Installing mpi4py and hdf5 [parallel] on H2P

commands.sh

# The installation below expects that HDF5 is compiled with shared and parallel capabilities

# 1. Load python and mpi libraries
module purge
module load python/3.7.0 venv/wrap openmpi/3.1.4 hdf5/1.10.7

# 2. Make a new virtual environment (or load an existing one)
mkvirtualenv test
workon test

# 3. Install mpi4py
OMPI_CC=/usr/bin/gcc pip install mpi4py

# Install Parallel HDF5
OMPI_CC=/usr/bin/gcc CC=$(which mpicc) HDF5_DIR=$HDF5_ROOT HDF5_MPI="ON" pip install --no-binary=h5py h5py