FS#61591 - [python-h5py-openmpi] importing h5py package prevents running mpiexec
Attached to Project:
Community Packages
Opened by Zach Jibben (threeofsix) - Thursday, 31 January 2019, 16:32 GMT
Last edited by Bruno Pagani (ArchangeGabriel) - Saturday, 31 October 2020, 15:41 GMT
Opened by Zach Jibben (threeofsix) - Thursday, 31 January 2019, 16:32 GMT
Last edited by Bruno Pagani (ArchangeGabriel) - Saturday, 31 October 2020, 15:41 GMT
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Details
Running mpiexec through subprocess after importing h5py
produces an exit code of 1 and empty stdout/stderr. This
does not occur with h5py 2.9.0 installed via pip.
I am using: - python-h5py-openmpi 2.9.0-1 - openmpi 3.1.3-1 - python 3.7.2-3 Steps to reproduce: Python 3.7.2 (default, Jan 10 2019, 23:51:51) [GCC 8.2.1 20181127] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import subprocess >>> subprocess.run("mpiexec -n 1 echo test", shell=True, capture_output=True) CompletedProcess(args='mpiexec -n 1 echo test', returncode=0, stdout=b'test\n', stderr=b'') >>> import h5py >>> subprocess.run("mpiexec -n 1 echo test", shell=True, capture_output=True) CompletedProcess(args='mpiexec -n 1 echo test', returncode=1, stdout=b'', stderr=b'') After uninstalling python-h5py-openmpi, the error goes away: $ pip install --user h5py $ python Python 3.7.2 (default, Jan 10 2019, 23:51:51) [GCC 8.2.1 20181127] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import subprocess >>> subprocess.run("mpiexec -n 1 echo test", shell=True, capture_output=True) CompletedProcess(args='mpiexec -n 1 echo test', returncode=0, stdout=b'test\n', stderr=b'') >>> import h5py >>> subprocess.run("mpiexec -n 1 echo test", shell=True, capture_output=True) CompletedProcess(args='mpiexec -n 1 echo test', returncode=0, stdout=b'test\n', stderr=b'') I also tested in a Python 3.6.8 virtual environment with h5py 2.9.0 installed via pip, which ran correctly. |
This task depends upon
Closed by Bruno Pagani (ArchangeGabriel)
Saturday, 31 October 2020, 15:41 GMT
Reason for closing: Fixed
Additional comments about closing: Upstream 3.0.0 fixed that issue, now available in our repos.
Saturday, 31 October 2020, 15:41 GMT
Reason for closing: Fixed
Additional comments about closing: Upstream 3.0.0 fixed that issue, now available in our repos.
Comment by
Bruno Pagani (ArchangeGabriel) -
Tuesday, 19 March 2019, 13:09 GMT
No idea why this is happening. You should likely ask upstream
about it.