These scripts will automatically build the latest development version of FEniCSX with PETSc and HDF5 support on the University of Luxembourg iris and aion clusters.
To build you need to have an account on and be familiar with using software modules the University of Luxembourg HPC first, see HPC uni.lu Technical documentation
First clone this repository:
cd ~
git clone https://github.com/jhale/fenicsx-iris-cluster.git
cd fenicsx-iris-cluster
Adjust the TAG and FLAGS in ./fenicsx-iris-cluster/env-build-fenics.sh appropriately and
then build FEniCSx:
sbatch build-all.sh
FEniCS jobs can be run in interactive mode using e.g.:
si # Start interactive session
source ${HOME}/fenicsx-<TAG>/bin/env-fenics.sh # <TAG> should be adjusted as appropriate.
srun python3 script_name.py
aion and iris have different OS and architecture so be careful with the FFCx cache.
Included in this repository is a very simple example launcher script to submit jobs on the cluster.
$ cd $HOME
$ cd fenicsx-iris-cluster
$ sbatch -n 4 fenics-launcher.sh python3 poisson.py
For large parallel jobs the time taken to load the shared object files from the cluster can dominate the overall runtime. By default we install the Spindle tool which seems to effectively deal with this issue on iris.
If you have issues then please remove the spindle prefix to srun in the
fenicsx-launcher.sh script.