[petsc-users] Re-initializing petsc again
Satish Balay
balay at mcs.anl.gov
Tue Sep 3 22:14:47 CDT 2013
This is incomplete info.
what compile command produced this error? And what do you get when you
compile a petsc example with a petsc makefile? [complete output]
Satish
On Wed, 4 Sep 2013, Suraj Prabhakaran wrote:
> Thanks a lot for the confirmation!!
> I am now compiling it with 3.4.2, but I get a strange error and could be great if someone can just point out whats wrong. (Might be something stupid, but just in case...)
>
> Thanks in advance!
>
> Suraj
>
> -------------------------------ERROR-----------------------------
>
> In file included from /opt/petsc-3.4.2/include/petsc.h:8,
> from Main/time_integration_dir/compute_tau_w_mean.c:91:
> /opt/petsc-3.4.2/include/petscbt.h: In function ‘compute_tau_w_mean’:
> /opt/petsc-3.4.2/include/petscbt.h:33: error: invalid storage class for function ‘PetscBTLength’
> /opt/petsc-3.4.2/include/petscbt.h:38: error: invalid storage class for function ‘PetscBTMemzero’
> /opt/petsc-3.4.2/include/petscbt.h:43: error: invalid storage class for function ‘PetscBTDestroy’
> /opt/petsc-3.4.2/include/petscbt.h:48: error: invalid storage class for function ‘PetscBTLookup’
> /opt/petsc-3.4.2/include/petscbt.h: In function ‘PetscBTLookup’:
> /opt/petsc-3.4.2/include/petscbt.h:47: warning: declaration of ‘index’ shadows a global declaration
> /usr/include/string.h:489: warning: shadowed declaration is here
> /opt/petsc-3.4.2/include/petscbt.h: In function ‘compute_tau_w_mean’:
> /opt/petsc-3.4.2/include/petscbt.h:59: error: invalid storage class for function ‘PetscBTView’
> /opt/petsc-3.4.2/include/petscbt.h:74: error: invalid storage class for function ‘PetscBTCreate’
> /opt/petsc-3.4.2/include/petscbt.h:79: error: invalid storage class for function ‘PetscBTLookupSet’
> /opt/petsc-3.4.2/include/petscbt.h: In function ‘PetscBTLookupSet’:
> /opt/petsc-3.4.2/include/petscbt.h:78: warning: declaration of ‘index’ shadows a global declaration
> /usr/include/string.h:489: warning: shadowed declaration is here
> /opt/petsc-3.4.2/include/petscbt.h: In function ‘compute_tau_w_mean’:
> /opt/petsc-3.4.2/include/petscbt.h:91: error: invalid storage class for function ‘PetscBTSet’
> /opt/petsc-3.4.2/include/petscbt.h: In function ‘PetscBTSet’:
> /opt/petsc-3.4.2/include/petscbt.h:90: warning: declaration of ‘index’ shadows a global declaration
> /usr/include/string.h:489: warning: shadowed declaration is here
> /opt/petsc-3.4.2/include/petscbt.h: In function ‘compute_tau_w_mean’:
> /opt/petsc-3.4.2/include/petscbt.h:103: error: invalid storage class for function ‘PetscBTLookupClear’
> /opt/petsc-3.4.2/include/petscbt.h: In function ‘PetscBTLookupClear’:
> /opt/petsc-3.4.2/include/petscbt.h:102: warning: declaration of ‘index’ shadows a global declaration
> /usr/include/string.h:489: warning: shadowed declaration is here
> /opt/petsc-3.4.2/include/petscbt.h: In function ‘compute_tau_w_mean’:
> /opt/petsc-3.4.2/include/petscbt.h:115: error: invalid storage class for function ‘PetscBTClear’
> /opt/petsc-3.4.2/include/petscbt.h: In function ‘PetscBTClear’:
