Add mpirun wrapper to scrub OpenMPI 5 env vars

Disables shared memory communication to prevent signal 7 bus errors, and
scrubs leaked PMIX/PRTE/OMPI variables from Python singletons to prevent
double-initialization crashes in subprocesses on Fedora.

Author: tomchapman

.ci_fedora.sh

@@ -34,31 +34,53 @@ fi
 test . != ".$1" && mpi="$1" || mpi=openmpi
 
 ## If we are called as normal user, run test
-    cp -a /tmp/BOUT-dev /home/test/
-    . /etc/profile.d/modules.sh
-    module load mpi/${1}-x86_64
-    export OMPI_MCA_rmaps_base_oversubscribe=yes
-    export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe
-    export TRAVIS=true
-    # Try limiting openmp threads
-    export FLEXIBLAS=NETLIB
-    export MKL_NUM_THREADS=1
-    export NUMEXPR_NUM_THREADS=1
-    export OMP_NUM_THREADS=1
-    cd
-    cd BOUT-dev
+cp -a /tmp/BOUT-dev /home/test/
+. /etc/profile.d/modules.sh
+module load mpi/${1}-x86_64
+export OMPI_MCA_rmaps_base_oversubscribe=yes
+export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe
+export TRAVIS=true
+# Try limiting openmp threads
+export FLEXIBLAS=NETLIB
+export MKL_NUM_THREADS=1
+export NUMEXPR_NUM_THREADS=1
+export OMP_NUM_THREADS=1
 
-    echo "Installing Python requirements inside Fedora container..."
-    # Install pytest and dependencies for the user inside the container
-    sudo dnf install -y python3-pip
-    python3 -m pip install --user -r requirements.txt
+# --- NEW FIXES FOR OPENMPI 5 IN DOCKER ---
 
-    echo "starting configure"
-    time cmake -S . -B build -DBOUT_USE_PETSC=ON \
-   -DBOUT_UPDATE_GIT_SUBMODULE=OFF \
-   -DBOUT_USE_SYSTEM_FMT=ON \
-   -DBOUT_USE_SYSTEM_MPARK_VARIANT=ON \
-	 -DBOUT_USE_SUNDIALS=ON
+# 1. Disable shared memory communication to prevent Signal 7 Bus Errors
+export OMPI_MCA_btl="tcp,self"
 
-    time make -C build build-check -j 2
-    time make -C build check
+# 2. Create an mpirun wrapper to scrub leaked environment variables
+#    from Python singletons before they poison the subprocesses.
+mkdir -p "$HOME/bin"
+
+cat << 'EOF' > "$HOME/bin/mpirun"
+#!/bin/bash
+vars=$(env | cut -d= -f1 | grep -E '^(OMPI_|PMIX_|PRTE_)')
+if [ -n "$vars" ]; then
+    unset $vars
+fi
+exec /usr/lib64/openmpi/bin/mpirun "$@"
+EOF
+
+chmod +x "$HOME/bin/mpirun"
+export PATH="$HOME/bin:$PATH"
+
+cd
+cd BOUT-dev
+
+echo "Installing Python requirements inside Fedora container..."
+# Install pytest and dependencies for the user inside the container
+sudo dnf install -y python3-pip
+python3 -m pip install --user -r requirements.txt
+
+echo "starting configure"
+time cmake -S . -B build -DBOUT_USE_PETSC=ON \
+-DBOUT_UPDATE_GIT_SUBMODULE=OFF \
+-DBOUT_USE_SYSTEM_FMT=ON \
+-DBOUT_USE_SYSTEM_MPARK_VARIANT=ON \
+-DBOUT_USE_SUNDIALS=ON
+
+time make -C build build-check -j 2
+time make -C build check