Running on HPC

ABI HPC Standard

If running on the ABI HPC, you can use a pre-installed (with all necessary libraries) OpenCOR pythonshell. To do this, clone the circulatory_autogen repo into a directory of your choice, then change the python_path in python_path.sh to:

python_path=/hpc/farg967/OpenCOR-0-8-3-Linux/pythonshell

To run in parallel you need to load MPI. Do the following from the {project_dir}/user_run_files dir:

. load_mpi.sh

Then you should be able to run as normal from the user_run_files dir (e.g. ./run_param_id.sh <NUM_CORES> or ./run_sensitivity_analysis.sh <NUM_CORES>).

ABI HPC Extra

If you need to install specific Python libraries that aren't installed in the above OpenCOR Python version, install a separate OpenCOR and then install the libraries. See Getting Started for how to install Python libraries; the process is the same on the HPC.

Warning

Before installing mpi4py in your separate OpenCOR, make sure you load mpi with

module load mpi/mpich-x86_64 && echo "succesfully loaded mpi/mpich-x86_64"