> /opt/petsc-3.4.2/include/petscbt.h:114: warning: declaration of ‘index’ shadows a global declaration
> /usr/include/string.h:489: warning: shadowed declaration is here
> In file included from /opt/petsc-3.4.2/include/petsc.h:9,
> from Main/time_integration_dir/compute_tau_w_mean.c:91:
> /opt/petsc-3.4.2/include/petscctable.h: In function ‘compute_tau_w_mean’:
> /opt/petsc-3.4.2/include/petscctable.h:20: error: invalid storage class for function ‘PetscHash’
> /opt/petsc-3.4.2/include/petscctable.h:40: error: invalid storage class for function ‘PetscTableAdd’
> In file included from /opt/petsc-3.4.2/include/petsc.h:9,
> from Main/time_integration_dir/compute_tau_w_mean.c:91:
> /opt/petsc-3.4.2/include/petscctable.h:83: error: invalid storage class for function ‘PetscTableAddCount’
> /opt/petsc-3.4.2/include/petscctable.h:120: error: invalid storage class for function ‘PetscTableFind’
> In file included from /opt/petsc-3.4.2/include/petscsnesfas.h:3,
> from /opt/petsc-3.4.2/include/petsc.h:27,
> from Main/time_integration_dir/compute_tau_w_mean.c:91:
> /opt/petsc-3.4.2/include/petscsnes.h:585: error: invalid storage class for function ‘SNESGetSNESLineSearch’
> /opt/petsc-3.4.2/include/petscsnes.h:586: error: invalid storage class for function ‘SNESSetSNESLineSearch’
> Main/time_integration_dir/compute_tau_w_mean.c:223: warning: implicit declaration of function ‘wall_thermoquants’
> Main/time_integration_dir/compute_tau_w_mean.c:155: warning: unused variable ‘iface_plus_one’
> Main/time_integration_dir/compute_tau_w_mean.c:330: warning: value computed is not used
> Main/time_integration_dir/compute_tau_w_mean.c:116: warning: unused variable ‘ierr’
> Main/time_integration_dir/compute_tau_w_mean.c:111: warning: unused variable ‘icell’
> Main/time_integration_dir/compute_tau_w_mean.c:105: warning: unused variable ‘mach’
> /opt/petsc-3.4.2/include/petscts.h:328: warning: unused variable ‘TSRegisterAllCalled’
> /opt/petsc-3.4.2/include/petscts.h:327: warning: unused variable ‘TSList’
> /opt/petsc-3.4.2/include/petscts.h:168: warning: unused variable ‘DMTS_CLASSID’
> /opt/petsc-3.4.2/include/petscts.h:167: warning: unused variable ‘TS_CLASSID’
> /opt/petsc-3.4.2/include/petscts.h:163: warning: unused variable ‘TSExactFinalTimeOptions’
> /opt/petsc-3.4.2/include/petscts.h:101: warning: unused variable ‘TSConvergedReasons’
> /opt/petsc-3.4.2/include/petscts.h:80: warning: unused variable ‘TSEquationTypes’
> /opt/petsc-3.4.2/include/petscsnesfas.h:19: warning: unused variable ‘SNESFASTypes’
> /opt/petsc-3.4.2/include/petscsnes.h:679: warning: unused variable ‘SNESQNRestartTypes’
> /opt/petsc-3.4.2/include/petscsnes.h:675: warning: unused variable ‘SNESQNScaleTypes’
> /opt/petsc-3.4.2/include/petscsnes.h:667: warning: unused variable ‘SNESNCGTypes’
> /opt/petsc-3.4.2/include/petscsnes.h:654: warning: unused variable ‘SNESNGMRESSelectTypes’
> /opt/petsc-3.4.2/include/petscsnes.h:648: warning: unused variable ‘SNESNGMRESRestartTypes’
> /opt/petsc-3.4.2/include/petscsnes.h:474: warning: unused variable ‘SNESLineSearch_Apply’
> /opt/petsc-3.4.2/include/petscsnes.h:473: warning: unused variable ‘SNESLineSearchList’
> /opt/petsc-3.4.2/include/petscsnes.h:472: warning: unused variable ‘SNESLineSearchRegisterAllCalled’
