setup.md

Install MPICH

1. Login to acfs.

2. Download source codes from the official website. Or equivalently I use:

   cd ~
   wget http://www.mpich.org/static/downloads/3.4.2/mpich-3.4.2.tar.gz

3. Unpack the tar file:

   tar xfz mpich-3.4.2.tar.gz

4. Choose/create an installation directory. MPICH will be installed to this directory:

   mkdir ~/.mpich

5. Choose/create a build directory, which will be deleted after installation.

   mkdir ~/mpich-build

6. Enter the build directory and run configuration. (Output to c.txt.)

   cd ~/mpich-build
   
   /homes/zhd1108/mpich-3.4.2/configure \
   -prefix=/homes/zhd1108/.mpich \
   --with-device=ch4:ofi 2>&1 | tee c.txt

7. Build MPICH (output to m.txt):

   make 2>&1 | m.txt

8. Install MPICH Commands (output to mi.txt):

   make install 2>&1 | tee mi.txt 

9. Add bin to PATH. In ~/.zshrc:

   export PATH="$HOME/.mpich/bin:$PATH"

10. Remove mpich-3.4.2.tar.gz, mpich-3.4.2 and mpich-build.

Install h5py and mpi4py

1. Create a virtual environment:

   cd ~
   mkdir envs
   cd envs
   python3.8 -m venv env_mpih5

2. activate virtual env:

   cd ~
   source ~/envs/env_mpih5/bin/activate

3. upgrade pip

   pip install --upgrade pip

4. install h5py and mpi4py

   pip install h5py
   pip install mpi4py

Install hdf5 for c

1. Download hdf5-1.12.1.tar.bz2 to $HOME
2. Unzip

   tar xvjf hdf5-1.12.1.tar.bz2

3. create build directory:

   mkdir ~/hdf5-build

4. create install folder:

   mkdir ~/.hdf5
   

5. configure:

   cd ~/hdf5-build
   CC=~/.mpich/bin/mpicc ../hdf5-1.12.1/configure --prefix=/homes/zhd1108/.hdf5  --enable-parallel

6. make

   # cd ~/hdf5-build
   make

7.  make check
    make install