From 1764ed63ff765e147c5d3bf75ac65190f03a1b36 Mon Sep 17 00:00:00 2001
From: paugier <pierre.augier@univ-grenoble-alpes.fr>
Date: Wed, 4 Sep 2024 15:06:16 +0200
Subject: [PATCH] examples/clusters/adastra

---
 doc/examples/clusters/adastra/README.md     | 84 +++++++++++++++++++++
 doc/examples/clusters/adastra/setup_venv.sh | 32 ++++++++
 doc/install-clusters.md                     |  1 +
 3 files changed, 117 insertions(+)
 create mode 100644 doc/examples/clusters/adastra/README.md
 create mode 100644 doc/examples/clusters/adastra/setup_venv.sh

diff --git a/doc/examples/clusters/adastra/README.md b/doc/examples/clusters/adastra/README.md
new file mode 100644
index 00000000..a7787b15
--- /dev/null
+++ b/doc/examples/clusters/adastra/README.md
@@ -0,0 +1,84 @@
+# Using Fluidsim on Adastra (CINES)
+
+We show in this directory
+(<https://foss.heptapod.net/fluiddyn/fluidsim/-/tree/branch/default/doc/examples/clusters/adastra>)
+how to use Fluidsim on Adastra. The main documentation for this HPC platform is
+[here](https://dci.dci-gitlab.cines.fr/webextranet/index.html).
+We use modules produced by [Spack](https://spack.io/).
+
+## Get a login and setup ssh
+
+Get an account on <https://www.edari.fr/>.
+
+Set the alias
+
+```sh
+alias sshadastra='ssh -X augier@adastra.cines.fr'
+```
+
+## Setup Mercurial and clone fluidsim
+
+Install and setup Mercurial as explained
+[here](https://fluidhowto.readthedocs.io/en/latest/mercurial/install-setup.html). Clone
+the Fluidsim repository in `$HOME/dev`.
+
+```{warning}
+The file `.bashrc` is not sourced at login so the user should to it is use pipx install applications.
+```
+
+```sh
+mkdir ~/dev
+cd ~/dev
+. ~/.bashrc
+hg clone https://foss.heptapod.net/fluiddyn/fluidsim
+cd ~/dev/fluidsim/doc/examples/clusters/adastra
+
+```
+
+## Setup a virtual environment
+
+Execute the script `setup_venv.sh`.
+
+```sh
+./setup_venv.sh
+```
+
+```{literalinclude} ./setup_venv.sh
+```
+
+Due to a bug in Meson (the build system used by few fluidfft pluggins, see
+https://github.com/mesonbuild/meson/pull/13619), we need to complete the installation:
+
+```sh
+module purge
+module load cpe/23.12
+module load craype-x86-genoa
+module load PrgEnv-gnu
+module load gcc/13.2.0
+module load cray-hdf5-parallel cray-fftw
+module load cray-python
+
+. ~/venv-fluidsim/bin/activate
+
+# --no-build-isolation because of the Meson bug
+
+# because of --no-build-isolation
+cd ~/dev
+hg clone https://github.com/paugier/meson.git
+cd meson
+hg up mpi-detection
+pip install -e .
+cd
+pip install ninja fluidfft-builder
+#
+
+pip install fluidfft-fftwmpi --no-binary fluidfft-fftwmpi --no-build-isolation --force-reinstall --no-cache-dir --no-deps -v
+```
+
+## Install Fluidsim from source
+
+```sh
+cd ~/dev/fluidsim
+# update to the wanted commit
+pip install . -v -C setup-args=-Dnative=true
+```
diff --git a/doc/examples/clusters/adastra/setup_venv.sh b/doc/examples/clusters/adastra/setup_venv.sh
new file mode 100644
index 00000000..f8a1bd70
--- /dev/null
+++ b/doc/examples/clusters/adastra/setup_venv.sh
@@ -0,0 +1,32 @@
+#!/usr/bin/env bash
+set -e
+
+module purge
+module load cpe/23.12
+module load craype-x86-genoa
+module load PrgEnv-gnu
+module load gcc/13.2.0
+module load cray-hdf5-parallel cray-fftw
+module load cray-python
+
+cd $HOME
+python -m venv venv-fluidsim
+.  ~/venv-fluidsim/bin/activate
+
+# install fluidsim and all dependencies from wheels!
+pip install "fluidsim[fft,test]"
+
+# fix/improve few packages (force recompilation)
+pip install fluidfft --no-binary fluidfft -C setup-args=-Dnative=true --force-reinstall --no-cache-dir --no-deps -v
+
+CC=mpicc pip install mpi4py --no-binary mpi4py --force-reinstall --no-cache-dir --no-deps -v
+CC="mpicc" HDF5_MPI="ON" pip install --no-binary=h5py h5py --force-reinstall --no-cache-dir --no-deps -v
+
+export LIBRARY_PATH=/opt/cray/pe/fftw/3.3.10.6/x86_genoa/lib
+export CFLAGS="-I/opt/cray/pe/fftw/3.3.10.6/x86_genoa/include"
+export PYFFTW_LIB_DIR="/opt/cray/pe/fftw/3.3.10.6/x86_genoa/lib"
+
+pip install pyfftw --no-binary pyfftw --force-reinstall --no-cache-dir --no-deps -v
+
+# install fluidfft pluggins
+pip install fluidfft-fftw --no-binary fluidfft-fftw --force-reinstall --no-cache-dir --no-deps -v
diff --git a/doc/install-clusters.md b/doc/install-clusters.md
index 35746b8d..39df1f2a 100644
--- a/doc/install-clusters.md
+++ b/doc/install-clusters.md
@@ -33,4 +33,5 @@ caption: Examples
 maxdepth: 1
 ---
 ./examples/clusters/gricad/README.md
+./examples/clusters/adastra/README.md
 ```