Implicit fork() while loading h5py

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mersenne zwirn

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Aug 10, 2020, 5:59:17 AM8/10/20
to h5py
h5py seems to do an implicit fork() while being loaded; 
this conflicts with loaded mpi4py module.
Minimal example:

******************************
$ module list
Currently Loaded Modulefiles:
2) gcc/7.4.0 3) openmpi/3.1.4

$ conda list | egrep h5py\|mpi
h5py 2.10.0 nompi_py38hfb01d0b_104 conda-forge
hdf5 1.10.6 nompi_h3c11f04_101 conda-forge
mpi4py 3.0.3 <pip>
$ conda list | egrep python
python 3.8.5 h6f2ec95_2_cpython conda-forge
python_abi 3.8 1_cp38 conda-forge

$ python -c "from mpi4py import MPI; import h5py" -------------------------------------------------------------------------- A process has executed an operation involving a call to the "fork()" system call to create a child process. Open MPI is currently operating in a condition that could result in memory corruption or other system errors; your job may hang, crash, or produce silent data corruption. The use of fork() (or system() or other calls that create child processes) is strongly discouraged. The process that invoked fork was: Local host: [[64729,1],0] (PID 8236) If you are *absolutely sure* that your application will successfully and correctly survive a call to fork(), you may disable this warning by setting the mpi_warn_on_fork MCA parameter to 0.


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h5py is deliberately not built against MPI.

Is the problem harmless?
Thanks
Alain


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