> /opt/petsc-3.4.2/include/petscsnes.h:471: warning: unused variable ‘SNESLINESEARCH_CLASSID’
> /opt/petsc-3.4.2/include/petscsnes.h:470: warning: unused variable ‘SNESList’
> /opt/petsc-3.4.2/include/petscsnes.h:469: warning: unused variable ‘SNESRegisterAllCalled’
> /opt/petsc-3.4.2/include/petscsnes.h:356: warning: unused variable ‘SNESNormTypes’
> /opt/petsc-3.4.2/include/petscsnes.h:217: warning: unused variable ‘SNESConvergedReasons’
> /opt/petsc-3.4.2/include/petscsnes.h:50: warning: unused variable ‘DMSNES_CLASSID’
> /opt/petsc-3.4.2/include/petscsnes.h:49: warning: unused variable ‘SNES_CLASSID’
> /opt/petsc-3.4.2/include/petsccharacteristic.h:44: warning: unused variable ‘CharacteristicList’
> /opt/petsc-3.4.2/include/petsccharacteristic.h:43: warning: unused variable ‘CharacteristicRegisterAllCalled’
> /opt/petsc-3.4.2/include/petscdmda.h:27: warning: unused variable ‘DMDABoundaryTypes’
> /opt/petsc-3.4.2/include/petscpf.h:50: warning: unused variable ‘PFRegisterAllCalled’
> /opt/petsc-3.4.2/include/petscpf.h:40: warning: unused variable ‘PF_CLASSID’
> /opt/petsc-3.4.2/include/petscpf.h:12: warning: unused variable ‘PFList’
> /opt/petsc-3.4.2/include/petscdm.h:34: warning: unused variable ‘DMRegisterAllCalled’
> /opt/petsc-3.4.2/include/petscdm.h:33: warning: unused variable ‘DMList’
> /opt/petsc-3.4.2/include/petscdm.h:11: warning: unused variable ‘DM_CLASSID’
> /opt/petsc-3.4.2/include/petscdraw.h:239: warning: unused variable ‘PETSC_DRAWHG_CLASSID’
> /opt/petsc-3.4.2/include/petscdraw.h:225: warning: unused variable ‘PETSC_DRAWSP_CLASSID’
> /opt/petsc-3.4.2/include/petscdraw.h:206: warning: unused variable ‘PETSC_DRAWLG_CLASSID’
> /opt/petsc-3.4.2/include/petscdraw.h:195: warning: unused variable ‘PETSC_DRAWAXIS_CLASSID’
> /opt/petsc-3.4.2/include/petscdraw.h:26: warning: unused variable ‘PetscDrawList’
> /opt/petsc-3.4.2/include/petscdraw.h:9: warning: unused variable ‘PETSC_DRAW_CLASSID’
> /opt/petsc-3.4.2/include/petscmatlab.h:8: warning: unused variable ‘MATLABENGINE_CLASSID’
> /opt/petsc-3.4.2/include/petscthreadcomm.h:35: warning: unused variable ‘PetscThreadCommReductionOps’
> /opt/petsc-3.4.2/include/petscthreadcomm.h:32: warning: unused variable ‘PetscThreadCommList’
>
>
>
> On Sep 3, 2013, at 9:03 PM, Satish Balay wrote:
>
> > Also you would have to call MPI_Init() before the first PetscInitialize() [and
> > similarly MPI_Finalize() after the last call to PetscFinalize()]
> >
> > Satish
> >
> > On Tue, 3 Sep 2013, Barry Smith wrote:
> >
> >>
> >> There is a problem with the 3.3 series when reinitializing PETSc. Can you switch to PETSc 3.4 which properly supports calling PetscInitialize() several times.
> >>
> >> Barry
> >>
> >> On Sep 3, 2013, at 1:58 PM, Suraj Prabhakaran <suraj.prabhakaran at gmail.com> wrote:
> >>
> >>> Hello,
> >>>
> >>> Again, this relates to finalizing and initializing petsc in my application. I basically want to finalize petsc and initialize it again with a different MPI communicator. A rough sketch of my quite huge application is as follows.
> >>>
> >>>
> >>> main()
> >>> {
> >>> PetscInitialize()
> >>> ...
> >>> ...
