Fenics¶
This uses Singularity containers, so you should refer to that page first for general information.
Fenics-images are based on these images.
Usage¶
This example shows how you can run a fenics example. To run example one should first copy the examples from the image to a suitable folder:
mkdir -p $WRKDIR/fenics
cd $WRKDIR/fenics
module load singularity-fenics
singularity_wrapper exec cp -r /usr/local/share/dolfin/demo demo
The examples try to use interactive windows to plot the results. This is not
available in the batch queue so to fix this one needs to specify an
alternative matplotlib backend.
This
patch file
fixes example demo_poisson.py. Download it into $WRKDIR/fenics
and run
patch -d demo -p1 < fenics_matplotlib.patch
to fix the example. After this one can run the example with the following
Slurm script
:
#!/bin/bash
#SBATCH --time=00:15:00
#SBATCH --mem=1G
#SBATCH -o fenics_out.out
module purge
module load singularity-fenics
cd demo/documented/poisson/python/
srun singularity_wrapper run demo_poisson.py
To submit the script one only needs to run:
sbatch fenics.sh
Resulting image can be checked with e.g.:
eog demo/documented/poisson/python/poisson.png