioning has attached null space using UNPRECONDITIONED norm type for convergence test PC Object:(ns_) 64 MPI processes type: fieldsplit FieldSplit with Schur preconditioner, factorization FULL Preconditioner for the Schur complement formed from the block diagonal part of A11 Split info: Split number 0 Defined by IS Split number 1 Defined by IS KSP solver for A00 block KSP Object: (ns_fieldsplit_velocity_) 64 MPI processes type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-05, absolute=1e-50, divergence=10000 left preconditioning using DEFAULT norm type for convergence test PC Object: (ns_fieldsplit_velocity_) 64 MPI processes type: none linear system matrix = precond matrix: Matrix Object: 64 MPI processes type: mpiaij rows=11068107, cols=11068107 total: nonzeros=315206535, allocated nonzeros=315206535 total number of mallocs used during MatSetValues calls =0 not using I-node (on process 0) routines KSP solver for S = A11 - A10 inv(A00) A01 KSP Object: (ns_fieldsplit_pressure_) 64 MPI processes type: gmres GMRES: restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative refinement GMRES: happy breakdown tolerance 1e-30 maximum iterations=10000, initial guess is zero tolerances: relative=1e-05, absolute=1e-50, divergence=10000 left preconditioning using DEFAULT norm type for convergence test PC Object: (ns_fieldsplit_pressure_) 64 MPI processes type: none linear system matrix followed by preconditioner matrix: Matrix Object: 64 MPI processes type: schurcomplement rows=469678, cols=469678 Schur complement A11 - A10 inv(A00) A01 A11 Matrix Object: 64 MPI processes type: mpiaij rows=469678, cols=469678 total: nonzeros=0, allocated nonzeros=0 total number of mallocs used during MatSetValues calls =0 using I-node (on process 0) routines: found 1304 nodes, limit used is 5 A10 Matrix Object: 64 MPI processes type: mpiaij rows=469678, cols=11068107 total: nonzeros=89122957, allocated nonzeros=89122957 total number of mallocs used during MatSetValues calls =0 not using I-node (on process 0) routines KSP of A00 KSP Object: (ns_fieldsplit_velocity_) 64 MPI processes type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-05, absolute=1e-50, divergence=10000 left preconditioning using DEFAULT norm type for convergence test PC Object: (ns_fieldsplit_velocity_) 64 MPI processes type: none linear system matrix = precond matrix: Matrix Object: 64 MPI processes type: mpiaij rows=11068107, cols=11068107 total: nonzeros=315206535, allocated nonzeros=315206535 total number of mallocs used during MatSetValues calls =0 not using I-node (on process 0) routines A01 Matrix Object: 64 MPI processes type: mpiaij rows=11068107, cols=469678 total: nonzeros=88821041, allocated nonzeros=88821041 total number of mallocs used during MatSetValues calls =0 not using I-node (on process 0) routines Matrix Object: 64 MPI processes type: mpiaij rows=469678, cols=469678 total: nonzeros=0, allocated nonzeros=0 total number of mallocs used during MatSetValues calls =0 using I-node (on process 0) routines: found 1304 nodes, limit used is 5 linear system matrix = precond matrix: Matrix Object: 64 MPI processes type: mpiaij rows=11537785, cols=11537785 total: nonzeros=493150533, allocated nonzeros=510309207 total number of mallocs used during MatSetValues calls =0 not using I-node (on process 0) routines Thomas From jedbrown at mcs.anl.gov Mon Nov 19 06:33:27 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Mon, 19 Nov 2012 13:33:27 +0100 Subject: [petsc-users] KSPSetUp does not scale In-Reply-To: <50AA0968.7050401@tu-dresden.de> References: <50AA0968.7050401@tu-dresden.de> Message-ID: Always, always, always send -log_summary when asking about performance. On Mon, Nov 19, 2012 at 11:26 AM, Thomas Witkowski < thomas.witkowski at tu-dresden.de> wrote: > I have some scaling problem in KSPSetUp, maybe some of you can help me to > fix it. It takes 4.5 seconds on 64 cores, and 4.0 cores on 128 cores. The > matrix has around 11 million rows and is not perfectly balanced, but the > number of maximum rows per core in the 128 cases is exactly halfe of the > number in the case when using 64 cores. Besides the scaling, why does the > setup takes so long? I though that just some objects are created but no > calculation is going on! > > The KSPView on the corresponding solver objects is as follows: > > KSP Object:(ns_) 64 MPI processes > type: fgmres > GMRES: restart=30, using Classical (unmodified) Gram-Schmidt > Orthogonalization with no iterative refinement > GMRES: happy breakdown tolerance 1e-30 > maximum iterations=100, initial guess is zero > tolerances: relative=1e-06, absolute=1e-08, divergence=10000 > right preconditioning > has attached null space > using UNPRECONDITIONED norm type for convergence test > PC Object:(ns_) 64 MPI processes > type: fieldsplit > FieldSplit with Schur preconditioner, factorization FULL > Preconditioner for the Schur complement formed from the block diagonal > part of A11 > Split info: > Split number 0 Defined by IS > Split number 1 Defined by IS > KSP solver for A00 block > KSP Object: (ns_fieldsplit_velocity_) 64 MPI processes > type: preonly > maximum iterations=10000, initial guess is zero > tolerances: relative=1e-05, absolute=1e-50, divergence=10000 > left preconditioning > using DEFAULT norm type for convergence test > PC Object: (ns_fieldsplit_velocity_) 64 MPI processes > type: none > linear system matrix = precond matrix: > Matrix Object: 64 MPI processes > type: mpiaij > rows=11068107, cols=11068107 > total: nonzeros=315206535, allocated nonzeros=315206535 > total number of mallocs used during MatSetValues calls =0 > not using I-node (on process 0) routines > KSP solver for S = A11 - A10 inv(A00) A01 > KSP Object: (ns_fieldsplit_pressure_) 64 MPI processes > type: gmres > GMRES: restart=30, using Classical (unmodified) Gram-Schmidt > Orthogonalization with no iterative refinement > GMRES: happy breakdown tolerance 1e-30 > maximum iterations=10000, initial guess is zero > tolerances: relative=1e-05, absolute=1e-50, divergence=10000 > left preconditioning > using DEFAULT norm type for convergence test > PC Object: (ns_fieldsplit_pressure_) 64 MPI processes > type: none > linear system matrix followed by preconditioner matrix: > Matrix Object: 64 MPI processes > type: schurcomplement > rows=469678, cols=469678 > Schur complement A11 - A10 inv(A00) A01 > A11 > Matrix Object: 64 MPI processes > type: mpiaij > rows=469678, cols=469678 > total: nonzeros=0, allocated nonzeros=0 > total number of mallocs used during MatSetValues calls =0 > using I-node (on process 0) routines: found 1304 nodes, > limit used is 5 > A10 > Matrix Object: 64 MPI processes > type: mpiaij > rows=469678, cols=11068107 > total: nonzeros=89122957, allocated nonzeros=89122957 > total number of mallocs used during MatSetValues calls =0 > not using I-node (on process 0) routines > KSP of A00 > KSP Object: (ns_fieldsplit_velocity_) 64 MPI > processes > type: preonly > maximum iterations=10000, initial guess is zero > tolerances: relative=1e-05, absolute=1e-50, > divergence=10000 > left preconditioning > using DEFAULT norm type for convergence test > PC Object: (ns_fieldsplit_velocity_) 64 MPI > processes > type: none > linear system matrix = precond matrix: > Matrix Object: 64 MPI processes > type: mpiaij > rows=11068107, cols=11068107 > total: nonzeros=315206535, allocated nonzeros=315206535 > total number of mallocs used during MatSetValues calls =0 > not using I-node (on process 0) routines > A01 > Matrix Object: 64 MPI processes > type: mpiaij > rows=11068107, cols=469678 > total: nonzeros=88821041, allocated nonzeros=88821041 > total number of mallocs used during MatSetValues calls =0 > not using I-node (on process 0) routines > Matrix Object: 64 MPI processes > type: mpiaij > rows=469678, cols=469678 > total: nonzeros=0, allocated nonzeros=0 > total number of mallocs used during MatSetValues calls =0 > using I-node (on process 0) routines: found 1304 nodes, limit > used is 5 > linear system matrix = precond matrix: > Matrix Object: 64 MPI processes > type: mpiaij > rows=11537785, cols=11537785 > total: nonzeros=493150533, allocated nonzeros=510309207 > total number of mallocs used during MatSetValues calls =0 > not using I-node (on process 0) routines > > > > > Thomas > -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.witkowski at tu-dresden.de Mon Nov 19 06:36:41 2012 From: thomas.witkowski at tu-dresden.de (Thomas Witkowski) Date: Mon, 19 Nov 2012 13:36:41 +0100 Subject: [petsc-users] KSPSetUp does not scale In-Reply-To: References: <50AA0968.7050401@tu-dresden.de> Message-ID: <50AA27D9.6020305@tu-dresden.de> I can do this! Should I stop the run after KSPSetUp? Or do you want to see the log_summary file from the whole run? Thomas Am 19.11.2012 13:33, schrieb Jed Brown: > Always, always, always send -log_summary when asking about performance. > > > On Mon, Nov 19, 2012 at 11:26 AM, Thomas Witkowski > > wrote: > > I have some scaling problem in KSPSetUp, maybe some of you can > help me to fix it. It takes 4.5 seconds on 64 cores, and 4.0 cores > on 128 cores. The matrix has around 11 million rows and is not > perfectly balanced, but the number of maximum rows per core in the > 128 cases is exactly halfe of the number in the case when using 64 > cores. Besides the scaling, why does the setup takes so long? I > though that just some objects are created but no calculation is > going on! > > The KSPView on the corresponding solver objects is as follows: > > KSP Object:(ns_) 64 MPI processes > type: fgmres > GMRES: restart=30, using Classical (unmodified) Gram-Schmidt > Orthogonalization with no iterative refinement > GMRES: happy breakdown tolerance 1e-30 > maximum iterations=100, initial guess is zero > tolerances: relative=1e-06, absolute=1e-08, divergence=10000 > right preconditioning > has attached null space > using UNPRECONDITIONED norm type for convergence test > PC Object:(ns_) 64 MPI processes > type: fieldsplit > FieldSplit with Schur preconditioner, factorization FULL > Preconditioner for the Schur complement formed from the block > diagonal part of A11 > Split info: > Split number 0 Defined by IS > Split number 1 Defined by IS > KSP solver for A00 block > KSP Object: (ns_fieldsplit_velocity_) 64 MPI > processes > type: preonly > maximum iterations=10000, initial guess is zero > tolerances: relative=1e-05, absolute=1e-50, divergence=10000 > left preconditioning > using DEFAULT norm type for convergence test > PC Object: (ns_fieldsplit_velocity_) 64 MPI processes > type: none > linear system matrix = precond matrix: > Matrix Object: 64 MPI processes > type: mpiaij > rows=11068107, cols=11068107 > total: nonzeros=315206535, allocated nonzeros=315206535 > total number of mallocs used during MatSetValues calls =0 > not using I-node (on process 0) routines > KSP solver for S = A11 - A10 inv(A00) A01 > KSP Object: (ns_fieldsplit_pressure_) 64 MPI > processes > type: gmres > GMRES: restart=30, using Classical (unmodified) > Gram-Schmidt Orthogonalization with no iterative refinement > GMRES: happy breakdown tolerance 1e-30 > maximum iterations=10000, initial guess is zero > tolerances: relative=1e-05, absolute=1e-50, divergence=10000 > left preconditioning > using DEFAULT norm type for convergence test > PC Object: (ns_fieldsplit_pressure_) 64 MPI processes > type: none > linear system matrix followed by preconditioner matrix: > Matrix Object: 64 MPI processes > type: schurcomplement > rows=469678, cols=469678 > Schur complement A11 - A10 inv(A00) A01 > A11 > Matrix Object: 64 MPI processes > type: mpiaij > rows=469678, cols=469678 > total: nonzeros=0, allocated nonzeros=0 > total number of mallocs used during MatSetValues > calls =0 > using I-node (on process 0) routines: found 1304 > nodes, limit used is 5 > A10 > Matrix Object: 64 MPI processes > type: mpiaij > rows=469678, cols=11068107 > total: nonzeros=89122957, allocated nonzeros=89122957 > total number of mallocs used during MatSetValues > calls =0 > not using I-node (on process 0) routines > KSP of A00 > KSP Object: (ns_fieldsplit_velocity_) 64 MPI > processes > type: preonly > maximum iterations=10000, initial guess is zero > tolerances: relative=1e-05, absolute=1e-50, > divergence=10000 > left preconditioning > using DEFAULT norm type for convergence test > PC Object: (ns_fieldsplit_velocity_) 64 MPI > processes > type: none > linear system matrix = precond matrix: > Matrix Object: 64 MPI processes > type: mpiaij > rows=11068107, cols=11068107 > total: nonzeros=315206535, allocated > nonzeros=315206535 > total number of mallocs used during MatSetValues > calls =0 > not using I-node (on process 0) routines > A01 > Matrix Object: 64 MPI processes > type: mpiaij > rows=11068107, cols=469678 > total: nonzeros=88821041, allocated nonzeros=88821041 > total number of mallocs used during MatSetValues > calls =0 > not using I-node (on process 0) routines > Matrix Object: 64 MPI processes > type: mpiaij > rows=469678, cols=469678 > total: nonzeros=0, allocated nonzeros=0 > total number of mallocs used during MatSetValues calls =0 > using I-node (on process 0) routines: found 1304 > nodes, limit used is 5 > linear system matrix = precond matrix: > Matrix Object: 64 MPI processes > type: mpiaij > rows=11537785, cols=11537785 > total: nonzeros=493150533, allocated nonzeros=510309207 > total number of mallocs used during MatSetValues calls =0 > not using I-node (on process 0) routines > > > > > Thomas > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Mon Nov 19 06:41:32 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Mon, 19 Nov 2012 13:41:32 +0100 Subject: [petsc-users] KSPSetUp does not scale In-Reply-To: <50AA27D9.6020305@tu-dresden.de> References: <50AA0968.7050401@tu-dresden.de> <50AA27D9.6020305@tu-dresden.de> Message-ID: Just have it do one or a few iterations. On Mon, Nov 19, 2012 at 1:36 PM, Thomas Witkowski < thomas.witkowski at tu-dresden.de> wrote: > I can do this! Should I stop the run after KSPSetUp? Or do you want to > see the log_summary file from the whole run? > > Thomas > > Am 19.11.2012 13:33, schrieb Jed Brown: > > Always, always, always send -log_summary when asking about performance. > > > On Mon, Nov 19, 2012 at 11:26 AM, Thomas Witkowski < > thomas.witkowski at tu-dresden.de> wrote: > >> I have some scaling problem in KSPSetUp, maybe some of you can help me to >> fix it. It takes 4.5 seconds on 64 cores, and 4.0 cores on 128 cores. The >> matrix has around 11 million rows and is not perfectly balanced, but the >> number of maximum rows per core in the 128 cases is exactly halfe of the >> number in the case when using 64 cores. Besides the scaling, why does the >> setup takes so long? I though that just some objects are created but no >> calculation is going on! >> >> The KSPView on the corresponding solver objects is as follows: >> >> KSP Object:(ns_) 64 MPI processes >> type: fgmres >> GMRES: restart=30, using Classical (unmodified) Gram-Schmidt >> Orthogonalization with no iterative refinement >> GMRES: happy breakdown tolerance 1e-30 >> maximum iterations=100, initial guess is zero >> tolerances: relative=1e-06, absolute=1e-08, divergence=10000 >> right preconditioning >> has attached null space >> using UNPRECONDITIONED norm type for convergence test >> PC Object:(ns_) 64 MPI processes >> type: fieldsplit >> FieldSplit with Schur preconditioner, factorization FULL >> Preconditioner for the Schur complement formed from the block >> diagonal part of A11 >> Split info: >> Split number 0 Defined by IS >> Split number 1 Defined by IS >> KSP solver for A00 block >> KSP Object: (ns_fieldsplit_velocity_) 64 MPI processes >> type: preonly >> maximum iterations=10000, initial guess is zero >> tolerances: relative=1e-05, absolute=1e-50, divergence=10000 >> left preconditioning >> using DEFAULT norm type for convergence test >> PC Object: (ns_fieldsplit_velocity_) 64 MPI processes >> type: none >> linear system matrix = precond matrix: >> Matrix Object: 64 MPI processes >> type: mpiaij >> rows=11068107, cols=11068107 >> total: nonzeros=315206535, allocated nonzeros=315206535 >> total number of mallocs used during MatSetValues calls =0 >> not using I-node (on process 0) routines >> KSP solver for S = A11 - A10 inv(A00) A01 >> KSP Object: (ns_fieldsplit_pressure_) 64 MPI processes >> type: gmres >> GMRES: restart=30, using Classical (unmodified) Gram-Schmidt >> Orthogonalization with no iterative refinement >> GMRES: happy breakdown tolerance 1e-30 >> maximum iterations=10000, initial guess is zero >> tolerances: relative=1e-05, absolute=1e-50, divergence=10000 >> left preconditioning >> using DEFAULT norm type for convergence test >> PC Object: (ns_fieldsplit_pressure_) 64 MPI processes >> type: none >> linear system matrix followed by preconditioner matrix: >> Matrix Object: 64 MPI processes >> type: schurcomplement >> rows=469678, cols=469678 >> Schur complement A11 - A10 inv(A00) A01 >> A11 >> Matrix Object: 64 MPI processes >> type: mpiaij >> rows=469678, cols=469678 >> total: nonzeros=0, allocated nonzeros=0 >> total number of mallocs used during MatSetValues calls =0 >> using I-node (on process 0) routines: found 1304 nodes, >> limit used is 5 >> A10 >> Matrix Object: 64 MPI processes >> type: mpiaij >> rows=469678, cols=11068107 >> total: nonzeros=89122957, allocated nonzeros=89122957 >> total number of mallocs used during MatSetValues calls =0 >> not using I-node (on process 0) routines >> KSP of A00 >> KSP Object: (ns_fieldsplit_velocity_) 64 MPI >> processes >> type: preonly >> maximum iterations=10000, initial guess is zero >> tolerances: relative=1e-05, absolute=1e-50, >> divergence=10000 >> left preconditioning >> using DEFAULT norm type for convergence test >> PC Object: (ns_fieldsplit_velocity_) 64 MPI >> processes >> type: none >> linear system matrix = precond matrix: >> Matrix Object: 64 MPI processes >> type: mpiaij >> rows=11068107, cols=11068107 >> total: nonzeros=315206535, allocated nonzeros=315206535 >> total number of mallocs used during MatSetValues calls >> =0 >> not using I-node (on process 0) routines >> A01 >> Matrix Object: 64 MPI processes >> type: mpiaij >> rows=11068107, cols=469678 >> total: nonzeros=88821041, allocated nonzeros=88821041 >> total number of mallocs used during MatSetValues calls =0 >> not using I-node (on process 0) routines >> Matrix Object: 64 MPI processes >> type: mpiaij >> rows=469678, cols=469678 >> total: nonzeros=0, allocated nonzeros=0 >> total number of mallocs used during MatSetValues calls =0 >> using I-node (on process 0) routines: found 1304 nodes, limit >> used is 5 >> linear system matrix = precond matrix: >> Matrix Object: 64 MPI processes >> type: mpiaij >> rows=11537785, cols=11537785 >> total: nonzeros=493150533, allocated nonzeros=510309207 >> total number of mallocs used during MatSetValues calls =0 >> not using I-node (on process 0) routines >> >> >> >> >> Thomas >> > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.witkowski at tu-dresden.de Mon Nov 19 07:40:03 2012 From: thomas.witkowski at tu-dresden.de (Thomas Witkowski) Date: Mon, 19 Nov 2012 14:40:03 +0100 Subject: [petsc-users] KSPSetUp does not scale In-Reply-To: References: <50AA0968.7050401@tu-dresden.de> <50AA27D9.6020305@tu-dresden.de> Message-ID: <50AA36B3.8050905@tu-dresden.de> Here are the two files. In this case, maybe you can also give me some hints, why the solver at all does not scale here. The solver runtime for 64 cores is 206 seconds, with the same problem size on 128 cores it takes 172 seconds. The number of inner and outer solver iterations are the same for both runs. I use CG with jacobi-preconditioner and hypre boomeramg for inner solver. Am 19.11.2012 13:41, schrieb Jed Brown: > Just have it do one or a few iterations. > > > On Mon, Nov 19, 2012 at 1:36 PM, Thomas Witkowski > > wrote: > > I can do this! Should I stop the run after KSPSetUp? Or do you > want to see the log_summary file from the whole run? > > Thomas > > Am 19.11.2012 13:33, schrieb Jed Brown: >> Always, always, always send -log_summary when asking about >> performance. >> >> >> On Mon, Nov 19, 2012 at 11:26 AM, Thomas Witkowski >> > > wrote: >> >> I have some scaling problem in KSPSetUp, maybe some of you >> can help me to fix it. It takes 4.5 seconds on 64 cores, and >> 4.0 cores on 128 cores. The matrix has around 11 million rows >> and is not perfectly balanced, but the number of maximum rows >> per core in the 128 cases is exactly halfe of the number in >> the case when using 64 cores. Besides the scaling, why does >> the setup takes so long? I though that just some objects are >> created but no calculation is going on! >> >> The KSPView on the corresponding solver objects is as follows: >> >> KSP Object:(ns_) 64 MPI processes >> type: fgmres >> GMRES: restart=30, using Classical (unmodified) >> Gram-Schmidt Orthogonalization with no iterative refinement >> GMRES: happy breakdown tolerance 1e-30 >> maximum iterations=100, initial guess is zero >> tolerances: relative=1e-06, absolute=1e-08, divergence=10000 >> right preconditioning >> has attached null space >> using UNPRECONDITIONED norm type for convergence test >> PC Object:(ns_) 64 MPI processes >> type: fieldsplit >> FieldSplit with Schur preconditioner, factorization FULL >> Preconditioner for the Schur complement formed from the >> block diagonal part of A11 >> Split info: >> Split number 0 Defined by IS >> Split number 1 Defined by IS >> KSP solver for A00 block >> KSP Object: (ns_fieldsplit_velocity_) 64 MPI >> processes >> type: preonly >> maximum iterations=10000, initial guess is zero >> tolerances: relative=1e-05, absolute=1e-50, >> divergence=10000 >> left preconditioning >> using DEFAULT norm type for convergence test >> PC Object: (ns_fieldsplit_velocity_) 64 MPI >> processes >> type: none >> linear system matrix = precond matrix: >> Matrix Object: 64 MPI processes >> type: mpiaij >> rows=11068107, cols=11068107 >> total: nonzeros=315206535, allocated nonzeros=315206535 >> total number of mallocs used during MatSetValues >> calls =0 >> not using I-node (on process 0) routines >> KSP solver for S = A11 - A10 inv(A00) A01 >> KSP Object: (ns_fieldsplit_pressure_) 64 MPI >> processes >> type: gmres >> GMRES: restart=30, using Classical (unmodified) >> Gram-Schmidt Orthogonalization with no iterative refinement >> GMRES: happy breakdown tolerance 1e-30 >> maximum iterations=10000, initial guess is zero >> tolerances: relative=1e-05, absolute=1e-50, >> divergence=10000 >> left preconditioning >> using DEFAULT norm type for convergence test >> PC Object: (ns_fieldsplit_pressure_) 64 MPI >> processes >> type: none >> linear system matrix followed by preconditioner matrix: >> Matrix Object: 64 MPI processes >> type: schurcomplement >> rows=469678, cols=469678 >> Schur complement A11 - A10 inv(A00) A01 >> A11 >> Matrix Object: 64 MPI processes >> type: mpiaij >> rows=469678, cols=469678 >> total: nonzeros=0, allocated nonzeros=0 >> total number of mallocs used during >> MatSetValues calls =0 >> using I-node (on process 0) routines: found >> 1304 nodes, limit used is 5 >> A10 >> Matrix Object: 64 MPI processes >> type: mpiaij >> rows=469678, cols=11068107 >> total: nonzeros=89122957, allocated >> nonzeros=89122957 >> total number of mallocs used during >> MatSetValues calls =0 >> not using I-node (on process 0) routines >> KSP of A00 >> KSP Object: (ns_fieldsplit_velocity_) >> 64 MPI processes >> type: preonly >> maximum iterations=10000, initial guess is zero >> tolerances: relative=1e-05, absolute=1e-50, >> divergence=10000 >> left preconditioning >> using DEFAULT norm type for convergence test >> PC Object: (ns_fieldsplit_velocity_) >> 64 MPI processes >> type: none >> linear system matrix = precond matrix: >> Matrix Object: 64 MPI processes >> type: mpiaij >> rows=11068107, cols=11068107 >> total: nonzeros=315206535, allocated >> nonzeros=315206535 >> total number of mallocs used during >> MatSetValues calls =0 >> not using I-node (on process 0) routines >> A01 >> Matrix Object: 64 MPI processes >> type: mpiaij >> rows=11068107, cols=469678 >> total: nonzeros=88821041, allocated >> nonzeros=88821041 >> total number of mallocs used during >> MatSetValues calls =0 >> not using I-node (on process 0) routines >> Matrix Object: 64 MPI processes >> type: mpiaij >> rows=469678, cols=469678 >> total: nonzeros=0, allocated nonzeros=0 >> total number of mallocs used during MatSetValues >> calls =0 >> using I-node (on process 0) routines: found 1304 >> nodes, limit used is 5 >> linear system matrix = precond matrix: >> Matrix Object: 64 MPI processes >> type: mpiaij >> rows=11537785, cols=11537785 >> total: nonzeros=493150533, allocated nonzeros=510309207 >> total number of mallocs used during MatSetValues calls =0 >> not using I-node (on process 0) routines >> >> >> >> >> Thomas >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- ************************************************************************************************************************ *** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r -fCourier9' to print this document *** ************************************************************************************************************************ ---------------------------------------------- PETSc Performance Summary: ---------------------------------------------- ./ns_diffuse on a arch-linux2-cxx-opt named jj15c52 with 64 processors, by hdr060 Mon Nov 19 14:09:02 2012 Using Petsc Development HG revision: a7fad1b276253926c2a6f6a2ded33d8595ea85e3 HG Date: Tue Oct 30 21:48:02 2012 -0500 Max Max/Min Avg Total Time (sec): 2.646e+02 1.00001 2.646e+02 Objects: 5.000e+02 1.00000 5.000e+02 Flops: 6.177e+09 1.26397 5.525e+09 3.536e+11 Flops/sec: 2.334e+07 1.26397 2.088e+07 1.336e+09 MPI Messages: 1.673e+04 4.59221 8.234e+03 5.270e+05 MPI Message Lengths: 2.267e+08 2.72709 1.745e+04 9.197e+09 MPI Reductions: 1.337e+03 1.00000 Flop counting convention: 1 flop = 1 real number operation of type (multiply/divide/add/subtract) e.g., VecAXPY() for real vectors of length N --> 2N flops and VecAXPY() for complex vectors of length N --> 8N flops Summary of Stages: ----- Time ------ ----- Flops ----- --- Messages --- -- Message Lengths -- -- Reductions -- Avg %Total Avg %Total counts %Total Avg %Total counts %Total 0: Main Stage: 2.6464e+02 100.0% 3.5359e+11 100.0% 5.270e+05 100.0% 1.745e+04 100.0% 1.336e+03 99.9% ------------------------------------------------------------------------------------------------------------------------ See the 'Profiling' chapter of the users' manual for details on interpreting output. Phase summary info: Count: number of times phase was executed Time and Flops: Max - maximum over all processors Ratio - ratio of maximum to minimum over all processors Mess: number of messages sent Avg. len: average message length Reduct: number of global reductions Global: entire computation Stage: stages of a computation. Set stages with PetscLogStagePush() and PetscLogStagePop(). %T - percent time in this phase %f - percent flops in this phase %M - percent messages in this phase %L - percent message lengths in this phase %R - percent reductions in this phase Total Mflop/s: 10e-6 * (sum of flops over all processors)/(max time over all processors) ------------------------------------------------------------------------------------------------------------------------ Event Count Time (sec) Flops --- Global --- --- Stage --- Total Max Ratio Max Ratio Max Ratio Mess Avg len Reduct %T %f %M %L %R %T %f %M %L %R Mflop/s ------------------------------------------------------------------------------------------------------------------------ --- Event Stage 0: Main Stage MatMult 707 1.0 8.2787e+00 1.1 4.27e+09 1.3 5.1e+05 1.7e+04 0.0e+00 3 68 97 92 0 3 68 97 92 0 29017 MatConvert 2 1.0 1.6090e-01 1.5 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 MatAssemblyBegin 12 1.0 2.7379e-01 4.4 0.00e+00 0.0 4.3e+03 1.4e+05 1.6e+01 0 0 1 6 1 0 0 1 6 1 0 MatAssemblyEnd 12 1.0 3.3810e-01 1.1 0.00e+00 0.0 1.0e+04 4.0e+03 6.8e+01 0 0 2 0 5 0 0 2 0 5 0 MatGetRowIJ 4 1.0 8.8716e-0435.8 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecMDot 100 1.0 1.0310e+00 1.8 5.68e+08 1.2 0.0e+00 0.0e+00 1.0e+02 0 9 0 0 7 0 9 0 0 7 32455 VecTDot 300 1.0 2.8301e-02 2.6 5.07e+06 1.4 0.0e+00 0.0e+00 3.0e+02 0 0 0 0 22 0 0 0 0 22 9957 VecNorm 508 1.0 7.5554e-01 3.3 8.64e+07 1.2 0.0e+00 0.0e+00 5.1e+02 0 1 0 0 38 0 1 0 0 38 6726 VecScale 205 1.0 3.1001e-02 1.3 2.14e+07 1.2 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 40594 VecCopy 201 1.0 9.6661e-02 1.3 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecSet 412 1.0 1.6734e-01 1.2 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecAXPY 401 1.0 1.8162e-01 1.2 8.03e+07 1.2 0.0e+00 0.0e+00 0.0e+00 0 1 0 0 0 0 1 0 0 0 26055 VecAYPX 201 1.0 8.2297e-02 2.1 2.06e+07 1.2 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 14731 VecWAXPY 5 1.0 6.2659e-03 2.1 9.79e+05 1.2 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 9207 VecMAXPY 201 1.0 1.6730e+00 1.2 1.14e+09 1.2 0.0e+00 0.0e+00 0.0e+00 1 19 0 0 0 1 19 0 0 0 40139 VecAssemblyBegin 4 1.0 6.0473e-0217.9 0.00e+00 0.0 7.1e+02 2.6e+04 1.2e+01 0 0 0 0 1 0 0 0 0 1 0 VecAssemblyEnd 4 1.0 2.9459e-03 7.3 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecPointwiseMult 300 1.0 6.2079e-03 1.3 2.53e+06 1.4 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 22697 VecScatterBegin 1107 1.0 4.0446e-01 1.6 0.00e+00 0.0 5.1e+05 1.7e+04 0.0e+00 0 0 97 92 0 0 0 97 92 0 0 VecScatterEnd 1107 1.0 1.6155e+0014.