> >>> AOCreate()..
> >>> AO operations..
> >>> AODestroy()..
> >>> ...
> >>> ...
> >>> PetscFinalize()
> >>> PETSC_COMM_WORLD = A new communicator (which includes more processes)
> >>> PetscInitialize()
> >>> ...
> >>> ...
> >>> AOCreate()..
> >>> AO operations..
> >>> AODestroy()
> >>> ...
> >>> ...
> >>> PetscFinalize()
> >>> }
> >>>
> >>> So after finalizing and initializing it back, I always get an error with one of the AO calls. Given below is the complete error I get when running with 8 procs. Can anyone give me a hint what the problem could be? I was told earlier, that finalizing and initializing petsc should not be a problem!
> >>>
> >>> Best,
> >>> Suraj
> >>>
> >>> -------------------------ERROR starts here-------------------------------
> >>> [0]PETSC ERROR: ------------------------------------------------------------------------
> >>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
> >>> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> >>> [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
> >>> [0]PETSC ERROR: likely location of problem given in stack below
> >>> [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------
> >>> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
> >>> [0]PETSC ERROR: INSTEAD the line number of the start of the function
> >>> [0]PETSC ERROR: is given.
> >>> [0]PETSC ERROR: [0] PetscStrcmp line 414 /root/petsc/petsc-3.3-p7/src/sys/utils/str.c
> >>> [0]PETSC ERROR: [0] PetscFListAdd line 202 /root/petsc/petsc-3.3-p7/src/sys/dll/reg.c
> >>> [0]PETSC ERROR: [0] AORegister line 99 /root/petsc/petsc-3.3-p7/src/dm/ao/interface/aoreg.c
> >>> [0]PETSC ERROR: [0] AORegisterAll line 28 /root/petsc/petsc-3.3-p7/src/dm/ao/interface/aoregall.c
> >>> [0]PETSC ERROR: [0] AOInitializePackage line 49 /root/petsc/petsc-3.3-p7/src/dm/ao/interface/dlregisdm.c
> >>> [0]PETSC ERROR: [0] AOCreate line 530 /root/petsc/petsc-3.3-p7/src/dm/ao/interface/ao.c
> >>> [0]PETSC ERROR: [0] AOCreateBasicIS line 381 /root/petsc/petsc-3.3-p7/src/dm/ao/impls/basic/aobasic.c
> >>> [0]PETSC ERROR: [0] AOCreateBasic line 336 /root/petsc/petsc-3.3-p7/src/dm/ao/impls/basic/aobasic.c
> >>> [0]PETSC ERROR: --------------------- Error Message ------------------------------------
> >>> [0]PETSC ERROR: Signal received!
> >>> [0]PETSC ERROR: ------------------------------------------------------------------------
> >>> [0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 CDT 2013
> >>> [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: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue Sep 3 20:56:21 2013
> >>> [0]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib
> >>> [0]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013
> >>> [0]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 --with-debugging
> >>> [0]PETSC ERROR: ------------------------------------------------------------------------
> >>> [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
> >>> --------------------------------------------------------------------------
> >>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> >>> with errorcode 59.
> >>>
> >>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> >>> You may or may not see output from other processes, depending on
> >>> exactly when Open MPI kills them.
> >>> --------------------------------------------------------------------------
> >>> [1]PETSC ERROR: ------------------------------------------------------------------------
> >>> [1]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the batch system) has told this process to end
> >>> [1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> >>> [1]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
> >>> [1]PETSC ERROR: likely location of problem given in stack below
> >>> [1]PETSC ERROR: --------------------- Stack Frames ------------------------------------
> >>> [1]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
> >>> [1]PETSC ERROR: INSTEAD the line number of the start of the function
> >>> [1]PETSC ERROR: is given.
> >>> [1]PETSC ERROR: --------------------- Error Message ------------------------------------
> >>> [1]PETSC ERROR: Signal received!
