How to Install H5PY-MPI

0. Preparation

• linux system
• gcc
• anaconda/miniconda

1. Install open-mpi

Go to "https://www.open-mpi.org/software/".

Download the lastest release (ended with ".tar.gz").

Open the terminal and change dir to the download destination.

Suppose the pack's name is "openmpi-4.1.5.tar.gz".

Run following command to decompress:

tar xvzf openmpi-4.1.5.tar.gz

You will get a folder named "openmpi-4.1.5" under the current dir.
Remember the path of the folder. We will get back here when testing.

In terminal, change dir into the folder.

Run following command to compile (Without --prefix argument, openmpi would be installed in a default location. MAKE SURE it is installed in the default location):

./configure

Run following command to install:

sudo make all install

Run following command to open .bashrc (If you do not want to use vim, use another text editor such as nano or gredit instead.):

sudo vim ~/.bashrc

Add following command at the bottom of .bashrc:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib

Run following command to activate changes immediately:

source ~/.bashrc

Change terminal dir to the example folder of the previous decompressed folder.
In my case, I should run following command:

cd ~/Downloads/openmpi-4.1.5/examples

Run following command to build:

make

Run following command to run test file

mpirun -np 4 hello_c

If the ouput is 4 lines of "Hello World", then you have successfully installed open-mpi.

2. Install HDF5

Go to "https://www.hdfgroup.org/downloads/hdf5/source-code" to download the latest release of HDF5 (which in my case is "hdf5-1.14.2.tar.gz)

Open ternimal. Change dir to the download dest. Run following code to decompress:

tar xvzf hdf5-1.14.2.tar.gz

Change dir into the decompressed folder.

Run following code to set MPI-C as compiler:

export CC=mpicc

Run following code to turn on HDF5_MPI:

export HDF5_MPI="ON"

Run following code to change build config:

./configure --enable-shared --enable-parallel --prefix=/usr/local/hdf5

Run following code to set default HDF5_dir:

export HDF5_DIR="/usr/local/hdf5"

Run following code to compile:

make

Run following code to install HDF5:

sudo make install

Run following code to install some other things (Sry. I'm not sure what "other things" are.):

sudo make check-install

3. Install h5py with MPI and HDF5 build

Create a new env.

Activate the new env and run following command:

conda install openmpi

Install tree additional packages:

conda install gcc_linux-64
conda install gxx_linux-64
conda install gfortran_linux-64

Run following code to set MPI-C as compiler:

export CC=mpicc

Run following code to turn on HDF5_MPI:

export HDF5_MPI="ON"

Run following code to set default HDF5_dir:

export HDF5_DIR="/usr/local/hdf5"

Run following code to build h5py from source:

pip install --no-binary=h5py h5py -i https://pypi.tuna.tsinghua.edu.cn/simple