Hi Matt, Thanks for your suggestion. I rebuilt with --with-64-bit-indices=1 but I get the same result. Any other ideas? Cheers, Dominic On 06/23/2015 09:23 AM, Matthew Knepley wrote:
On Tue, Jun 23, 2015 at 9:38 AM, Dominic Meiser <[email protected] <mailto:[email protected]>> 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 <http://longspeak.txcorp.com> by dmeiser Mon Jun 22 16:59:21 2015 ./testcase on a fftw_test named longspeak.txcorp.com <http://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 [email protected] ----------------End of Error Message -------send entire error message to [email protected] [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 <http://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 <tel:303-996-2036> Fax: 303-448-7756 <tel:303-448-7756> www.txcorp.com <http://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
-- Dominic Meiser Tech-X Corporation 5621 Arapahoe Avenue Boulder, CO 80303 USA Telephone: 303-996-2036 Fax: 303-448-7756 www.txcorp.com