FEniCS is available to all users at HPC2N.
FEniCS is free software for automated solution of differential equations.
If you use FEniCS in your research, the developers would be grateful if you would cite the relevant publications. FEniCS is organized as a collection of components, so to give proper credit to the developers of FEniCS, please cite the indicated references for each relevant component.
More about citing FEniCS here.
The FEniCS Project is is a collaborative project for the development of innovative concepts and tools for automated scientific computing, with a particular focus on automated solution of differential equations by finite element methods.
On HPC2N we have FEniCS available on Abisko.
To use the fenics module, add it to your environment:
module add fenics
The recommended usage for FEniCS is as a batch job.
During a job run, FEniCS uses a directory for some cache files, which will be placed in
After a failed run, it is often a good idea to clean the directory, which can be done with
NOTE: Parallel XML mesh output is no longer supported by fenics. It was removed very recently. Use HDF5 format instead.
Example, batch script:
Since parallelism does not work yet, ask for only one core.
#!/bin/bash # Change to your actual SNIC project number #SBATCH -A SNICXXX-YY-ZZ # Asking for 1 core #SBATCH -n 1 # Change to the amount of time you expect your job to use #SBATCH -t 00:30:00 #SBATCH --error=fenics_%J.err #SBATCH --output=fenics_%J.out module add fenics/1.5.0 srun python <file.py>
It is also possible to run FEniCS interactively, instead of as a batch job. If you need to use graphics/the plotting functionality, it is important that you log in with ssh -X username@host to set the display correctly.
NOTE that it will complain about not being able to use/initialize infiniband, since that is not available on the login node. It will instead use other, slower means of communication.
Load the module
module load fenics/1.5.0
and run your program