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecNormalize 1 1.0 1.5441e-01 1.0 5.87e+05 1.2 0.0e+00 0.0e+00 1.0e+00 0 0 0 0 0 0 0 0 0 0 224 KSPGMRESOrthog 100 1.0 1.7406e+00 1.3 1.14e+09 1.2 0.0e+00 0.0e+00 1.0e+02 1 19 0 0 7 1 19 0 0 7 38447 KSPSetUp 5 1.0 1.4701e-02 1.2 0.00e+00 0.0 0.0e+00 0.0e+00 4.0e+00 0 0 0 0 0 0 0 0 0 0 0 KSPSolve 1 1.0 2.0766e+02 1.0 6.16e+09 1.3 5.1e+05 1.7e+04 1.1e+03 78100 97 92 83 78100 97 92 84 1698 PCSetUp 5 1.0 3.2241e+01 1.0 0.00e+00 0.0 4.6e+03 2.6e+04 1.3e+02 12 0 1 1 10 12 0 1 1 10 0 PCApply 100 1.0 1.9821e+02 1.0 7.54e+08 1.4 3.6e+05 8.4e+03 8.1e+02 75 12 69 33 61 75 12 69 33 61 210 ------------------------------------------------------------------------------------------------------------------------ Memory usage is given in bytes: Object Type Creations Destructions Memory Descendants' Mem. Reports information only for process 0. --- Event Stage 0: Main Stage Matrix 29 29 271125592 0 Matrix Null Space 3 3 1756 0 Vector 415 408 390453064 0 Vector Scatter 10 10 10360 0 Index Set 26 26 425372 0 Krylov Solver 8 7 25864 0 Preconditioner 8 7 6192 0 Viewer 1 0 0 0 ======================================================================================================================== Average time to get PetscTime(): 0 Average time for MPI_Barrier(): 1.94073e-05 Average time for zero size MPI_Send(): 1.19545e-05 #PETSc Option Table entries: -log_summary -ns_ksp_max_it 100 #End of PETSc Option Table entries Compiled without FORTRAN kernels Compiled with full precision matrices (default) sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 sizeof(PetscScalar) 8 sizeof(PetscInt) 4 Configure run at: Wed Oct 31 15:22:38 2012 Configure options: --known-level1-dcache-size=32768 --known-level1-dcache-linesize=64 --known-level1-dcache-assoc=8 --known-memcmp-ok=1 --known-sizeof-char=1 --known-sizeof-void-p=8 --known-sizeof-short=2 --known-sizeof-int=4 --known-sizeof-long=8 --known-sizeof-long-long=8 --known-sizeof-float=4 --known-sizeof-double=8 --known-sizeof-size_t=8 --known-bits-per-byte=8 --known-sizeof-MPI_Comm=4 --known-sizeof-MPI_Fint=4 --known-mpi-long-double=1 --prefix=/lustre/jhome22/hdr06/hdr060/petsc/install/petsc-dev-opt --with-batch=1 --with-blacs-include=/usr/local/intel/mkl/10.2.5.035/include --with-blacs-lib="-L/usr/local/intel/mkl/10.2.5.035/lib/em64t -lmkl_blacs_intelmpi_lp64 -lmkl_core" --with-blas-lapack-lib="-L/usr/local/intel/mkl/10.2.5.035/lib/em64t -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread" --with-c++-support --with-cc=mpicc --with-clanguage=cxx --with-cxx=mpicxx --with-debugging=1 --with-fc=mpif90 --with-scalapack-include=/usr/local/intel/mkl/10.2.5.035/include --with-scalapack-lib="-L/usr/local/intel/mkl/10.2.5.035/lib/em64t -lmkl_scalapack_lp64 -lmkl_core" --with-x=0 --known-mpi-shared-libraries=0 --download-hypre --download-metis --download-mumps --download-parmetis --download-superlu --download-superlu_dist --download-umfpack --with-debugging=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 ----------------------------------------- Libraries compiled on Wed Oct 31 15:22:38 2012 on jj28l05 Machine characteristics: Linux-2.6.32.59-0.3-default-x86_64-with-SuSE-11-x86_64 Using PETSc directory: /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev Using PETSc arch: arch-linux2-cxx-opt ----------------------------------------- Using C compiler: mpicxx -wd1572 -O3 ${COPTFLAGS} ${CFLAGS} Using Fortran compiler: mpif90 -O3 ${FOPTFLAGS} ${FFLAGS} ----------------------------------------- Using include paths: -I/lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/arch-linux2-cxx-opt/include -I/lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/include -I/lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/include -I/lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/arch-linux2-cxx-opt/include -I/lustre/jsoft/usr_local/parastation/mpi2-intel-5.0.26-1/include ----------------------------------------- Using C linker: mpicxx Using Fortran linker: mpif90 Using libraries: -Wl,-rpath,/lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/arch-linux2-cxx-opt/lib -L/lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/arch-linux2-cxx-opt/lib -lpetsc -Wl,-rpath,/lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/arch-linux2-cxx-opt/lib -L/lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/arch-linux2-cxx-opt/lib -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -L/usr/local/intel/mkl/10.2.5.035/lib/em64t -lmkl_scalapack_lp64 -lmkl_core -lmkl_blacs_intelmpi_lp64 -lmkl_core -lsuperlu_dist_3.1 -lparmetis -lmetis -lsuperlu_4.3 -lHYPRE -lpthread -lumfpack -lamd -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -L/lustre/jsoft/usr_local/parastation/mpi2-intel-5.0.26-1/lib -L/opt/parastation/lib64 -L/usr/local/intel/Compiler/11.1/072/lib/intel64 -L/usr/lib64/gcc/x86_64-suse-linux/4.3 -L/usr/x86_64-suse-linux/lib -lmpichf90 -Wl,-rpath,/lustre/jsoft/usr_local/parastation/mpi2-intel-5.0.26-1/lib -Wl,-rpath,/opt/parastation/lib64 -lifport -lifcore -lm -lm -lmpichcxx -lstdc++ -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lpthread -lpscom -lrt -limf -lsvml -lipgo -ldecimal -lgcc_s -lirc -lirc_s -ldl ----------------------------------------- -------------- next part -------------- ************************************************************************************************************************ *** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r -fCourier9' to print this document *** ************************************************************************************************************************ ---------------------------------------------- PETSc Performance Summary: ---------------------------------------------- ./ns_diffuse on a arch-linux2-cxx-opt named jj05c86 with 128 processors, by hdr060 Mon Nov 19 14:03:54 2012 Using Petsc Development HG revision: a7fad1b276253926c2a6f6a2ded33d8595ea85e3 HG Date: Tue Oct 30 21:48:02 2012 -0500 Max Max/Min Avg Total Time (sec): 2.031e+02 1.00001 2.031e+02 Objects: 5.000e+02 1.00000 5.000e+02 Flops: 3.252e+09 1.40504 2.761e+09 3.534e+11 Flops/sec: 1.601e+07 1.40506 1.359e+07 1.739e+09 MPI Messages: 2.435e+04 5.32757 9.772e+03 1.251e+06 MPI Message Lengths: 1.547e+08 2.72759 9.141e+03 1.143e+10 MPI Reductions: 1.374e+03 1.00000 Flop counting convention: 1 flop = 1 real number operation of type (multiply/divide/add/subtract) e.g., VecAXPY() for real vectors of length N --> 2N flops and VecAXPY() for complex vectors of length N --> 8N flops Summary of Stages: ----- Time ------ ----- Flops ----- --- Messages --- -- Message Lengths -- -- Reductions -- Avg %Total Avg %Total counts %Total Avg %Total counts %Total 0: Main Stage: 2.0315e+02 100.0% 3.5336e+11 100.0% 1.251e+06 100.0% 9.141e+03 100.0% 1.373e+03 99.9% ------------------------------------------------------------------------------------------------------------------------ See the 'Profiling' chapter of the users' manual for details on interpreting output. Phase summary info: Count: number of times phase was executed Time and Flops: Max - maximum over all processors Ratio - ratio of maximum to minimum over all processors Mess: number of messages sent Avg. len: average message length Reduct: number of global reductions Global: entire computation Stage: stages of a computation. Set stages with PetscLogStagePush() and PetscLogStagePop(). %T - percent time in this phase %f - percent flops in this phase %M - percent messages in this phase %L - percent message lengths in this phase %R - percent reductions in this phase Total Mflop/s: 10e-6 * (sum of flops over all processors)/(max time over all processors) ------------------------------------------------------------------------------------------------------------------------ Event Count Time (sec) Flops --- Global --- --- Stage --- Total Max Ratio Max Ratio Max Ratio Mess Avg len Reduct %T %f %M %L %R %T %f %M %L %R Mflop/s ------------------------------------------------------------------------------------------------------------------------ --- Event Stage 0: Main Stage MatMult 740 1.0 4.1607e+00 1.3 2.25e+09 1.5 1.2e+06 8.7e+03 0.0e+00 2 68 97 92 0 2 68 97 92 0 57719 MatConvert 2 1.0 8.6766e-02 1.6 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 MatAssemblyBegin 12 1.0 2.0412e-01 6.1 0.00e+00 0.0 9.5e+03 7.5e+04 1.6e+01 0 0 1 6 1 0 0 1 6 1 0 MatAssemblyEnd 12 1.0 2.3422e-01 1.1 0.00e+00 0.0 2.3e+04 2.2e+03 6.8e+01 0 0 2 0 5 0 0 2 0 5 0 MatGetRowIJ 4 1.0 1.6210e-03147.8 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecMDot 100 1.0 6.7637e-01 2.2 2.96e+08 1.3 0.0e+00 0.0e+00 1.0e+02 0 9 0 0 7 0 9 0 0 7 49366 VecTDot 335 1.0 4.2665e-02 2.9 3.05e+06 1.6 0.0e+00 0.0e+00 3.4e+02 0 0 0 0 24 0 0 0 0 24 7360 VecNorm 510 1.0 8.5397e-01 2.7 4.51e+07 1.3 0.0e+00 0.0e+00 5.1e+02 0 1 0 0 37 0 1 0 0 37 5940 VecScale 205 1.0 1.3045e-02 1.4 1.12e+07 1.3 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 96270 VecCopy 201 1.0 3.9065e-02 1.4 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecSet 412 1.0 7.5919e-02 1.4 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecAXPY 405 1.0 6.7209e-02 1.4 4.19e+07 1.3 0.0e+00 0.0e+00 0.0e+00 0 1 0 0 0 0 1 0 0 0 70318 VecAYPX 234 1.0 3.8888e-02 2.6 1.10e+07 1.3 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 31905 VecWAXPY 5 1.0 2.6548e-03 2.7 5.10e+05 1.3 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 21685 VecMAXPY 201 1.0 8.4197e-01 1.3 5.93e+08 1.3 0.0e+00 0.0e+00 0.0e+00 0 19 0 0 0 0 19 0 0 0 79587 VecAssemblyBegin 4 1.0 3.6471e-02 5.6 0.00e+00 0.0 1.6e+03 1.5e+04 1.2e+01 0 0 0 0 1 0 0 0 0 1 0 VecAssemblyEnd 4 1.0 1.4598e-03 2.5 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecPointwiseMult 302 1.0 4.0665e-03 1.6 1.37e+06 1.6 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 34811 VecScatterBegin 1140 1.0 2.3255e-01 1.8 0.00e+00 0.0 1.2e+06 8.7e+03 0.0e+00 0 0 97 92 0 0 0 97 92 0 0 VecScatterEnd 1140 1.0 1.2122e+0014.5 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecNormalize 1 1.0 2.7853e-01 1.0 3.06e+05 1.3 0.0e+00 0.0e+00 1.0e+00 0 0 0 0 0 0 0 0 0 0 124 KSPGMRESOrthog 100 1.0 1.0198e+00 1.5 5.91e+08 1.3 0.0e+00 0.0e+00 1.0e+02 0 19 0 0 7 0 19 0 0 7 65484 KSPSetUp 5 1.0 1.4089e-02 1.2 0.00e+00 0.0 0.0e+00 0.0e+00 4.0e+00 0 0 0 0 0 0 0 0 0 0 0 KSPSolve 1 1.0 1.7274e+02 1.0 3.24e+09 1.4 1.2e+06 8.7e+03 1.2e+03 85100 97 92 84 85100 97 92 84 2040 PCSetUp 5 1.0 3.0170e+01 1.0 0.00e+00 0.0 1.0e+04 1.2e+04 1.3e+02 15 0 1 1 9 15 0 1 1 9 0 PCApply 100 1.0 1.6804e+02 1.0 4.04e+08 1.5 8.7e+05 4.4e+03 8.5e+02 83 12 70 33 62 83 12 70 33 62 250 ------------------------------------------------------------------------------------------------------------------------ Memory usage is given in bytes: Object Type Creations Destructions Memory Descendants' Mem. Reports information only for process 0. --- Event Stage 0: Main Stage Matrix 29 29 128412168 0 Matrix Null Space 3 3 1756 0 Vector 415 408 182178800 0 Vector Scatter 10 10 10360 0 Index Set 26 26 266496 0 Krylov Solver 8 7 25864 0 Preconditioner 8 7 6192 0 Viewer 1 0 0 0 ======================================================================================================================== Average time to get PetscTime(): 1.19209e-07 Average time for MPI_Barrier(): 2.90394e-05 Average time for zero size MPI_Send(): 1.24779e-05 #PETSc Option Table entries: -log_summary -ns_ksp_max_it 100 #End of PETSc Option Table entries Compiled without FORTRAN kernels Compiled with full precision matrices (default) sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 sizeof(PetscScalar) 8 sizeof(PetscInt) 4 Configure run at: Wed Oct 31 15:22:38 2012 Configure options: --known-level1-dcache-size=32768 --known-level1-dcache-linesize=64 --known-level1-dcache-assoc=8 --known-memcmp-ok=1 --known-sizeof-char=1 --known-sizeof-void-p=8 --known-sizeof-short=2 --known-sizeof-int=4 --known-sizeof-long=8 --known-sizeof-long-long=8 --known-sizeof-float=4 --known-sizeof-double=8 --known-sizeof-size_t=8 --known-bits-per-byte=8 --known-sizeof-MPI_Comm=4 --known-sizeof-MPI_Fint=4 --known-mpi-long-double=1 --prefix=/lustre/jhome22/hdr06/hdr060/petsc/install/petsc-dev-opt --with-batch=1 --with-blacs-include=/usr/local/intel/mkl/10.2.5.035/include --with-blacs-lib="-L/usr/local/intel/mkl/10.2.5.035/lib/em64t -lmkl_blacs_intelmpi_lp64 -lmkl_core" --with-blas-lapack-lib="-L/usr/local/intel/mkl/10.2.5.035/lib/em64t -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread" --with-c++-support --with-cc=mpicc --with-clanguage=cxx --with-cxx=mpicxx --with-debugging=1 --with-fc=mpif90 --with-scalapack-include=/usr/local/intel/mkl/10.2.5.035/include --with-scalapack-lib="-L/usr/local/intel/mkl/10.2.5.035/lib/em64t -lmkl_scalapack_lp64 -lmkl_core" --with-x=0 --known-mpi-shared-libraries=0 --download-hypre --download-metis --download-mumps --download-parmetis --download-superlu --download-superlu_dist --download-umfpack --with-debugging=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 ----------------------------------------- Libraries compiled on Wed Oct 31 15:22:38 2012 on jj28l05 Machine characteristics: Linux-2.6.32.59-0.3-default-x86_64-with-SuSE-11-x86_64 Using PETSc directory: /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev Using PETSc arch: arch-linux2-cxx-opt ----------------------------------------- Using C compiler: mpicxx -wd1572 -O3 ${COPTFLAGS} ${CFLAGS} Using Fortran compiler: mpif90 -O3 ${FOPTFLAGS} ${FFLAGS} ----------------------------------------- Using include paths: -I/lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/arch-linux2-cxx-opt/include -I/lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/include -I/lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/include -I/lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/arch-linux2-cxx-opt/include -I/lustre/jsoft/usr_local/parastation/mpi2-intel-5.0.26-1/include ----------------------------------------- Using C linker: mpicxx Using Fortran linker: mpif90 Using libraries: -Wl,-rpath,/lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/arch-linux2-cxx-opt/lib -L/lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/arch-linux2-cxx-opt/lib -lpetsc -Wl,-rpath,/lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/arch-linux2-cxx-opt/lib -L/lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/arch-linux2-cxx-opt/lib -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -L/usr/local/intel/mkl/10.2.5.035/lib/em64t -lmkl_scalapack_lp64 -lmkl_core -lmkl_blacs_intelmpi_lp64 -lmkl_core -lsuperlu_dist_3.1 -lparmetis -lmetis -lsuperlu_4.3 -lHYPRE -lpthread -lumfpack -lamd -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -L/lustre/jsoft/usr_local/parastation/mpi2-intel-5.0.26-1/lib -L/opt/parastation/lib64 -L/usr/local/intel/Compiler/11.1/072/lib/intel64 -L/usr/lib64/gcc/x86_64-suse-linux/4.3 -L/usr/x86_64-suse-linux/lib -lmpichf90 -Wl,-rpath,/lustre/jsoft/usr_local/parastation/mpi2-intel-5.0.26-1/lib -Wl,-rpath,/opt/parastation/lib64 -lifport -lifcore -lm -lm -lmpichcxx -lstdc++ -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lpthread -lpscom -lrt -limf -lsvml -lipgo -ldecimal -lgcc_s -lirc -lirc_s -ldl ----------------------------------------- From bsmith at mcs.anl.gov Mon Nov 19 07:45:28 2012 From: bsmith at mcs.anl.gov (Barry Smith) Date: Mon, 19 Nov 2012 07:45:28 -0600 Subject: [petsc-users] Creating PCFieldSplit Preconditioner in source code In-Reply-To: <50A9DFE7.9030407@tu-dresden.de> References: <50A9DFE7.9030407@tu-dresden.de> Message-ID: On Nov 19, 2012, at 1:29 AM, Thomas Witkowski wrote: > In the implementation of my Navier-Stokes solver, I initialize the PCFieldSplit preconditioner in my source code (thus not on the command line) in the following way: > > PCSetType(pc, PCFIELDSPLIT); > PCFieldSplitSetType(pc, PC_COMPOSITE_SCHUR); > PCFieldSplitSetSchurFactType(pc, PC_FIELDSPLIT_SCHUR_FACT_FULL); > ... > KSPSetUp(ksp); > KSP *subKsp; > PetscInt nSubKsp; > PCFieldSplitGetSubKSP(pc, &nSubKsp, &subKsp); > KSP kspVelocity = subKsp[0]; > KSP kspSchur = subKsp[1]; > ... > > And then kspVelocity and kspSchur are filled with appropriate options. The point is now, that to get the sub solver objects, I have to run KSPSetUp before. In this case, the sub solver objects are also initialized with some predefined options (block jacobi ILU), which I don't need and what takes some time and memory. These are just little stubs, they don't take but a trivial amount of memory and time to create they are not complete solvers so you shouldn't worry about them. Barry > Is there any other way to get the sub solver objects before and to initialize than the outer solver correctly with the inner solver I have specified? > > > Thomas From thomas.witkowski at tu-dresden.de Mon Nov 19 07:48:36 2012 From: thomas.witkowski at tu-dresden.de (Thomas Witkowski) Date: Mon, 19 Nov 2012 14:48:36 +0100 Subject: [petsc-users] Creating PCFieldSplit Preconditioner in source code In-Reply-To: References: <50A9DFE7.9030407@tu-dresden.de> Message-ID: <50AA38B4.1040606@tu-dresden.de> Am 19.11.2012 14:45, schrieb Barry Smith: > On Nov 19, 2012, at 1:29 AM, Thomas Witkowski wrote: > >> In the implementation of my Navier-Stokes solver, I initialize the PCFieldSplit preconditioner in my source code (thus not on the command line) in the following way: >> >> PCSetType(pc, PCFIELDSPLIT); >> PCFieldSplitSetType(pc, PC_COMPOSITE_SCHUR); >> PCFieldSplitSetSchurFactType(pc, PC_FIELDSPLIT_SCHUR_FACT_FULL); >> ... >> KSPSetUp(ksp); >> KSP *subKsp; >> PetscInt nSubKsp; >> PCFieldSplitGetSubKSP(pc, &nSubKsp, &subKsp); >> KSP kspVelocity = subKsp[0]; >> KSP kspSchur = subKsp[1]; >> ... >> >> And then kspVelocity and kspSchur are filled with appropriate options. The point is now, that to get the sub solver objects, I have to run KSPSetUp before. In this case, the sub solver objects are also initialized with some predefined options (block jacobi ILU), which I don't need and what takes some time and memory. > These are just little stubs, they don't take but a trivial amount of memory and time to create they are not complete solvers so you shouldn't worry about them. > > Barry > Just the KSPSetUp takes 4 to 5 seconds, for no computation at all. I don't think, this is negligible. It destroys my parallel scaling of initializing the solver. > >> Is there any other way to get the sub solver objects before and to initialize than the outer solver correctly with the inner solver I have specified? >> >> >> Thomas From knepley at gmail.com Mon Nov 19 07:56:31 2012 From: knepley at gmail.com (Matthew Knepley) Date: Mon, 19 Nov 2012 08:56:31 -0500 Subject: [petsc-users] KSPSetUp does not scale In-Reply-To: <50AA36B3.8050905@tu-dresden.de> References: <50AA0968.7050401@tu-dresden.de> <50AA27D9.6020305@tu-dresden.de> <50AA36B3.8050905@tu-dresden.de> Message-ID: On Mon, Nov 19, 2012 at 8:40 AM, Thomas Witkowski wrote: > Here are the two files. In this case, maybe you can also give me some hints, > why the solver at all does not scale here. The solver runtime for 64 cores > is 206 seconds, with the same problem size on 128 cores it takes 172 > seconds. The number of inner and outer solver iterations are the same for > both runs. I use CG with jacobi-preconditioner and hypre boomeramg for inner > solver. This appears to have nothing at all to do with SetUp(). You have 64 procs PCSetUp 5 1.0 3.2241e+01 1.0 0.00e+00 0.0 4.6e+03 2.6e+04 1.3e+02 12 0 1 1 10 12 0 1 1 10 0 KSPSolve 1 1.0 2.0766e+02 1.0 6.16e+09 1.3 5.1e+05 1.7e+04 1.1e+03 78100 97 92 83 78100 97 92 84 1698 PCApply 100 1.0 1.9821e+02 1.0 7.54e+08 1.4 3.6e+05 8.4e+03 8.1e+02 75 12 69 33 61 75 12 69 33 61 210 128 procs PCSetUp 5 1.0 3.0170e+01 1.0 0.00e+00 0.0 1.0e+04 1.2e+04 1.3e+02 15 0 1 1 9 15 0 1 1 9 0 KSPSolve 1 1.0 1.7274e+02 1.0 3.24e+09 1.4 1.2e+06 8.7e+03 1.2e+03 85100 97 92 84 85100 97 92 84 2040 PCApply 100 1.0 1.6804e+02 1.0 4.04e+08 1.5 8.7e+05 4.4e+03 8.5e+02 83 12 70 33 62 83 12 70 33 62 250 The PCApply time is the nonscalable part, and it all Hypre it looks like. Matt > Am 19.11.2012 13:41, schrieb Jed Brown: > > Just have it do one or a few iterations. > > > On Mon, Nov 19, 2012 at 1:36 PM, Thomas Witkowski > wrote: >> >> I can do this! Should I stop the run after KSPSetUp? Or do you want to see >> the log_summary file from the whole run? >> >> Thomas >> >> Am 19.11.2012 13:33, schrieb Jed Brown: >> >> Always, always, always send -log_summary when asking about performance. >> >> >> On Mon, Nov 19, 2012 at 11:26 AM, Thomas Witkowski >> wrote: >>> >>> I have some scaling problem in KSPSetUp, maybe some of you can help me to >>> fix it. It takes 4.5 seconds on 64 cores, and 4.0 cores on 128 cores. The >>> matrix has around 11 million rows and is not perfectly balanced, but the >>> number of maximum rows per core in the 128 cases is exactly halfe of the >>> number in the case when using 64 cores. Besides the scaling, why does the >>> setup takes so long? I though that just some objects are created but no >>> calculation is going on! >>> >>> The KSPView on the corresponding solver objects is as follows: >>> >>> KSP Object:(ns_) 64 MPI processes >>> type: fgmres >>> GMRES: restart=30, using Classical (unmodified) Gram-Schmidt >>> Orthogonalization with no iterative refinement >>> GMRES: happy breakdown tolerance 1e-30 >>> maximum iterations=100, initial guess is zero >>> tolerances: relative=1e-06, absolute=1e-08, divergence=10000 >>> right preconditioning >>> has attached null space >>> using UNPRECONDITIONED norm type for convergence test >>> PC Object:(ns_) 64 MPI processes >>> type: fieldsplit >>> FieldSplit with Schur preconditioner, factorization FULL >>> Preconditioner for the Schur complement formed from the block >>> diagonal part of A11 >>> Split info: >>> Split number 0 Defined by IS >>> Split number 1 Defined by IS >>> KSP solver for A00 block >>> KSP Object: (ns_fieldsplit_velocity_) 64 MPI processes >>> type: preonly >>> maximum iterations=10000, initial guess is zero >>> tolerances: relative=1e-05, absolute=1e-50, divergence=10000 >>> left preconditioning >>> using DEFAULT norm type for convergence test >>> PC Object: (ns_fieldsplit_velocity_) 64 MPI processes >>> type: none >>> linear system matrix = precond matrix: >>> Matrix Object: 64 MPI processes >>> type: mpiaij >>> rows=11068107, cols=11068107 >>> total: nonzeros=315206535, allocated nonzeros=315206535 >>> total number of mallocs used during MatSetValues calls =0 >>> not using I-node (on process 0) routines >>> KSP solver for S = A11 - A10 inv(A00) A01 >>> KSP Object: (ns_fieldsplit_pressure_) 64 MPI processes >>> type: gmres >>> GMRES: restart=30, using Classical (unmodified) Gram-Schmidt >>> Orthogonalization with no iterative refinement >>> GMRES: happy breakdown tolerance 1e-30 >>> maximum iterations=10000, initial guess is zero >>> tolerances: relative=1e-05, absolute=1e-50, divergence=10000 >>> left preconditioning >>> using DEFAULT norm type for convergence test >>> PC Object: (ns_fieldsplit_pressure_) 64 MPI processes >>> type: none >>> linear system matrix followed by preconditioner matrix: >>> Matrix Object: 64 MPI processes >>> type: schurcomplement >>> rows=469678, cols=469678 >>> Schur complement A11 - A10 inv(A00) A01 >>> A11 >>> Matrix Object: 64 MPI processes >>> type: mpiaij >>> rows=469678, cols=469678 >>> total: nonzeros=0, allocated nonzeros=0 >>> total number of mallocs used during MatSetValues calls =0 >>> using I-node (on process 0) routines: found 1304 nodes, >>> limit used is 5 >>> A10 >>> Matrix Object: 64 MPI processes >>> type: mpiaij >>> rows=469678, cols=11068107 >>> total: nonzeros=89122957, allocated nonzeros=89122957 >>> total number of mallocs used during MatSetValues calls =0 >>> not using I-node (on process 0) routines >>> KSP of A00 >>> KSP Object: (ns_fieldsplit_velocity_) 64 MPI >>> processes >>> type: preonly >>> maximum iterations=10000, initial guess is zero >>> tolerances: relative=1e-05, absolute=1e-50, >>> divergence=10000 >>> left preconditioning >>> using DEFAULT norm type for convergence test >>> PC Object: (ns_fieldsplit_velocity_) 64 MPI >>> processes >>> type: none >>> linear system matrix = precond matrix: >>> Matrix Object: 64 MPI processes >>> type: mpiaij >>> rows=11068107, cols=11068107 >>> total: nonzeros=315206535, allocated nonzeros=315206535 >>> total number of