On Wed, 4 Sep 2013, Barry Smith wrote: > > >> 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’ > > > Ok, nothing wrong with the static inline or build; There must be something > wonky in compute_tau_w_mean.c or a file it includes that is causing the error. > > I would start debugging by removing stuff from compute_tau_w_mean.c before > the #include "petsc.h" until the error goes away and that will show the > culprit.
Also you have a huge list of -I dirs. Make sure a wrong petscconf.h isn't getting included from one of these locations. I would do a 'make CFLAGS=-E' compute_tau_w_mean.o and look at the preprocessed 'PetscBTLength' reference in there. Also 'grep petscconf.h compute_tau_w_mean.o' Satish > > Barry > > > > On Sep 3, 2013, at 10:21 PM, Suraj Prabhakaran <[email protected]> > wrote: > > > Hi Barry, > > > > Thanks a lot! Here are the files attached. > > > > Suraj > > > > <configure.log><make.log> > > > > On Sep 4, 2013, at 5:13 AM, Barry Smith wrote: > > > >> > >> Something is going wrong with the PETSC_STATIC_INLINE definition. Please > >> send configure.log and make.log > >> > >> Barry > >> > >> On Sep 3, 2013, at 10:01 PM, Suraj Prabhakaran > >> <[email protected]> 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). > >>>>> > >>>>> > >>>> > >>> > >> > > > >
