Using Fluidsim on Gricad clusters

We show in this directory (https://foss.heptapod.net/fluiddyn/fluidsim/-/tree/branch/default/doc/examples/clusters/gricad) how to use Fluidsim on Gricad clusters. The main documentation for this HPC platform is here. We will use Guix, which is one of the recommended package managers for this platform.

Setup Guix

The first thing to do, is to create the following file ~/.config/guix/channels.scm:

(cons* (channel
          (name 'gricad-guix-packages)
          (url "https://gricad-gitlab.univ-grenoble-alpes.fr/bouttiep/gricad_guix_packages.git")
          (branch "WIP_Benjamin"))
       %default-channels)

Once this is done, you can load and update the Guix environment:

source /applis/site/guix-start.sh
guix pull  # This will take a while

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 should run the following command to be sure you use the lastest guix command:

GUIX_PROFILE="$HOME/.config/guix/current"
. "$GUIX_PROFILE/etc/profile"

Install Fluidsim from source

Install and setup Mercurial as explained here. Clone the Fluidsim repository in $HOME/dev.

Change the changeset used for the Guix environment

One needs to choose a changeset reference (a hash). One can study them with:

cd ~/dev/fluidsim
hg log -G

Get the hash with (note: guix download does not support Mercurial):

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 python-fluidsim.scm.

Build-install from source

source /applis/site/guix-start.sh
DIR_MANIFEST=$HOME/dev/fluidsim/doc/examples/clusters/gricad
# This will take a while
guix shell --pure -m $DIR_MANIFEST/manifest.scm -f $DIR_MANIFEST/python-fluidsim.scm

Test Fluidsim in sequential

source /applis/site/guix-start.sh
DIR_MANIFEST=$HOME/dev/fluidsim/doc/examples/clusters/gricad
guix shell --pure -m $DIR_MANIFEST/manifest.scm -f $DIR_MANIFEST/python-fluidsim.scm
python3 -m pytest --pyargs fluidsim

Submit a Fluidfft benchmark

cd ~/dev/fluidsim/doc/examples/clusters/gricad
oarsub -S ./job_fluidfft_bench.oar

Submit a Fluidsim benchmark

Hand written OAR script

cd ~/dev/fluidsim/doc/examples/clusters/gricad
oarsub -S ./job_fluidsim_bench.oar

With fluiddyn

Prepare a virtual env (1 time).

source /applis/environments/conda.sh
conda create -n env-fluiddyn fluiddyn

Submit with

cd ~/dev/fluidsim/doc/examples/clusters/gricad
source /applis/environments/conda.sh
conda activate env-fluiddyn
python submit_bench_fluidsim.py