mallocs used during MatSetValues calls >>> =0 >>> not using I-node (on process 0) routines >>> A01 >>> Matrix Object: 64 MPI processes >>> type: mpiaij >>> rows=11068107, cols=469678 >>> total: nonzeros=88821041, allocated nonzeros=88821041 >>> total number of mallocs used during MatSetValues calls =0 >>> not using I-node (on process 0) routines >>> Matrix Object: 64 MPI processes >>> type: mpiaij >>> rows=469678, cols=469678 >>> total: nonzeros=0, allocated nonzeros=0 >>> total number of mallocs used during MatSetValues calls =0 >>> using I-node (on process 0) routines: found 1304 nodes, limit >>> used is 5 >>> linear system matrix = precond matrix: >>> Matrix Object: 64 MPI processes >>> type: mpiaij >>> rows=11537785, cols=11537785 >>> total: nonzeros=493150533, allocated nonzeros=510309207 >>> total number of mallocs used during MatSetValues calls =0 >>> not using I-node (on process 0) routines >>> >>> >>> >>> >>> Thomas >> >> >> > > -- 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 From knepley at gmail.com Mon Nov 19 07:57:34 2012 From: knepley at gmail.com (Matthew Knepley) Date: Mon, 19 Nov 2012 08:57:34 -0500 Subject: [petsc-users] Creating PCFieldSplit Preconditioner in source code In-Reply-To: <50AA38B4.1040606@tu-dresden.de> References: <50A9DFE7.9030407@tu-dresden.de> <50AA38B4.1040606@tu-dresden.de> Message-ID: On Mon, Nov 19, 2012 at 8:48 AM, Thomas Witkowski wrote: > Am 19.11.2012 14:45, schrieb Barry Smith: > >> On Nov 19, 2012, at 1:29 AM, Thomas Witkowski >> wrote: >> >>> In the implementation of my Navier-Stokes solver, I initialize the >>> PCFieldSplit preconditioner in my source code (thus not on the command line) >>> in the following way: >>> >>> PCSetType(pc, PCFIELDSPLIT); >>> PCFieldSplitSetType(pc, PC_COMPOSITE_SCHUR); >>> PCFieldSplitSetSchurFactType(pc, PC_FIELDSPLIT_SCHUR_FACT_FULL); >>> ... >>> KSPSetUp(ksp); >>> KSP *subKsp; >>> PetscInt nSubKsp; >>> PCFieldSplitGetSubKSP(pc, &nSubKsp, &subKsp); >>> KSP kspVelocity = subKsp[0]; >>> KSP kspSchur = subKsp[1]; >>> ... >>> >>> And then kspVelocity and kspSchur are filled with appropriate options. >>> The point is now, that to get the sub solver objects, I have to run KSPSetUp >>> before. In this case, the sub solver objects are also initialized with some >>> predefined options (block jacobi ILU), which I don't need and what takes >>> some time and memory. >> >> These are just little stubs, they don't take but a trivial amount of >> memory and time to create they are not complete solvers so you shouldn't >> worry about them. >> >> Barry >> > Just the KSPSetUp takes 4 to 5 seconds, for no computation at all. I don't > think, this is negligible. It destroys my parallel scaling of initializing > the solver. You are wrong. Read my latest reply. Matt >> >>> Is there any other way to get the sub solver objects before and to >>> initialize than the outer solver correctly with the inner solver I have >>> specified? >>> >>> >>> Thomas > > -- 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 From thomas.witkowski at tu-dresden.de Mon Nov 19 08:47:24 2012 From: thomas.witkowski at tu-dresden.de (Thomas Witkowski) Date: Mon, 19 Nov 2012 15:47:24 +0100 Subject: [petsc-users] KSPSetUp does not scale In-Reply-To: References: <50AA0968.7050401@tu-dresden.de> <50AA27D9.6020305@tu-dresden.de> <50AA36B3.8050905@tu-dresden.de> Message-ID: <50AA467C.5020309@tu-dresden.de> Your assumption is right. A removed the Hypre preconditioner with an iterative non-preconditioned solver. The solver is now much slower, but it scales. But, even in this case, the KSPSetUp takes 4.5 seconds on 64 cores and 3.8 seconds on 128 cores! Thomas Am 19.11.2012 14:56, schrieb Matthew Knepley: > On Mon, Nov 19, 2012 at 8:40 AM, Thomas Witkowski > wrote: >> Here are the two files. In this case, maybe you can also give me some hints, >> why the solver at all does not scale here. The solver runtime for 64 cores >> is 206 seconds, with the same problem size on 128 cores it takes 172 >> seconds. The number of inner and outer solver iterations are the same for >> both runs. I use CG with jacobi-preconditioner and hypre boomeramg for inner >> solver. > This appears to have nothing at all to do with SetUp(). You have > > 64 procs > PCSetUp 5 1.0 3.2241e+01 1.0 0.00e+00 0.0 4.6e+03 > 2.6e+04 1.3e+02 12 0 1 1 10 12 0 1 1 10 0 > KSPSolve 1 1.0 2.0766e+02 1.0 6.16e+09 1.3 5.1e+05 > 1.7e+04 1.1e+03 78100 97 92 83 78100 97 92 84 1698 > PCApply 100 1.0 1.9821e+02 1.0 7.54e+08 1.4 3.6e+05 > 8.4e+03 8.1e+02 75 12 69 33 61 75 12 69 33 61 210 > > 128 procs > PCSetUp 5 1.0 3.0170e+01 1.0 0.00e+00 0.0 1.0e+04 > 1.2e+04 1.3e+02 15 0 1 1 9 15 0 1 1 9 0 > KSPSolve 1 1.0 1.7274e+02 1.0 3.24e+09 1.4 1.2e+06 > 8.7e+03 1.2e+03 85100 97 92 84 85100 97 92 84 2040 > PCApply 100 1.0 1.6804e+02 1.0 4.04e+08 1.5 8.7e+05 > 4.4e+03 8.5e+02 83 12 70 33 62 83 12 70 33 62 250 > > The PCApply time is the nonscalable part, and it all Hypre it looks like. > > Matt > >> Am 19.11.2012 13:41, schrieb Jed Brown: >> >> Just have it do one or a few iterations. >> >> >> On Mon, Nov 19, 2012 at 1:36 PM, Thomas Witkowski >> wrote: >>> I can do this! Should I stop the run after KSPSetUp? Or do you want to see >>> the log_summary file from the whole run? >>> >>> Thomas >>> >>> Am 19.11.2012 13:33, schrieb Jed Brown: >>> >>> Always, always, always send -log_summary when asking about performance. >>> >>> >>> On Mon, Nov 19, 2012 at 11:26 AM, Thomas Witkowski >>> wrote: >>>> I have some scaling problem in KSPSetUp, maybe some of you can help me to >>>> fix it. It takes 4.5 seconds on 64 cores, and 4.0 cores on 128 cores. The >>>> matrix has around 11 million rows and is not perfectly balanced, but the >>>> number of maximum rows per core in the 128 cases is exactly halfe of the >>>> number in the case when using 64 cores. Besides the scaling, why does the >>>> setup takes so long? I though that just some objects are created but no >>>> calculation is going on! >>>> >>>> The KSPView on the corresponding solver objects is as follows: >>>> >>>> KSP Object:(ns_) 64 MPI processes >>>> type: fgmres >>>> GMRES: restart=30, using Classical (unmodified) Gram-Schmidt >>>> Orthogonalization with no iterative refinement >>>> GMRES: happy breakdown tolerance 1e-30 >>>> maximum iterations=100, initial guess is zero >>>> tolerances: relative=1e-06, absolute=1e-08, divergence=10000 >>>> right preconditioning >>>> has attached null space >>>> using UNPRECONDITIONED norm type for convergence test >>>> PC Object:(ns_) 64 MPI processes >>>> type: fieldsplit >>>> FieldSplit with Schur preconditioner, factorization FULL >>>> Preconditioner for the Schur complement formed from the block >>>> diagonal part of A11 >>>> Split info: >>>> Split number 0 Defined by IS >>>> Split number 1 Defined by IS >>>> KSP solver for A00 block >>>> KSP Object: (ns_fieldsplit_velocity_) 64 MPI processes >>>> type: preonly >>>> maximum iterations=10000, initial guess is zero >>>> tolerances: relative=1e-05, absolute=1e-50, divergence=10000 >>>> left preconditioning >>>> using DEFAULT norm type for convergence test >>>> PC Object: (ns_fieldsplit_velocity_) 64 MPI processes >>>> type: none >>>> linear system matrix = precond matrix: >>>> Matrix Object: 64 MPI processes >>>> type: mpiaij >>>> rows=11068107, cols=11068107 >>>> total: nonzeros=315206535, allocated nonzeros=315206535 >>>> total number of mallocs used during MatSetValues calls =0 >>>> not using I-node (on process 0) routines >>>> KSP solver for S = A11 - A10 inv(A00) A01 >>>> KSP Object: (ns_fieldsplit_pressure_) 64 MPI processes >>>> type: gmres >>>> GMRES: restart=30, using Classical (unmodified) Gram-Schmidt >>>> Orthogonalization with no iterative refinement >>>> GMRES: happy breakdown tolerance 1e-30 >>>> maximum iterations=10000, initial guess is zero >>>> tolerances: relative=1e-05, absolute=1e-50, divergence=10000 >>>> left preconditioning >>>> using DEFAULT norm type for convergence test >>>> PC Object: (ns_fieldsplit_pressure_) 64 MPI processes >>>> type: none >>>> linear system matrix followed by preconditioner matrix: >>>> Matrix Object: 64 MPI processes >>>> type: schurcomplement >>>> rows=469678, cols=469678 >>>> Schur complement A11 - A10 inv(A00) A01 >>>> A11 >>>> Matrix Object: 64 MPI processes >>>> type: mpiaij >>>> rows=469678, cols=469678 >>>> total: nonzeros=0, allocated nonzeros=0 >>>> total number of mallocs used during MatSetValues calls =0 >>>> using I-node (on process 0) routines: found 1304 nodes, >>>> limit used is 5 >>>> A10 >>>> Matrix Object: 64 MPI processes >>>> type: mpiaij >>>> rows=469678, cols=11068107 >>>> total: nonzeros=89122957, allocated nonzeros=89122957 >>>> total number of mallocs used during MatSetValues calls =0 >>>> not using I-node (on process 0) routines >>>> KSP of A00 >>>> KSP Object: (ns_fieldsplit_velocity_) 64 MPI >>>> processes >>>> type: preonly >>>> maximum iterations=10000, initial guess is zero >>>> tolerances: relative=1e-05, absolute=1e-50, >>>> divergence=10000 >>>> left preconditioning >>>> using DEFAULT norm type for convergence test >>>> PC Object: (ns_fieldsplit_velocity_) 64 MPI >>>> processes >>>> type: none >>>> linear system matrix = precond matrix: >>>> Matrix Object: 64 MPI processes >>>> type: mpiaij >>>> rows=11068107, cols=11068107 >>>> total: nonzeros=315206535, allocated nonzeros=315206535 >>>> total number of mallocs used during MatSetValues calls >>>> =0 >>>> not using I-node (on process 0) routines >>>> A01 >>>> Matrix Object: 64 MPI processes >>>> type: mpiaij >>>> rows=11068107, cols=469678 >>>> total: nonzeros=88821041, allocated nonzeros=88821041 >>>> total number of mallocs used during MatSetValues calls =0 >>>> not using I-node (on process 0) routines >>>> Matrix Object: 64 MPI processes >>>> type: mpiaij >>>> rows=469678, cols=469678 >>>> total: nonzeros=0, allocated nonzeros=0 >>>> total number of mallocs used during MatSetValues calls =0 >>>> using I-node (on process 0) routines: found 1304 nodes, limit >>>> used is 5 >>>> linear system matrix = precond matrix: >>>> Matrix Object: 64 MPI processes >>>> type: mpiaij >>>> rows=11537785, cols=11537785 >>>> total: nonzeros=493150533, allocated nonzeros=510309207 >>>> total number of mallocs used during MatSetValues calls =0 >>>> not using I-node (on process 0) routines >>>> >>>> >>>> >>>> >>>> Thomas >>> >>> >> > > > -- > 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 From bsmith at mcs.anl.gov Mon Nov 19 11:26:20 2012 From: bsmith at mcs.anl.gov (Barry Smith) Date: Mon, 19 Nov 2012 11:26:20 -0600 Subject: [petsc-users] KSPSetUp does not scale In-Reply-To: <50AA467C.5020309@tu-dresden.de> References: <50AA0968.7050401@tu-dresden.de> <50AA27D9.6020305@tu-dresden.de> <50AA36B3.8050905@tu-dresden.de> <50AA467C.5020309@tu-dresden.de> Message-ID: <486777F2-15D0-46C6-A397-3E9F65E72B4D@mcs.anl.gov> On Nov 19, 2012, at 8:47 AM, Thomas Witkowski wrote: > Your assumption is right. A removed the Hypre preconditioner with an iterative non-preconditioned solver. The solver is now much slower, but it scales. > > But, even in this case, the KSPSetUp takes 4.5 seconds on 64 cores and 3.8 seconds on 128 cores! What is it setting up? It is definitely NOT suppose to be setting up some preconditioner and then immediately destroying it and setting up a different one; if it is doing that then it is our bug. Barry > > Thomas > > Am 19.11.2012 14:56, schrieb Matthew Knepley: >> On Mon, Nov 19, 2012 at 8:40 AM, Thomas Witkowski >> wrote: >>> Here are the two files. In this case, maybe you can also give me some hints, >>> why the solver at all does not scale here. The solver runtime for 64 cores >>> is 206 seconds, with the same problem size on 128 cores it takes 172 >>> seconds. The number of inner and outer solver iterations are the same for >>> both runs. I use CG with jacobi-preconditioner and hypre boomeramg for inner >>> solver. >> This appears to have nothing at all to do with SetUp(). You have >> >> 64 procs >> PCSetUp 5 1.0 3.2241e+01 1.0 0.00e+00 0.0 4.6e+03 >> 2.6e+04 1.3e+02 12 0 1 1 10 12 0 1 1 10 0 >> KSPSolve 1 1.0 2.0766e+02 1.0 6.16e+09 1.3 5.1e+05 >> 1.7e+04 1.1e+03 78100 97 92 83 78100 97 92 84 1698 >> PCApply 100 1.0 1.9821e+02 1.0 7.54e+08 1.4 3.6e+05 >> 8.4e+03 8.1e+02 75 12 69 33 61 75 12 69 33 61 210 >> >> 128 procs >> PCSetUp 5 1.0 3.0170e+01 1.0 0.00e+00 0.0 1.0e+04 >> 1.2e+04 1.3e+02 15 0 1 1 9 15 0 1 1 9 0 >> KSPSolve 1 1.0 1.7274e+02 1.0 3.24e+09 1.4 1.2e+06 >> 8.7e+03 1.2e+03 85100 97 92 84 85100 97 92 84 2040 >> PCApply 100 1.0 1.6804e+02 1.0 4.04e+08 1.5 8.7e+05 >> 4.4e+03 8.5e+02 83 12 70 33 62 83 12 70 33 62 250 >> >> The PCApply time is the nonscalable part, and it all Hypre it looks like. >> >> Matt >> >>> Am 19.11.2012 13:41, schrieb Jed Brown: >>> >>> Just have it do one or a few iterations. >>> >>> >>> On Mon, Nov 19, 2012 at 1:36 PM, Thomas Witkowski >>> wrote: >>>> I can do this! Should I stop the run after KSPSetUp? Or do you want to see >>>> the log_summary file from the whole run? >>>> >>>> Thomas >>>> >>>> Am 19.11.2012 13:33, schrieb Jed Brown: >>>> >>>> Always, always, always send -log_summary when asking about performance. >>>> >>>> >>>> On Mon, Nov 19, 2012 at 11:26 AM, Thomas Witkowski >>>> wrote: >>>>> I have some scaling problem in KSPSetUp, maybe some of you can help me to >>>>> fix it. It takes 4.5 seconds on 64 cores, and 4.0 cores on 128 cores. The >>>>> matrix has around 11 million rows and is not perfectly balanced, but the >>>>> number of maximum rows per core in the 128 cases is exactly halfe of the >>>>> number in the case when using 64 cores. Besides the scaling, why does the >>>>> setup takes so long? I though that just some objects are created but no >>>>> calculation is going on! >>>>> >>>>> The KSPView on the corresponding solver objects is as follows: >>>>> >>>>> KSP Object:(ns_) 64 MPI processes >>>>> type: fgmres >>>>> GMRES: restart=30, using Classical (unmodified) Gram-Schmidt >>>>> Orthogonalization with no iterative refinement >>>>> GMRES: happy breakdown tolerance 1e-30 >>>>> maximum iterations=100, initial guess is zero >>>>> tolerances: relative=1e-06, absolute=1e-08, divergence=10000 >>>>> right preconditioning >>>>> has attached null space >>>>> using UNPRECONDITIONED norm type for convergence test >>>>> PC Object:(ns_) 64 MPI processes >>>>> type: fieldsplit >>>>> FieldSplit with Schur preconditioner, factorization FULL >>>>> Preconditioner for the Schur complement formed from the block >>>>> diagonal part of A11 >>>>> Split info: >>>>> Split number 0 Defined by IS >>>>> Split number 1 Defined by IS >>>>> KSP solver for A00 block >>>>> KSP Object: (ns_fieldsplit_velocity_) 64 MPI processes >>>>> type: preonly >>>>> maximum iterations=10000, initial guess is zero >>>>> tolerances: relative=1e-05, absolute=1e-50, divergence=10000 >>>>> left preconditioning >>>>> using DEFAULT norm type for convergence test >>>>> PC Object: (ns_fieldsplit_velocity_) 64 MPI processes >>>>> type: none >>>>> linear system matrix = precond matrix: >>>>> Matrix Object: 64 MPI processes >>>>> type: mpiaij >>>>> rows=11068107, cols=11068107 >>>>> total: nonzeros=315206535, allocated nonzeros=315206535 >>>>> total number of mallocs used during MatSetValues calls =0 >>>>> not using I-node (on process 0) routines >>>>> KSP solver for S = A11 - A10 inv(A00) A01 >>>>> KSP Object: (ns_fieldsplit_pressure_) 64 MPI processes >>>>> type: gmres >>>>> GMRES: restart=30, using Classical (unmodified) Gram-Schmidt >>>>> Orthogonalization with no iterative refinement >>>>> GMRES: happy breakdown tolerance 1e-30 >>>>> maximum iterations=10000, initial guess is zero >>>>> tolerances: relative=1e-05, absolute=1e-50, divergence=10000 >>>>> left preconditioning >>>>> using DEFAULT norm type for convergence test >>>>> PC Object: (ns_fieldsplit_pressure_) 64 MPI processes >>>>> type: none >>>>> linear system matrix followed by preconditioner matrix: >>>>> Matrix Object: 64 MPI processes >>>>> type: schurcomplement >>>>> rows=469678, cols=469678 >>>>> Schur complement A11 - A10 inv(A00) A01 >>>>> A11 >>>>> Matrix Object: 64 MPI processes >>>>> type: mpiaij >>>>> rows=469678, cols=469678 >>>>> total: nonzeros=0, allocated nonzeros=0 >>>>> total number of mallocs used during MatSetValues calls =0 >>>>> using I-node (on process 0) routines: found 1304 nodes, >>>>> limit used is 5 >>>>> A10 >>>>> Matrix Object: 64 MPI processes >>>>> type: mpiaij >>>>> rows=469678, cols=11068107 >>>>> total: nonzeros=89122957, allocated nonzeros=89122957 >>>>> total number of mallocs used during MatSetValues calls =0 >>>>> not using I-node (on process 0) routines >>>>> KSP of A00 >>>>> KSP Object: (ns_fieldsplit_velocity_) 64 MPI >>>>> processes >>>>> type: preonly >>>>> maximum iterations=10000, initial guess is zero >>>>> tolerances: relative=1e-05, absolute=1e-50, >>>>> divergence=10000 >>>>> left preconditioning >>>>> using DEFAULT norm type for convergence test >>>>> PC Object: (ns_fieldsplit_velocity_) 64 MPI >>>>> processes >>>>> type: none >>>>> linear system matrix = precond matrix: >>>>> Matrix Object: 64 MPI processes >>>>> type: mpiaij >>>>> rows=11068107, cols=11068107 >>>>> total: nonzeros=315206535, allocated nonzeros=315206535 >>>>> total number of mallocs used during MatSetValues calls >>>>> =0 >>>>> not using I-node (on process 0) routines >>>>> A01 >>>>> Matrix Object: 64 MPI processes >>>>> type: mpiaij >>>>> rows=11068107, cols=469678 >>>>> total: nonzeros=88821041, allocated nonzeros=88821041 >>>>> total number of mallocs used during MatSetValues calls =0 >>>>> not using I-node (on process 0) routines >>>>> Matrix Object: 64 MPI processes >>>>> type: mpiaij >>>>> rows=469678, cols=469678 >>>>> total: nonzeros=0, allocated nonzeros=0 >>>>> total number of mallocs used during MatSetValues calls =0 >>>>> using I-node (on process 0) routines: found 1304 nodes, limit >>>>> used is 5 >>>>> linear system matrix = precond matrix: >>>>> Matrix Object: 64 MPI processes >>>>> type: mpiaij >>>>> rows=11537785, cols=11537785 >>>>> total: nonzeros=493150533, allocated nonzeros=510309207 >>>>> total number of mallocs used during MatSetValues calls =0 >>>>> not using I-node (on process 0) routines >>>>> >>>>> >>>>> >>>>> >>>>> Thomas >>>> >>>> >>> >> >> >> -- >> 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 > From fande.kong at colorado.edu Mon Nov 19 17:27:40 2012 From: fande.kong at colorado.edu (Fande Kong) Date: Mon, 19 Nov 2012 16:27:40 -0700 Subject: [petsc-users] How to read/write unstructured mesh in parallel Message-ID: Hi all, Are there functions that can be used to implement parallel read and write? -- Fande Kong Department of Computer Science University of Colorado at Boulder -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Mon Nov 19 17:32:55 2012 From: knepley at gmail.com (Matthew Knepley) Date: Mon, 19 Nov 2012 18:32:55 -0500 Subject: [petsc-users] How to read/write unstructured mesh in parallel In-Reply-To: References: Message-ID: On Mon, Nov 19, 2012 at 6:27 PM, Fande Kong wrote: > Hi all, > > Are there functions that can be used to implement parallel read and write? Now, all the reads are in serial right now. Is this a bottleneck? Matt > -- > Fande Kong > Department of Computer Science > University of Colorado at Boulder > > -- 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 From bourdin at lsu.edu Mon Nov 19 17:37:28 2012 From: bourdin at lsu.edu (Blaise A Bourdin) Date: Mon, 19 Nov 2012 23:37:28 +0000 Subject: [petsc-users] How to read/write unstructured mesh in parallel In-Reply-To: References: , Message-ID: Actually, there is _some_ support for distributed IO on exodusII files using DMMesh. I assume that porting the existing code to DMComplex would not be too difficult, but I don't have time to work on it right now. The mesh geometry initial reading is sequential, but distributed meshes and result files can be written. The caveat is that there is no interface matching, which can be a problem with some post processing functions. Blaise Sent from a mobile device On Nov 19, 2012, at 5:33 PM, "Matthew Knepley" wrote: > On Mon, Nov 19, 2012 at 6:27 PM, Fande Kong wrote: >> Hi all, >> >> Are there functions that can be used to implement parallel read and write? > > Now, all the reads are in serial right now. Is this a bottleneck? > > Matt > >> -- >> Fande Kong >> Department of Computer Science >> University of Colorado at Boulder > > > > -- > 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 > From fd.kong at siat.ac.cn Mon Nov 19 17:38:35 2012 From: fd.kong at siat.ac.cn (Fande Kong) Date: Mon, 19 Nov 2012 16:38:35 -0700 Subject: [petsc-users] How to read/write unstructured mesh in parallel In-Reply-To: References: Message-ID: I want to try very 'large' mesh. I guess it should be bottleneck. On Mon, Nov 19, 2012 at 4:32 PM, Matthew Knepley wrote: > On Mon, Nov 19, 2012 at 6:27 PM, Fande Kong > wrote: > > Hi all, > > > > Are there functions that can be used to implement parallel read and > write? > > Now, all the reads are in serial right now. Is this a bottleneck? > > Matt > > > -- > > Fande Kong > > Department of Computer Science > > University of Colorado at Boulder > > > > > > > > -- > 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 > > -- Fande Kong ShenZhen Institutes of Advanced Technology Chinese Academy of Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Mon Nov 19 17:52:04 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Tue, 20 Nov 2012 00:52:04 +0100 Subject: [petsc-users] How to read/write unstructured mesh in parallel In-Reply-To: References: Message-ID: On Tue, Nov 20, 2012 at 12:38 AM, Fande Kong wrote: > I want to try very 'large' mesh. I guess it should be bottleneck. It's really worth profiling. Having every process read directly is no more scalable (frequently less, actually) than having rank 1 read incrementally and send to whoever should own it. You can do full parallel IO, but the code depends on the mesh format. -------------- next part -------------- An HTML attachment was scrubbed... URL: From fd.kong at siat.ac.cn Mon Nov 19 18:08:16 2012 From: fd.kong at siat.ac.cn (Fande Kong) Date: Mon, 19 Nov 2012 17:08:16 -0700 Subject: [petsc-users] How to read/write unstructured mesh in parallel In-Reply-To: References: Message-ID: It seems to be a good idea. I have another related question. If all processors read the same file at the same time, would it be very slow for conflicting access? On Mon, Nov 19, 2012 at 4:52 PM, Jed Brown wrote: > On Tue, Nov 20, 2012 at 12:38 AM, Fande Kong wrote: > >> I want to try very 'large' mesh. I guess it should be bottleneck. > > > It's really worth profiling. Having every process read directly is no more > scalable (frequently less, actually) than having rank 1 read incrementally > and send to whoever should own it. You can do full parallel IO, but the > code depends on the mesh format. > -- Fande Kong ShenZhen Institutes of Advanced Technology Chinese Academy of Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Mon Nov 19 18:09:53 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Tue, 20 Nov 2012 01:09:53 +0100 Subject: [petsc-users] How to read/write unstructured mesh in parallel In-Reply-To: References: Message-ID: On Tue, Nov 20, 2012 at 1:08 AM, Fande Kong wrote: > It seems to be a good idea. I have another related question. If all > processors read the same file at the same time, would it be very slow for > conflicting access? Yes, though it's much better if you use MPI-IO collective IO. The worst is if every process reads a different file. > > > On Mon, Nov 19, 2012 at 4:52 PM, Jed Brown wrote: > >> On Tue, Nov 20, 2012 at 12:38 AM, Fande Kong wrote: >> >>> I want to try very 'large' mesh. I guess it should be bottleneck. >> >> >> It's really worth profiling. Having every process read directly is no >> more scalable (frequently less, actually) than having rank 1 read >> incrementally and send to whoever should own it. You can do full parallel >> IO, but the code depends on the mesh format. >> > > > > -- > Fande Kong > ShenZhen Institutes of Advanced Technology > Chinese Academy of Sciences > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stali at geology.wisc.edu Mon Nov 19 19:15:12 2012 From: stali at geology.wisc.edu (Tabrez Ali) Date: Mon, 19 Nov 2012 19:15:12 -0600 Subject: [petsc-users] How to read/write unstructured mesh in parallel In-Reply-To: References: Message-ID: <50AAD9A0.50104@geology.wisc.edu> I have used Fortran I/O (serial) where all processes access the same input file to read part of the mesh. For runs on 1K-4K cores it is fairly fast. For example it takes under 2 mins to read a unstructured mesh of 16 million elements (larger mesh is also fine) on 1000 cores. Though I guess its not good for the file system (Lustre) but then you're only doing it once. MPI collective I/O is supposed to be faster as smaller requests get merged into a single large one. However its binary only so you may be better off using higher level libs (HDF5/Parallel NetCDF). However it seems that after certain number of processors even that gets too slow, e.g., see sec 4.2 in the following paper http://climate.ornl.gov/~rmills/pubs/mills-PFLOTRAN_CUG2009.pdf T On 11/19/2012 06:08 PM, Fande Kong wrote: > It seems to be a good idea. I have another related question. If all > processors read the same file at the same time, would it be very slow > for conflicting access? > > On Mon, Nov 19, 2012 at 4:52 PM, Jed Brown > wrote: > > On Tue, Nov 20, 2012 at 12:38 AM, Fande Kong > wrote: > > I want to try very 'large' mesh. I guess it should be bottleneck. > > > It's really worth profiling. Having every process read directly is > no more scalable (frequently less, actually) than having rank 1 > read incrementally and send to whoever should own it. You can do > full parallel IO, but the code depends on the mesh format. > > > > > -- > Fande Kong > ShenZhen Institutes of Advanced Technology > Chinese Academy of Sciences > -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.witkowski at tu-dresden.de Tue Nov 20 00:56:40 2012 From: thomas.witkowski at tu-dresden.de (Thomas Witkowski) Date: Tue, 20 Nov 2012 07:56:40 +0100 Subject: [petsc-users] Using GAMG for solving singular systems Message-ID: <50AB29A8.9070107@tu-dresden.de> When I try to use GAMG for solviing a singular system (Laplace matrix with Neuman boundaries), it crashes with the following error: [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Detected zero pivot in LU factorization: [0]PETSC ERROR: Zero pivot row 65 value 9.19403e-17 tolerance 2.22045e-14! [0]PETSC ERROR: MatPivotCheck_none() line 585 in /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/include/petsc-private/matimpl.h [0]PETSC ERROR: MatPivotCheck() line 604 in /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/include/petsc-private/matimpl.h [0]PETSC ERROR: MatLUFactorNumeric_SeqAIJ() line 570 in /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/mat/impls/aij/seq/aijfact.c [0]PETSC ERROR: MatLUFactorNumeric() line 2862 in /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/mat/interface/matrix.c [0]PETSC ERROR: PCSetUp_LU() line 160 in /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/factor/lu/lu.c [0]PETSC ERROR: PCSetUp() line 832 in /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/interface/precon.c [0]PETSC ERROR: KSPSetUp() line 278 in /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/ksp/interface/itfunc.c [0]PETSC ERROR: PCSetUpOnBlocks_BJacobi_Singleblock() line 719 in /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/bjacobi/bjacobi.c [0]PETSC ERROR: PCSetUpOnBlocks() line 865 in /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/interface/precon.c [0]PETSC ERROR: KSPSetUpOnBlocks() line 154 in /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/ksp/interface/itfunc.c [0]PETSC ERROR: KSPSolve() line 403 in /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/ksp/interface/itfunc.c [0]PETSC ERROR: PCMGMCycle_Private() line 20 in /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/mg/mg.c [0]PETSC ERROR: PCMGMCycle_Private() line 49 in /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/mg/mg.c [0]PETSC ERROR: PCMGMCycle_Private() line 49 in /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/mg/mg.c [0]PETSC ERROR: PCMGMCycle_Private() line 49 in /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/mg/mg.c [0]PETSC ERROR: PCApplyRichardson_MG() line 104 in /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/mg/mg.c [0]PETSC ERROR: PCApplyRichardson() line 780 in /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/interface/precon.c [0]PETSC ERROR: KSPSolve_Richardson() line 69 in /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/ksp/impls/rich/rich.c [0]PETSC ERROR: KSPSolve() line 446 in /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/ksp/interface/itfunc.c How to fix this problem? I already checked the gamg options, but I have not found something what could be related to this problem. Thomas From jedbrown at mcs.anl.gov Tue Nov 20 01:19:39 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Tue, 20 Nov 2012 08:19:39 +0100 Subject: [petsc-users] Using GAMG for solving singular systems In-Reply-To: <50AB29A8.9070107@tu-dresden.de> References: <50AB29A8.9070107@tu-dresden.de> Message-ID: -mg_coarse_pc_type svd (or configure any other coarse solver that works for singular systems, including adding a shift or using an iterative method) On Tue, Nov 20, 2012 at 7:56 AM, Thomas Witkowski < thomas.witkowski at tu-dresden.de> wrote: > When I try to use GAMG for solviing a singular system (Laplace matrix with > Neuman boundaries), it crashes with the following error: > > [0]PETSC ERROR: --------------------- Error Message > ------------------------------**------ > [0]PETSC ERROR: Detected zero pivot in LU factorization: > [0]PETSC ERROR: Zero pivot row 65 value 9.19403e-17 tolerance 2.22045e-14! > [0]PETSC ERROR: MatPivotCheck_none() line 585 in > /lustre/jhome22/hdr06/hdr060/**petsc/build/petsc-dev/include/** > petsc-private/matimpl.h > [0]PETSC ERROR: MatPivotCheck() line 604 in /lustre/jhome22/hdr06/hdr060/* > *petsc/build/petsc-dev/include/**petsc-private/matimpl.h > [0]PETSC ERROR: MatLUFactorNumeric_SeqAIJ() line 570 in > /lustre/jhome22/hdr06/hdr060/**petsc/build/petsc-dev/src/mat/** > impls/aij/seq/aijfact.c > [0]PETSC ERROR: MatLUFactorNumeric() line 2862 in > /lustre/jhome22/hdr06/hdr060/**petsc/build/petsc-dev/src/mat/** > interface/matrix.c > [0]PETSC ERROR: PCSetUp_LU() line 160 in /lustre/jhome22/hdr06/hdr060/** > petsc/build/petsc-dev/src/ksp/**pc/impls/factor/lu/lu.c > [0]PETSC ERROR: PCSetUp() line 832 in /lustre/jhome22/hdr06/hdr060/** > petsc/build/petsc-dev/src/ksp/**pc/interface/precon.c > [0]PETSC ERROR: KSPSetUp() line 278 in /lustre/jhome22/hdr06/hdr060/** > petsc/build/petsc-dev/src/ksp/**ksp/interface/itfunc.c > [0]PETSC ERROR: PCSetUpOnBlocks_BJacobi_**Singleblock() line 719 in > /lustre/jhome22/hdr06/hdr060/**petsc/build/petsc-dev/src/ksp/** > pc/impls/bjacobi/bjacobi.c > [0]PETSC ERROR: PCSetUpOnBlocks() line 865 in /lustre/jhome22/hdr06/hdr060/ > **petsc/build/petsc-dev/src/ksp/**pc/interface/precon.c > [0]PETSC ERROR: KSPSetUpOnBlocks() line 154 in > /lustre/jhome22/hdr06/hdr060/**petsc/build/petsc-dev/src/ksp/** > ksp/interface/itfunc.c > [0]PETSC ERROR: KSPSolve() line 403 in /lustre/jhome22/hdr06/hdr060/** > petsc/build/petsc-dev/src/ksp/**ksp/interface/itfunc.c > [0]PETSC ERROR: PCMGMCycle_Private() line 20 in > /lustre/jhome22/hdr06/hdr060/**petsc/build/petsc-dev/src/ksp/** > pc/impls/mg/mg.c > [0]PETSC ERROR: PCMGMCycle_Private() line 49 in > /lustre/jhome22/hdr06/hdr060/**petsc/build/petsc-dev/src/ksp/** > pc/impls/mg/mg.c > [0]PETSC ERROR: PCMGMCycle_Private() line 49 in > /lustre/jhome22/hdr06/hdr060/**petsc/build/petsc-dev/src/ksp/** > pc/impls/mg/mg.c > [0]PETSC ERROR: PCMGMCycle_Private() line 49 in > /lustre/jhome22/hdr06/hdr060/**petsc/build/petsc-dev/src/ksp/** > pc/impls/mg/mg.c > [0]PETSC ERROR: PCApplyRichardson_MG() line 104 in > /lustre/jhome22/hdr06/hdr060/**petsc/build/petsc-dev/src/ksp/** > pc/impls/mg/mg.c > [0]PETSC ERROR: PCApplyRichardson() line 780 in > /lustre/jhome22/hdr06/hdr060/**petsc/build/petsc-dev/src/ksp/** > pc/interface/precon.c > [0]PETSC ERROR: KSPSolve_Richardson() line 69 in > /lustre/jhome22/hdr06/hdr060/**petsc/build/petsc-dev/src/ksp/** > ksp/impls/rich/rich.c > [0]PETSC ERROR: KSPSolve() line 446 in /lustre/jhome22/hdr06/hdr060/** > petsc/build/petsc-dev/src/ksp/**ksp/interface/itfunc.c > > How to fix this problem? I already checked the gamg options, but I have > not found something what could be related to this problem. > > Thomas > -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.witkowski at tu-dresden.de Tue Nov 20 01:22:16 2012 From: thomas.witkowski at tu-dresden.de (Thomas Witkowski) Date: Tue, 20 Nov 2012 08:22:16 +0100 Subject: [petsc-users] Using GAMG for solving singular systems In-Reply-To: References: <50AB29A8.9070107@tu-dresden.de> Message-ID: <50AB2FA8.6050408@tu-dresden.de> Which prefix must be added here? When I use "-laplace_pc_type gamg", must this parameter be set with "-laplace_mg_coarse_pc_type svd" ? Thomas Am 20.11.2012 08:19, schrieb Jed Brown: > -mg_coarse_pc_type svd > > (or configure any other coarse solver that works for singular systems, > including adding a shift or using an iterative method) > > > On Tue, Nov 20, 2012 at 7:56 AM, Thomas Witkowski > > wrote: > > When I try to use GAMG for solviing a singular system (Laplace > matrix with Neuman boundaries), it crashes with the following error: > > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [0]PETSC ERROR: Detected zero pivot in LU factorization: > [0]PETSC ERROR: Zero pivot row 65 value 9.19403e-17 tolerance > 2.22045e-14! > [0]PETSC ERROR: MatPivotCheck_none() line 585 in > /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/include/petsc-private/matimpl.h > [0]PETSC ERROR: MatPivotCheck() line 604 in > /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/include/petsc-private/matimpl.h > [0]PETSC ERROR: MatLUFactorNumeric_SeqAIJ() line 570 in > /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/mat/impls/aij/seq/aijfact.c > [0]PETSC ERROR: MatLUFactorNumeric() line 2862 in > /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/mat/interface/matrix.c > [0]PETSC ERROR: PCSetUp_LU() line 160 in > /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/factor/lu/lu.c > [0]PETSC ERROR: PCSetUp() line 832 in > /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/interface/precon.c > [0]PETSC ERROR: KSPSetUp() line 278 in > /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/ksp/interface/itfunc.c > [0]PETSC ERROR: PCSetUpOnBlocks_BJacobi_Singleblock() line 719 in > /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/bjacobi/bjacobi.c > [0]PETSC ERROR: PCSetUpOnBlocks() line 865 in > /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/interface/precon.c > [0]PETSC ERROR: KSPSetUpOnBlocks() line 154 in > /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/ksp/interface/itfunc.c > [0]PETSC ERROR: KSPSolve() line 403 in > /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/ksp/interface/itfunc.c > [0]PETSC ERROR: PCMGMCycle_Private() line 20 in > /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/mg/mg.c > [0]PETSC ERROR: PCMGMCycle_Private() line 49 in > /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/mg/mg.c > [0]PETSC ERROR: PCMGMCycle_Private() line 49 in > /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/mg/mg.c > [0]PETSC ERROR: PCMGMCycle_Private() line 49 in > /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/mg/mg.c > [0]PETSC ERROR: PCApplyRichardson_MG() line 104 in > /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/mg/mg.c > [0]PETSC ERROR: PCApplyRichardson() line 780 in > /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/interface/precon.c > [0]PETSC ERROR: KSPSolve_Richardson() line 69 in > /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/ksp/impls/rich/rich.c > [0]PETSC ERROR: KSPSolve() line 446 in > /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/ksp/interface/itfunc.c > > How to fix this problem? I already checked the gamg options, but I > have not found something what could be related to this problem. > > Thomas > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.witkowski at tu-dresden.de Tue Nov 20 01:34:02 2012 From: thomas.witkowski at tu-dresden.de (Thomas Witkowski) Date: Tue, 20 Nov 2012 08:34:02 +0100 Subject: [petsc-users] Using GAMG for solving singular systems In-Reply-To: <50AB2FA8.6050408@tu-dresden.de> References: <50AB29A8.9070107@tu-dresden.de> <50AB2FA8.6050408@tu-dresden.de> Message-ID: <50AB326A.9010901@tu-dresden.de> Okay, I found it in the parameter list from -help! Am 20.11.2012 08:22, schrieb Thomas Witkowski: > Which prefix must be added here? When I use "-laplace_pc_type gamg", > must this parameter be set with "-laplace_mg_coarse_pc_type svd" ? > > Thomas > > Am 20.11.2012 08:19, schrieb Jed Brown: >> -mg_coarse_pc_type svd >> >> (or configure any other coarse solver that works for singular >> systems, including adding a shift or using an iterative method) >> >> >> On Tue, Nov 20, 2012 at 7:56 AM, Thomas Witkowski >> > > wrote: >> >> When I try to use GAMG for solviing a singular system (Laplace >> matrix with Neuman boundaries), it crashes with the following error: >> >> [0]PETSC ERROR: --------------------- Error Message >> ------------------------------------ >> [0]PETSC ERROR: Detected zero pivot in LU factorization: >> [0]PETSC ERROR: Zero pivot row 65 value 9.19403e-17 tolerance >> 2.22045e-14! >> [0]PETSC ERROR: MatPivotCheck_none() line 585 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/include/petsc-private/matimpl.h >> [0]PETSC ERROR: MatPivotCheck() line 604 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/include/petsc-private/matimpl.h >> [0]PETSC ERROR: MatLUFactorNumeric_SeqAIJ() line 570 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/mat/impls/aij/seq/aijfact.c >> [0]PETSC ERROR: MatLUFactorNumeric() line 2862 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/mat/interface/matrix.c >> [0]PETSC ERROR: PCSetUp_LU() line 160 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/factor/lu/lu.c >> [0]PETSC ERROR: PCSetUp() line 832 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/interface/precon.c >> [0]PETSC ERROR: KSPSetUp() line 278 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/ksp/interface/itfunc.c >> [0]PETSC ERROR: PCSetUpOnBlocks_BJacobi_Singleblock() line 719 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/bjacobi/bjacobi.c >> [0]PETSC ERROR: PCSetUpOnBlocks() line 865 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/interface/precon.c >> [0]PETSC ERROR: KSPSetUpOnBlocks() line 154 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/ksp/interface/itfunc.c >> [0]PETSC ERROR: KSPSolve() line 403 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/ksp/interface/itfunc.c >> [0]PETSC ERROR: PCMGMCycle_Private() line 20 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/mg/mg.c >> [0]PETSC ERROR: PCMGMCycle_Private() line 49 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/mg/mg.c >> [0]PETSC ERROR: PCMGMCycle_Private() line 49 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/mg/mg.c >> [0]PETSC ERROR: PCMGMCycle_Private() line 49 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/mg/mg.c >> [0]PETSC ERROR: PCApplyRichardson_MG() line 104 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/mg/mg.c >> [0]PETSC ERROR: PCApplyRichardson() line 780 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/interface/precon.c >> [0]PETSC ERROR: KSPSolve_Richardson() line 69 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/ksp/impls/rich/rich.c >> [0]PETSC ERROR: KSPSolve() line 446 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/ksp/interface/itfunc.c >> >> How to fix this problem? I already checked the gamg options, but >> I have not found something what could be related to this problem. >> >> Thomas >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Tue Nov 20 02:10:56 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Tue, 20 Nov 2012 09:10:56 +0100 Subject: [petsc-users] Using GAMG for solving singular systems In-Reply-To: <50AB2FA8.6050408@tu-dresden.de> References: <50AB29A8.9070107@tu-dresden.de> <50AB2FA8.6050408@tu-dresden.de> Message-ID: Yes, as usual. Run with -help to see all options. On Tue, Nov 20, 2012 at 8:22 AM, Thomas Witkowski < thomas.witkowski at tu-dresden.de> wrote: > Which prefix must be added here? When I use "-laplace_pc_type gamg", > must this parameter be set with "-laplace_mg_coarse_pc_type svd" ? > > Thomas > > Am 20.11.2012 08:19, schrieb Jed Brown: > > -mg_coarse_pc_type svd > > (or configure any other coarse solver that works for singular systems, > including adding a shift or using an iterative method) > > > On Tue, Nov 20, 2012 at 7:56 AM, Thomas Witkowski < > thomas.witkowski at tu-dresden.de> wrote: > >> When I try to use GAMG for solviing a singular system (Laplace matrix >> with Neuman boundaries), it crashes with the following error: >> >> [0]PETSC ERROR: --------------------- Error Message >> ------------------------------------ >> [0]PETSC ERROR: Detected zero pivot in LU factorization: >> [0]PETSC ERROR: Zero pivot row 65 value 9.19403e-17 tolerance 2.22045e-14! >> [0]PETSC ERROR: MatPivotCheck_none() line 585 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/include/petsc-private/matimpl.h >> [0]PETSC ERROR: MatPivotCheck() line 604 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/include/petsc-private/matimpl.h >> [0]PETSC ERROR: MatLUFactorNumeric_SeqAIJ() line 570 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/mat/impls/aij/seq/aijfact.c >> [0]PETSC ERROR: MatLUFactorNumeric() line 2862 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/mat/interface/matrix.c >> [0]PETSC ERROR: PCSetUp_LU() line 160 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/factor/lu/lu.c >> [0]PETSC ERROR: PCSetUp() line 832 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/interface/precon.c >> [0]PETSC ERROR: KSPSetUp() line 278 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/ksp/interface/itfunc.c >> [0]PETSC ERROR: PCSetUpOnBlocks_BJacobi_Singleblock() line 719 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/bjacobi/bjacobi.c >> [0]PETSC ERROR: PCSetUpOnBlocks() line 865 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/interface/precon.c >> [0]PETSC ERROR: KSPSetUpOnBlocks() line 154 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/ksp/interface/itfunc.c >> [0]PETSC ERROR: KSPSolve() line 403 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/ksp/interface/itfunc.c >> [0]PETSC ERROR: PCMGMCycle_Private() line 20 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/mg/mg.c >> [0]PETSC ERROR: PCMGMCycle_Private() line 49 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/mg/mg.c >> [0]PETSC ERROR: PCMGMCycle_Private() line 49 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/mg/mg.c >> [0]PETSC ERROR: PCMGMCycle_Private() line 49 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/mg/mg.c >> [0]PETSC ERROR: PCApplyRichardson_MG() line 104 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/impls/mg/mg.c >> [0]PETSC ERROR: PCApplyRichardson() line 780 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/pc/interface/precon.c >> [0]PETSC ERROR: KSPSolve_Richardson() line 69 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/ksp/impls/rich/rich.c >> [0]PETSC ERROR: KSPSolve() line 446 in >> /lustre/jhome22/hdr06/hdr060/petsc/build/petsc-dev/src/ksp/ksp/interface/itfunc.c >> >> How to fix this problem? I already checked the gamg options, but I have >> not found something what could be related to this problem. >> >> Thomas >> > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From billingsjj at ornl.gov Tue Nov 20 09:36:27 2012 From: billingsjj at ornl.gov (Jay Jay Billings) Date: Tue, 20 Nov 2012 10:36:27 -0500 Subject: [petsc-users] Supported mpich versions? Message-ID: <50ABA37B.9080605@ornl.gov> Hello! Can you tell me what versions of mpich are supported by PetSc? Is it OK to use version 3.0? The download for mpich2-1.5 is down today. Jay From knepley at gmail.com Tue Nov 20 09:37:40 2012 From: knepley at gmail.com (Matthew Knepley) Date: Tue, 20 Nov 2012 10:37:40 -0500 Subject: [petsc-users] Supported mpich versions? In-Reply-To: <50ABA37B.9080605@ornl.gov> References: <50ABA37B.9080605@ornl.gov> Message-ID: On Tue, Nov 20, 2012 at 10:36 AM, Jay Jay Billings wrote: > Hello! > > Can you tell me what versions of mpich are supported by PetSc? Is it OK to > use version 3.0? Yes. Matt > The download for mpich2-1.5 is down today. > > Jay -- 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 From balay at mcs.anl.gov Tue Nov 20 10:29:51 2012 From: balay at mcs.anl.gov (Satish Balay) Date: Tue, 20 Nov 2012 10:29:51 -0600 (CST) Subject: [petsc-users] Supported mpich versions? In-Reply-To: References: <50ABA37B.9080605@ornl.gov> Message-ID: mpich-3.0 is sitll alpha/beta - and we never tested with it. But it might be ok. http://lists.mpich.org/pipermail/announce/2012-November/000001.html Satish On Tue, 20 Nov 2012, Matthew Knepley wrote: > On Tue, Nov 20, 2012 at 10:36 AM, Jay Jay Billings wrote: > > Hello! > > > > Can you tell me what versions of mpich are supported by PetSc? Is it OK to > > use version 3.0? > > Yes. > > Matt > > > The download for mpich2-1.5 is down today. > > > > Jay > > > > -- > 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 > From balay at mcs.anl.gov Tue Nov 20 10:37:35 2012 From: balay at mcs.anl.gov (Satish Balay) Date: Tue, 20 Nov 2012 10:37:35 -0600 (CST) Subject: [petsc-users] Supported mpich versions? In-Reply-To: References: <50ABA37B.9080605@ornl.gov> Message-ID: BTW: MPICH website has migrated to a new location and some links are broken. mpich2-1.5 can be downloaded from http://www.mpich.org/files/tarballs/1.5/mpich2-1.5.tar.gz Satish On Tue, 20 Nov 2012, Satish Balay wrote: > mpich-3.0 is sitll alpha/beta - and we never tested with it. But it might be ok. > > http://lists.mpich.org/pipermail/announce/2012-November/000001.html > > Satish > > On Tue, 20 Nov 2012, Matthew Knepley wrote: > > > On Tue, Nov 20, 2012 at 10:36 AM, Jay Jay Billings wrote: > > > Hello! > > > > > > Can you tell me what versions of mpich are supported by PetSc? Is it OK to > > > use version 3.0? > > > > Yes. > > > > Matt > > > > > The download for mpich2-1.5 is down today. > > > > > > Jay > > > > > > > > -- > > 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 > > > > From balay at mcs.anl.gov Tue Nov 20 10:38:24 2012 From: balay at mcs.anl.gov (Satish Balay) Date: Tue, 20 Nov 2012 10:38:24 -0600 (CST) Subject: [petsc-users] Supported mpich versions? In-Reply-To: References: <50ABA37B.9080605@ornl.gov> Message-ID: I see this link is fixed now [on the website] satish On Tue, 20 Nov 2012, Satish Balay wrote: > BTW: MPICH website has migrated to a new location and some links are broken. > > > mpich2-1.5 can be downloaded from > http://www.mpich.org/files/tarballs/1.5/mpich2-1.5.tar.gz > > Satish > > On Tue, 20 Nov 2012, Satish Balay wrote: > > > mpich-3.0 is sitll alpha/beta - and we never tested with it. But it might be ok. > > > > http://lists.mpich.org/pipermail/announce/2012-November/000001.html > > > > Satish > > > > On Tue, 20 Nov 2012, Matthew Knepley wrote: > > > > > On Tue, Nov 20, 2012 at 10:36 AM, Jay Jay Billings wrote: > > > > Hello! > > > > > > > > Can you tell me what versions of mpich are supported by PetSc? Is it OK to > > > > use version 3.0? > > > > > > Yes. > > > > > > Matt > > > > > > > The download for mpich2-1.5 is down today. > > > > > > > > Jay > > > > > > > > > > > > -- > > > 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 > > > > > > > > > From billingsjj at ornl.gov Tue Nov 20 10:39:28 2012 From: billingsjj at ornl.gov (Jay Jay Billings) Date: Tue, 20 Nov 2012 11:39:28 -0500 Subject: [petsc-users] Supported mpich versions? In-Reply-To: References: <50ABA37B.9080605@ornl.gov> Message-ID: <50ABB240.7080804@ornl.gov> Satish, Thanks very much. I'll download that and use it instead. I think I'll still test PetSc with mpich3 since I already have it built. I'll report any interesting results. Jay On 11/20/2012 11:37 AM, Satish Balay wrote: > BTW: MPICH website has migrated to a new location and some links are broken. > > > mpich2-1.5 can be downloaded from > http://www.mpich.org/files/tarballs/1.5/mpich2-1.5.tar.gz > > Satish > > On Tue, 20 Nov 2012, Satish Balay wrote: > >> mpich-3.0 is sitll alpha/beta - and we never tested with it. But it might be ok. >> >> http://lists.mpich.org/pipermail/announce/2012-November/000001.html >> >> Satish >> >> On Tue, 20 Nov 2012, Matthew Knepley wrote: >> >>> On Tue, Nov 20, 2012 at 10:36 AM, Jay Jay Billings wrote: >>>> Hello! >>>> >>>> Can you tell me what versions of mpich are supported by PetSc? Is it OK to >>>> use version 3.0? >>> Yes. >>> >>> Matt >>> >>>> The download for mpich2-1.5 is down today. >>>> >>>> Jay >>> >>> >>> -- >>> 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 >>> >> From billingsjj at ornl.gov Tue Nov 20 10:42:42 2012 From: billingsjj at ornl.gov (Jay Jay Billings) Date: Tue, 20 Nov 2012 11:42:42 -0500 Subject: [petsc-users] Supported mpich versions? In-Reply-To: References: <50ABA37B.9080605@ornl.gov> Message-ID: <50ABB302.3070808@ornl.gov> Satish, Yes, I just noticed it too. It was tarballs1.5 instead of tarballs/1.5. Jay On 11/20/2012 11:38 AM, Satish Balay wrote: > I see this link is fixed now [on the website] > > satish > > On Tue, 20 Nov 2012, Satish Balay wrote: > >> BTW: MPICH website has migrated to a new location and some links are broken. >> >> >> mpich2-1.5 can be downloaded from >> http://www.mpich.org/files/tarballs/1.5/mpich2-1.5.tar.gz >> >> Satish >> >> On Tue, 20 Nov 2012, Satish Balay wrote: >> >>> mpich-3.0 is sitll alpha/beta - and we never tested with it. But it might be ok. >>> >>> http://lists.mpich.org/pipermail/announce/2012-November/000001.html >>> >>> Satish >>> >>> On Tue, 20 Nov 2012, Matthew Knepley wrote: >>> >>>> On Tue, Nov 20, 2012 at 10:36 AM, Jay Jay Billings wrote: >>>>> Hello! >>>>> >>>>> Can you tell me what versions of mpich are supported by PetSc? Is it OK to >>>>> use version 3.0? >>>> Yes. >>>> >>>> Matt >>>> >>>>> The download for mpich2-1.5 is down today. >>>>> >>>>> Jay >>>> >>>> >>>> -- >>>> 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 >>>> >>> >> From bsmith at mcs.anl.gov Tue Nov 20 10:26:22 2012 From: bsmith at mcs.anl.gov (Barry Smith) Date: Tue, 20 Nov 2012 10:26:22 -0600 Subject: [petsc-users] Supported mpich versions? In-Reply-To: <50ABA37B.9080605@ornl.gov> References: <50ABA37B.9080605@ornl.gov> Message-ID: <516EDCE5-0C2C-4F90-BEB5-0257466AF9CE@mcs.anl.gov> On Nov 20, 2012, at 9:36 AM, Jay Jay Billings wrote: > Hello! > > Can you tell me what versions of mpich are supported by PetSc? PETSc, not some other weird combination of capitalizations Barry > Is it OK to use version 3.0? > > The download for mpich2-1.5 is down today. > > Jay From billingsjj at ornl.gov Tue Nov 20 11:21:01 2012 From: billingsjj at ornl.gov (Jay Jay Billings) Date: Tue, 20 Nov 2012 12:21:01 -0500 Subject: [petsc-users] Supported mpich versions? In-Reply-To: <50ABB302.3070808@ornl.gov> References: <50ABA37B.9080605@ornl.gov> <50ABB302.3070808@ornl.gov> Message-ID: <50ABBBFD.70605@ornl.gov> mpich3.0 seemed to work fine: make PETSC_DIR=/opt/petsc-3.3-p4_mpich-3.0rc1_debug test Running test examples to verify correct installation Using PETSC_DIR=/opt/petsc-3.3-p4_mpich-3.0rc1_debug and PETSC_ARCH=arch-linux2-c-debug C/C++ example src/snes/examples/tutorials/ex19 run successfully with 1 MPI process C/C++ example src/snes/examples/tutorials/ex19 run successfully with 2 MPI processes Fortran example src/snes/examples/tutorials/ex5f run successfully with 1 MPI process Completed test examples Jay On 11/20/2012 11:42 AM, Jay Jay Billings wrote: > Satish, > > Yes, I just noticed it too. It was tarballs1.5 instead of tarballs/1.5. > > Jay > > On 11/20/2012 11:38 AM, Satish Balay wrote: >> I see this link is fixed now [on the website] >> >> satish >> >> On Tue, 20 Nov 2012, Satish Balay wrote: >> >>> BTW: MPICH website has migrated to a new location and some links are broken. >>> >>> >>> mpich2-1.5 can be downloaded from >>> http://www.mpich.org/files/tarballs/1.5/mpich2-1.5.tar.gz >>> >>> Satish >>> >>> On Tue, 20 Nov 2012, Satish Balay wrote: >>> >>>> mpich-3.0 is sitll alpha/beta - and we never tested with it. But it might be ok. >>>> >>>> http://lists.mpich.org/pipermail/announce/2012-November/000001.html >>>> >>>> Satish >>>> >>>> On Tue, 20 Nov 2012, Matthew Knepley wrote: >>>> >>>>> On Tue, Nov 20, 2012 at 10:36 AM, Jay Jay Billings wrote: >>>>>> Hello! >>>>>> >>>>>> Can you tell me what versions of mpich are supported by PetSc? Is it OK to >>>>>> use version 3.0? >>>>> Yes. >>>>> >>>>> Matt >>>>> >>>>>> The download for mpich2-1.5 is down today. >>>>>> >>>>>> Jay >>>>> >>>>> -- >>>>> 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 >>>>> From w_ang_temp at 163.com Thu Nov 22 10:20:51 2012 From: w_ang_temp at 163.com (w_ang_temp) Date: Fri, 23 Nov 2012 00:20:51 +0800 (CST) Subject: [petsc-users] installation error of 3.3 Message-ID: Hello, When I install petsc-3.3-p4 in the cluster, I get an error information. When 'make PETSC_DIR=/public/soft/ddc/soft/petsc/petsc-3.3-p4 PETSC_ARCH=arch-linux2-c-opt test', the error information is as follows: [root at node21 petsc-3.3-p4]# make PETSC_DIR=/public/soft/ddc/soft/petsc/petsc-3.3-p4 PETSC_ARCH=arch-linux2-c-opt test Running test examples to verify correct installation Using PETSC_DIR=/public/soft/ddc/soft/petsc/petsc-3.3-p4 and PETSC_ARCH=arch-linux2-c-opt --------------Error detected during compile or link!