Hi,
I’d like to compile hdf5 in parallel using opempi compiled with intel 2018.
When executing make check, some tests like t_mpi run without problems but the parallel testphdf5 fails with this error
===================================
Testing testphdf5
===================================
testphdf5 Test Log
===================================
PHDF5 TESTS START
===================================
MPI-process 1. hostname=piscopia
For help use: /home/magaldi/Softwares/Hdf5/parallel_ver/hdf5-1.10.2/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.10 release 2
MPI-process 0. hostname=piscopia
For help use: /home/magaldi/Softwares/Hdf5/parallel_ver/hdf5-1.10.2/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.10 release 2
MPI-process 4. hostname=piscopia
For help use: /home/magaldi/Softwares/Hdf5/parallel_ver/hdf5-1.10.2/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.10 release 2
MPI-process 2. hostname=piscopia
For help use: /home/magaldi/Softwares/Hdf5/parallel_ver/hdf5-1.10.2/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.10 release 2
MPI-process 3. hostname=piscopia
For help use: /home/magaldi/Softwares/Hdf5/parallel_ver/hdf5-1.10.2/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.10 release 2
MPI-process 5. hostname=piscopia
For help use: /home/magaldi/Softwares/Hdf5/parallel_ver/hdf5-1.10.2/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.10 release 2
Test filenames are:
ParaTest.h5
Testing – fapl_mpio duplicate (mpiodup)
Test filenames are:
ParaTest.h5
Testing – fapl_mpio duplicate (mpiodup)
Test filenames are:
ParaTest.h5
Testing – fapl_mpio duplicate (mpiodup)
*** Hint ***
You can use environment variable HDF5_PARAPREFIX to run parallel test files in a
different directory or to add file type prefix. E.g.,
HDF5_PARAPREFIX=pfs:/PFS/user/me
export HDF5_PARAPREFIX
*** End of Hint ***
Test filenames are:
ParaTest.h5
Testing – fapl_mpio duplicate (mpiodup)
Test filenames are:
ParaTest.h5
Testing – fapl_mpio duplicate (mpiodup)
Test filenames are:
ParaTest.h5
Testing – fapl_mpio duplicate (mpiodup)
Testing – dataset using split communicators (split)
Testing – dataset using split communicators (split)
Testing – dataset using split communicators (split)
Testing – dataset using split communicators (split)
Testing – dataset using split communicators (split)
Testing – dataset using split communicators (split)
Testing – Coll Metadata file property settings (props)
Testing – Coll Metadata file property settings (props)
Testing – Coll Metadata file property settings (props)
Testing – Coll Metadata file property settings (props)
Testing – Coll Metadata file property settings (props)
Testing – Coll Metadata file property settings (props)
Testing – dataset independent write (idsetw)
Testing – dataset independent write (idsetw)
Testing – dataset independent write (idsetw)
Testing – dataset independent write (idsetw)
Testing – dataset independent write (idsetw)
Testing – dataset independent write (idsetw)
Testing – dataset independent read (idsetr)
Testing – dataset independent read (idsetr)
Testing – dataset independent read (idsetr)
Testing – dataset independent read (idsetr)
Testing – dataset independent read (idsetr)
Testing – dataset independent read (idsetr)
Testing – dataset collective write (cdsetw)
Testing – dataset collective write (cdsetw)
Testing – dataset collective write (cdsetw)
Testing – dataset collective write (cdsetw)
Testing – dataset collective write (cdsetw)
Testing – dataset collective write (cdsetw)
Testing – dataset collective read (cdsetr)
Testing – dataset collective read (cdsetr)
Testing – dataset collective read (cdsetr)
Testing – dataset collective read (cdsetr)
Testing – dataset collective read (cdsetr)
Testing – dataset collective read (cdsetr)
Testing – extendible dataset independent write (eidsetw)
Testing – extendible dataset independent write (eidsetw)
Testing – extendible dataset independent write (eidsetw)
Testing – extendible dataset independent write (eidsetw)
Testing – extendible dataset independent write (eidsetw)
Testing – extendible dataset independent write (eidsetw)
Testing – extendible dataset independent read (eidsetr)
Testing – extendible dataset independent read (eidsetr)
Testing – extendible dataset independent read (eidsetr)
Testing – extendible dataset independent read (eidsetr)
Testing – extendible dataset independent read (eidsetr)
Testing – extendible dataset independent read (eidsetr)
Testing – extendible dataset collective write (ecdsetw)
Testing – extendible dataset collective write (ecdsetw)
Testing – extendible dataset collective write (ecdsetw)
Testing – extendible dataset collective write (ecdsetw)
Testing – extendible dataset collective write (ecdsetw)
Testing – extendible dataset collective write (ecdsetw)
Proc 1: *** Parallel ERROR ***
VRFY (H5Dwrite succeeded) failed at line 2211 in t_dset.c
aborting MPI processes
Proc 4: *** Parallel ERROR ***
VRFY (H5Dwrite succeeded) failed at line 2211 in t_dset.c
aborting MPI processes
Proc 2: *** Parallel ERROR ***
VRFY (H5Dwrite succeeded) failed at line 2211 in t_dset.c
aborting MPI processes
Proc 0: *** Parallel ERROR ***
VRFY (H5Dwrite succeeded) failed at line 2211 in t_dset.c
aborting MPI processes
Proc 3: *** Parallel ERROR ***
VRFY (H5Dwrite succeeded) failed at line 2211 in t_dset.c
aborting MPI processes
Proc 5: *** Parallel ERROR ***
VRFY (H5Dwrite succeeded) failed at line 2211 in t_dset.c
aborting MPI processes
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 4 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[piscopia:34187] 5 more processes have sent help message help-mpi-api.txt / mpi-abort
[piscopia:34187] Set MCA parameter “orte_base_help_aggregate” to 0 to see all help / error messages
Makefile:1432: recipe for target ‘testphdf5.chkexe_’ failed
make[4]: *** [testphdf5.chkexe_] Error 1
make[4]: Leaving directory ‘/home/magaldi/Softwares/Hdf5/parallel_ver/hdf5-1.10.2/testpar’
Makefile:1541: recipe for target ‘build-check-p’ failed
make[3]: *** [build-check-p] Error 1
make[3]: Leaving directory ‘/home/magaldi/Softwares/Hdf5/parallel_ver/hdf5-1.10.2/testpar’
Makefile:1412: recipe for target ‘test’ failed
make[2]: *** [test] Error 2
make[2]: Leaving directory ‘/home/magaldi/Softwares/Hdf5/parallel_ver/hdf5-1.10.2/testpar’
Makefile:1213: recipe for target ‘check-am’ failed
make[1]: *** [check-am] Error 2
make[1]: Leaving directory ‘/home/magaldi/Softwares/Hdf5/parallel_ver/hdf5-1.10.2/testpar’
Makefile:652: recipe for target ‘check-recursive’ failed
make: *** [check-recursive] Error 1
Could you please help me find out what’s going on?
Thanks,
m