From c612b367005d4207f0f36085dfe73bd15af04345 Mon Sep 17 00:00:00 2001
From: Alexandre l'Heritier <alexandre.lheritier@cea.fr>
Date: Mon, 15 Jun 2026 12:35:25 +0200
Subject: [PATCH 1/2] [Minimal] Patch OpenMPI -- Add Pythonnet

---
 .../minimal/build_scripts/minimal_apt.sh      | 30 +++++++++++++++++++
 dockerfiles/minimal/build_scripts/pip.sh      |  4 +--
 2 files changed, 31 insertions(+), 3 deletions(-)

diff --git a/dockerfiles/minimal/build_scripts/minimal_apt.sh b/dockerfiles/minimal/build_scripts/minimal_apt.sh
index ed6e142..5ff8879 100755
--- a/dockerfiles/minimal/build_scripts/minimal_apt.sh
+++ b/dockerfiles/minimal/build_scripts/minimal_apt.sh
@@ -9,6 +9,11 @@ set -e
 #---------------------------------------------------------------------------
 
 apt-get update
+
+# https://github.com/open-mpi/ompi/issues/13886
+echo "path-include=/usr/share/doc/libprrte-dev/help-*" >> /etc/dpkg/dpkg.cfg.d/excludes
+# libprrte-dev gzip
+
 apt-get install -y --no-install-recommends \
   apt-utils \
   gnupg \
@@ -16,15 +21,19 @@ apt-get install -y --no-install-recommends \
   curl \
   rsync \
   build-essential \
+  \
   gcc-15 g++-15 \
   gcc g++ \
+  \
   clang-22 \
   clang-20 \
+  \
   make \
   cmake \
   ccache \
   ninja-build \
   mold \
+  \
   iputils-ping \
   python3-dev \
   python3-pip \
@@ -35,9 +44,14 @@ apt-get install -y --no-install-recommends \
   libboost-program-options-dev \
   libopenblas-dev \
   libxml2-dev \
+  \
   libhdf5-dev \
   libhdf5-openmpi-dev \
+  \
   libopenmpi-dev \
+  gzip \
+  libprrte-dev \
+  \
   libmetis-dev \
   libtbb-dev \
   libunwind-dev \
@@ -61,6 +75,22 @@ update-alternatives --install /usr/bin/clang++ clang++ /usr/bin/clang++-20 90
 #---------------------------------------------------------------------------
 #---------------------------------------------------------------------------
 
+# https://github.com/open-mpi/ompi/issues/13886
+ARCH=`uname -m`
+if [ ! -f /usr/lib/${ARCH}-linux-gnu/prrte3/share/prte/help-prun.txt ]; then
+  # fix a packaging issue: https://bugs.launchpad.net/ubuntu/+source/openmpi/+bug/2155666
+  mkdir -p /usr/lib/${ARCH}-linux-gnu/prrte3/share/prte
+  cp /usr/share/doc/libprrte-dev/help-schizo-ompi.txt /usr/lib/${ARCH}-linux-gnu/prrte3/share/prte/
+  cp /usr/share/doc/libprrte-dev/help-prun.txt.gz /usr/lib/${ARCH}-linux-gnu/prrte3/share/prte/
+  gzip -d /usr/lib/${ARCH}-linux-gnu/prrte3/share/prte/help-prun.txt.gz ;
+fi
+
+# https://github.com/open-mpi/ompi/issues/12517
+echo "export OMPI_MCA_osc=sm" >> /etc/bash.bashrc
+
+#---------------------------------------------------------------------------
+#---------------------------------------------------------------------------
+
 # Cleanup
 rm -rf /var/lib/apt/lists/*
 rm -rf /var/cache/*
diff --git a/dockerfiles/minimal/build_scripts/pip.sh b/dockerfiles/minimal/build_scripts/pip.sh
index 5e615bb..3a32d3f 100755
--- a/dockerfiles/minimal/build_scripts/pip.sh
+++ b/dockerfiles/minimal/build_scripts/pip.sh
@@ -7,10 +7,8 @@ set -e
 #---------------------------------------------------------------------------
 
 # Installation de PythonNet et de NumPy.
-# pip install --break-system-packages \
-#   pythonnet \
-#   numpy
 pip install --break-system-packages \
+  pythonnet \
   numpy
 
 # Cleanup

From 78e141131578c769b3fc6882cef50abc1d41e79f Mon Sep 17 00:00:00 2001
From: Alexandre l'Heritier <alexandre.lheritier@cea.fr>
Date: Tue, 16 Jun 2026 11:48:35 +0200
Subject: [PATCH 2/2] [Minimal] Add env var for login bash

---
 .../minimal/build_scripts/minimal_apt.sh       |  1 +
 dockerfiles/minimal/scripts/config_env.sh      | 18 ++++++++++++++++++
 2 files changed, 19 insertions(+)
 create mode 100644 dockerfiles/minimal/scripts/config_env.sh

diff --git a/dockerfiles/minimal/build_scripts/minimal_apt.sh b/dockerfiles/minimal/build_scripts/minimal_apt.sh
index 5ff8879..c7f21b4 100755
--- a/dockerfiles/minimal/build_scripts/minimal_apt.sh
+++ b/dockerfiles/minimal/build_scripts/minimal_apt.sh
@@ -87,6 +87,7 @@ fi
 
 # https://github.com/open-mpi/ompi/issues/12517
 echo "export OMPI_MCA_osc=sm" >> /etc/bash.bashrc
+echo "export OMPI_MCA_osc=sm" > /etc/profile.d/patch_mpi.sh
 
 #---------------------------------------------------------------------------
 #---------------------------------------------------------------------------
diff --git a/dockerfiles/minimal/scripts/config_env.sh b/dockerfiles/minimal/scripts/config_env.sh
new file mode 100644
index 0000000..77034a3
--- /dev/null
+++ b/dockerfiles/minimal/scripts/config_env.sh
@@ -0,0 +1,18 @@
+#!/bin/sh
+
+# Script permettant de configurer l'environnement initial.
+# Nécessaire uniquement si /etc/profile et/ou /etc/bash.bashrc ne sont sourcés
+# (par exemple avec les options --norc --noprofile).
+
+#---------------------------------------------------------------------------
+#---------------------------------------------------------------------------
+
+export OMPI_MCA_osc=sm
+echo "OMPI_MCA_osc=${OMPI_MCA_osc}"
+
+#---------------------------------------------------------------------------
+#---------------------------------------------------------------------------
+
+if [ -f "/root/scripts/config_env_full.sh" ]; then
+    . /root/scripts/config_env_full.sh
+fi