[petsc-dev] hdf5 viewer question
Matthew Knepley
knepley at gmail.com
Tue Jun 23 12:24:17 CDT 2015
On Tue, Jun 23, 2015 at 12:39 PM, Dominic Meiser <dmeiser at txcorp.com> wrote:
> Hi Matt,
>
> Thanks for your suggestion. I rebuilt with --with-64-bit-indices=1 but I
> get the same result. Any other ideas?
>
There could be a bug with the calculation of chunksize. I will run your
example as soon as I can.
Thanks,
Matt
> 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
>
--
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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