Merge branch 'topic/default/apptainer' into 'branch/default'

First apptainer .def file

See merge request fluiddyn/fluidsim!386

doc/apptainer/README.md

@@ -0,0 +1,42 @@
+# 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:
+
+```sh
+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!):
+
+```sh
+cd ~/apptainer
+apptainer shell --no-home image-fluidsim.sif
+```
+
+From the container:
+
+```sh
+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
+```

doc/apptainer/hgrc

@@ -0,0 +1,32 @@
+[ui]
+# TODO: correct this line.
+username=user_apptainer
+editor=nano
+# another alternative
+# editor=emacs -nw -Q
+tweakdefaults = True
+ignore = ~/.hgignore
+
+[alias]
+lg = log -G
+up = up -v
+
+[extensions]
+hgext.extdiff =
+# only to use Mercurial with GitHub and Gitlab
+hggit =
+# specific extension for FluidDyn dev
+hgfluiddyn =
+# more advanced extensions (really useful for FluidDyn dev)
+churn =
+shelve =
+rebase =
+absorb =
+evolve =
+topic =
+
+[extdiff]
+cmd.meld =
+
+# [subrepos]
+# git:allowed = true

doc/apptainer/image-fluidsim.def

@@ -0,0 +1,54 @@
+BootStrap: docker
+From: python:3.11
+
+%post
+   apt-get -y update
+   apt-get -y install mercurial git less meld nano
+
+   apt-get install -y --no-install-recommends \
+     libfftw3-dev libfftw3-mpi-dev openmpi-bin libhdf5-openmpi-dev libopenblas-dev \
+     gfortran
+
+   mkdir -p /root/.local/include
+   mkdir -p /root/.local/lib
+   export PATH=/root/.local/bin:$PATH
+   export CPATH=/root/.local/include
+   export LIBRARY_PATH=/root/.local/lib
+   export LD_LIBRARY_PATH=/root/.local/lib
+
+   python -m pip install pipx
+
+   pipx install mercurial
+   pipx inject mercurial hg-git hg-evolve hg-fluiddyn
+   wget https://foss.heptapod.net/fluiddyn/fluidsim/-/raw/topic/default/apptainer/doc/apptainer/hgrc -O ~/hgrc
+
+   pipx install pdm
+   pipx install nox
+
+   ln -s /usr/include/fftw* /root/.local/include
+   ln -s /usr/lib/x86_64-linux-gnu/libfftw3* /root/.local/lib
+
+   wget https://foss.heptapod.net/fluiddyn/fluidfft/raw/branch/default/doc/install/install_p3dfft.sh -O ./install_p3dfft.sh
+   chmod +x install_p3dfft.sh
+   export FCFLAGS="-w -fallow-argument-mismatch -O2"
+   export FFLAGS="-w -fallow-argument-mismatch -O2"
+   ./install_p3dfft.sh
+
+   wget https://foss.heptapod.net/fluiddyn/fluidfft/raw/branch/default/doc/install/install_pfft.sh -O ./install_pfft.sh
+   chmod +x install_pfft.sh
+   ./install_pfft.sh
+
+%startscript
+   mkdir -p home
+
+%environment
+   export LC_ALL=C
+   export PATH=/root/.local/bin:$PATH
+   export CPATH=/root/.local/include
+   export LIBRARY_PATH=/root/.local/lib
+   export LD_LIBRARY_PATH=/root/.local/lib
+   export HOME=$HOME/apptainer/home
+   export HGRCPATH=/root/hgrc
+
+%labels
+   Author Pierre Augier

doc/build-from-source.md

@@ -291,6 +291,15 @@ export MESONPY_EDITABLE_VERBOSE=1
 See
 https://meson-python.readthedocs.io/en/latest/how-to-guides/editable-installs.html#verbose-mode
 
+## Installation with Apptainer
+
+```{toctree}
+---
+maxdepth: 1
+---
+apptainer/README.md
+```
+
 [conda-forge]: https://conda-forge.org/
 [evolve]: https://www.mercurial-scm.org/doc/evolution/
 [mercurial]: https://www.mercurial-scm.org/