On Fri, Apr 11, 2014 at 12:11 PM, Andrés Alessandro León Baldelli < [email protected]> wrote:
> Hi, > I am trying to use the new Plex to HDF5 interface. From what I understand, > it only works in sequential mode. > I would like to write a sequential DM, created e.g. from an exodusII mesh > via DMPlexCreateExodusFromFile. > What puzzles me is that I only can do it if I run on a single processor, > since it crashes as soon its communicator contains more than one proc. > > My understanding is that, if numproc>1, the crash is due to the call to > ISView in src/dm/impls/plex/plex.c:785 which fails because its two > arguments do not share the same communicator. > > Could you help me understand a little more what is going on, what I am > doing wrong and what could help solving this issue? > Use 'next', not 'master' Matt > I attach the error message, a minimal code to reproduce the crash and a > test mesh. > > Best, > > ---------- begin output---------- > geothermal:dmcomplex kumiori$ mpirun -n 2 ./testHDF5Plex -i data/TwoTri.gen > cubit(/Users/blaise/Development/DMComplex/data/junkTri.gen): 08/31/2013: > 19:01:0 in 2 dimensions: > 0-cells: 6 0 > 2-cells: 4 0 > Labels: > depth: 2 strata of sizes (6, 4) > Cell Sets: 1 strata of sizes (4) > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [0]PETSC ERROR: Arguments must have same communicators > [0]PETSC ERROR: Different communicators in the two objects: Argument # 1 > and 2 flag 3 > [0]PETSC ERROR: See http:// > http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. > [0]PETSC ERROR: Petsc Development GIT revision: v3.4.4-3957-g24a0f54 GIT > Date: 2014-04-02 15:35:24 -0500 > [0]PETSC ERROR: ./testHDF5Plex on a Darwin-llvm50-g named > geothermal.lsu.edu by kumiori Fri Apr 11 12:06:44 2014 > [0]PETSC ERROR: Configure options --CFLAGS=-Wno-unused --download-chaco=1 > --download-exodusii=1 --download-hdf5=1 --download-metis=1 > --download-mpich=1 --download-netcdf=1 --download-parmetis=1 > --download-sowing=1 --download-triangle=1 --download-yaml=1 > --with-cmake=cmake --with-debugging=1 --with-pic --with-shared-libraries=1 > --with-x11=1 PETSC_ARCH=Darwin-llvm50-g > [0]PETSC ERROR: #1 ISView() line 756 in > /opt/HPC/petsc/src/vec/is/is/interface/index.c > [0]PETSC ERROR: #2 DMPlexView_HDF5() line 785 in > /opt/HPC/petsc/src/dm/impls/plex/plex.c > [0]PETSC ERROR: #3 DMView_Plex() line 812 in > /opt/HPC/petsc/src/dm/impls/plex/plex.c > [0]PETSC ERROR: #4 main() line 61 in > /Users/kumiori/Code/dmcomplex/testHDF5Plex.c > [0]PETSC ERROR: ----------------End of Error Message -------send entire > error message to [email protected] > application called MPI_Abort(MPI_COMM_WORLD, 80) - process 0 > [cli_0]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 80) - process 0 > HDF5-DIAG: Error detected in HDF5 (1.8.10-patch1) MPI-process 1: > #000: H5F.c line 2058 in H5Fclose(): decrementing file ID failed > major: Object atom > minor: Unable to close file > #001: H5I.c line 1479 in H5I_dec_app_ref(): can't decrement ID ref count > major: Object atom > minor: Unable to decrement reference count > #002: H5F.c line 1835 in H5F_close(): can't close file > major: File accessability > minor: Unable to close file > #003: H5F.c line 1997 in H5F_try_close(): problems closing file > major: File accessability > minor: Unable to close file > #004: H5F.c line 1142 in H5F_dest(): low level truncate failed > major: File accessability > minor: Write failed > #005: H5FD.c line 1897 in H5FD_truncate(): driver truncate request failed > major: Virtual File Layer > minor: Can't update object > #006: H5FDmpio.c line 1984 in H5FD_mpio_truncate(): MPI_File_set_size > failed > major: Internal error (too specific to document in detail) > minor: Some MPI function failed > #007: H5FDmpio.c line 1984 in H5FD_mpio_truncate(): Invalid argument, > error stack: > MPI_FILE_SET_SIZE(74): Inconsistent arguments to collective routine > major: Internal error (too specific to document in detail) > minor: MPI Error String > [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]PETSCERROR: 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] PetscError line 363 /opt/HPC/petsc/src/sys/error/err.c > [0]PETSC ERROR: [0] ISView line 750 > /opt/HPC/petsc/src/vec/is/is/interface/index.c > [0]PETSC ERROR: [0] DMPlexView_HDF5 line 656 > /opt/HPC/petsc/src/dm/impls/plex/plex.c > [0]PETSC ERROR: [0] DMView_Plex line 803 > /opt/HPC/petsc/src/dm/impls/plex/plex.c > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [0]PETSC ERROR: Signal received > [0]PETSC ERROR: See http:// > http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. > [0]PETSC ERROR: Petsc Development GIT revision: v3.4.4-3957-g24a0f54 GIT > Date: 2014-04-02 15:35:24 -0500 > [0]PETSC ERROR: ./testHDF5Plex on a Darwin-llvm50-g named > geothermal.lsu.edu by kumiori Fri Apr 11 12:06:44 2014 > [0]PETSC ERROR: Configure options --CFLAGS=-Wno-unused --download-chaco=1 > --download-exodusii=1 --download-hdf5=1 --download-metis=1 > --download-mpich=1 --download-netcdf=1 --download-parmetis=1 > --download-sowing=1 --download-triangle=1 --download-yaml=1 > --with-cmake=cmake --with-debugging=1 --with-pic --with-shared-libraries=1 > --with-x11=1 PETSC_ARCH=Darwin-llvm50-g > [0]PETSC ERROR: #5 User provided function() line 0 in unknown file > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > [cli_0]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > > > =================================================================================== > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = EXIT CODE: 59 > = CLEANING UP REMAINING PROCESSES > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > > =================================================================================== > geothermal:dmcomplex kumiori$ > > ---------- end output---------- > > ----------begin C source code testHDF5plex.c -------------- > /* usage: testHDF5plex -i meshfilename > */ > #include <petscdmplex.h> > #include <petscsf.h> > #include <exodusII.h> > #include <petsc-private/dmimpl.h> /*I "petscdm.h" I*/ > #include <petscsf.h> > #include <petscviewerhdf5.h> > #include <petscdmplex.h> > > #undef __FUNCT__ > #define __FUNCT__ "main" > int main(int argc,char **argv) > { > PetscErrorCode ierr; > DM dm; > char ifilename[PETSC_MAX_PATH_LEN]; > PetscBool flg; > int CPU_word_size = 0,IO_word_size = 0,exoid; > float version; > PetscMPIInt numproc,rank; > PetscViewer hdf5Viewer; > PetscInt dim; > PetscInt numFields = 2; > PetscInt numComp[2] = {1,1}; > PetscInt numDof[6] = {1, 0, 0, > 0, 0, 1}; /*{Vertex, Edge, Cell} > */ > PetscInt bcFields[1] = {0}, numBC=0; > IS bcPoints[1] = {NULL}; > PetscSection section; > MPI_Comm comm; > > ierr = PetscInitialize(&argc, &argv, (char*)0, help);CHKERRQ(ierr); > comm = PETSC_COMM_WORLD; > > ierr = PetscOptionsBegin(PETSC_COMM_WORLD,"","testHDF5Plex Test > Options","none");CHKERRQ(ierr); > ierr = PetscOptionsEnd(); > ierr = PetscOptionsGetString(PETSC_NULL,"-i",ifilename,sizeof > ifilename,&flg);CHKERRQ(ierr); > > ierr = MPI_Comm_size(PETSC_COMM_WORLD,&numproc); > ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank); > > ierr = DMPlexCreateExodusFromFile(PETSC_COMM_WORLD, ifilename, > PETSC_FALSE, &dm);CHKERRQ(ierr); > ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); > ierr = DMPlexCreateSection(dm, dim, numFields, numComp, numDof, > numBC, bcFields, bcPoints, NULL, §ion);CHKERRQ(ierr); > ierr = DMSetDefaultSection(dm, section);CHKERRQ(ierr); > ierr = PetscViewerHDF5Open(PetscObjectComm((PetscObject) dm), > "out/seqDM.h5", FILE_MODE_WRITE, &hdf5Viewer); CHKERRQ(ierr); > // Crashes if numproc > 1, > ierr = DMView_Plex(dm, hdf5Viewer); CHKERRQ(ierr); > PetscViewerDestroy(&hdf5Viewer); > > ierr = DMDestroy(&dm);CHKERRQ(ierr); > ierr = PetscFinalize(); > return 0; > } > > ----------end C source code testHDF5plex.c -------------- > > ---------- test mesh > > Andrés A. León Baldelli > -- > LSU Center for Computation & Technology > 2099 Louisiana Digital Media Center > > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener
