Installing h5py with Parallel HDF5

Last updated: April 1, 2021

The following guide is if you want to install h5py with parallel (mpi) IO features. Therefore, h5py also requires a system-mpi linked mpi4py installation as well.

Installation:

Load the current latest parallel HDF5 module (e.g. HDF5/1.10.6-CrayGNU-20.11-parallel).
```
module load HDF5/1.10.6-CrayGNU-20.11-parallel
```

Update environment variables

export MPI_DIR=$MPICH_DIR
export MPI_INCLUDE=$MPICH_DIR/include
export MPI_LIB=$MPICH_DIR/lib
export LB_LIBRARY_PATH=$MPI_DIR/lib:$LD_LIBRARY_PATH
export MPICC=CC
export mpicc=CC

export HDF5_MPI="ON"
export HDF5_DIR=/apps/daint/UES/jenkins/7.0.UP02-20.11/gpu/easybuild/software/HDF5/1.10.6-CrayGNU-20.11-parallel

Install h5py from source.

a. Clone repo locally:
```
git clone https://github.com/h5py/h5py
```
b. Update the setup_build.py file with the additional following include_dirs:
```
settings['include_dirs'] += ['/opt/cray/pe/mpt/7.7.16/gni/mpich-gnu/8.2/include/']
```
c. Install from locally using pip:
```
pip install .
```

Testing:

Test h5py parallel build using following example script (parallel_h5py.py):

from mpi4py import MPI
import h5py

comm = MPI.COMM_WORLD
rank = comm.rank
size = comm.size

f = h5py.File('parallel_test.hdf5', 'w', driver='mpio', comm=MPI.COMM_WORLD)

dset = f.create_dataset('test', (size,), dtype='i')
dset[rank] = rank

f.close()

Load system HDF5/xxx-parallel and your custom python environment with h5py and mpi4py. Run parallel_h5py.py script:
```
srun python parallel_h5py.py
```
Inspect output:
```
h5dump parallel_test.h5
```

Last update: March 9, 2022