----------------------- See http://www.mcs.anl.gov/petsc/documentation/faq.html /public/soft/ddc/soft/petsc/petsc-3.3-p4/src/snes/examples/tutorials ex19 --------------------------------------------------------------------------- /public/soft/ddc/soft/mpich2/bin/mpicc -o ex19.o -c -wd1572 -O3 -I/public/soft/ddc/soft/petsc/petsc-3.3-p4/include -I/public/soft/ddc/soft/petsc/petsc-3.3-p4/arch- linux2-c-opt/include -I/public/soft/ddc/soft/mpich2/include -D__INSDIR__=src/snes/examples/tutorials/ ex19.c /public/soft/ddc/soft/mpich2/bin/mpicc -wd1572 -O3 -o ex19 ex19.o -L/public/soft/ddc/soft/petsc/petsc-3.3-p4/arch-linux2-c-opt/lib -lpetsc -lX11 -Wl,-rpath,/pub lic/soft/ddc/soft/petsc/petsc-3.3-p4/arch-linux2-c-opt/lib -lHYPRE -L/public/soft/ddc/soft/mpich2/lib -L/public/soft/compiler/intel/11/056/mkl/lib/em64t -L/public/ soft/compiler/intel/11/056/lib/intel64 -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -lmpichcxx -lstdc++ -lpthread -lflapack -lfblas -lmpichf90 -lifport -lifcore -lm -l m -lmpichcxx -lstdc++ -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lmpl -lrt -lpthread -limf -lsvml -lipgo -ldecimal -lgcc_s -lirc -lirc_s -ldl /public/soft/compiler/intel/11/056/lib/intel64/libimf.so: warning: warning: feupdateenv is not implemented and will always fail /bin/rm -f ex19.o C/C++ example src/snes/examples/tutorials/ex19 run successfully with 1 MPI process C/C++ example src/snes/examples/tutorials/ex19 run successfully with 2 MPI processes --------------Error detected during compile or link!----------------------- See http://www.mcs.anl.gov/petsc/documentation/faq.html /public/soft/ddc/soft/petsc/petsc-3.3-p4/src/snes/examples/tutorials ex5f --------------------------------------------------------------------------- /public/soft/ddc/soft/mpich2/bin/mpif90 -c -O3 -I/public/soft/ddc/soft/petsc/petsc-3.3-p4/include -I/public/soft/ddc/soft/petsc/petsc-3.3-p4/arch-linux2-c-opt/i nclude -I/public/soft/ddc/soft/mpich2/include -o ex5f.o ex5f.F /public/soft/ddc/soft/mpich2/bin/mpif90 -O3 -o ex5f ex5f.o -L/public/soft/ddc/soft/petsc/petsc-3.3-p4/arch-linux2-c-opt/lib -lpetsc -lX11 -Wl,-rpath,/public/sof t/ddc/soft/petsc/petsc-3.3-p4/arch-linux2-c-opt/lib -lHYPRE -L/public/soft/ddc/soft/mpich2/lib -L/public/soft/compiler/intel/11/056/mkl/lib/em64t -L/public/soft/co mpiler/intel/11/056/lib/intel64 -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -lmpichcxx -lstdc++ -lpthread -lflapack -lfblas -lmpichf90 -lifport -lifcore -lm -lm -lmpi chcxx -lstdc++ -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lmpl -lrt -lpthread -limf -lsvml -lipgo -ldecimal -lgcc_s -lirc -lirc_s -ldl /public/soft/compiler/intel/11/056/lib/intel64/libimf.so: warning: warning: feupdateenv is not implemented and will always fail /bin/rm -f ex5f.o Fortran example src/snes/examples/tutorials/ex5f run successfully with 1 MPI process Completed test examples [root at node21 petsc-3.3-p4]# And in order to find the reason, I install 'petsc-3.2-p7.tar.gz' with the same procedure and it is ok. So what is the reason? Thanks. Jim -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Thu Nov 22 10:31:56 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Thu, 22 Nov 2012 17:31:56 +0100 Subject: [petsc-users] installation error of 3.3 In-Reply-To: References: Message-ID: This ran fine, so it's okay. You won't be able to use the -fp_trap option, however. On Thu, Nov 22, 2012 at 5:20 PM, w_ang_temp wrote: > Hello, > When I install petsc-3.3-p4 in the cluster, I get an error information. > When 'make PETSC_DIR=/public/soft/ddc/soft/petsc/petsc-3.3-p4 > PETSC_ARCH=arch-linux2-c-opt test', > the error information is as follows: > [root at node21 petsc-3.3-p4]# make > PETSC_DIR=/public/soft/ddc/soft/petsc/petsc-3.3-p4 > PETSC_ARCH=arch-linux2-c-opt test > Running test examples to verify correct installation > Using PETSC_DIR=/public/soft/ddc/soft/petsc/petsc-3.3-p4 and > PETSC_ARCH=arch-linux2-c-opt > --------------Error detected during compile or link!----------------------- > See http://www.mcs.anl.gov/petsc/documentation/faq.html > /public/soft/ddc/soft/petsc/petsc-3.3-p4/src/snes/examples/tutorials ex19 > --------------------------------------------------------------------------- > /public/soft/ddc/soft/mpich2/bin/mpicc -o ex19.o -c -wd1572 -O3 > -I/public/soft/ddc/soft/petsc/petsc-3.3-p4/include > -I/public/soft/ddc/soft/petsc/petsc-3.3-p4/arch- > linux2-c-opt/include -I/public/soft/ddc/soft/mpich2/include > -D__INSDIR__=src/snes/examples/tutorials/ ex19.c > /public/soft/ddc/soft/mpich2/bin/mpicc -wd1572 -O3 -o ex19 ex19. o > -L/public/soft/ddc/soft/petsc/petsc-3.3-p4/arch-linux2-c-opt/lib -lpetsc > -lX11 -Wl,-rpath,/pub > lic/soft/ddc/soft/petsc/petsc-3.3-p4/arch-linux2-c-opt/lib -lHYPRE > -L/public/soft/ddc/soft/mpich2/lib > -L/public/soft/compiler/intel/11/056/mkl/lib/em64t -L/public/ > soft/compiler/intel/11/056/lib/intel64 > -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -lmpichcxx -lstdc++ -lpthread > -lflapack -lfblas -lmpichf90 -lifport -lifcore -lm -l > m -lmpichcxx -lstdc++ -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lmpl -lrt > -lpthread -limf -lsvml -lipgo -ldecimal -lgcc_s -lirc -lirc_s -ldl > /public/soft/compiler/intel/11/056/lib/intel64/libimf.so: warning: > warning: feupdateenv is not implemented and will always fail > /bin/rm -f ex19.o > C/C++ example src/snes/examples/tutorials/ex19 run successfully with 1 MPI > process > C/C++ example src/snes/examples/tutorials/ex19 run successfully with 2 MPI > processes > --------------Error detected during compile or link!----------------------- > S ee http://www.mcs.anl.gov/petsc/documentation/faq.html > /public/soft/ddc/soft/petsc/petsc-3.3-p4/src/snes/examples/tutorials ex5f > --------------------------------------------------------------------------- > /public/soft/ddc/soft/mpich2/bin/mpif90 -c -O3 > -I/public/soft/ddc/soft/petsc/petsc-3.3-p4/include > -I/public/soft/ddc/soft/petsc/petsc-3.3-p4/arch-linux2-c-opt/i > nclude -I/public/soft/ddc/soft/mpich2/include -o ex5f.o ex5f.F > /public/soft/ddc/soft/mpich2/bin/mpif90 -O3 -o ex5f ex5f.o > -L/public/soft/ddc/soft/petsc/petsc-3.3-p4/arch-linux2-c-opt/lib -lpetsc > -lX11 -Wl,-rpath,/public/sof > t/ddc/soft/petsc/petsc-3.3-p4/arch-linux2-c-opt/lib -lHYPRE > -L/public/soft/ddc/soft/mpich2/lib > -L/public/soft/compiler/intel/11/056/mkl/lib/em64t -L/public/soft/co > mpiler/intel/11/056/lib/intel64 -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 > -lmpichcxx -lstdc++ - lpthread -lflapack -lfblas -lmpichf90 -lifport > -lifcore -lm -lm -lmpi > chcxx -lstdc++ -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lmpl -lrt -lpthread > -limf -lsvml -lipgo -ldecimal -lgcc_s -lirc -lirc_s -ldl > /public/soft/compiler/intel/11/056/lib/intel64/libimf.so: warning: > warning: feupdateenv is not implemented and will always fail > These jerks didn't bother to implement a function that is required for standards compliance, so instead of leaving it out, they made a stub that fails. One can only assume that this is a malicious scheme to force projects to test for availability of every function by attempting to link (not just compile/parse) so that configure tests run slower, thus decreasing the productivity of both developers and users. /bin/rm -f ex5f.o > Fortran example src/snes/examples/tutorials/ex5f run successfully with 1 > MPI process > Completed test examples > [root at node21 petsc-3.3-p4]# > And in order to find the reason, I install 'petsc-3.2-p7.tar.gz' with > the same procedure and it is ok. > So what is the reason? > Thanks. > > Jim > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From w_ang_temp at 163.com Thu Nov 22 11:02:46 2012 From: w_ang_temp at 163.com (w_ang_temp) Date: Fri, 23 Nov 2012 01:02:46 +0800 (CST) Subject: [petsc-users] installation error of 3.3 In-Reply-To: References: Message-ID: <4ef53d61.11.13b29125a8a.Coremail.w_ang_temp@163.com> >At 2012-11-23 00:31:56,"Jed Brown" wrote: >This ran fine, so it's okay. You won't be able to use the -fp_trap option, however. >These jerks didn't bother to implement a function that is required for standards compliance, so instead of leaving it out, they made a stub that fails. One can Hello, Jed Thanks for your reply. I am sorry that I am not sure about my understanding. So, can I ignore them ('Error detected during compile or link!-') and think that my installation of petsc is ok? Thanks. Jim >only assume that this is a malicious scheme to force projects to test for availability of every function by attempting to link (not just compile/parse) so that >configure tests run slower, thus decreasing the productivity of both developers and users. -------------- next part -------------- An HTML attachment was scrubbed... URL: From popov at uni-mainz.de Thu Nov 22 12:07:08 2012 From: popov at uni-mainz.de (Anton Popov) Date: Thu, 22 Nov 2012 19:07:08 +0100 Subject: [petsc-users] Which IDE you use to develop petsc application In-Reply-To: References: <50A76201.8010607@uni-mainz.de> Message-ID: <50AE69CC.2030607@uni-mainz.de> As promised, description files how to use Eclipse PTP for development/parallel debugging of PETSc applications are in the attachment. I recommend installing debug versions of MPICH2, PETSc, parallel SDM debugger, and valgrind (if necessary) to /opt directory Just follow the instructions. Cheers, Anton On 11/18/12 4:43 PM, Fande Kong wrote: > yeap, It sounds very interesting. Could you please give some > instructions on how to use eclipse link both Petsc and MPI? > > On Sat, Nov 17, 2012 at 3:08 AM, Anton Popov > wrote: > > On 11/16/12 2:03 AM, Barry Smith wrote: > > Because we are developing PETSc as a library that must be > portable to many users most people who develop the PETSc > libraries do not use a IDE. > > For someone who is writing AN APPLICATION that uses PETSc > (especially an application with guis) it makes sense to use an > IDL to do that development. What you chose should depend on > what machine you develop on and what your are experienced with > or comfortable with. In the users manual we try to provide > some information on using PETSc from a variety of IDEs. We are > interested in collecting information on using PETSc from IDEs > and improving our documentation. > > I managed Eclipse PTP on Mac OS (probably the same on Linux). > Provided that a debug (preferably valgrind-clean) version of > MPICH2 library with MPD process manager can be installed, Eclipse > Indigo can be easily configured for using PARALLEL SDM debugger > with PETSc applications. > > If you're interested, I can send detailed configuration / setup > instructions. > > Anton > > > > Barry > > > On Nov 15, 2012, at 4:52 PM, Fande Kong > wrote: > > Got it. Thanks. > On Thu, Nov 15, 2012 at 3:49 PM, Matthew Knepley > > wrote: > On Thu, Nov 15, 2012 at 5:41 PM, Fande Kong > > > wrote: > > Hi all, > > In order to improve development the efficient of the > petsc application > development, which IDE are you using? > > Emacs+gdb. > > Matt > > Regards, > -- > Fande Kong > Department of Computer Science > University of Colorado at Boulder > > > > > -- > 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 > > > > > -- > Fande Kong > ShenZhen Institutes of Advanced Technology > Chinese Academy of Sciences > > > > > > > -- > Fande Kong > ShenZhen Institutes of Advanced Technology > Chinese Academy of Sciences > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- # configure ./configure \ CC= ... \ set here C compiler command (e.g. gcc) CXX= ... \ set here C++ compiler command (e.g. g++) F77= ... \ set here FORTRAN 77 compiler command (e.g. gfortran) FC= ... \ set here FORTRAN 90 compiler command (e.g. gfortran) CPPFLAGS='-I...' \ full path to valgrind include directory (if you have valgrind) --prefix= ... \ set installation directory (I recommend /opt/mpich2-debug) --enable-f77 \ --enable-fc \ --enable-cxx \ --enable-threads=runtime \ --enable-g=dbg,mem,meminit \ --enable-debuginfo \ --enable-shared \ --enable-sharedlibs="..." \ osx-gcc for Mac OS, gcc for Linux --enable-fast=none \ --with-thread-package=pthreads \ --with-pm=mpd # build make all # install sudo make install # update the path in .bash_profile (.bashrc on Linux) export PATH=$PATH:/opt/mpich2-debug/bin # create file .mpd.conf in the home directory # put the following string in this file MPD_SECRETWORD=mr45-j9z ################################################################## # IMPORTANT!!! # when using debug version you should make sure that # mpiexec doesn't complain about mpd # open a separate console and type the following command there mpd & # do not close the console while you're using mpiexec # otherwise it cannot be guaranteed that mpiexec won't complain ################################################################## # after installation check if everything works, type in the console: mpicc -show mpicxx -show mpif90 -show # compile and run C and FORTRAN hello_world examples mpicc mpi_hello.c mpiexec -np 4 ./a.out mpif90 mpi_hello.f mpiexec -np 4 ./a.out -------------- next part -------------- #==================================== # Configuring debug version (example): #==================================== NOTE: use mpi compiler that you've installed in previous step Read the file 01_install_mpich2.txt ./configure \ --prefix= ... \ set installation path here (I recommend /opt/petsc/petsc-int32-debug) --download-f-blas-lapack=1 \ --with-debugging=1 \ --with-valgrind=1 \ request valgrind (if you have one) --with-valgrind-dir= ... \ set paths to valgrind root directory (if you have one) --COPTFLAGS="-g -O0" \ --FOPTFLAGS="-g -O0" \ --CXXOPTFLAGS="-g -O0" \ --with-c++-support=1 \ --with-fortran=1 \ --with-fortran-kernels=1 \ --with-large-file-io=1 \ --with-mpi-compilers=1 \ --with-cc=mpicc \ --with-cxx=mpicxx \ --with-fc=mpif90 \ --with-shared-libraries=1 \ --download-ml=1 \ --download-hypre=1 \ --download-blacs=1 \ --download-scalapack=1 \ --download-metis=1 \ --download-parmetis=1 \ --download-mumps=1 \ --download-superlu_dist=1 Add more (less) packages (options) if you like make sudo make install # After installation, modify .bash_profile (.bashrc) file to point out to valid petsc directory. export PETSC_DIR=/opt/petsc/petsc-int32-debug -------------- next part -------------- Installation of Eclipse on OSX for parallel debugging NOTE: On Linux just use appropriate version of Eclipse and PTP Proxy =================================== Eclipse Installation (Mac OS only): =================================== 0. Download and unpack into Applications folder: eclipse-parallel-indigo-SR1-incubation-macosx-cocoa-x86_64.tar.gz 1. Go to eclipse folder and create file eclipse.command, put the string inside: /Applications/eclipse/eclipse & 2. Change permissions, execute in console chmod 755 eclipse.command 3. Drag eclipse.command to desktop 4. Right click desktop icon -> Get Info -> Name & Extension, change to Eclipse (optional) 5. Change desktop icon to original Eclipse logo with Command+c, Command+v (optional) ================= Install PTP Proxy ================= - Download PTP Proxy from this website: http://www.eclipse.org/ptp/downloads_5_0.php or directly, using the link: http://www.eclipse.org/downloads/download.php?file=/tools/ptp/updates/indigo/ptp-proxy-5.0.7.zip - unpack & cd to the following folder: org.eclipse.ptp.macosx.x86_5.0.7.201203231315 - build Scalable Debug Manager (SDM) sh BUILD - install executable to /opt sudo cp -r bin/ /opt/sdm-bin More info is found here (eclipse help): Parallel Tools Platform (PTP) User Guide -> PTP - Prerequisites -> http://wiki.eclipse.org/PTP/release_notes/5.0 -> Install optional PTP server components ===================== Also helpful: Eclipse->Preferences->General->Editors, check box Show line numbers ->C/C++->Editor, uncheck box Highlight inactive code -------------- next part -------------- ========================================= Configuring and building Eclipse project: ========================================= 0. Start Eclipse by double clicking desktop icon 1. Right click in Project Explorer -> New -> Project -> C/C++ -> Makefile Project with Existing Code 2. Click Next and set Project Name and location of project ROOT! directory (not just src), click Finish 3. Right click on your project in the Explorer, select Properties -> C/C++ Build 4. Builder Settings tab -> Build directory -> File System, select full path path to project source directory 5. Behaviour tab -> Build (incremental build) set command to buld yor application (e.g. all), set Clean to clean the application (e.g. distclean) 6. Unfold C/C++ Build -> Settings -> Binary Parser (select Mach-O 64 Parser on Mac OS, On Linux select appropriate option) 7. Add full paths to header files used in your project. Petsc applications would require setting: /opt/mpich2-debug/include /opt/petsc/petsc-int32-debug/include Each path can be added as follows: In the project properties select Path and Symbols -> Includes -> Add Place directory path here, also check boxes: Add to all configurations Add to all languages 8. Build your application by clicking Hammer icon ========================================= -------------- next part -------------- ====================================== Running and debugging Eclipse project: ====================================== 0. Run -> Run configurations -> double click C/C++ application -> Main tab -> Browse, select full path to application executable (e.g. in the /bin directory) 1. Swich to Arguments tab -> Program aruments, insert all command line options that you want to use with your application Arguments tab -> Working directory -> File System, select full path to working directory (e.g. /tests, to avoid copying input files) 2. Switch to debugging perspective: Window -> Open Perspective -> Debug, then click the bug icon ====================================== -------------- next part -------------- ================================== Configure & start Resource Manager ================================== - Window -> Open Perspective -> Other -> Parallel Runtime - right click Resource Manager tab Add Resource Manager -> MPICH2 - click finish - right click on MPICH2 at Local manager -> Start Resource Manager If there is an error at this stage, most likely mpd is not running, as usual, just open console and type mpd & (don't close the console afterwards) More info is found here (eclipse help): Parallel Tools Platform (PTP) User Guide -> Resource Managers -> Configuring Resource Managers ================================== Configure Parallel Debug ================================== Run -> Debug Configurations -> Parallel Application - Resources tab -> Resource manger -> select MPICH2 at local, set number of processors - Application tab -> Parallel Project (enter project name), Application program (set full path to application executable) - Arguments tab -> Parallel program arguments (enter application command line options), Directory (set full path to working directory (e.g. tests)) - Debugger tab -> Path to debugger executable (/opt/sdm-bin/sdm) - lunch debugging session, by clicking Debug button NOTE: Resource manager must be started before the debug launch goto Parallel Runtime perspective and start it (see "Configure & start Resource Manager") More info is found here (eclipse help): Parallel Tools Platform (PTP) User Guide -> Parallel Debugging -> Creating a Debug Launch Configuration and here: -> Running Parallel Programs ================================== Debug your application ================================== ... More info is found here (eclipse help): Parallel Tools Platform (PTP) User Guide -> Parallel Debugging ================================== -------------- next part -------------- /* C Example */ #include #include int main(int argc, char *argv[]) { int rank, size; MPI_Init (&argc, &argv); /* starts MPI */ MPI_Comm_rank (MPI_COMM_WORLD, &rank); /* get current process id */ MPI_Comm_size (MPI_COMM_WORLD, &size); /* get number of processes */ printf( "Hello world from process %d of %d\n", rank, size ); MPI_Finalize(); return 0; } -------------- next part -------------- c Fortran example program hello include 'mpif.h' integer rank, size, ierror, tag, status(MPI_STATUS_SIZE) call MPI_INIT(ierror) call MPI_COMM_SIZE(MPI_COMM_WORLD, size, ierror) call MPI_COMM_RANK(MPI_COMM_WORLD, rank, ierror) print*, 'node', rank, ': Hello world' call MPI_FINALIZE(ierror) end From jedbrown at mcs.anl.gov Thu Nov 22 13:57:06 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Thu, 22 Nov 2012 20:57:06 +0100 Subject: [petsc-users] installation error of 3.3 In-Reply-To: <4ef53d61.11.13b29125a8a.Coremail.w_ang_temp@163.com> References: <4ef53d61.11.13b29125a8a.Coremail.w_ang_temp@163.com> Message-ID: On Thu, Nov 22, 2012 at 6:02 PM, w_ang_temp wrote: > Thanks for your reply. > I am sorry that I am not sure about my understanding. So, can I ignore > them > ('Error detected during compile or link!-') and think that my installation > of > petsc is ok? > Yes, but -fp_trap won't work. -------------- next part -------------- An HTML attachment was scrubbed... URL: From w_ang_temp at 163.com Sat Nov 24 06:14:51 2012 From: w_ang_temp at 163.com (w_ang_temp) Date: Sat, 24 Nov 2012 20:14:51 +0800 (CST) Subject: [petsc-users] How to choose a suitable restarted m when using GMRES? Message-ID: <62750067.156fe.13b3257788b.Coremail.w_ang_temp@163.com> Hello, As is know, GMRES(m) is a very efficient solver when dealing with symmetric indefinite system. And the restarted parameter m is critical. When the system is small, I can do several tests to find a suitable m. But when the system is very large, it is very difficult to do that. I read lots of papers about GMRES(m) and find that almost none told the way to get a suitable m. Someone told me that I can just choose the matrix dimension as the m, but I find that it is not right. So, generally, when using GMRES(m) as the sovler, how to use a suitable restarted m? Thanks. Jim -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Sat Nov 24 09:28:51 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Sat, 24 Nov 2012 16:28:51 +0100 Subject: [petsc-users] How to choose a suitable restarted m when using GMRES? In-Reply-To: <62750067.156fe.13b3257788b.Coremail.w_ang_temp@163.com> References: <62750067.156fe.13b3257788b.Coremail.w_ang_temp@163.com> Message-ID: On Sat, Nov 24, 2012 at 1:14 PM, w_ang_temp wrote: > Hello, > As is know, GMRES(m) is a very efficient solver when dealing with > symmetric indefinite > system. > If you use an SPD preconditioner, then MINRES is equivalent to full GMRES (without restarts), but uses a short recurrence. > And the restarted parameter *m* is critical. When the system is small, I > can do > several tests to find a suitable *m*. But when the system is very large, > it is very difficult > to do that. I read lots of papers about GMRES(*m*) and find that almost > none told the way to > get a suitable *m*. Someone told me that I can just choose the matrix > dimension as the *m*, but > I find that it is not right. > Using that restart makes GMRES just an inefficient way to compute a dense QR factorization, impractical unless the method converges much sooner. In practice, you choose the restart length to balance the cost of orthogonalizing and storage with the convergence rate. > So, generally, when using GMRES(*m*) as the sovler, how to use a > suitable restarted *m*? > Thanks. > Jim > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From w_ang_temp at 163.com Sat Nov 24 10:38:09 2012 From: w_ang_temp at 163.com (w_ang_temp) Date: Sun, 25 Nov 2012 00:38:09 +0800 (CST) Subject: [petsc-users] How to choose a suitable restarted m when using GMRES? In-Reply-To: References: <62750067.156fe.13b3257788b.Coremail.w_ang_temp@163.com> Message-ID: <231b6335.18132.13b3348876c.Coremail.w_ang_temp@163.com> >>On 2012-11-24 23:28:51?"Jed Brown" ??? >>On Sat, Nov 24, 2012 at 1:14 PM, w_ang_temp wrote: >>Hello, >> As is know, GMRES(m) is a very efficient solver when dealing with symmetric indefinite >>system. >If you use an SPD preconditioner, then MINRES is equivalent to full GMRES (without restarts), but uses a short recurrence. >>And the restarted parameter m is critical. When the system is small, I can do >>several tests to find a suitable m. But when the system is very large, it is very difficult >>to do that. I read lots of papers about GMRES(m) and find that almost none told the way to >>get a suitable m. Someone told me that I can just choose the matrix dimension as the m, but >>I find that it is not right. >Using that restart makes GMRES just an inefficient way to compute a dense QR factorization, impractical unless the method converges much sooner. >In practice, you choose the restart length to balance the cost of orthogonalizing and storage with the convergence rate. So, is there no effective way to determine a suitable m? Only by doing lots of tests to find an appropriate value in practical application? Or something need to be noticeable of using GMRES with an effective way? Jim >> So, generally, when using GMRES(m) as the sovler, how to use a suitable restarted m? >> Thanks. >> Jim -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Sat Nov 24 10:46:29 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Sat, 24 Nov 2012 17:46:29 +0100 Subject: [petsc-users] How to choose a suitable restarted m when using GMRES? In-Reply-To: <231b6335.18132.13b3348876c.Coremail.w_ang_temp@163.com> References: <62750067.156fe.13b3257788b.Coremail.w_ang_temp@163.com> <231b6335.18132.13b3348876c.Coremail.w_ang_temp@163.com> Message-ID: On Sat, Nov 24, 2012 at 5:38 PM, w_ang_temp wrote: > So, is there no effective way to determine a suitable m? Only by doing > lots of tests to find > an appropriate value in practical application? Or something need to be > noticeable of using GMRES > with an effective way? > Just use the default until it doesn't converge well or until you run out of memory. You're not going to have any theory here unless you know a lot of about your problem and want to think carefully about it, neither of which seem to be true, and even if it was, it's unlikely to be practically important. If you want some entertainment, read Mark Embree's 2003 SIAM Review article "The tortoise and the hare restart GMRES". Consider using MINRES instead of GMRES. -------------- next part -------------- An HTML attachment was scrubbed... URL: From w_ang_temp at 163.com Sat Nov 24 11:14:47 2012 From: w_ang_temp at 163.com (w_ang_temp) Date: Sun, 25 Nov 2012 01:14:47 +0800 (CST) Subject: [petsc-users] How to choose a suitable restarted m when using GMRES? In-Reply-To: References: <62750067.156fe.13b3257788b.Coremail.w_ang_temp@163.com> <231b6335.18132.13b3348876c.Coremail.w_ang_temp@163.com> Message-ID: <6f8a68da.90.13b336a0fbe.Coremail.w_ang_temp@163.com> >> 2012-11-25 00:46:29?"Jed Brown" ??? >>On Sat, Nov 24, 2012 at 5:38 PM, w_ang_temp wrote: >> So, is there no effective way to determine a suitable m? Only by doing lots of tests to find >>an appropriate value in practical application? Or something need to be noticeable of using GMRES >>with an effective way? >Just use the default until it doesn't converge well or until you run out of memory. You're not going to have any theory here unless you know a lot of about your >problem and want to think carefully about it, neither of which seem to be true, and even if it was, it's unlikely to be practically important. If you want some >entertainment, read Mark Embree's 2003 SIAM Review article "The tortoise and the hare restart GMRES". This article is interesting and helpful. Thanks. >Consider using MINRES instead of GMRES. -------------- next part -------------- An HTML attachment was scrubbed... URL: From pengxwang at hotmail.com Sat Nov 24 11:17:49 2012 From: pengxwang at hotmail.com (Roc Wang) Date: Sat, 24 Nov 2012 11:17:49 -0600 Subject: [petsc-users] PETSC ERROR: Floating point exception! Message-ID: Hello, I met a wierd problem. I am trying to solve linear system by calling KSPSolve(). But sometimes, the error information of Floating point exception! I tried to track down the error, but unfortunately, it's pretty random. Sometimes the executable runs fine. Other times it will crash with floating point exceptions as below. I cannot find the exact line causing the error. Could you please give me some suggestions or hints? Thanks a lot! [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Floating point exception! [0]PETSC ERROR: Infinite or not-a-number generated in norm! