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 > >> <[email protected]> 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). > >> > >> > > > >
