Update doc/examples/clusters/gricad_guix

Author: paugier

doc/examples/clusters/gricad/README.md

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+# Using Fluidsim on Gricad clusters
+
+We show in this directory
+(<https://foss.heptapod.net/fluiddyn/fluidsim/-/tree/branch/default/doc/examples/clusters/gricad_guix>)
+how to use Fluidsim on Gricad clusters. The main documentation for this HPC platform is
+[here](https://gricad-doc.univ-grenoble-alpes.fr/hpc/). We will use
+[Guix](https://gricad-doc.univ-grenoble-alpes.fr/hpc/softenv/guix/), which is one of the
+recommended package managers for this platform.
+
+## Get a login and setup ssh
+
+Get an account on <https://perseus.univ-grenoble-alpes.fr/>.
+
+Set an ssh key and the alias
+
+```sh
+alias sshdahu='ssh -X dahu.ciment'
+```
+
+## Setup Mercurial with UV
+
+Install UV with
+
+```sh
+wget -qO- https://astral.sh/uv/install.sh | sh
+```
+
+Logout and login to get a new shell. UV should be available.
+
+```sh
+uv --version
+```
+
+Install and setup Mercurial:
+
+```sh
+uv tool install mercurial --with hg-evolve --with hg-git
+uvx hg-setup init -f
+```
+
+## Setup Guix
+
+The first thing to do, is to create the file `~/.config/guix/channels.scm` with the
+following content:
+
+```lisp
+(cons* (channel
+          (name 'gricad-guix-packages)
+          (url "https://gricad-gitlab.univ-grenoble-alpes.fr/bouttiep/gricad_guix_packages.git")
+          (branch "master"))
+       %default-channels)
+```
+
+Once this is done, you can load and update the Guix environment:
+
+```sh
+source /applis/site/guix-start.sh
+guix pull  # This can take a very long time
+```
+
+You only need to update the Guix environment (and thus run `guix pull`) when a package
+you want to use has been created or updated.
+
+After `guix pull`, you have to run the following command to be sure you use the latest
+`guix` command:
+
+```sh
+GUIX_PROFILE="$HOME/.config/guix/current"
+. "$GUIX_PROFILE/etc/profile"
+```
+
+## Install Fluidsim from source
+
+Clone the Fluidsim repository in `$HOME/dev`:
+
+```sh
+hg clone https://foss.heptapod.net/fluiddyn/fluidsim ~/dev/fluidsim
+```
+
+Update to
+
+```sh
+cd ~/dev/fluidsim
+hg up doc-gricad-guix
+```
+
+### Change the changeset used for the Guix environment
+
+One needs to choose a changeset (a commit) and get its changeset reference (its hash).
+One can study them with:
+
+```sh
+cd ~/dev/fluidsim
+# get the node (changeset reference, hash) of the current commit
+# (you can choose this commit)
+hg log -r . -T "{node}"
+# study all commits
+# (you can choose another commit)
+hg log -G
+```
+
+Get the Guix hash with (note: `guix download` does not support Mercurial). In a new
+terminal (replace `<changeset_ref>` with the chosen Mercurial node):
+
+```sh
+source /applis/site/guix-start.sh
+hg clone https://foss.heptapod.net/fluiddyn/fluidsim ~/dev/fluidsim-clean
+cd ~/dev/fluidsim-clean
+hg up <changeset_ref> --clean
+hg purge --all
+guix hash -x -r .
+```
+
+Change the Mercurial reference and the hash in
+`~/dev/fluidsim/doc/examples/clusters/gricad_guix/python-fluidsim.scm`.
+
+### Build-install from source
+
+```sh
+source /applis/site/guix-start.sh
+DIR_MANIFEST=$HOME/dev/fluidsim/doc/examples/clusters/gricad_guix
+# This will take a while
+guix shell --pure -m $DIR_MANIFEST/manifest.scm -f $DIR_MANIFEST/python-fluidsim.scm
+```
+
+## Test Fluidsim in sequential
+
+```sh
+source /applis/site/guix-start.sh
+DIR_MANIFEST=$HOME/dev/fluidsim/doc/examples/clusters/gricad_guix
+guix shell --pure -m $DIR_MANIFEST/manifest.scm -f $DIR_MANIFEST/python-fluidsim.scm
+python3 -m pytest --pyargs fluidsim
+```
+
+## Submit a Fluidfft benchmark
+
+```sh
+cd ~/dev/fluidsim/doc/examples/clusters/gricad_guix
+oarsub -S ./job_fluidfft_bench.oar
+```
+
+## Submit a Fluidsim benchmark
+
+Here, we are going to show how to do it with two strategies, either manually write a OAR
+script or use fluiddyn to write it.
+
+### Hand written OAR script
+
+```sh
+cd ~/dev/fluidsim/doc/examples/clusters/gricad_guix
+oarsub -S ./job_fluidsim_bench.oar
+```
+
+### With fluiddyn
+
+Prepare a virtual env (1 time). From a new terminal:
+
+```sh
+python3 -m venv ~/venv_fluiddyn
+. ~/venv_fluiddyn/bin/activate
+pip install fluiddyn
+```
+
+Submit with
+
+```sh
+. ~/venv_fluiddyn/bin/activate
+cd ~/dev/fluidsim/doc/examples/clusters/gricad_guix
+python submit_bench_fluidsim.py
+```
+
+````{note}
+Note that the script `submit_bench_fluidsim.py` contains the line:
+
+```python
+from fluiddyn.clusters.gricad import DahuGuix16_6130 as Cluster
+```
+
+The classes `DahuGuix...` are able to write OAR scripts for using Dahu with Guix.
+
+````