Serial and MPI Builds ===================== h5py is available for both serial and MPI builds of HDF5, provided by python3-h5py-serial and python3-h5py-mpi, respectively. The serial build is provided to avoid the library overheads associated with the MPI build, when only serial use is required. In order to provide flexibility, both can be installed at the same time. The choice of which build to use is determined at runtime. In general you would want a serial job to use HDF5-serial and an MPI job to use HDF5-mpi. The installation is set up so that if the job is run in a serial process, then the serial build is invoked (h5py/_debian_h5py_serial). If the job is run in an MPI process (openmpi or mpich), then the MPI build is invoked (h5py/_debian_h5py_mpi). The test for MPI uses the environment variables OMPI_COMM_WORLD_SIZE and MPI_LOCALNRANKS, set automatically at runtime by OpenMPI and MPICH (mpirun), respectively. Selection between serial and mpi builds of h5py is automatic by default (performed in h5py/__init__.py). In normal usage you need only specify "import h5py" as usual without having to specify if you need the serial or mpi version. You can check at runtime if mpi is active from h5py.get_config().mpi. $ python3 -c "import h5py; print(h5py.get_config().mpi)" should return "False" (serial mode) $ mpirun -n 1 python3 -c "import h5py; print(h5py.get_config().mpi)" should return "True" (MPI mode) Enforcing use of h5py-mpi in a serial job ========================================= There may be particular circumstances in which you want to access the MPI build of HDF5 even from a serial job. This might be the case if you have an app that accesses the HDF5 MPI API directly, and so is built against libhdf5-*mpi.so not libhdf5-serial.so. If the same app also uses h5py for convenience, then it should use the equivalent build, i.e. h5py-mpi not h5py-serial, even if it might be run as a serial job. Or you may have reason to access h5py's MPI API (file handling with mpio) even from a serial job. In this case you have three options for enforcing the use of the MPI build in a serial job. 1) You could invoke as a single process MPI job $ mpirun -n 1 python3 myscript.py (technically this is not a serial job as such, but an MPI job with one process) 2) You may import the MPI build directly, using import h5py._debian_h5py_mpi as h5py instead of import h5py 3) Alternatively, you can force the use of the MPI build by setting the environment variable H5PY_ALWAYS_USE_MPI. Option 2 is probably the most transparent, but the other alternatives will work. Obviously python3-h5py-mpi must be installed for any of these to be effective.
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