Dear HDF community,
I’m experiencing some troubles with the PHDF5 libraries for the Monte Carlo code OpenMC.
I’m running the software on HPC system where the HDF5 libraries have benn compiled starting from the source of the latest release.
The HPC systems uses SLURM as scheduler for the jobs submission, anche the HFD libraries have been compiles with MPICH 4.0.3 adopting the CFLAGS for read/write large files (>2 GB).
At the moment the reading of the .h5 libraries of OpenMC is correctly performed, but when the code has to write a statepoint (a .h5 file) the code is stuck.
All these operations are performed by using a parallelization MPI/OpenMP on several nodes.
I’m suspecting that there are some errors in the configuration phase, since also the tests on the HDF5 libraries produce some errors
Test filenames are:
ParaTest.h5
Testing -- fapl_mpio duplicate (mpiodup)
Testing -- dataset using split communicators (split)
Testing -- H5Oflush failure (h5oflusherror)
Testing -- H5Oflush failure (h5oflusherror)
Testing -- H5Oflush failure (h5oflusherror)
Testing -- H5Oflush failure (h5oflusherror)
Testing -- H5Oflush failure (h5oflusherror)
Testing -- H5Oflush failure (h5oflusherror)
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 -- MPI-IO VFD file delete (delete)
Testing -- MPI-IO VFD file delete (delete)
Testing -- MPI-IO VFD file delete (delete)
Testing -- MPI-IO VFD file delete (delete)
Testing -- MPI-IO VFD file delete (delete)
Testing -- MPI-IO VFD file delete (delete)
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 grp/dset write - independent grp/dset read (cngrpw-ingrpr)
Testing -- collective grp/dset write - independent grp/dset read (cngrpw-ingrpr)
Testing -- collective grp/dset write - independent grp/dset read (cngrpw-ingrpr)
Testing -- collective grp/dset write - independent grp/dset read (cngrpw-ingrpr)
Testing -- collective grp/dset write - independent grp/dset read (cngrpw-ingrpr)
Testing -- collective grp/dset write - independent grp/dset read (cngrpw-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)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- null dataset test (null)
Testing -- null dataset test (null)
Testing -- null dataset test (null)
Testing -- null dataset test (null)
Testing -- null dataset test (null)
Testing -- null dataset test (null)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- Chunk allocation with alignment bug. (alnbg1)
Testing -- Chunk allocation with alignment bug. (alnbg1)
Testing -- Chunk allocation with alignment bug. (alnbg1)
Testing -- Chunk allocation with alignment bug. (alnbg1)
Testing -- Chunk allocation with alignment bug. (alnbg1)
Testing -- Chunk allocation with alignment bug. (alnbg1)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 2154276 RUNNING AT boot-hpc
= EXIT CODE: 139
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
Thank you!
Domenico