| # Run in dolfinx-nightly container | |
| from pathlib import Path | |
| from mpi4py import MPI | |
| import dolfinx | |
| import gmsh | |
| def generate_mesh( | |
| path: Path = Path("annulus.msh"), |
| import logging | |
| from mpi4py import MPI | |
| mode2mpi_mode = { | |
| "w": MPI.MODE_WRONLY | MPI.MODE_CREATE | MPI.MODE_EXCL, | |
| "a": MPI.MODE_WRONLY | MPI.MODE_CREATE | MPI.MODE_APPEND, | |
| } | |
| from dataclasses import dataclass | |
| import shutil | |
| from mpi4py import MPI | |
| from petsc4py import PETSc | |
| import dolfinx.fem.petsc | |
| from dolfinx_external_operator import ( | |
| FEMExternalOperator, | |
| evaluate_external_operators, | |
| evaluate_operands, |
| from ghcr.io/fenics/test-env:current-mpich | |
| ENV PETSC_ARCH=linux-gnu-real32-32 | |
| ARG UFL_BRANCH=main | |
| ARG FFCX_BRANCH=main | |
| ARG BUILD_MODE=Release | |
| RUN python3 -m pip install pybind11 | |
| RUN git clone --branch=main --single-branch https://github.com/FEniCS/dolfinx.git |
Here we will explain the steps needed to install fenics development version on ex3 (the HPC cluster at Simula).
Note that the recipe here is rather general and could probalby be adopted to most HPC systems. Note that at the time of writing there is an open PR to add FEniCS devlopment version, and this has to merged (or you need to use my fork) to make it work.
First we need a working C and Fortran compiler before installing anything. To get this I used
module purge
| { | |
| "588e6dc941ef2f6e85f77fa64e1303665906c037": { | |
| "dx0.2_dt0.025": { | |
| "import_time": 6.809999604229233e-07, | |
| "timestamp": "2025-02-14T17:45:30.415965", | |
| "simcardems_version": "2024.0.0", | |
| "dt": 0.025, | |
| "dx": 0.2, | |
| "sha": "588e6dc941ef2f6e85f77fa64e1303665906c037", | |
| "coupling_type": "fully_coupled_ORdmm_Land", |
| import dolfin | |
| import ufl | |
| def subplus(x): | |
| r""" | |
| Ramp function | |
| .. math:: | |
| \max\{x,0\} | |
| """ |
First log in to an ifi machine, i.e
ssh [email protected]
Here you can list the teachers using the command
lsng gin1910
| # Change prefix to what ever you want - I usually install everything in a python virtual environment | |
| export PREFIX=$HOME/.venv | |
| # Activate the virtual environment | |
| source $PREFIX/bin/activate | |
| export HDF5_MPI="ON" | |
| export CC=mpicc | |
| wget https://hdf-wordpress-1.s3.amazonaws.com/wp-content/uploads/manual/HDF5/HDF5_1_12_2/source/hdf5-1.12.2.tar | |
| tar -xvf hdf5-1.12.2.tar && cd hdf5-1.12.2/ && ./configure --enable-parallel --prefix=$PREFIX && make install && cd .. |
| import matplotlib.pyplot as plt | |
| import dolfin | |
| from pulse import Constant | |
| def boundary(x): | |
| return x[0] < dolfin.DOLFIN_EPS or x[0] > 1.0 - dolfin.DOLFIN_EPS | |
| def rhs(x, y): |