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
