[petsc-dev] hdf5 viewer question
Dominic Meiser
dmeiser at txcorp.com
Tue Jun 23 12:39:37 CDT 2015
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 <dmeiser at txcorp.com
> <mailto:dmeiser at 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
> <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 petsc-maint at mcs.anl.gov----------
> ----------------End of Error Message -------send entire error
> message to petsc-maint at 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
> <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
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