> >>> [1]PETSC ERROR: ------------------------------------------------------------------------
> >>> [1]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 CDT 2013
> >>> [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: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue Sep 3 20:56:21 2013
> >>> [1]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib
> >>> [1]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013
> >>> [1]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 --with-debugging
> >>> [1]PETSC ERROR: ------------------------------------------------------------------------
> >>> [1]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
> >>> [2]PETSC ERROR: ------------------------------------------------------------------------
> >>> [2]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the batch system) has told this process to end
> >>> [2]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> >>> [2]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[2]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
> >>> [2]PETSC ERROR: likely location of problem given in stack below
> >>> [2]PETSC ERROR: --------------------- Stack Frames ------------------------------------
> >>> [2]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
> >>> [2]PETSC ERROR: INSTEAD the line number of the start of the function
> >>> [2]PETSC ERROR: is given.
> >>> [2]PETSC ERROR: --------------------- Error Message ------------------------------------
> >>> [2]PETSC ERROR: Signal received!
> >>> [2]PETSC ERROR: ------------------------------------------------------------------------
> >>> [2]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 CDT 2013
> >>> [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: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue Sep 3 20:56:21 2013
> >>> [2]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib
> >>> [2]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013
> >>> [2]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 --with-debugging
> >>> [2]PETSC ERROR: ------------------------------------------------------------------------
> >>> [2]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
> >>> [3]PETSC ERROR: ------------------------------------------------------------------------
> >>> [3]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the batch system) has told this process to end
> >>> [3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> >>> [3]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[3]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
> >>> [3]PETSC ERROR: likely location of problem given in stack below
> >>> [3]PETSC ERROR: --------------------- Stack Frames ------------------------------------
> >>> [3]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
> >>> [3]PETSC ERROR: INSTEAD the line number of the start of the function
> >>> [3]PETSC ERROR: is given.
> >>> [3]PETSC ERROR: --------------------- Error Message ------------------------------------
> >>> [3]PETSC ERROR: Signal received!
> >>> [3]PETSC ERROR: ------------------------------------------------------------------------
> >>> [3]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 CDT 2013
> >>> [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: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue Sep 3 20:56:21 2013
> >>> [3]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib
> >>> [3]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013
> >>> [3]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 --with-debugging
> >>> [3]PETSC ERROR: ------------------------------------------------------------------------
> >>> [3]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
> >>> [4]PETSC ERROR: ------------------------------------------------------------------------
> >>> [4]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the batch system) has told this process to end
> >>> [4]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> >>> [4]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[4]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
> >>> [4]PETSC ERROR: likely location of problem given in stack below
> >>> [4]PETSC ERROR: --------------------- Stack Frames ------------------------------------
> >>> [4]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
> >>> [4]PETSC ERROR: INSTEAD the line number of the start of the function
> >>> [4]PETSC ERROR: is given.
> >>> [4]PETSC ERROR: --------------------- Error Message ------------------------------------
> >>> [4]PETSC ERROR: Signal received!
> >>> [4]PETSC ERROR: ------------------------------------------------------------------------
> >>> [4]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 CDT 2013
> >>> [4]PETSC ERROR: See docs/changes/index.html for recent updates.
> >>> [4]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> >>> [4]PETSC ERROR: See docs/index.html for manual pages.
> >>> [4]PETSC ERROR: ------------------------------------------------------------------------
> >>> [4]PETSC ERROR: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue Sep 3 20:56:21 2013
> >>> [4]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib
> >>> [4]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013
> >>> [4]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 --with-debugging
> >>> [4]PETSC ERROR: ------------------------------------------------------------------------
> >>> [4]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
> >>> [5]PETSC ERROR: ------------------------------------------------------------------------
> >>> [5]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the batch system) has told this process to end
> >>> [5]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> >>> [5]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[5]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
> >>> [5]PETSC ERROR: likely location of problem given in stack below
> >>> [5]PETSC ERROR: --------------------- Stack Frames ------------------------------------
> >>> [5]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
> >>> [5]PETSC ERROR: INSTEAD the line number of the start of the function
> >>> [5]PETSC ERROR: is given.
> >>> [5]PETSC ERROR: --------------------- Error Message ------------------------------------
> >>> [5]PETSC ERROR: Signal received!
