On Tue, Jun 23, 2015 at 9:38 AM, Dominic Meiser <dmei...@txcorp.com> wrote:
> Hi, > > I'm running into an issue with the Hdf5 viewer. For parallel vectors of > length larger than 2^16 I get the error message below. The vector is > created from a 1D DMDA with 2 dofs. Serial vectors work fine as do vectors > of length <= 2^16. The error message is reproduced below. The issue can be > reproduced with the attached example with 'mpirun -np 2 ./testcase > -da_grid_x 65537'. > > Do I need to configure the viewer in some way before using it? > You may have to configure with --with-64-bit-indices Thanks, Matt > Thanks, > Dominic > > > > HDF5-DIAG: Error detected in HDF5 (1.8.12) MPI-process 0: > #000: H5D.c line 170 in H5Dcreate2(): unable to create dataset > major: Dataset > minor: Unable to initialize object > #001: H5Dint.c line 439 in H5D__create_named(): unable to create and > link to dataset > major: Dataset > minor: Unable to initialize object > #002: H5L.c line 1638 in H5L_link_object(): unable to create new link to > object > major: Links > minor: Unable to initialize object > #003: H5L.c line 1882 in H5L_create_real(): can't insert link > major: Symbol table > minor: Unable to insert object > #004: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal > failed > major: Symbol table > minor: Object not found > #005: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator > failed > major: Symbol table > minor: Callback failed > #006: H5L.c line 1685 in H5L_link_cb(): unable to create object > major: Object header > minor: Unable to initialize object > #007: H5O.c line 3015 in H5O_obj_create(): unable to open object > major: Object header > HDF5-DIAG: Error detected in HDF5 (1.8.12) MPI-process 1: > #000: H5D.c line 170 in H5Dcreate2(): unable to create dataset > major: Dataset > minor: Unable to initialize object > #001: H5Dint.c line 439 in H5D__create_named(): unable to create and > link to dataset > major: Dataset > minor: Unable to initialize object > #002: H5L.c line 1638 in H5L_link_object(): unable to create new link to > object > major: Links > minor: Unable to initialize object > #003: H5L.c line 1882 in H5L_create_real(): can't insert link > major: Symbol table > minor: Unable to insert object > #004: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal > failed > major: Symbol table > minor: Object not found > #005: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator > failed > major: Symbol table > minor: Callback failed > #006: H5L.c line 1685 in H5L_link_cb(): unable to create object > major: Object header > minor: Unable to initialize object > #007: H5O.c line 3015 in H5O_obj_create(): unable to open object > major: Object header > minor: Can't open object > #008: H5Doh.c line 293 in H5O__dset_create(): unable to create dataset > major: Dataset > minor: Unable to initialize object > #009: H5Dint.c line 1044 in H5D__create(): unable to construct layout > information > major: Dataset > minor: Unable to initialize object > #010: H5Dchunk.c line 539 in H5D__chunk_construct(): chunk size must be > <= maximum dimension size for fixed-sized dimensions > major: Dataset > minor: Unable to initialize object > minor: Can't open object > #008: H5Doh.c line 293 in H5O__dset_create(): unable to create dataset > major: Dataset > minor: Unable to initialize object > #009: H5Dint.c line 1044 in H5D__create(): unable to construct layout > information > major: Dataset > minor: Unable to initialize object > #010: H5Dchunk.c line 539 in H5D__chunk_construct(): chunk size must be > <= maximum dimension size for fixed-sized dimensions > major: Dataset > minor: Unable to initialize object > [0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > --------------------- Error Message > -------------------------------------------------------------- > [0]PETSC ERROR: [1]PETSC ERROR: Error in external library > Error in external library > [0]PETSC ERROR: Error in HDF5 call H5Dcreate2() Status -1 > [0]PETSC ERROR: [1]PETSC ERROR: Error in HDF5 call H5Dcreate2() Status -1 > [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > shooting. > [0]PETSC ERROR: Petsc Release Version 3.6.0, unknown > [0]PETSC ERROR: [1]PETSC ERROR: Petsc Release Version 3.6.0, unknown > [1]PETSC ERROR: ./testcase on a fftw_test named longspeak.txcorp.com by > dmeiser Mon Jun 22 16:59:21 2015 > ./testcase on a fftw_test named longspeak.txcorp.com by dmeiser Mon Jun > 22 16:59:21 2015 > [0]PETSC ERROR: Configure options --download-hdf5=1 --download-fftw=1 > --with-mpi=1 PETSC_ARCH=fftw_test > [0]PETSC ERROR: [1]PETSC ERROR: Configure options --download-hdf5=1 > --download-fftw=1 --with-mpi=1 PETSC_ARCH=fftw_test > [1]PETSC ERROR: #1 VecView_MPI_HDF5_DA() line 535 in > /home/scratch/petsc/src/dm/impls/da/gr2.c > #1 VecView_MPI_HDF5_DA() line 535 in > /home/scratch/petsc/src/dm/impls/da/gr2.c > [0]PETSC ERROR: #2 VecView_MPI_DA() line 713 in > /home/scratch/petsc/src/dm/impls/da/gr2.c > [1]PETSC ERROR: #2 VecView_MPI_DA() line 713 in > /home/scratch/petsc/src/dm/impls/da/gr2.c > [0]PETSC ERROR: #3 VecView() line 618 in > /home/scratch/petsc/src/vec/vec/interface/vector.c > [1]PETSC ERROR: #3 VecView() line 618 in > /home/scratch/petsc/src/vec/vec/interface/vector.c > [0]PETSC ERROR: [1]PETSC ERROR: #4 dump() line 75 in testcase.c > #4 dump() line 75 in testcase.c > [0]PETSC ERROR: #5 main() line 31 in testcase.c > [1]PETSC ERROR: #5 main() line 31 in testcase.c > [0]PETSC ERROR: [1]PETSC ERROR: PETSc Option Table entries: > [1]PETSC ERROR: PETSc Option Table entries: > [0]PETSC ERROR: -da_grid_x 65537 > [0]PETSC ERROR: -da_grid_x 65537 > [1]PETSC ERROR: ----------------End of Error Message -------send entire > error message to petsc-ma...@mcs.anl.gov---------- > ----------------End of Error Message -------send entire error message to > petsc-ma...@mcs.anl.gov---------- > [cli_0]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 76) - process 0 > [cli_1]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 76) - process 1 > > > =================================================================================== > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = PID 15847 RUNNING AT longspeak.txcorp.com > = EXIT CODE: 76 > = CLEANING UP REMAINING PROCESSES > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > > =================================================================================== > > -- > Dominic Meiser > Tech-X Corporation > 5621 Arapahoe Avenue > Boulder, CO 80303 > USA > Telephone: 303-996-2036 > Fax: 303-448-7756 > www.txcorp.com > > -- 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