Notes setting up PyNEMO on ARCHER2

Install miniconda

cd /work/n01/n01/<user>
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod u+x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh

Install in /work/n01/n01/$USER/miniconda3 when prompted.

Allow it to modify PYTHONPATH in .bashrc Close and open shell

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Install PyNEMO

cd /work/n01/n01/$USER
git clone https://github.com/NOC-MSM/PyNEMO.git

cd PyNEMO
git checkout IMMERSE
conda env create -f pynemo_37.yml
conda activate pynemo3

# Build and install pynemo
#export JAVA_HOME=/usr/lib64/jvm/java  # Already set, but in the past has not being set has caused trouble.

python setup.py build
export PYTHONPATH=/work/n01/n01/$USER/miniconda3/envs/pynemo3/lib/python3.7/site-packages:$PYTHONPATH
python setup.py install

Verify it works:

pynemo -h

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Subsequent use of PyNEMO build might require explicitly updating the PYTHONPATH variable. E.g.

conda activate pynemo3
export PYTHONPATH=/work/n01/n01/$USER/miniconda3/envs/pynemo3/lib/python3.7/site-packages:$PYTHONPATH