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 7, Thu Mar 15 09:30:51 CDT 2012 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: /gpfs/home/pzw2/work/MLPIC03_3dCart_20121118/a.out on a arch-linu named lionxo64.hpc.aset.psu.edu by pzw2 Sat Nov 24 11:01:49 2012 [0]PETSC ERROR: Libraries linked from /usr/global/petsc/3.2-p7/lib [0]PETSC ERROR: Configure run at Thu Apr 5 10:32:29 2012 [0]PETSC ERROR: Configure options --prefix=/usr/global/petsc/3.2-p7/ --with-blas-lapack-dir=/usr/global/intel/mkl/10.2.6.038/lib/em64t/ [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: VecNorm() line 167 in src/vec/vec/interface/rvector.c [0]PETSC ERROR: VecNormalize() line 261 in src/vec/vec/interface/rvector.c [0]PETSC ERROR: GMREScycle() line 128 in src/ksp/ksp/impls/gmres/gmres.c [0]PETSC ERROR: KSPSolve_GMRES() line 231 in src/ksp/ksp/impls/gmres/gmres.c [0]PETSC ERROR: KSPSolve() line 423 in src/ksp/ksp/interface/itfunc.c -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Sat Nov 24 11:26:10 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Sat, 24 Nov 2012 18:26:10 +0100 Subject: [petsc-users] PETSC ERROR: Floating point exception! In-Reply-To: References: Message-ID: Lack of reproducibility points its huge foam finger at memory corruption. You can try 1. running with -fp_trap to see where the bad values are first computed 2. running in valgrind to look for memory corruption 3. linking to a different BLAS/Lapack to rule out linking problems with MKL On Sat, Nov 24, 2012 at 6:17 PM, Roc Wang wrote: > Hello, > > I met a wierd problem. I am trying to solve linear system by calling > KSPSolve(). But sometimes, the error information of Floating point > exception! I tried to track down the error, but unfortunately, it's > pretty random. Sometimes the executable runs fine. Other times it will > crash with floating point exceptions as below. I cannot find the exact line > causing the error. Could you please give me some suggestions or hints? > Thanks a lot! > > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ [0]PETSC ERROR: Floating point > exception! [0]PETSC ERROR: Infinite or not-a-number generated in norm! > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 7, Thu Mar 15 09:30:51 > CDT 2012 [0]PETSC ERROR: See docs/changes/index.html for recent updates. > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: /gpfs/home/pzw2/work/MLPIC03_3dCart_20121118/a.out on a > arch-linu named lionxo64.hpc.aset.psu.edu by pzw2 Sat Nov 24 11:01:49 > 2012 [0]PETSC ERROR: Libraries linked from /usr/global/petsc/3.2-p7/lib > [0]PETSC ERROR: Configure run at Thu Apr 5 10:32:29 2012 [0]PETSC ERROR: > Configure options --prefix=/usr/global/petsc/3.2-p7/ > --with-blas-lapack-dir=/usr/global/intel/mkl/10.2.6.038/lib/em64t/[0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: VecNorm() line 167 in src/vec/vec/interface/rvector.c > [0]PETSC ERROR: VecNormalize() line 261 in src/vec/vec/interface/rvector.c > [0]PETSC ERROR: GMREScycle() line 128 in src/ksp/ksp/impls/gmres/gmres.c > [0]PETSC ERROR: KSPSolve_GMRES() line 231 in > src/ksp/ksp/impls/gmres/gmres.c [0]PETSC ERROR: KSPSolve() line 423 in > src/ksp/ksp/interface/itfunc.c > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pengxwang at hotmail.com Sat Nov 24 12:06:16 2012 From: pengxwang at hotmail.com (Roc Wang) Date: Sat, 24 Nov 2012 12:06:16 -0600 Subject: [petsc-users] PETSC ERROR: Floating point exception! In-Reply-To: References: , Message-ID: Thanks, Jed. It seems the error comes more often when I asked a larger array or Mat than a smaller one. Is it because the outage of memories on the node? Thanks. Date: Sat, 24 Nov 2012 18:26:10 +0100 From: jedbrown at mcs.anl.gov To: petsc-users at mcs.anl.gov Subject: Re: [petsc-users] PETSC ERROR: Floating point exception! Lack of reproducibility points its huge foam finger at memory corruption. You can try 1. running with -fp_trap to see where the bad values are first computed2. running in valgrind to look for memory corruption 3. linking to a different BLAS/Lapack to rule out linking problems with MKL On Sat, Nov 24, 2012 at 6:17 PM, Roc Wang wrote: Hello, I met a wierd problem. I am trying to solve linear system by calling KSPSolve(). But sometimes, the error information of Floating point exception! I tried to track down the error, but unfortunately, it's pretty random. Sometimes the executable runs fine. Other times it will crash with floating point exceptions as below. I cannot find the exact line causing the error. Could you please give me some suggestions or hints? Thanks a lot! [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Floating point exception! [0]PETSC ERROR: Infinite or not-a-number generated in norm! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 7, Thu Mar 15 09:30:51 CDT 2012 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: /gpfs/home/pzw2/work/MLPIC03_3dCart_20121118/a.out on a arch-linu named lionxo64.hpc.aset.psu.edu by pzw2 Sat Nov 24 11:01:49 2012 [0]PETSC ERROR: Libraries linked from /usr/global/petsc/3.2-p7/lib [0]PETSC ERROR: Configure run at Thu Apr 5 10:32:29 2012 [0]PETSC ERROR: Configure options --prefix=/usr/global/petsc/3.2-p7/ --with-blas-lapack-dir=/usr/global/intel/mkl/10.2.6.038/lib/em64t/ [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: VecNorm() line 167 in src/vec/vec/interface/rvector.c [0]PETSC ERROR: VecNormalize() line 261 in src/vec/vec/interface/rvector.c [0]PETSC ERROR: GMREScycle() line 128 in src/ksp/ksp/impls/gmres/gmres.c [0]PETSC ERROR: KSPSolve_GMRES() line 231 in src/ksp/ksp/impls/gmres/gmres.c [0]PETSC ERROR: KSPSolve() line 423 in src/ksp/ksp/interface/itfunc.c -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Sat Nov 24 12:09:27 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Sat, 24 Nov 2012 19:09:27 +0100 Subject: [petsc-users] PETSC ERROR: Floating point exception! In-Reply-To: References: Message-ID: If the operating system is not crashing regularly, then it is probably not a hardware failure. Do what I wrote in the last email. On Sat, Nov 24, 2012 at 7:06 PM, Roc Wang wrote: > Thanks, Jed. > > It seems the error comes more often when I asked a larger array or Mat > than a smaller one. Is it because the outage of memories on the node? > Thanks. > > ------------------------------ > Date: Sat, 24 Nov 2012 18:26:10 +0100 > From: jedbrown at mcs.anl.gov > To: petsc-users at mcs.anl.gov > Subject: Re: [petsc-users] PETSC ERROR: Floating point exception! > > > Lack of reproducibility points its huge foam finger at memory corruption. > You can try > > 1. running with -fp_trap to see where the bad values are first computed > 2. running in valgrind to look for memory corruption > 3. linking to a different BLAS/Lapack to rule out linking problems with MKL > > > On Sat, Nov 24, 2012 at 6:17 PM, Roc Wang wrote: > > Hello, > > I met a wierd problem. I am trying to solve linear system by calling > KSPSolve(). But sometimes, the error information of Floating point > exception! I tried to track down the error, but unfortunately, it's > pretty random. Sometimes the executable runs fine. Other times it will > crash with floating point exceptions as below. I cannot find the exact line > causing the error. Could you please give me some suggestions or hints? > Thanks a lot! > > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ [0]PETSC ERROR: Floating point > exception! [0]PETSC ERROR: Infinite or not-a-number generated in norm! > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 7, Thu Mar 15 09:30:51 > CDT 2012 [0]PETSC ERROR: See docs/changes/index.html for recent updates. > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: /gpfs/home/pzw2/work/MLPIC03_3dCart_20121118/a.out on a > arch-linu named lionxo64.hpc.aset.psu.edu by pzw2 Sat Nov 24 11:01:49 > 2012 [0]PETSC ERROR: Libraries linked from /usr/global/petsc/3.2-p7/lib > [0]PETSC ERROR: Configure run at Thu Apr 5 10:32:29 2012 [0]PETSC ERROR: > Configure options --prefix=/usr/global/petsc/3.2-p7/ > --with-blas-lapack-dir=/usr/global/intel/mkl/10.2.6.038/lib/em64t/[0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: VecNorm() line 167 in src/vec/vec/interface/rvector.c > [0]PETSC ERROR: VecNormalize() line 261 in src/vec/vec/interface/rvector.c > [0]PETSC ERROR: GMREScycle() line 128 in src/ksp/ksp/impls/gmres/gmres.c > [0]PETSC ERROR: KSPSolve_GMRES() line 231 in > src/ksp/ksp/impls/gmres/gmres.c [0]PETSC ERROR: KSPSolve() line 423 in > src/ksp/ksp/interface/itfunc.c > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhenglun.wei at gmail.com Sun Nov 25 11:05:34 2012 From: zhenglun.wei at gmail.com (Alan) Date: Sun, 25 Nov 2012 11:05:34 -0600 Subject: [petsc-users] When pull the petsc-dev for update:Connection timed out Message-ID: <50B24FDE.7050207@gmail.com> Dear folks, I hope you had a nice Thanksgiving. I was trying to 'hg pull -u' for the PETSc development update; however, an error message saying: abort: error: Connection timed out Is the update server down? Or what should I do for this? I tested that my internet is on. thanks, Alan From sean at mcs.anl.gov Sun Nov 25 11:32:12 2012 From: sean at mcs.anl.gov (Sean Farley) Date: Sun, 25 Nov 2012 11:32:12 -0600 Subject: [petsc-users] When pull the petsc-dev for update:Connection timed out In-Reply-To: <50B24FDE.7050207@gmail.com> References: <50B24FDE.7050207@gmail.com> Message-ID: On Sun, Nov 25, 2012 at 11:05 AM, Alan wrote: > Dear folks, > I hope you had a nice Thanksgiving. > I was trying to 'hg pull -u' for the PETSc development update; however, > an error message saying: > abort: error: Connection timed out > Is the update server down? Or what should I do for this? I tested that > my internet is on. Unfortunately, the petsc.cs.iit.edu server died. So, we moved the repos to bitbucket, http://www.mcs.anl.gov/petsc/developers/mercurial-hosting.html Basically, you just need to change the urls in your $PETSC_DIR/.hg/hgrc and $PETSC_DIR/config/buildsystem/.hg/hgrc From zhenglun.wei at gmail.com Sun Nov 25 12:09:25 2012 From: zhenglun.wei at gmail.com (Alan) Date: Sun, 25 Nov 2012 12:09:25 -0600 Subject: [petsc-users] When pull the petsc-dev for update:Connection timed out In-Reply-To: References: <50B24FDE.7050207@gmail.com> Message-ID: <50B25ED5.3020403@gmail.com> Thanks Sean, I tried the method you recommend. However, it shows; warning: bitbucket.org certificate not verified (check web.cacerts config setting) I missed this step: [Optional:] For ssh access - register your public ssh key at:'YourName' -> 'Account' -> 'SSH keys'. Since I think it is a option. When it pulls the petsc-dev, it is fine. However, when it pulls the BuildSystem, it says: abort: repository is unrelated What should I do for this? thanks, Alan > On Sun, Nov 25, 2012 at 11:05 AM, Alan wrote: >> Dear folks, >> I hope you had a nice Thanksgiving. >> I was trying to 'hg pull -u' for the PETSc development update; however, >> an error message saying: >> abort: error: Connection timed out >> Is the update server down? Or what should I do for this? I tested that >> my internet is on. > Unfortunately, the petsc.cs.iit.edu server died. So, we moved the > repos to bitbucket, > > http://www.mcs.anl.gov/petsc/developers/mercurial-hosting.html > > Basically, you just need to change the urls in your > $PETSC_DIR/.hg/hgrc and $PETSC_DIR/config/buildsystem/.hg/hgrc -------------- next part -------------- An HTML attachment was scrubbed... URL: From sean at mcs.anl.gov Sun Nov 25 12:23:27 2012 From: sean at mcs.anl.gov (Sean Farley) Date: Sun, 25 Nov 2012 12:23:27 -0600 Subject: [petsc-users] When pull the petsc-dev for update:Connection timed out In-Reply-To: <50B25ED5.3020403@gmail.com> References: <50B24FDE.7050207@gmail.com> <50B25ED5.3020403@gmail.com> Message-ID: On Sun, Nov 25, 2012 at 12:09 PM, Alan wrote: > Thanks Sean, > I tried the method you recommend. However, it shows; > warning: bitbucket.org certificate not verified (check web.cacerts config > setting) To suppress that warning, you could add this to your ~/.hgrc [hostfingerprints] bitbucket.org = 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b > I missed this step: > [Optional:] For ssh access - register your public ssh key at: 'YourName' -> > 'Account' -> 'SSH keys'. > Since I think it is a option. This is only if you want to push (over ssh as opposed to https). If you don't plan on patching petsc, you don't need this option. You can always change it later since it's just changing the wire protocol method. > When it pulls the petsc-dev, it is fine. However, when it pulls the > BuildSystem, it says: > abort: repository is unrelated > > > What should I do for this? What does $PETSC_DIR/config/buildsystem/.hg/hgrc contain? The default url should be [paths] default = https://bitbucket.org/petsc/buildsystem From zhenglun.wei at gmail.com Sun Nov 25 12:30:13 2012 From: zhenglun.wei at gmail.com (Alan) Date: Sun, 25 Nov 2012 12:30:13 -0600 Subject: [petsc-users] When pull the petsc-dev for update:Connection timed out In-Reply-To: References: <50B24FDE.7050207@gmail.com> <50B25ED5.3020403@gmail.com> Message-ID: <50B263B5.606@gmail.com> Thanks Sean, my /petsc-dev/.hg/hgrc shows: [paths] default = https://bitbucket.org/petsc/petsc-dev [hostfingerprints] bitbucket.org = 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b When pulling the petsc-dev, it shows: abort: no certificate for bitbucket.org with configured hostfingerprint The same thing happens if it pull the BuildSystem with: [paths] default = https://bitbucket.org/petsc/buildsystem thanks, Alan > On Sun, Nov 25, 2012 at 12:09 PM, Alan wrote: >> Thanks Sean, >> I tried the method you recommend. However, it shows; >> warning: bitbucket.org certificate not verified (check web.cacerts config >> setting) > To suppress that warning, you could add this to your ~/.hgrc > > [hostfingerprints] > bitbucket.org = 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b > >> I missed this step: >> [Optional:] For ssh access - register your public ssh key at: 'YourName' -> >> 'Account' -> 'SSH keys'. >> Since I think it is a option. > This is only if you want to push (over ssh as opposed to https). If > you don't plan on patching petsc, you don't need this option. You can > always change it later since it's just changing the wire protocol > method. > >> When it pulls the petsc-dev, it is fine. However, when it pulls the >> BuildSystem, it says: >> abort: repository is unrelated >> >> >> What should I do for this? > What does $PETSC_DIR/config/buildsystem/.hg/hgrc contain? The > default url should be > > [paths] > default = https://bitbucket.org/petsc/buildsystem From sean at mcs.anl.gov Sun Nov 25 12:42:49 2012 From: sean at mcs.anl.gov (Sean Farley) Date: Sun, 25 Nov 2012 12:42:49 -0600 Subject: [petsc-users] When pull the petsc-dev for update:Connection timed out In-Reply-To: <50B263B5.606@gmail.com> References: <50B24FDE.7050207@gmail.com> <50B25ED5.3020403@gmail.com> <50B263B5.606@gmail.com> Message-ID: On Sun, Nov 25, 2012 at 12:30 PM, Alan wrote: > Thanks Sean, > my /petsc-dev/.hg/hgrc shows: > [paths] > default = https://bitbucket.org/petsc/petsc-dev > > > [hostfingerprints] > bitbucket.org = 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b Good. > When pulling the petsc-dev, it shows: > abort: no certificate for bitbucket.org with configured hostfingerprint Weird. Are you behind a proxy? > The same thing happens if it pull the BuildSystem with: > > [paths] > default = https://bitbucket.org/petsc/buildsystem Something is being misconfigured because I'm guessing that buildsystem is trying to pull petsc-dev or vice-versa. Let's be sure, by $ cd $PETSC_DIR $ hg showconfig paths.default $ cd config/buildsystem $ hg showconfig paths.default And might as well send your mercurial version, too, $ hg version From zhenglun.wei at gmail.com Sun Nov 25 12:48:44 2012 From: zhenglun.wei at gmail.com (Alan) Date: Sun, 25 Nov 2012 12:48:44 -0600 Subject: [petsc-users] When pull the petsc-dev for update:Connection timed out In-Reply-To: References: <50B24FDE.7050207@gmail.com> <50B25ED5.3020403@gmail.com> <50B263B5.606@gmail.com> Message-ID: <50B2680C.7050700@gmail.com> Dear Sean, > On Sun, Nov 25, 2012 at 12:30 PM, Alan wrote: >> Thanks Sean, >> my /petsc-dev/.hg/hgrc shows: >> [paths] >> default = https://bitbucket.org/petsc/petsc-dev >> >> >> [hostfingerprints] >> bitbucket.org = 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b > Good. > >> When pulling the petsc-dev, it shows: >> abort: no certificate for bitbucket.org with configured hostfingerprint > Weird. Are you behind a proxy? It is. The server is behind a university net. > >> The same thing happens if it pull the BuildSystem with: >> >> [paths] >> default = https://bitbucket.org/petsc/buildsystem > Something is being misconfigured because I'm guessing that buildsystem > is trying to pull petsc-dev or vice-versa. Let's be sure, by > > $ cd $PETSC_DIR > $ hg showconfig paths.default It shows: https://bitbucket.org/petsc/petsc-dev > $ cd config/buildsystem > $ hg showconfig paths.default It shows: https://bitbucket.org/petsc/petsc-dev > > And might as well send your mercurial version, too, > > $ hg version Mercurial Distributed SCM (version 1.8.3) (see http://mercurial.selenic.com for more information) Copyright (C) 2005-2011 Matt Mackall and others This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Thanks for you help, Sean. Alan From sean at mcs.anl.gov Sun Nov 25 13:06:08 2012 From: sean at mcs.anl.gov (Sean Farley) Date: Sun, 25 Nov 2012 13:06:08 -0600 Subject: [petsc-users] When pull the petsc-dev for update:Connection timed out In-Reply-To: <50B2680C.7050700@gmail.com> References: <50B24FDE.7050207@gmail.com> <50B25ED5.3020403@gmail.com> <50B263B5.606@gmail.com> <50B2680C.7050700@gmail.com> Message-ID: On Sun, Nov 25, 2012 at 12:48 PM, Alan wrote: > Dear Sean, > >> On Sun, Nov 25, 2012 at 12:30 PM, Alan wrote: >>> >>> Thanks Sean, >>> my /petsc-dev/.hg/hgrc shows: >>> [paths] >>> default = https://bitbucket.org/petsc/petsc-dev >>> >>> >>> [hostfingerprints] >>> bitbucket.org = >>> 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b >> >> Good. >> >>> When pulling the petsc-dev, it shows: >>> abort: no certificate for bitbucket.org with configured hostfingerprint >> >> Weird. Are you behind a proxy? > > It is. The server is behind a university net. Ok, that explains why you still get a warning. You could just try http:// (without the 's') but I think bitbucket redirects to https. You could try Atlassian's advice here, but your mileage may vary, https://answers.atlassian.com/questions/103526/proxy-fakes-certificate-for-mercurial-hg >>> The same thing happens if it pull the BuildSystem with: >>> >>> [paths] >>> default = https://bitbucket.org/petsc/buildsystem >> >> Something is being misconfigured because I'm guessing that buildsystem >> is trying to pull petsc-dev or vice-versa. Let's be sure, by >> >> $ cd $PETSC_DIR >> $ hg showconfig paths.default > > It shows: > https://bitbucket.org/petsc/petsc-dev Good. >> $ cd config/buildsystem >> $ hg showconfig paths.default > > It shows: > https://bitbucket.org/petsc/petsc-dev This is the problem. Make sure that within the buildsystem directory, the .hg/hgrc file (different from the petsc-dev one) has the path for bitbucket's buildsystem. If all else fails, you could just reclone. >> And might as well send your mercurial version, too, >> >> $ hg version > > > Mercurial Distributed SCM (version 1.8.3) > (see http://mercurial.selenic.com for more information) > > Copyright (C) 2005-2011 Matt Mackall and others > This is free software; see the source for copying conditions. There is NO > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. You may want to upgrade to the latest mercurial which is currently 2.4 but your version is fine for now. From zhenglun.wei at gmail.com Sun Nov 25 16:16:43 2012 From: zhenglun.wei at gmail.com (Zhenglun (Alan) Wei) Date: Sun, 25 Nov 2012 16:16:43 -0600 Subject: [petsc-users] When pull the petsc-dev for update:Connection timed out In-Reply-To: References: <50B24FDE.7050207@gmail.com> <50B25ED5.3020403@gmail.com> <50B263B5.606@gmail.com> <50B2680C.7050700@gmail.com> Message-ID: <50B298CB.3050208@gmail.com> Thank you Sean, I changed the $ cd config/buildsystem $ hg showconfig paths.default to https://bitbucket.org/petsc/buildsystem It gives me 2 extra changes. Although, it always giev me the warning of 'certificate not verified', it updated lots of files. Should I just ignore this warning? BTW, the reason I used 'https' instead of 'http' is that 'https' is shown in the website you gave to me. :) It may needs to be changed. thanks, Alan > On Sun, Nov 25, 2012 at 12:48 PM, Alan wrote: >> Dear Sean, >> >>> On Sun, Nov 25, 2012 at 12:30 PM, Alan wrote: >>>> Thanks Sean, >>>> my /petsc-dev/.hg/hgrc shows: >>>> [paths] >>>> default = https://bitbucket.org/petsc/petsc-dev >>>> >>>> >>>> [hostfingerprints] >>>> bitbucket.org = >>>> 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b >>> Good. >>> >>>> When pulling the petsc-dev, it shows: >>>> abort: no certificate for bitbucket.org with configured hostfingerprint >>> Weird. Are you behind a proxy? >> It is. The server is behind a university net. > Ok, that explains why you still get a warning. You could just try > http:// (without the 's') but I think bitbucket redirects to https. > You could try Atlassian's advice here, but your mileage may vary, > > https://answers.atlassian.com/questions/103526/proxy-fakes-certificate-for-mercurial-hg > >>>> The same thing happens if it pull the BuildSystem with: >>>> >>>> [paths] >>>> default = https://bitbucket.org/petsc/buildsystem >>> Something is being misconfigured because I'm guessing that buildsystem >>> is trying to pull petsc-dev or vice-versa. Let's be sure, by >>> >>> $ cd $PETSC_DIR >>> $ hg showconfig paths.default >> It shows: >> https://bitbucket.org/petsc/petsc-dev > Good. > >>> $ cd config/buildsystem >>> $ hg showconfig paths.default >> It shows: >> https://bitbucket.org/petsc/petsc-dev > This is the problem. Make sure that within the buildsystem directory, > the .hg/hgrc file (different from the petsc-dev one) has the path for > bitbucket's buildsystem. If all else fails, you could just reclone. > >>> And might as well send your mercurial version, too, >>> >>> $ hg version >> >> Mercurial Distributed SCM (version 1.8.3) >> (see http://mercurial.selenic.com for more information) >> >> Copyright (C) 2005-2011 Matt Mackall and others >> This is free software; see the source for copying conditions. There is NO >> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. > You may want to upgrade to the latest mercurial which is currently 2.4 > but your version is fine for now. From sean at mcs.anl.gov Sun Nov 25 17:37:58 2012 From: sean at mcs.anl.gov (Sean Farley) Date: Sun, 25 Nov 2012 17:37:58 -0600 Subject: [petsc-users] When pull the petsc-dev for update:Connection timed out In-Reply-To: <50B298CB.3050208@gmail.com> References: <50B24FDE.7050207@gmail.com> <50B25ED5.3020403@gmail.com> <50B263B5.606@gmail.com> <50B2680C.7050700@gmail.com> <50B298CB.3050208@gmail.com> Message-ID: On Sun, Nov 25, 2012 at 4:16 PM, Zhenglun (Alan) Wei wrote: > Thank you Sean, > I changed the > > > $ cd config/buildsystem > $ hg showconfig paths.default > to > https://bitbucket.org/petsc/buildsystem > > It gives me 2 extra changes. Great! Glad to know it's working. > Although, it always giev me the warning of 'certificate not verified', > it updated lots of files. Should I just ignore this warning? You could ignore those warnings, yes, but it would probably be better to upgrade your mercurial and see if the host fingerprint option works. Or you could try to use the ssh protocol, assuming your university proxy allows ssh out. > BTW, the reason I used 'https' instead of 'http' is that 'https' is shown > in the website you gave to me. :) It may needs to be changed. Well, as I said previously, bitbucket redirects all http traffic to https, so I don't think changing it to just http would really work. From zhenglun.wei at gmail.com Sun Nov 25 17:59:49 2012 From: zhenglun.wei at gmail.com (Zhenglun (Alan) Wei) Date: Sun, 25 Nov 2012 17:59:49 -0600 Subject: [petsc-users] When pull the petsc-dev for update:Connection timed out In-Reply-To: References: <50B24FDE.7050207@gmail.com> <50B25ED5.3020403@gmail.com> <50B263B5.606@gmail.com> <50B2680C.7050700@gmail.com> <50B298CB.3050208@gmail.com> Message-ID: <50B2B0F5.2060901@gmail.com> Dear Sean, Thank you so much for your help. Here I have another question. After updating the PETSc, I tried to 'make ex45' in /src/ksp/ksp/example/tutorial/. It says that 'petscksp.h' can not be found; therefore, I commented this library in ex45.c to see what will happen. It, then, shows that the 'petscdmmg.h' can not be found. Any idea on this? :) thanks, Alan > On Sun, Nov 25, 2012 at 4:16 PM, Zhenglun (Alan) Wei > wrote: >> Thank you Sean, >> I changed the >> >> >> $ cd config/buildsystem >> $ hg showconfig paths.default >> to >> https://bitbucket.org/petsc/buildsystem >> >> It gives me 2 extra changes. > Great! Glad to know it's working. > >> Although, it always giev me the warning of 'certificate not verified', >> it updated lots of files. Should I just ignore this warning? > You could ignore those warnings, yes, but it would probably be better > to upgrade your mercurial and see if the host fingerprint option > works. Or you could try to use the ssh protocol, assuming your > university proxy allows ssh out. > >> BTW, the reason I used 'https' instead of 'http' is that 'https' is shown >> in the website you gave to me. :) It may needs to be changed. > Well, as I said previously, bitbucket redirects all http traffic to > https, so I don't think changing it to just http would really work. From jedbrown at mcs.anl.gov Sun Nov 25 18:03:01 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Mon, 26 Nov 2012 01:03:01 +0100 Subject: [petsc-users] When pull the petsc-dev for update:Connection timed out In-Reply-To: <50B2B0F5.2060901@gmail.com> References: <50B24FDE.7050207@gmail.com> <50B25ED5.3020403@gmail.com> <50B263B5.606@gmail.com> <50B2680C.7050700@gmail.com> <50B298CB.3050208@gmail.com> <50B2B0F5.2060901@gmail.com> Message-ID: On Mon, Nov 26, 2012 at 12:59 AM, Zhenglun (Alan) Wei < zhenglun.wei at gmail.com> wrote: > Dear Sean, > Thank you so much for your help. Here I have another question. > After updating the PETSc, I tried to 'make ex45' in > /src/ksp/ksp/example/tutorial/**. It says that 'petscksp.h' can not be > found; therefore, I commented this library in ex45.c to see what will > happen. It, then, shows that the 'petscdmmg.h' can not be found. Any idea > on this? :) > Since DMMG is gone, baby gone, this means your environment (PETSC_DIR) is still pointing to an old version of PETSc. > > thanks, > Alan > > On Sun, Nov 25, 2012 at 4:16 PM, Zhenglun (Alan) Wei >> wrote: >> >>> Thank you Sean, >>> I changed the >>> >>> >>> $ cd config/buildsystem >>> $ hg showconfig paths.default >>> to >>> https://bitbucket.org/petsc/**buildsystem >>> >>> It gives me 2 extra changes. >>> >> Great! Glad to know it's working. >> >> Although, it always giev me the warning of 'certificate not >>> verified', >>> it updated lots of files. Should I just ignore this warning? >>> >> You could ignore those warnings, yes, but it would probably be better >> to upgrade your mercurial and see if the host fingerprint option >> works. Or you could try to use the ssh protocol, assuming your >> university proxy allows ssh out. >> >> BTW, the reason I used 'https' instead of 'http' is that 'https' is >>> shown >>> in the website you gave to me. :) It may needs to be changed. >>> >> Well, as I said previously, bitbucket redirects all http traffic to >> https, so I don't think changing it to just http would really work. >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhenglun.wei at gmail.com Sun Nov 25 18:25:30 2012 From: zhenglun.wei at gmail.com (Zhenglun (Alan) Wei) Date: Sun, 25 Nov 2012 18:25:30 -0600 Subject: [petsc-users] When pull the petsc-dev for update:Connection timed out In-Reply-To: References: <50B24FDE.7050207@gmail.com> <50B25ED5.3020403@gmail.com> <50B263B5.606@gmail.com> <50B2680C.7050700@gmail.com> <50B298CB.3050208@gmail.com> <50B2B0F5.2060901@gmail.com> Message-ID: <50B2B6FA.5000706@gmail.com> > On Mon, Nov 26, 2012 at 12:59 AM, Zhenglun (Alan) Wei > > wrote: > > Dear Sean, > Thank you so much for your help. Here I have another question. > After updating the PETSc, I tried to 'make ex45' in > /src/ksp/ksp/example/tutorial/. It says that 'petscksp.h' can not > be found; therefore, I commented this library in ex45.c to see > what will happen. It, then, shows that the 'petscdmmg.h' can not > be found. Any idea on this? :) > > > Since DMMG is gone, baby gone, this means your environment (PETSC_DIR) > is still pointing to an old version of PETSc. Since my PETSc was updated, the PETSC_DIR of the new version of the PETSc should be the same as the old version of the PETSc, isn't it? BTW, it works after I re-configure and make the PETSc. However, I found that it as a lot of dummy things in the ex45.c, i.e.: <<<<<<<<<>>>>>>>>other ========= It seems that the update changes the original program of ex45.c by adding fractions of the new code into the old code. It confused me a lot. Is there any way that I can just replace the old code by the new code? thanks, Alan > > thanks, > Alan > > On Sun, Nov 25, 2012 at 4:16 PM, Zhenglun (Alan) Wei > > wrote: > > Thank you Sean, > I changed the > > > $ cd config/buildsystem > $ hg showconfig paths.default > to > https://bitbucket.org/petsc/buildsystem > > It gives me 2 extra changes. > > Great! Glad to know it's working. > > Although, it always giev me the warning of > 'certificate not verified', > it updated lots of files. Should I just ignore this warning? > > You could ignore those warnings, yes, but it would probably be > better > to upgrade your mercurial and see if the host fingerprint option > works. Or you could try to use the ssh protocol, assuming your > university proxy allows ssh out. > > BTW, the reason I used 'https' instead of 'http' is > that 'https' is shown > in the website you gave to me. :) It may needs to be changed. > > Well, as I said previously, bitbucket redirects all http > traffic to > https, so I don't think changing it to just http would really > work. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Sun Nov 25 18:30:59 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Mon, 26 Nov 2012 01:30:59 +0100 Subject: [petsc-users] When pull the petsc-dev for update:Connection timed out In-Reply-To: <50B2B6FA.5000706@gmail.com> References: <50B24FDE.7050207@gmail.com> <50B25ED5.3020403@gmail.com> <50B263B5.606@gmail.com> <50B2680C.7050700@gmail.com> <50B298CB.3050208@gmail.com> <50B2B0F5.2060901@gmail.com> <50B2B6FA.5000706@gmail.com> Message-ID: Sounds like you didn't "hg update" and had a bad mergetool or something. You can use hg revert to discard any local changes. Since you have many stale files around, you may want to use hg clean (this will delete all untracked files!) to get back to a state like if you had a fresh clone. On Mon, Nov 26, 2012 at 1:25 AM, Zhenglun (Alan) Wei wrote: > > On Mon, Nov 26, 2012 at 12:59 AM, Zhenglun (Alan) Wei < > zhenglun.wei at gmail.com> wrote: > >> Dear Sean, >> Thank you so much for your help. Here I have another question. >> After updating the PETSc, I tried to 'make ex45' in >> /src/ksp/ksp/example/tutorial/. It says that 'petscksp.h' can not be found; >> therefore, I commented this library in ex45.c to see what will happen. It, >> then, shows that the 'petscdmmg.h' can not be found. Any idea on this? :) >> > > Since DMMG is gone, baby gone, this means your environment (PETSC_DIR) > is still pointing to an old version of PETSc. > > Since my PETSc was updated, the PETSC_DIR of the new version of the > PETSc should be the same as the old version of the PETSc, isn't it? > BTW, it works after I re-configure and make the PETSc. However, I > found that it as a lot of dummy things in the ex45.c, i.e.: > <<<<<<<<< > ======== > > >>>>>>>>>other > > ========= > > It seems that the update changes the original program of ex45.c by > adding fractions of the new code into the old code. It confused me a lot. > Is there any way that I can just replace the old code by the new code? > > thanks, > Alan > > > >> >> thanks, >> Alan >> >> On Sun, Nov 25, 2012 at 4:16 PM, Zhenglun (Alan) Wei >>> wrote: >>> >>>> Thank you Sean, >>>> I changed the >>>> >>>> >>>> $ cd config/buildsystem >>>> $ hg showconfig paths.default >>>> to >>>> https://bitbucket.org/petsc/buildsystem >>>> >>>> It gives me 2 extra changes. >>>> >>> Great! Glad to know it's working. >>> >>> Although, it always giev me the warning of 'certificate not >>>> verified', >>>> it updated lots of files. Should I just ignore this warning? >>>> >>> You could ignore those warnings, yes, but it would probably be better >>> to upgrade your mercurial and see if the host fingerprint option >>> works. Or you could try to use the ssh protocol, assuming your >>> university proxy allows ssh out. >>> >>> BTW, the reason I used 'https' instead of 'http' is that 'https' is >>>> shown >>>> in the website you gave to me. :) It may needs to be changed. >>>> >>> Well, as I said previously, bitbucket redirects all http traffic to >>> https, so I don't think changing it to just http would really work. >>> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhenglun.wei at gmail.com Sun Nov 25 18:35:02 2012 From: zhenglun.wei at gmail.com (Zhenglun (Alan) Wei) Date: Sun, 25 Nov 2012 18:35:02 -0600 Subject: [petsc-users] When pull the petsc-dev for update:Connection timed out In-Reply-To: References: <50B24FDE.7050207@gmail.com> <50B25ED5.3020403@gmail.com> <50B263B5.606@gmail.com> <50B2680C.7050700@gmail.com> <50B298CB.3050208@gmail.com> <50B2B0F5.2060901@gmail.com> <50B2B6FA.5000706@gmail.com> Message-ID: <50B2B936.4030004@gmail.com> Thank you so much, Dr. Brown. Another little question is that: After I update the PETSc, the ${PETSC_ARCH}/conf/bin/mpiexec does not work and shows: [mpiexec at ...edu] set_default_values (./ui/mpich/utils.c:1541): no executable provided [mpiexec at ...edu] HYD_uii_mpx_get_parameters (./ui/mpich/utils.c:1745): setting default values failed [mpiexec at ...edu] main (./ui/mpich/mpiexec.c:154): error parsing parameters Any idea on this? thanks, Alan > Sounds like you didn't "hg update" and had a bad mergetool or > something. You can use hg revert to discard any local changes. Since > you have many stale files around, you may want to use hg clean (this > will delete all untracked files!) to get back to a state like if you > had a fresh clone. > > > On Mon, Nov 26, 2012 at 1:25 AM, Zhenglun (Alan) Wei > > wrote: > > >> On Mon, Nov 26, 2012 at 12:59 AM, Zhenglun (Alan) Wei >> > wrote: >> >> Dear Sean, >> Thank you so much for your help. Here I have another >> question. >> After updating the PETSc, I tried to 'make ex45' in >> /src/ksp/ksp/example/tutorial/. It says that 'petscksp.h' can >> not be found; therefore, I commented this library in ex45.c >> to see what will happen. It, then, shows that the >> 'petscdmmg.h' can not be found. Any idea on this? :) >> >> >> Since DMMG is gone, baby gone, this means your environment >> (PETSC_DIR) is still pointing to an old version of PETSc. > Since my PETSc was updated, the PETSC_DIR of the new version > of the PETSc should be the same as the old version of the PETSc, > isn't it? > BTW, it works after I re-configure and make the PETSc. > However, I found that it as a lot of dummy things in the ex45.c, i.e.: > <<<<<<<<< > ======== > > >>>>>>>>>other > > ========= > > It seems that the update changes the original program of > ex45.c by adding fractions of the new code into the old code. It > confused me a lot. Is there any way that I can just replace the > old code by the new code? > > thanks, > Alan > >> >> thanks, >> Alan >> >> On Sun, Nov 25, 2012 at 4:16 PM, Zhenglun (Alan) Wei >> > >> wrote: >> >> Thank you Sean, >> I changed the >> >> >> $ cd config/buildsystem >> $ hg showconfig paths.default >> to >> https://bitbucket.org/petsc/buildsystem >> >> It gives me 2 extra changes. >> >> Great! Glad to know it's working. >> >> Although, it always giev me the warning of >> 'certificate not verified', >> it updated lots of files. Should I just ignore this >> warning? >> >> You could ignore those warnings, yes, but it would >> probably be better >> to upgrade your mercurial and see if the host fingerprint >> option >> works. Or you could try to use the ssh protocol, assuming >> your >> university proxy allows ssh out. >> >> BTW, the reason I used 'https' instead of 'http' >> is that 'https' is shown >> in the website you gave to me. :) It may needs to be >> changed. >> >> Well, as I said previously, bitbucket redirects all http >> traffic to >> https, so I don't think changing it to just http would >> really work. >> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Sun Nov 25 18:39:45 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Mon, 26 Nov 2012 01:39:45 +0100 Subject: [petsc-users] When pull the petsc-dev for update:Connection timed out In-Reply-To: <50B2B936.4030004@gmail.com> References: <50B24FDE.7050207@gmail.com> <50B25ED5.3020403@gmail.com> <50B263B5.606@gmail.com> <50B2680C.7050700@gmail.com> <50B298CB.3050208@gmail.com> <50B2B0F5.2060901@gmail.com> <50B2B6FA.5000706@gmail.com> <50B2B936.4030004@gmail.com> Message-ID: It tries to find the executable in PATH, maybe you need mpiexec -n ./app instead of mpiexec -n app. On Mon, Nov 26, 2012 at 1:35 AM, Zhenglun (Alan) Wei wrote: > Thank you so much, Dr. Brown. > Another little question is that: > After I update the PETSc, the ${PETSC_ARCH}/conf/bin/mpiexec does > not work and shows: > [mpiexec at ...edu] set_default_values (./ui/mpich/utils.c:1541): no > executable provided > [mpiexec at ...edu] HYD_uii_mpx_get_parameters (./ui/mpich/utils.c:1745): > setting default values failed > [mpiexec at ...edu] main (./ui/mpich/mpiexec.c:154): error parsing parameters > Any idea on this? > > thanks, > Alan > > Sounds like you didn't "hg update" and had a bad mergetool or something. > You can use hg revert to discard any local changes. Since you have many > stale files around, you may want to use hg clean (this will delete all > untracked files!) to get back to a state like if you had a fresh clone. > > > On Mon, Nov 26, 2012 at 1:25 AM, Zhenglun (Alan) Wei < > zhenglun.wei at gmail.com> wrote: > >> >> On Mon, Nov 26, 2012 at 12:59 AM, Zhenglun (Alan) Wei < >> zhenglun.wei at gmail.com> wrote: >> >>> Dear Sean, >>> Thank you so much for your help. Here I have another question. >>> After updating the PETSc, I tried to 'make ex45' in >>> /src/ksp/ksp/example/tutorial/. It says that 'petscksp.h' can not be found; >>> therefore, I commented this library in ex45.c to see what will happen. It, >>> then, shows that the 'petscdmmg.h' can not be found. Any idea on this? :) >>> >> >> Since DMMG is gone, baby gone, this means your environment (PETSC_DIR) >> is still pointing to an old version of PETSc. >> >> Since my PETSc was updated, the PETSC_DIR of the new version of the >> PETSc should be the same as the old version of the PETSc, isn't it? >> BTW, it works after I re-configure and make the PETSc. However, I >> found that it as a lot of dummy things in the ex45.c, i.e.: >> <<<<<<<<<> >> ======== >> >> >>>>>>>>>other >> >> ========= >> >> It seems that the update changes the original program of ex45.c by >> adding fractions of the new code into the old code. It confused me a lot. >> Is there any way that I can just replace the old code by the new code? >> >> thanks, >> Alan >> >> >> >>> >>> thanks, >>> Alan >>> >>> On Sun, Nov 25, 2012 at 4:16 PM, Zhenglun (Alan) Wei >>>> wrote: >>>> >>>>> Thank you Sean, >>>>> I changed the >>>>> >>>>> >>>>> $ cd config/buildsystem >>>>> $ hg showconfig paths.default >>>>> to >>>>> https://bitbucket.org/petsc/buildsystem >>>>> >>>>> It gives me 2 extra changes. >>>>> >>>> Great! Glad to know it's working. >>>> >>>> Although, it always giev me the warning of 'certificate not >>>>> verified', >>>>> it updated lots of files. Should I just ignore this warning? >>>>> >>>> You could ignore those warnings, yes, but it would probably be better >>>> to upgrade your mercurial and see if the host fingerprint option >>>> works. Or you could try to use the ssh protocol, assuming your >>>> university proxy allows ssh out. >>>> >>>> BTW, the reason I used 'https' instead of 'http' is that 'https' is >>>>> shown >>>>> in the website you gave to me. :) It may needs to be changed. >>>>> >>>> Well, as I said previously, bitbucket redirects all http traffic to >>>> https, so I don't think changing it to just http would really work. >>>> >>> >>> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhenglun.wei at gmail.com Sun Nov 25 18:42:19 2012 From: zhenglun.wei at gmail.com (Zhenglun (Alan) Wei) Date: Sun, 25 Nov 2012 18:42:19 -0600 Subject: [petsc-users] When pull the petsc-dev for update:Connection timed out In-Reply-To: References: <50B24FDE.7050207@gmail.com> <50B25ED5.3020403@gmail.com> <50B263B5.606@gmail.com> <50B2680C.7050700@gmail.com> <50B298CB.3050208@gmail.com> <50B2B0F5.2060901@gmail.com> <50B2B6FA.5000706@gmail.com> <50B2B936.4030004@gmail.com> Message-ID: <50B2BAEB.5080007@gmail.com> Dear Dr. Brown, You're totally right. Thank you so much, Alan > It tries to find the executable in PATH, maybe you need mpiexec -n > ./app instead of mpiexec -n app. > > > On Mon, Nov 26, 2012 at 1:35 AM, Zhenglun (Alan) Wei > > wrote: > > Thank you so much, Dr. Brown. > Another little question is that: > After I update the PETSc, the > ${PETSC_ARCH}/conf/bin/mpiexec does not work and shows: > [mpiexec at ...edu ] set_default_values > (./ui/mpich/utils.c:1541): no executable provided > [mpiexec at ...edu ] > HYD_uii_mpx_get_parameters (./ui/mpich/utils.c:1745): setting > default values failed > [mpiexec at ...edu ] main > (./ui/mpich/mpiexec.c:154): error parsing parameters > Any idea on this? > > thanks, > Alan > >> Sounds like you didn't "hg update" and had a bad mergetool or >> something. You can use hg revert to discard any local changes. >> Since you have many stale files around, you may want to use hg >> clean (this will delete all untracked files!) to get back to a >> state like if you had a fresh clone. >> >> >> On Mon, Nov 26, 2012 at 1:25 AM, Zhenglun (Alan) Wei >> > wrote: >> >> >>> On Mon, Nov 26, 2012 at 12:59 AM, Zhenglun (Alan) Wei >>> > wrote: >>> >>> Dear Sean, >>> Thank you so much for your help. Here I have >>> another question. >>> After updating the PETSc, I tried to 'make ex45' in >>> /src/ksp/ksp/example/tutorial/. It says that >>> 'petscksp.h' can not be found; therefore, I commented >>> this library in ex45.c to see what will happen. It, >>> then, shows that the 'petscdmmg.h' can not be found. Any >>> idea on this? :) >>> >>> >>> Since DMMG is gone, baby gone, this means your environment >>> (PETSC_DIR) is still pointing to an old version of PETSc. >> Since my PETSc was updated, the PETSC_DIR of the new >> version of the PETSc should be the same as the old version of >> the PETSc, isn't it? >> BTW, it works after I re-configure and make the PETSc. >> However, I found that it as a lot of dummy things in the >> ex45.c, i.e.: >> <<<<<<<<<> >> ======== >> >> >>>>>>>>>other >> >> ========= >> >> It seems that the update changes the original program of >> ex45.c by adding fractions of the new code into the old code. >> It confused me a lot. Is there any way that I can just >> replace the old code by the new code? >> >> thanks, >> Alan >> >>> >>> thanks, >>> Alan >>> >>> On Sun, Nov 25, 2012 at 4:16 PM, Zhenglun (Alan) Wei >>> >> > wrote: >>> >>> Thank you Sean, >>> I changed the >>> >>> >>> $ cd config/buildsystem >>> $ hg showconfig paths.default >>> to >>> https://bitbucket.org/petsc/buildsystem >>> >>> It gives me 2 extra changes. >>> >>> Great! Glad to know it's working. >>> >>> Although, it always giev me the warning of >>> 'certificate not verified', >>> it updated lots of files. Should I just ignore >>> this warning? >>> >>> You could ignore those warnings, yes, but it would >>> probably be better >>> to upgrade your mercurial and see if the host >>> fingerprint option >>> works. Or you could try to use the ssh protocol, >>> assuming your >>> university proxy allows ssh out. >>> >>> BTW, the reason I used 'https' instead of >>> 'http' is that 'https' is shown >>> in the website you gave to me. :) It may needs >>> to be changed. >>> >>> Well, as I said previously, bitbucket redirects all >>> http traffic to >>> https, so I don't think changing it to just http >>> would really work. >>> >>> >>> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhenglun.wei at gmail.com Sun Nov 25 19:16:14 2012 From: zhenglun.wei at gmail.com (Zhenglun (Alan) Wei) Date: Sun, 25 Nov 2012 19:16:14 -0600 Subject: [petsc-users] When pull the petsc-dev for update:Connection timed out In-Reply-To: References: <50B24FDE.7050207@gmail.com> <50B25ED5.3020403@gmail.com> <50B263B5.606@gmail.com> <50B2680C.7050700@gmail.com> <50B298CB.3050208@gmail.com> <50B2B0F5.2060901@gmail.com> <50B2B6FA.5000706@gmail.com> <50B2B936.4030004@gmail.com> Message-ID: <50B2C2DE.6060105@gmail.com> Dear folks, Here are some problems when I'm using the new PETSc and tried to run src/ksp/ksp/example/tutorial/ex45.c 1, when I compile it, it says that 'DMSetInitialGuess' can not be found. So, I commented it out; however, this command still appears in http://www.mcs.anl.gov/petsc/petsc-current/src/ksp/ksp/examples/tutorials/ex45.c.html. Therefore, I wonder if my PETSc has not been updated correctly. 2, in old version code, I implemented a post-processing code using: ierr = DMDAGetCoordinateDA(da, &cda); ierr = DMDAGetGhostedCoordinates(da, &gc); ierr = DMDAVecGetArray(cda, gc, &coors); in order to get the locations of 'coors' stored in 'DM da'. However, the current version seems does not have 'DMDAGetCoordinateDA' and 'DMDAGetGhostedCoordinates'. Then, what should I do to get the 'coors'? Specifically, what should I do to get 'Vec gc'. thanks, Alan From jedbrown at mcs.anl.gov Sun Nov 25 19:20:38 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Mon, 26 Nov 2012 02:20:38 +0100 Subject: [petsc-users] When pull the petsc-dev for update:Connection timed out In-Reply-To: <50B2C2DE.6060105@gmail.com> References: <50B24FDE.7050207@gmail.com> <50B25ED5.3020403@gmail.com> <50B263B5.606@gmail.com> <50B2680C.7050700@gmail.com> <50B298CB.3050208@gmail.com> <50B2B0F5.2060901@gmail.com> <50B2B6FA.5000706@gmail.com> <50B2B936.4030004@gmail.com> <50B2C2DE.6060105@gmail.com> Message-ID: On Mon, Nov 26, 2012 at 2:16 AM, Zhenglun (Alan) Wei wrote: > Dear folks, > Here are some problems when I'm using the new PETSc and tried to run > src/ksp/ksp/example/tutorial/**ex45.c > 1, when I compile it, it says that 'DMSetInitialGuess' can not be found. > So, I commented it out; however, this command still appears in > http://www.mcs.anl.gov/petsc/**petsc-current/src/ksp/ksp/** > examples/tutorials/ex45.c.html > **. Therefore, I wonder if my PETSc has not been updated correctly. > You still don't have a current clone of petsc-dev. The HTML file is from the release version, in which that function was deprecated but still present. Look at the petsc-dev docs if that's what you're using. > 2, in old version code, I implemented a post-processing code using: > ierr = DMDAGetCoordinateDA(da, &cda); > ierr = DMDAGetGhostedCoordinates(da, &gc); > ierr = DMDAVecGetArray(cda, gc, &coors); > in order to get the locations of 'coors' stored in 'DM da'. However, > the current version seems does not have 'DMDAGetCoordinateDA' and > 'DMDAGetGhostedCoordinates'. Then, what should I do to get the 'coors'? > Specifically, what should I do to get 'Vec gc'. > These routines were promoted. http://www.mcs.anl.gov/petsc/documentation/changes/dev.html > > thanks, > Alan > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhenglun.wei at gmail.com Sun Nov 25 22:44:47 2012 From: zhenglun.wei at gmail.com (Alan) Date: Sun, 25 Nov 2012 22:44:47 -0600 Subject: [petsc-users] When pull the petsc-dev for update:Connection timed out In-Reply-To: References: <50B24FDE.7050207@gmail.com> <50B25ED5.3020403@gmail.com> <50B263B5.606@gmail.com> <50B2680C.7050700@gmail.com> <50B298CB.3050208@gmail.com> <50B2B0F5.2060901@gmail.com> <50B2B6FA.5000706@gmail.com> <50B2B936.4030004@gmail.com> <50B2C2DE.6060105@gmail.com> Message-ID: <50B2F3BF.6080903@gmail.com> Thanks Dr. Brown, What I did are: hg pull -u: under /petsc-dev hg update make all test what else should I do? how can I check the PETSc version in my computer? thanks, Alan > On Mon, Nov 26, 2012 at 2:16 AM, Zhenglun (Alan) Wei > > wrote: > > Dear folks, > Here are some problems when I'm using the new PETSc and tried > to run src/ksp/ksp/example/tutorial/ex45.c > 1, when I compile it, it says that 'DMSetInitialGuess' can not be > found. So, I commented it out; however, this command still appears > in > http://www.mcs.anl.gov/petsc/petsc-current/src/ksp/ksp/examples/tutorials/ex45.c.html. > Therefore, I wonder if my PETSc has not been updated correctly. > > > You still don't have a current clone of petsc-dev. The HTML file is > from the release version, in which that function was deprecated but > still present. Look at the petsc-dev docs if that's what you're using. > > 2, in old version code, I implemented a post-processing code using: > ierr = DMDAGetCoordinateDA(da, &cda); > ierr = DMDAGetGhostedCoordinates(da, &gc); > ierr = DMDAVecGetArray(cda, gc, &coors); > in order to get the locations of 'coors' stored in 'DM da'. > However, the current version seems does not have > 'DMDAGetCoordinateDA' and 'DMDAGetGhostedCoordinates'. Then, what > should I do to get the 'coors'? Specifically, what should I do to > get 'Vec gc'. > > > These routines were promoted. > > http://www.mcs.anl.gov/petsc/documentation/changes/dev.html > > > thanks, > Alan > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Sun Nov 25 23:07:58 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Mon, 26 Nov 2012 06:07:58 +0100 Subject: [petsc-users] When pull the petsc-dev for update:Connection timed out In-Reply-To: <50B2F3BF.6080903@gmail.com> References: <50B24FDE.7050207@gmail.com> <50B25ED5.3020403@gmail.com> <50B263B5.606@gmail.com> <50B2680C.7050700@gmail.com> <50B298CB.3050208@gmail.com> <50B2B0F5.2060901@gmail.com> <50B2B6FA.5000706@gmail.com> <50B2B936.4030004@gmail.com> <50B2C2DE.6060105@gmail.com> <50B2F3BF.6080903@gmail.com> Message-ID: Check again whether ex45.c contains DMSetInitialGuess. On Mon, Nov 26, 2012 at 5:44 AM, Alan wrote: > Thanks Dr. Brown, > What I did are: > hg pull -u: under /petsc-dev > hg update > make all test > > what else should I do? how can I check the PETSc version in my computer? > > thanks, > Alan > > On Mon, Nov 26, 2012 at 2:16 AM, Zhenglun (Alan) Wei < > zhenglun.wei at gmail.com> wrote: > >> Dear folks, >> Here are some problems when I'm using the new PETSc and tried to run >> src/ksp/ksp/example/tutorial/ex45.c >> 1, when I compile it, it says that 'DMSetInitialGuess' can not be found. >> So, I commented it out; however, this command still appears in >> http://www.mcs.anl.gov/petsc/petsc-current/src/ksp/ksp/examples/tutorials/ex45.c.html. >> Therefore, I wonder if my PETSc has not been updated correctly. >> > > You still don't have a current clone of petsc-dev. The HTML file is from > the release version, in which that function was deprecated but still > present. Look at the petsc-dev docs if that's what you're using. > > >> 2, in old version code, I implemented a post-processing code using: >> ierr = DMDAGetCoordinateDA(da, &cda); >> ierr = DMDAGetGhostedCoordinates(da, &gc); >> ierr = DMDAVecGetArray(cda, gc, &coors); >> in order to get the locations of 'coors' stored in 'DM da'. However, >> the current version seems does not have 'DMDAGetCoordinateDA' and >> 'DMDAGetGhostedCoordinates'. Then, what should I do to get the 'coors'? >> Specifically, what should I do to get 'Vec gc'. >> > > These routines were promoted. > > http://www.mcs.anl.gov/petsc/documentation/changes/dev.html > > >> >> thanks, >> Alan >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From icksa1 at gmail.com Mon Nov 26 10:28:55 2012 From: icksa1 at gmail.com (Milad Fatenejad) Date: Mon, 26 Nov 2012 10:28:55 -0600 Subject: [petsc-users] Segmentation Fault in ts tutorial ex23 Message-ID: Hello: I was trying to run example ts/examples/tutorial/ex23 and I seem to get an error similar to the one I've shown below no matter what options I use. For the error below, I simply ran ex23 with no arguments. I've tried running with the released petsc version and the development version from bitbucket. Any suggestions? Thanks Milad [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Argument out of range! [0]PETSC ERROR: New nonzero at (2,9) caused a malloc! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Development HG revision: f86d5620e977ae10ba0f45b74b5f06746e16ab61 HG Date: Mon Nov 19 18:09:55 2012 +0100 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: ./ex23 on a arch-linu named animal5 by milad Mon Nov 26 10:12:42 2012 [0]PETSC ERROR: Libraries linked from /home/milad/petsc/petsc-dev-bb/arch-linux2-c-debug/lib [0]PETSC ERROR: Configure run at Mon Nov 19 13:22:07 2012 [0]PETSC ERROR: Configure options --with-moab=1 --with-moab-dir=/home/milad/Downloads/moab/moab-opt-parallel/install --with-hdf5=1 --with-hdf5-dir=/usr/local/hdf5-1.8.8-parallel --with-netcdf=1 --with-netcdf-dir=/usr/local/netcdf-4.1.3-serial --with-clanguage=C++ [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: MatSetValues_SeqAIJ() line 353 in /home/milad/petsc/petsc-dev-bb/src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: MatSetValues() line 1080 in /home/milad/petsc/petsc-dev-bb/src/mat/interface/matrix.c [0]PETSC ERROR: MatSetValuesLocal() line 1941 in /home/milad/petsc/petsc-dev-bb/src/mat/interface/matrix.c [0]PETSC ERROR: SetUpMatrices() line 396 in src/ts/examples/tutorials/ex23.c [0]PETSC ERROR: main() line 76 in src/ts/examples/tutorials/ex23.c application called MPI_Abort(MPI_COMM_WORLD, 63) - process 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: From bourdin at lsu.edu Mon Nov 26 10:49:38 2012 From: bourdin at lsu.edu (Blaise A Bourdin) Date: Mon, 26 Nov 2012 16:49:38 +0000 Subject: [petsc-users] ts_type euler Message-ID: <6C4AE5741C2B874282F58DA136A2CCB832E151@BY2PRD0611MB441.namprd06.prod.outlook.com> Hi, I am working with a student on converting an existing code from hand-written ODE solver to a TS. In order to validate the port, we want to compare the results of the existing code with the same methods implemented in TS. When running the examples in src/ts/examples/tutorials, it seems that -ts_type euler doesn't work, and that the iterate is simply equal to the initial value. Try for example ./ex17 -da_grid_x 40 -drawcontours -draw_pause .1 -ts_type euler in petsc-3.3 Are we missing something? Blaise -- Department of Mathematics and Center for Computation & Technology Louisiana State University, Baton Rouge, LA 70803, USA Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 http://www.math.lsu.edu/~bourdin From bourdin at lsu.edu Mon Nov 26 11:25:54 2012 From: bourdin at lsu.edu (Blaise A Bourdin) Date: Mon, 26 Nov 2012 17:25:54 +0000 Subject: [petsc-users] Fortran binding for MatZeroRowsColumnsStencil Message-ID: <6C4AE5741C2B874282F58DA136A2CCB832F2CA@BY2PRD0611MB441.namprd06.prod.outlook.com> Hi, Is it possible to add fortran binding for MatZeroRowsColumnsStencil in petsc-3.3 or petsc-dev? The attached patch (module line endings, sorry) should do the job. Regards, Blaise -- Department of Mathematics and Center for Computation & Technology Louisiana State University, Baton Rouge, LA 70803, USA Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 http://www.math.lsu.edu/~bourdin -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MatZeroRowsColumnsStencil.patch Type: application/octet-stream Size: 1702 bytes Desc: MatZeroRowsColumnsStencil.patch URL: From rlmackie862 at gmail.com Mon Nov 26 12:16:14 2012 From: rlmackie862 at gmail.com (Randall Mackie) Date: Mon, 26 Nov 2012 10:16:14 -0800 Subject: [petsc-users] output after updating to petsc-3.3-p4 from p3 Message-ID: I just updated from patch level 3 to patch level 4, and after recompiling and rerunning, I am getting output like the following: [0]Total space allocated 1091174672 bytes [ 0]48 bytes PetscObjectComposedDataIncreaseReal() line 170 in /home/MackieR/PETSc/petsc-3.3-p4/src/sys/objects/state.c [0] VecSet() line 494 in /home/MackieR/PETSc/petsc-3.3-p4/src/vec/vec/interface/rvector.c [0] VecZeroEntries() line 1365 in /home/MackieR/PETSc/petsc-3.3-p4/src/vec/vec/interface/vector.c [0] PCApply_ASM() line 432 in /home/MackieR/PETSc/petsc-3.3-p4/src/ksp/pc/impls/asm/asm.c [0] PCApply() line 373 in /home/MackieR/PETSc/petsc-3.3-p4/src/ksp/pc/interface/precon.c [0] PCApplyBAorAB() line 581 in /home/MackieR/PETSc/petsc-3.3-p4/src/ksp/pc/interface/precon.c [0] KSPSolve_BCGS() line 54 in /home/MackieR/PETSc/petsc-3.3-p4/src/ksp/ksp/impls/bcgs/bcgs.c [0] KSPSolve() line 351 in /home/MackieR/PETSc/petsc-3.3-p4/src/ksp/ksp/interface/itfunc.c etc This must be something new in patch level 4, but what is this and how can it be turned off? Thanks, Randy M. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Mon Nov 26 12:37:01 2012 From: bsmith at mcs.anl.gov (Barry Smith) Date: Mon, 26 Nov 2012 12:37:01 -0600 Subject: [petsc-users] output after updating to petsc-3.3-p4 from p3 In-Reply-To: References: Message-ID: <54A6C259-05EE-4616-B613-92091A838303@mcs.anl.gov> Randy, This output comes from having a memory leak in the code. By default we don't print this information. Do you perhaps have an environmental variable PETSC_OPTIONS set to -malloc_test or -malloc_debug etc? Likely this is not a direct result of changing the patch level but something else that changed in your configuration, options etc. Barry On Nov 26, 2012, at 12:16 PM, Randall Mackie wrote: > I just updated from patch level 3 to patch level 4, and after recompiling and rerunning, I am getting output like the following: > > > [0]Total space allocated 1091174672 bytes > [ 0]48 bytes PetscObjectComposedDataIncreaseReal() line 170 in /home/MackieR/PETSc/petsc-3.3-p4/src/sys/objects/state.c > [0] VecSet() line 494 in /home/MackieR/PETSc/petsc-3.3-p4/src/vec/vec/interface/rvector.c > [0] VecZeroEntries() line 1365 in /home/MackieR/PETSc/petsc-3.3-p4/src/vec/vec/interface/vector.c > [0] PCApply_ASM() line 432 in /home/MackieR/PETSc/petsc-3.3-p4/src/ksp/pc/impls/asm/asm.c > [0] PCApply() line 373 in /home/MackieR/PETSc/petsc-3.3-p4/src/ksp/pc/interface/precon.c > [0] PCApplyBAorAB() line 581 in /home/MackieR/PETSc/petsc-3.3-p4/src/ksp/pc/interface/precon.c > [0] KSPSolve_BCGS() line 54 in /home/MackieR/PETSc/petsc-3.3-p4/src/ksp/ksp/impls/bcgs/bcgs.c > [0] KSPSolve() line 351 in /home/MackieR/PETSc/petsc-3.3-p4/src/ksp/ksp/interface/itfunc.c > > > etc > > > This must be something new in patch level 4, but what is this and how can it be turned off? > > > Thanks, > > Randy M. From bsmith at mcs.anl.gov Mon Nov 26 12:44:09 2012 From: bsmith at mcs.anl.gov (Barry Smith) Date: Mon, 26 Nov 2012 12:44:09 -0600 Subject: [petsc-users] ts_type euler In-Reply-To: <6C4AE5741C2B874282F58DA136A2CCB832E151@BY2PRD0611MB441.namprd06.prod.outlook.com> References: <6C4AE5741C2B874282F58DA136A2CCB832E151@BY2PRD0611MB441.namprd06.prod.outlook.com> Message-ID: <0F90FF3F-A78A-4788-825C-8C65BA82E50C@mcs.anl.gov> On Nov 26, 2012, at 10:49 AM, Blaise A Bourdin wrote: > Hi, > > I am working with a student on converting an existing code from hand-written ODE solver to a TS. In order to validate the port, we want to compare the results of the existing code with the same methods implemented in TS. When running the examples in src/ts/examples/tutorials, it seems that -ts_type euler doesn't work, and that the iterate is simply equal to the initial value. Try for example > ./ex17 -da_grid_x 40 -drawcontours -draw_pause .1 -ts_type euler > in petsc-3.3 > > Are we missing something? ex17 is a DAE so euler won't work properly. Hence ex17 behaves badly as you report (yes, we should somehow have the code tell you this). Other examples that are not DAEs should work for Euler, but the time-step may be so small you don't see much change without running for a very large number of time-steps Barry > > Blaise > > > > -- > Department of Mathematics and Center for Computation & Technology > Louisiana State University, Baton Rouge, LA 70803, USA > Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 http://www.math.lsu.edu/~bourdin > > > > > > > > From zhenglun.wei at gmail.com Mon Nov 26 14:37:30 2012 From: zhenglun.wei at gmail.com (Zhenglun (Alan) Wei) Date: Mon, 26 Nov 2012 14:37:30 -0600 Subject: [petsc-users] When pull the petsc-dev for update:Connection timed out In-Reply-To: References: <50B24FDE.7050207@gmail.com> <50B25ED5.3020403@gmail.com> <50B263B5.606@gmail.com> <50B2680C.7050700@gmail.com> <50B298CB.3050208@gmail.com> <50B2B0F5.2060901@gmail.com> <50B2B6FA.5000706@gmail.com> <50B2B936.4030004@gmail.com> <50B2C2DE.6060105@gmail.com> <50B2F3BF.6080903@gmail.com> Message-ID: <50B3D30A.5050903@gmail.com> Dear Dr. Brown, Yes, it changes to KSPSetComputeInitialGuess. thanks, Alan > Check again whether ex45.c contains DMSetInitialGuess. > > > On Mon, Nov 26, 2012 at 5:44 AM, Alan > wrote: > > Thanks Dr. Brown, > What I did are: > hg pull -u: under /petsc-dev > hg update > make all test > > what else should I do? how can I check the PETSc version in my > computer? > > thanks, > Alan >> On Mon, Nov 26, 2012 at 2:16 AM, Zhenglun (Alan) Wei >> > wrote: >> >> Dear folks, >> Here are some problems when I'm using the new PETSc and >> tried to run src/ksp/ksp/example/tutorial/ex45.c >> 1, when I compile it, it says that 'DMSetInitialGuess' can >> not be found. So, I commented it out; however, this command >> still appears in >> http://www.mcs.anl.gov/petsc/petsc-current/src/ksp/ksp/examples/tutorials/ex45.c.html. >> Therefore, I wonder if my PETSc has not been updated correctly. >> >> >> You still don't have a current clone of petsc-dev. The HTML file >> is from the release version, in which that function was >> deprecated but still present. Look at the petsc-dev docs if >> that's what you're using. >> >> 2, in old version code, I implemented a post-processing code >> using: >> ierr = DMDAGetCoordinateDA(da, &cda); >> ierr = DMDAGetGhostedCoordinates(da, &gc); >> ierr = DMDAVecGetArray(cda, gc, &coors); >> in order to get the locations of 'coors' stored in 'DM >> da'. However, the current version seems does not have >> 'DMDAGetCoordinateDA' and 'DMDAGetGhostedCoordinates'. Then, >> what should I do to get the 'coors'? Specifically, what >> should I do to get 'Vec gc'. >> >> >> These routines were promoted. >> >> http://www.mcs.anl.gov/petsc/documentation/changes/dev.html >> >> >> thanks, >> Alan >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From rupp at mcs.anl.gov Tue Nov 27 14:32:11 2012 From: rupp at mcs.anl.gov (Karl Rupp) Date: Tue, 27 Nov 2012 14:32:11 -0600 Subject: [petsc-users] Which IDE you use to develop petsc application In-Reply-To: <50AE69CC.2030607@uni-mainz.de> References: <50A76201.8010607@uni-mainz.de> <50AE69CC.2030607@uni-mainz.de> Message-ID: <50B5234B.70207@mcs.anl.gov> Hi Anton, thanks for the detailed instructions. I will make sure that they are moved to an appropriate place :-) Best regards, Karli On 11/22/2012 12:07 PM, Anton Popov wrote: > As promised, description files how to use Eclipse PTP for > development/parallel debugging of PETSc applications are in the attachment. > I recommend installing debug versions of MPICH2, PETSc, parallel SDM > debugger, and valgrind (if necessary) to /opt directory > Just follow the instructions. > Cheers, > Anton > > > On 11/18/12 4:43 PM, Fande Kong wrote: >> yeap, It sounds very interesting. Could you please give some >> instructions on how to use eclipse link both Petsc and MPI? >> >> On Sat, Nov 17, 2012 at 3:08 AM, Anton Popov > > wrote: >> >> On 11/16/12 2:03 AM, Barry Smith wrote: >> >> Because we are developing PETSc as a library that must be >> portable to many users most people who develop the PETSc >> libraries do not use a IDE. >> >> For someone who is writing AN APPLICATION that uses PETSc >> (especially an application with guis) it makes sense to use an >> IDL to do that development. What you chose should depend on >> what machine you develop on and what your are experienced with >> or comfortable with. In the users manual we try to provide >> some information on using PETSc from a variety of IDEs. We are >> interested in collecting information on using PETSc from IDEs >> and improving our documentation. >> >> I managed Eclipse PTP on Mac OS (probably the same on Linux). >> Provided that a debug (preferably valgrind-clean) version of >> MPICH2 library with MPD process manager can be installed, Eclipse >> Indigo can be easily configured for using PARALLEL SDM debugger >> with PETSc applications. >> >> If you're interested, I can send detailed configuration / setup >> instructions. >> >> Anton >> >> >> >> Barry >> >> >> On Nov 15, 2012, at 4:52 PM, Fande Kong > > wrote: >> >> Got it. Thanks. >> On Thu, Nov 15, 2012 at 3:49 PM, Matthew Knepley >> > wrote: >> On Thu, Nov 15, 2012 at 5:41 PM, Fande Kong >> > >> wrote: >> >> Hi all, >> >> In order to improve development the efficient of the >> petsc application >> development, which IDE are you using? >> >> Emacs+gdb. >> >> Matt >> >> Regards, >> -- >> Fande Kong >> Department of Computer Science >> University of Colorado at Boulder >> >> >> >> >> -- >> 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 >> >> >> >> >> -- >> Fande Kong >> ShenZhen Institutes of Advanced Technology >> Chinese Academy of Sciences >> >> >> >> >> >> >> -- >> Fande Kong >> ShenZhen Institutes of Advanced Technology >> Chinese Academy of Sciences >> > From jedbrown at mcs.anl.gov Tue Nov 27 17:46:10 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Tue, 27 Nov 2012 17:46:10 -0600 Subject: [petsc-users] Segmentation Fault in ts tutorial ex23 In-Reply-To: References: Message-ID: Change STAR to BOX as in the patch below. I'll push this to petsc-dev later. diff --git a/src/ts/examples/tutorials/ex23.c b/src/ts/examples/tutorials/ex23.c --- a/src/ts/examples/tutorials/ex23.c +++ b/src/ts/examples/tutorials/ex23.c @@ -52,7 +52,7 @@ /* Get physics and time parameters */ ierr = GetParams(&user);CHKERRQ(ierr); /* Create a 2D DA with dof = 2 */ - ierr = DMDACreate2d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,2,1,PETSC_NULL,PETSC_NULL,&user.da);CHKERRQ(ierr); + ierr = DMDACreate2d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_BOX,-4,-4,PETSC_DECIDE,PETSC_DECIDE,2,1,PETSC_NULL,PETSC_NULL,&user.da);CHKERRQ(ierr); /* Set Element type (triangular) */ ierr = DMDASetElementType(user.da,DMDA_ELEMENT_P1);CHKERRQ(ierr); On Mon, Nov 26, 2012 at 10:28 AM, Milad Fatenejad wrote: > Hello: > > I was trying to run example ts/examples/tutorial/ex23 and I seem to get an > error similar to the one I've shown below no matter what options I use. For > the error below, I simply ran ex23 with no arguments. I've tried running > with the released petsc version and the development version from bitbucket. > Any suggestions? > > Thanks > Milad > > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [0]PETSC ERROR: Argument out of range! > [0]PETSC ERROR: New nonzero at (2,9) caused a malloc! > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Development HG revision: > f86d5620e977ae10ba0f45b74b5f06746e16ab61 HG Date: Mon Nov 19 18:09:55 2012 > +0100 > [0]PETSC ERROR: See docs/changes/index.html for recent updates. > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [0]PETSC ERROR: See docs/index.html for manual pages. > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: ./ex23 on a arch-linu named animal5 by milad Mon Nov 26 > 10:12:42 2012 > [0]PETSC ERROR: Libraries linked from > /home/milad/petsc/petsc-dev-bb/arch-linux2-c-debug/lib > [0]PETSC ERROR: Configure run at Mon Nov 19 13:22:07 2012 > [0]PETSC ERROR: Configure options --with-moab=1 > --with-moab-dir=/home/milad/Downloads/moab/moab-opt-parallel/install > --with-hdf5=1 --with-hdf5-dir=/usr/local/hdf5-1.8.8-parallel > --with-netcdf=1 --with-netcdf-dir=/usr/local/netcdf-4.1.3-serial > --with-clanguage=C++ > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: MatSetValues_SeqAIJ() line 353 in > /home/milad/petsc/petsc-dev-bb/src/mat/impls/aij/seq/aij.c > [0]PETSC ERROR: MatSetValues() line 1080 in > /home/milad/petsc/petsc-dev-bb/src/mat/interface/matrix.c > [0]PETSC ERROR: MatSetValuesLocal() line 1941 in > /home/milad/petsc/petsc-dev-bb/src/mat/interface/matrix.c > [0]PETSC ERROR: SetUpMatrices() line 396 in > src/ts/examples/tutorials/ex23.c > [0]PETSC ERROR: main() line 76 in src/ts/examples/tutorials/ex23.c > application called MPI_Abort(MPI_COMM_WORLD, 63) - process 0 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jedbrown at mcs.anl.gov Wed Nov 28 06:27:44 2012 From: jedbrown at mcs.anl.gov (Jed Brown) Date: Wed, 28 Nov 2012 06:27:44 -0600 Subject: [petsc-users] Fortran binding for MatZeroRowsColumnsStencil In-Reply-To: <6C4AE5741C2B874282F58DA136A2CCB832F2CA@BY2PRD0611MB441.namprd06.prod.outlook.com> References: <6C4AE5741C2B874282F58DA136A2CCB832F2CA@BY2PRD0611MB441.namprd06.prod.outlook.com> Message-ID: Evidently I applied this patch and pushed to petsc.cs.iit.edu just before that server died (after the last backup) so it didn't show up in the bitbucket repository. Lisandro just pointed this out to me, so now the original is on bitbucket. https://bitbucket.org/petsc/petsc-3.3/changeset/ca8b914ed0710d0b9159d4b1592de91d5d973e6f Sorry about that. On Mon, Nov 26, 2012 at 11:25 AM, Blaise A Bourdin wrote: > Hi, > > Is it possible to add fortran binding for MatZeroRowsColumnsStencil in > petsc-3.3 or petsc-dev? > > The attached patch (module line endings, sorry) should do the job. > > Regards, > Blaise > > -- > Department of Mathematics and Center for Computation & Technology > Louisiana State University, Baton Rouge, LA 70803, USA > Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 > http://www.math.lsu.edu/~bourdin > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From malexe at vt.edu Thu Nov 29 09:48:48 2012 From: malexe at vt.edu (Mihai Alexe) Date: Thu, 29 Nov 2012 16:48:48 +0100 Subject: [petsc-users] Is MatSetUp required with MatCreateNormal and MatCreateMPIAIJWithSplitArrays? Message-ID: Hello all, I am creating a large rectangular MPIAIJ matrix, then a shell NormalMatrix that eventually gets passed to a KSP object (all part of a constrained least-squares solver). Code looks as follows: //user.A_mat and user.Hess are PETSc Mat info = MatCreateMPIAIJWithSplitArrays( PETSC_COMM_WORLD, *locrow, *loccol, nrow, *ncol, onrowidx, oncolidx, (PetscScalar*) onvals, offrowidx, offcolidx, (PetscScalar*) values, &user.A_mat ); CHKERRQ(info); info = MatCreateNormal( user.A_mat, &user.Hess ); CHKERRQ(info); info = MatSetUp( user.Hess ); Is MatSetUp() required for A or Hess to be initialized correctly? Or some call to MatSetPreallocation? My code crashes after displaying (with -info -mat_view_info): [0] PetscCommDuplicate(): Duplicating a communicator 47534399113024 67425648 max tags = 2147483647 [0] PetscCommDuplicate(): Duplicating a communicator 47534399112000 67760592 max tags = 2147483647 [0] MatCreate_SeqAIJ_Inode(): Not using Inode routines due to -mat_no_inode [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 8920860 X 1508490; storage space: 0 unneeded,34572269 used [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0 [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 615 Matrix Object: 1 MPI processes type: seqaij rows=8920860, cols=1508490 total: nonzeros=34572269, allocated nonzeros=0 total number of mallocs used during MatSetValues calls =0 not using I-node routines [0] PetscCommDuplicate(): Using internal PETSc communicator 47534399112000 67760592 [0] MatCreate_SeqAIJ_Inode(): Not using Inode routines due to -mat_no_inode [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 8920860 X 18752388; storage space: 0 unneeded,1762711 used [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0 [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 349 Matrix Object: 1 MPI processes type: seqaij rows=8920860, cols=18752388 total: nonzeros=1762711, allocated nonzeros=0 total number of mallocs used during MatSetValues calls =0 not using I-node routines [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 8920860 X 1508490; storage space: 0 unneeded,34572269 used [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0 [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 615 Matrix Object: 1 MPI processes type: seqaij rows=8920860, cols=1508490 total: nonzeros=34572269, allocated nonzeros=0 total number of mallocs used during MatSetValues calls =0 not using I-node routines [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 8920860 X 18752388; storage space: 0 unneeded,1762711 used [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0 [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 349 Matrix Object: 1 MPI processes type: seqaij rows=8920860, cols=18752388 total: nonzeros=1762711, allocated nonzeros=0 total number of mallocs used during MatSetValues calls =0 not using I-node routines [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 8920860 X 1508490; storage space: 0 unneeded,34572269 used [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0 [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 615 [0] PetscCommDuplicate(): Using internal PETSc communicator 47534399112000 67760592 [0] PetscCommDuplicate(): Using internal PETSc communicator 47534399112000 67760592 [0] VecScatterCreateCommon_PtoS(): Using blocksize 1 scatter [0] VecScatterCreate(): General case: MPI to Seq [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 8920860 X 38109; storage space: 0 unneeded,1762711 used [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0 [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 349 Matrix Object: 160 MPI processes type: mpiaij rows=131858910, cols=18752388 The code ran just fine on a smaller (pruned) input dataset. I don't get a stacktrace unfortunately... (running in production mode, trying to switch to debug mode now). Regards, Mihai -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at mcs.anl.gov Thu Nov 29 11:25:31 2012 From: bsmith at mcs.anl.gov (Barry Smith) Date: Thu, 29 Nov 2012 11:25:31 -0600 Subject: [petsc-users] Is MatSetUp required with MatCreateNormal and MatCreateMPIAIJWithSplitArrays? In-Reply-To: References: Message-ID: <269A4421-4AB1-4829-A578-5B66CEF5C6C9@mcs.anl.gov> On Nov 29, 2012, at 9:48 AM, Mihai Alexe wrote: > Hello all, > > I am creating a large rectangular MPIAIJ matrix, then a shell NormalMatrix that eventually gets passed to a KSP object (all part of a constrained least-squares solver). > Code looks as follows: > > //user.A_mat and user.Hess are PETSc Mat > > info = MatCreateMPIAIJWithSplitArrays( PETSC_COMM_WORLD, *locrow, *loccol, nrow, > *ncol, onrowidx, oncolidx, > (PetscScalar*) onvals, offrowidx, offcolidx, > (PetscScalar*) values, &user.A_mat ); CHKERRQ(info); > > info = MatCreateNormal( user.A_mat, &user.Hess ); CHKERRQ(info); > info = MatSetUp( user.Hess ); > > Is MatSetUp() required for A or Hess to be initialized correctly? Or some call to MatSetPreallocation? ' No you shouldn't need them. Try with valgrind http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind Barry > > My code crashes after displaying (with -info -mat_view_info): > > [0] PetscCommDuplicate(): Duplicating a communicator 47534399113024 67425648 max tags = 2147483647 > [0] PetscCommDuplicate(): Duplicating a communicator 47534399112000 67760592 max tags = 2147483647 > [0] MatCreate_SeqAIJ_Inode(): Not using Inode routines due to -mat_no_inode > [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 8920860 X 1508490; storage space: 0 unneeded,34572269 used > [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0 > [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 615 > Matrix Object: 1 MPI processes > type: seqaij > rows=8920860, cols=1508490 > total: nonzeros=34572269, allocated nonzeros=0 > total number of mallocs used during MatSetValues calls =0 > not using I-node routines > [0] PetscCommDuplicate(): Using internal PETSc communicator 47534399112000 67760592 > [0] MatCreate_SeqAIJ_Inode(): Not using Inode routines due to -mat_no_inode > [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 8920860 X 18752388; storage space: 0 unneeded,1762711 used > [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0 > [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 349 > Matrix Object: 1 MPI processes > type: seqaij > rows=8920860, cols=18752388 > total: nonzeros=1762711, allocated nonzeros=0 > total number of mallocs used during MatSetValues calls =0 > not using I-node routines > [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 8920860 X 1508490; storage space: 0 unneeded,34572269 used > [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0 > [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 615 > Matrix Object: 1 MPI processes > type: seqaij > rows=8920860, cols=1508490 > total: nonzeros=34572269, allocated nonzeros=0 > total number of mallocs used during MatSetValues calls =0 > not using I-node routines > [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 8920860 X 18752388; storage space: 0 unneeded,1762711 used > [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0 > [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 349 > Matrix Object: 1 MPI processes > type: seqaij > rows=8920860, cols=18752388 > total: nonzeros=1762711, allocated nonzeros=0 > total number of mallocs used during MatSetValues calls =0 > not using I-node routines > [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 8920860 X 1508490; storage space: 0 unneeded,34572269 used > [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0 > [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 615 > [0] PetscCommDuplicate(): Using internal PETSc communicator 47534399112000 67760592 > [0] PetscCommDuplicate(): Using internal PETSc communicator 47534399112000 67760592 > [0] VecScatterCreateCommon_PtoS(): Using blocksize 1 scatter > [0] VecScatterCreate(): General case: MPI to Seq > [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 8920860 X 38109; storage space: 0 unneeded,1762711 used > [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0 > [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 349 > Matrix Object: 160 MPI processes > type: mpiaij > rows=131858910, cols=18752388 > > The code ran just fine on a smaller (pruned) input dataset. > I don't get a stacktrace unfortunately... (running in production mode, trying to switch to debug mode now). > > > Regards, > Mihai >