Fenics

Please note that this application page is referring to the old CentOS software stack which is obsolete and does not work any more with the new Ubuntu setup. You can find an overview on the Ubuntu software stack on this wiki page.

Category

Differential equations, Finite elements

Description

FEniCS is a project for the development of concepts and tools for automated scientific computing, with a focus on automated solution of differential equations by finite element methods. It has a list of features for automated, efficient solution of differential equations, including automated solution of variational problems, automated error control and adaptivity, a comprehensive library of finite elements, high performance linear algebra and many more. FEniCS is organized as a collection of interoperable components that together form the FEniCS Project. These components include the problem-solving environment DOLFIN, the form compiler FFC, the finite element tabulator FIAT, the just-in-time compiler Instant, the code generation interface UFC, the form language UFL and a range of additional components.

Available versions (Euler, old software stack)

Legacy versions	Supported versions	New versions
	0.8.0

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

Environment modules (Euler, old software stack)

Version	Module load command	Additional modules loaded automatically
0.8.0	module load stack/2024-06 gcc/12.2.0 openmpi/4.1.6 fenics-dolfinx/0.8.0 py-fenics-ufl/2024.1.0.post1 py-fenics-ffcx/0.8.0 py-fenics-dolfinx/0.8.0 py-fenics-basix/0.8.0 fenics-ufcx/0.8.0 fenics-basix/0.8.0 fenics-ufcx/0.8.0 fenics-basix/0.8.0 python/3.11.6 py-mpi4py/3.1.4 py-petsc4py/3.20.1

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

How to submit a job

You can submit a Python FEniCS job with the following command.

module load stack/2024-06 gcc/12.2.0  openmpi/4.1.6 fenics-dolfinx/0.8.0 py-fenics-ufl/2024.1.0.post1 py-fenics-ffcx/0.8.0 py-fenics-dolfinx/0.8.0 py-fenics-basix/0.8.0 fenics-ufcx/0.8.0 fenics-basix/0.8.0 fenics-ufcx/0.8.0 fenics-basix/0.8.0 python/3.11.6 py-mpi4py/3.1.4 py-petsc4py/3.20.1
sbatch [Slurm options] --wrap="python3 my_fenics_python_script.py"

Here you need to replace [Slurm options] with Slurm parameters for the resource requirements of the job. Please find a documentation about the parameters of sbatch on the wiki page about the batch system.

Example

As an example for using fenics, we are running a script that solves a differential equation:

[eu-login-01 ~]$ module load stack/2024-06 gcc/12.2.0  openmpi/4.1.6 fenics-dolfinx/0.8.0 py-fenics-ufl/2024.1.0.post1 py-fenics-ffcx/0.8.0 py-fenics-dolfinx/0.8.0 py-fenics-basix/0.8.0 fenics-ufcx/0.8.0 fenics-basix/0.8.0 fenics-ufcx/0.8.0 fenics-basix/0.8.0 python/3.11.6 py-mpi4py/3.1.4 py-petsc4py/3.20.1
[eu-login-01 ~]$ ls -ltr
total 4
-rwxr-xr-x 1 euler T0000 219 Sep 14 08:20 test.py
[eu-login-01 ~]$ cat test.py
#!/usr/bin/env python

from mpi4py import MPI
from petsc4py.PETSc import ScalarType  # type: ignore
import numpy as np
import ufl
from dolfinx import fem, io, mesh, plot
from dolfinx.fem.petsc import LinearProblem
from ufl import ds, dx, grad, inner

msh = mesh.create_rectangle(
    comm=MPI.COMM_WORLD,
    points=((0.0, 0.0), (2.0, 1.0)),
    n=(32, 16),
    cell_type=mesh.CellType.triangle,
)
V = fem.functionspace(msh, ("Lagrange", 1))

facets = mesh.locate_entities_boundary(
    msh,
    dim=(msh.topology.dim - 1),
    marker=lambda x: np.isclose(x[0], 0.0) | np.isclose(x[0], 2.0),
)

dofs = fem.locate_dofs_topological(V=V, entity_dim=1, entities=facets)
bc = fem.dirichletbc(value=ScalarType(0), dofs=dofs, V=V)

u = ufl.TrialFunction(V)
v = ufl.TestFunction(V)
x = ufl.SpatialCoordinate(msh)
f = 10 * ufl.exp(-((x[0] - 0.5) ** 2 + (x[1] - 0.5) ** 2) / 0.02)
g = ufl.sin(5 * x[0])
a = inner(grad(u), grad(v)) * dx
L = inner(f, v) * dx + inner(g, v) * ds

problem = LinearProblem(a, L, bcs=[bc], petsc_options={"ksp_type": "preonly", "pc_type": "lu"})
uh = problem.solve()

with io.XDMFFile(msh.comm, "poisson1.xdmf", "w") as file:
    file.write_mesh(msh)
    file.write_function(uh)
[eu-login-1 ~]$ sbatch --mem-per-cpu=4g --wrap="python3 ./test.py"
Generic job.
Job <27435524> is submitted to queue <normal.4h>.

The resource usage summary as well as the job logs can be found in the LSF log file lsf.o27435524.

License information

All FEniCS core components are licensed under the GNU LGPL as published by the Free Software Foundation, either version 3 of the license, or (at your option) any later version. All other FEniCS components are licensed under either the GNU GPL or the GNU LGPL, either version 3 of the license, or (at your option) any later version. Authors and institutions have given their consent to licensing under these terms.

Links

https://fenicsproject.org/

http://hplgit.github.io/fenics-tutorial/doc/pub/ftut.html