Install Fluidsim from source in an Apptainer container
The directory fluidsim/doc/apptainer
contains what is needed to run Fluidsim
with Apptainer. See also
https://gricad-doc.univ-grenoble-alpes.fr/hpc/softenv/container/.
Build the image locally on a node
From the host:
mkdir ~/apptainer
cd ~/apptainer
wget https://foss.heptapod.net/fluiddyn/fluidsim/-/raw/topic/default/apptainer/doc/apptainer/image-fluidsim.def
apptainer build image-fluidsim.sif image-fluidsim.def
Run the image to install Fluidsim from source
From the host (a node of the cluster!):
cd ~/apptainer
apptainer shell --no-home image-fluidsim.sif
From the container:
python -m venv venv-fluidsim
. venv-fluidsim/bin/activate
HDF5_MPI="ON" pip install --no-binary=h5py h5py pytest pytest-mpi
python -c 'import h5py; h5py.run_tests()'
hg clone https://foss.heptapod.net/fluiddyn/fluidsim
cd fluidsim/
pip install ".[test,mpi,fft]"
pytest --pyargs fluidsim
pip install fluidfft-fftw fluidfft-fftwmpi fluidfft-mpi_with_fftw
mpirun -np 2 pytest --pyargs fluidsim
pip install fluidfft-p3dfft
pip install fluidfft-pfft