Hi,
I’ve built parallel HDF5 1.8.21 against OpenMPI 4.0.1 on CentOS 7 and a
Lustre 2.12 filesystem using the OS-provided GCC 4.8.5 and am trying to
run the testsuite. I’m failing the testphdf5 test: could anyone help,
please?
I’ve successfully used the same method to pass tests when building HDF5
1.8.21 against different MPIs - MVAPICH2 2.3.1 and IntelMPI 2019.4.243.
I’ve built openmpi 4.0.1 with configure options:
./configure --prefix=$prefix
–with-sge
–with-io-romio-flags=–with-file-system=lustre+ufs
–enable-mpi-cxx
–with-cma
–enable-mpi1-compatibility
–with-ucx=$prefix --without-verbs
–enable-mca-no-build=btl-uct
I’ve set the following MCA param to try and force ROMIO:
export OMPI_MCA_io=romio321
For OpenMPI 4.0.1, I’m getting this failure - any ideas, please?
Thanks,
Mark
$ cat testphdf5.chklog
============================
testphdf5 Test Log
============================
===================================
PHDF5 TESTS START
===================================
MPI-process 1. hostname=login2.arc4.leeds.ac.uk
MPI-process 3. hostname=login2.arc4.leeds.ac.uk
MPI-process 4. hostname=login2.arc4.leeds.ac.uk
MPI-process 5. hostname=login2.arc4.leeds.ac.uk
For help use:
/nobackup/issmcd/login2.arc4.leeds.ac.uk.u4q9A9ALkN/hdf5-1.8.21/testpar/.libs/testphdf5
-help
Linked with hdf5 version 1.8 release 21
For help use:
/nobackup/issmcd/login2.arc4.leeds.ac.uk.u4q9A9ALkN/hdf5-1.8.21/testpar/.libs/testphdf5
-help
Linked with hdf5 version 1.8 release 21
For help use:
/nobackup/issmcd/login2.arc4.leeds.ac.uk.u4q9A9ALkN/hdf5-1.8.21/testpar/.libs/testphdf5
-help
Linked with hdf5 version 1.8 release 21
For help use:
/nobackup/issmcd/login2.arc4.leeds.ac.uk.u4q9A9ALkN/hdf5-1.8.21/testpar/.libs/testphdf5
-help
Linked with hdf5 version 1.8 release 21
MPI-process 2. hostname=login2.arc4.leeds.ac.uk
For help use:
/nobackup/issmcd/login2.arc4.leeds.ac.uk.u4q9A9ALkN/hdf5-1.8.21/testpar/.libs/testphdf5
-help
Linked with hdf5 version 1.8 release 21
MPI-process 0. hostname=login2.arc4.leeds.ac.uk
For help use:
/nobackup/issmcd/login2.arc4.leeds.ac.uk.u4q9A9ALkN/hdf5-1.8.21/testpar/.libs/testphdf5
-help
Linked with hdf5 version 1.8 release 21
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)
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)
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 -- 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)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- chunked dataset with none-selection (selnone)
Testing -- chunked dataset with none-selection (selnone)
Testing -- chunked dataset with none-selection (selnone)
Testing -- chunked dataset with none-selection (selnone)
Testing -- chunked dataset with none-selection (selnone)
Testing -- chunked dataset with none-selection (selnone)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- zero dim dset (zerodsetr)
Testing -- zero dim dset (zerodsetr)
Testing -- zero dim dset (zerodsetr)
Testing -- zero dim dset (zerodsetr)
Testing -- zero dim dset (zerodsetr)
Testing -- zero dim dset (zerodsetr)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups read (ngrpr)
Testing -- multiple groups read (ngrpr)
Testing -- multiple groups read (ngrpr)
Testing -- multiple groups read (ngrpr)
Testing -- multiple groups read (ngrpr)
Testing -- multiple groups read (ngrpr)
Testing -- compact dataset test (compact)
Testing -- compact dataset test (compact)
Testing -- compact dataset test (compact)
Testing -- compact dataset test (compact)
Testing -- compact dataset test (compact)
Testing -- compact dataset test (compact)
Testing -- collective group and dataset write (cngrpw)
Testing -- collective group and dataset write (cngrpw)
Testing -- collective group and dataset write (cngrpw)
Testing -- collective group and dataset write (cngrpw)
Testing -- collective group and dataset write (cngrpw)
Testing -- collective group and dataset write (cngrpw)
Testing -- independent group and dataset read (ingrpr)
Testing -- independent group and dataset read (ingrpr)
Testing -- independent group and dataset read (ingrpr)
Testing -- independent group and dataset read (ingrpr)
Testing -- independent group and dataset read (ingrpr)
Testing -- independent group and dataset read (ingrpr)
Testing -- big dataset test (bigdset)
Testing -- big dataset test (bigdset)
Testing -- big dataset test (bigdset)
Testing -- big dataset test (bigdset)
Testing -- big dataset test (bigdset)
Testing -- big dataset test (bigdset)
Testing -- dataset fill value (fill)
Testing -- dataset fill value (fill)
Testing -- dataset fill value (fill)
Testing -- dataset fill value (fill)
Testing -- dataset fill value (fill)
Testing -- dataset fill value (fill)
Testing -- simple collective chunk io (cchunk1)
Testing -- simple collective chunk io (cchunk1)
Testing -- simple collective chunk io (cchunk1)
Testing -- simple collective chunk io (cchunk1)
Testing -- simple collective chunk io (cchunk1)
Testing -- simple collective chunk io (cchunk1)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- multi-chunk collective chunk io (cchunk3)
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 5 with PID 0 on node login2 exited on signal
14 (Alarm clock).
--------------------------------------------------------------------------
4200.49user 2983.56system 20:01.98elapsed 597%CPU (0avgtext+0avgdata
121548maxresident)k
10480inputs+73472outputs (23major+98853minor)pagefaults 0swaps
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