>> 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. 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). >>>>> >>>>> >>>> >>> >> >
