HDF5 file not correctly closed #402
Description
There is currently an issue with submitting jobs on a shared file system. A simple test setup:
- Create a job on your own system
- Login to your system via ssh using pysqa and execute the job
- The calculation fails as the HDF5 file remains open after submission
/Software/anaconda3/envs/pyiron_test/lib/python3.9/site-packages/pysqa/utils/remote.py:238: UserWarning: Traceback (most recent call last):
File "/isi/programs/anaconda/anaconda3/envs/pyiron_test/lib/python3.9/runpy.py", line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/isi/programs/anaconda/anaconda3/envs/pyiron_test/lib/python3.9/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/isi/programs/anaconda/anaconda3/envs/pyiron_test/lib/python3.9/site-packages/pyiron_base/cli/__main__.py", line 2, in <module>
main()
File "/isi/programs/anaconda/anaconda3/envs/pyiron_test/lib/python3.9/site-packages/pyiron_base/cli/__init__.py", line 61, in main
args.cli(args)
File "/isi/programs/anaconda/anaconda3/envs/pyiron_test/lib/python3.9/site-packages/pyiron_base/cli/wrapper.py", line 34, in main
job_wrapper_function(
File "/isi/programs/anaconda/anaconda3/envs/pyiron_test/lib/python3.9/site-packages/pyiron_base/job/wrapper.py", line 139, in job_wrapper_function
job = JobWrapper(
File "/isi/programs/anaconda/anaconda3/envs/pyiron_test/lib/python3.9/site-packages/pyiron_base/job/wrapper.py", line 65, in __init__
"status": get_job_status_from_file(
File "/isi/programs/anaconda/anaconda3/envs/pyiron_test/lib/python3.9/site-packages/pyiron_base/database/filetable.py", line 334, in get_job_status_from_file
return h5io.read_hdf5(hdf5_file, job_name + '/status')
File "/isi/programs/anaconda/anaconda3/envs/pyiron_test/lib/python3.9/site-packages/h5io/_h5io.py", line 263, in read_hdf5
with h5py.File(fname, mode='r') as fid:
File "/isi/programs/anaconda/anaconda3/envs/pyiron_test/lib/python3.9/site-packages/h5py/_hl/files.py", line 444, in __init__
fid = make_fid(name, mode, userblock_size,
File "/isi/programs/anaconda/anaconda3/envs/pyiron_test/lib/python3.9/site-packages/h5py/_hl/files.py", line 199, in make_fid
fid = h5f.open(name, flags, fapl=fapl)
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 100, in h5py.h5f.open
OSError: Unable to open file (truncated file: eof = 16384, sblock->base_addr = 0, stored_eof = 284121)
The required modifications to pysqa to work with a shared filesystem are included in pyiron/pysqa#92