> >>> [5]PETSC ERROR: ------------------------------------------------------------------------
> >>> [5]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 CDT 2013
> >>> [5]PETSC ERROR: See docs/changes/index.html for recent updates.
> >>> [5]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> >>> [5]PETSC ERROR: See docs/index.html for manual pages.
> >>> [5]PETSC ERROR: ------------------------------------------------------------------------
> >>> [5]PETSC ERROR: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue Sep 3 20:56:21 2013
> >>> [5]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib
> >>> [5]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013
> >>> [5]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 --with-debugging
> >>> [5]PETSC ERROR: ------------------------------------------------------------------------
> >>> [5]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
> >>> [6]PETSC ERROR: ------------------------------------------------------------------------
> >>> [6]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the batch system) has told this process to end
> >>> [6]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> >>> [6]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[6]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
> >>> [6]PETSC ERROR: likely location of problem given in stack below
> >>> [6]PETSC ERROR: --------------------- Stack Frames ------------------------------------
> >>> [6]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
> >>> [6]PETSC ERROR: INSTEAD the line number of the start of the function
> >>> [6]PETSC ERROR: is given.
> >>> [6]PETSC ERROR: --------------------- Error Message ------------------------------------
> >>> [6]PETSC ERROR: Signal received!
> >>> [6]PETSC ERROR: ------------------------------------------------------------------------
> >>> [6]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 CDT 2013
> >>> [6]PETSC ERROR: See docs/changes/index.html for recent updates.
> >>> [6]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> >>> [6]PETSC ERROR: See docs/index.html for manual pages.
> >>> [6]PETSC ERROR: ------------------------------------------------------------------------
> >>> [6]PETSC ERROR: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue Sep 3 20:56:21 2013
> >>> [6]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib
> >>> [6]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013
> >>> [6]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 --with-debugging
> >>> [6]PETSC ERROR: ------------------------------------------------------------------------
> >>> [6]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
> >>> [7]PETSC ERROR: ------------------------------------------------------------------------
> >>> [7]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the batch system) has told this process to end
> >>> [7]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> >>> [7]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[7]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
> >>> [7]PETSC ERROR: likely location of problem given in stack below
> >>> [7]PETSC ERROR: --------------------- Stack Frames ------------------------------------
> >>> [7]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
> >>> [7]PETSC ERROR: INSTEAD the line number of the start of the function
> >>> [7]PETSC ERROR: is given.
> >>> [7]PETSC ERROR: --------------------- Error Message ------------------------------------
> >>> [7]PETSC ERROR: Signal received!
> >>> [7]PETSC ERROR: ------------------------------------------------------------------------
> >>> [7]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 CDT 2013
> >>> [7]PETSC ERROR: See docs/changes/index.html for recent updates.
> >>> [7]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> >>> [7]PETSC ERROR: See docs/index.html for manual pages.
> >>> [7]PETSC ERROR: ------------------------------------------------------------------------
> >>> [7]PETSC ERROR: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue Sep 3 20:56:21 2013
> >>> [7]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib
> >>> [7]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013
> >>> [7]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 --with-debugging
> >>> [7]PETSC ERROR: ------------------------------------------------------------------------
> >>> [7]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
> >>> --------------------------------------------------------------------------
> >>> mpiexec has exited due to process rank 0 with PID 2670 on
> >>> node grsacc17 exiting improperly. There are two reasons this could occur:
> >>>
> >>> 1. this process did not call "init" before exiting, but others in
> >>> the job did. This can cause a job to hang indefinitely while it waits
> >>> for all processes to call "init". By rule, if one process calls "init",
> >>> then ALL processes must call "init" prior to termination.
> >>>
> >>> 2. this process called "init", but exited without calling "finalize".
> >>> By rule, all processes that call "init" MUST call "finalize" prior to
> >>> exiting or it will be considered an "abnormal termination"
> >>>
> >>> This may have caused other processes in the application to be
> >>> terminated by signals sent by mpiexec (as reported here).
> >>
> >>
> >
>
>
More information about the petsc-users
mailing list