[Darshan-users] HDF5 version support

[Jiří Nádvorník]

Hi all,

I was able to successfully run the darshan runtime without any warnings
withou HDF5.

Now when I compile with HDF5 (the results above are without it):
./configure --with-log-path=/gpfs/raid/darshan-logs
--with-jobid-env=PBS_JOBID CC=mpicc --enable-hdf5-mod
--with-hdf5=/gpfs/raid/SDSSCube/ext_lib//hdf5-1.12.0/hdf5/

It messes up my runtime and causes python to crash:
mpirun -x DARSHAN_CONFIG_PATH=/gpfs/raid/SDSSCube/darshan.conf -x
LD_PRELOAD=/gpfs/raid/shared_libs/darshan/darshan-runtime/lib/.libs/libdarshan.so:/gpfs/raid/SDSSCube/ext_lib/hdf5-1.12.0/hdf5/lib/libhdf5.so
-np 65 --hostfile hosts --map-by node
/gpfs/raid/SDSSCube/venv_par/bin/python hisscube.py --truncate
../sdss_data/ results/SDSS_cube_c_par.h5

Resulting in:
INFO:rank[0]:Rank 0 pid: 137058
Darshan HDF5 module error: runtime library version (1.12) incompatible with
Darshan module (1.10-).
Traceback (most recent call last):
  File "hisscube.py", line 74, in <module>
    writer.ingest(fits_image_path, fits_spectra_path,
truncate_file=args.truncate)
  File "/gpfs/raid/SDSSCube/hisscube/ParallelWriterMWMR.py", line 45, in
ingest
    self.process_metadata(image_path, image_pattern, spectra_path,
spectra_pattern, truncate_file)
  File "/gpfs/raid/SDSSCube/hisscube/CWriter.py", line 150, in
process_metadata
    h5_file = self.open_h5_file_serial(truncate_file)
  File "/gpfs/raid/SDSSCube/hisscube/CWriter.py", line 170, in
open_h5_file_serial
    return h5py.File(self.h5_path, 'w', fs_strategy="page",
fs_page_size=4096, libver="latest")
  File
"/gpfs/raid/SDSSCube/venv_par/lib/python3.8/site-packages/h5py-3.6.0-py3.8-linux-x86_64.egg/h5py/_hl/files.py",
line 533, in __init__
    fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
  File
"/gpfs/raid/SDSSCube/venv_par/lib/python3.8/site-packages/h5py-3.6.0-py3.8-linux-x86_64.egg/h5py/_hl/files.py",
line 232, in make_fid
    fid = h5f.create(name, h5f.ACC_TRUNC, fapl=fapl, fcpl=fcpl)
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5f.pyx", line 126, in h5py.h5f.create
  File "h5py/defs.pyx", line 693, in h5py.defs.H5Fcreate
RuntimeError: Unspecified error in H5Fcreate (return value <0)

You are saying that darshan should be compatible with HDF5 > 1.8, which
1.12 should be, right? I checked the source and there is hardcoded if minor
version > 10: not supported.

Thanks for explaining what's supported.

Cheers,

Jiri Nadvornik
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