[petsc-users] parallel IO messages

[Fande Kong]

HI Matt,

Thanks for your reply. I put my application data into PETSc Vec and IS that
take advantage of HDF5 viewer (you implemented). In fact, I did not add any
new output and input functions.

Thanks,

Fande,

On Fri, Nov 27, 2015 at 12:08 PM, Matthew Knepley <knepley at gmail.com> wrote:

> On Fri, Nov 27, 2015 at 1:05 PM, Fande Kong <fdkong.jd at gmail.com> wrote:
>
>> Hi all,
>>
>> I implemented a parallel IO based on the Vec and IS which uses HDF5. I am
>> testing this loader on a supercomputer. I occasionally (not always)
>> encounter the following errors (using 8192 cores):
>>
>
> What is different from the current HDF5 output routines?
>
>   Thanks,
>
>     Matt
>
>
>> [7689]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [7689]PETSC ERROR: Caught signal number 5 TRAP
>> [7689]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> [7689]PETSC ERROR: or see
>> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>> [7689]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac
>> OS X to find memory corruption errors
>> [7689]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> [7689]PETSC ERROR: to get more information on the crash.
>> [7689]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [7689]PETSC ERROR: Signal received
>> [7689]PETSC ERROR: See
>> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
>> [7689]PETSC ERROR: Petsc Release Version 3.6.2, unknown
>> [7689]PETSC ERROR: ./fsi on a arch-linux2-cxx-opt named ys6103 by fandek
>> Fri Nov 27 11:26:30 2015
>> [7689]PETSC ERROR: Configure options --with-clanguage=cxx
>> --with-shared-libraries=1 --download-fblaslapack=1 --with-mpi=1
>> --download-parmetis=1 --download-metis=1 --with-netcdf=1
>> --download-exodusii=1
>> --with-hdf5-dir=/glade/apps/opt/hdf5-mpi/1.8.12/intel/12.1.5
>> --with-debugging=no --with-c2html=0 --with-64-bit-indices=1
>> [7689]PETSC ERROR: #1 User provided function() line 0 in  unknown file
>> Abort(59) on node 7689 (rank 7689 in comm 1140850688): application called
>> MPI_Abort(MPI_COMM_WORLD, 59) - process 7689
>> ERROR: 0031-300  Forcing all remote tasks to exit due to exit code 1 in
>> task 7689
>>
>> Make and configure logs are attached.
>>
>> Thanks,
>>
>> Fande Kong,
>>
>>
>
>
> --
> 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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