[petsc-dev] DMView_Plex crash with sequential DM and numproc>1
Matthew Knepley
knepley at gmail.com
Fri Apr 11 12:35:52 CDT 2014
On Fri, Apr 11, 2014 at 12:11 PM, Andrés Alessandro León Baldelli <
a.leon.baldelli at gmail.com> 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 petsc-maint at mcs.anl.gov----------
> 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
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