fix: environment for hpctoolkit container

Author: FoamScience

basic/hpctoolkit.def

@@ -50,7 +50,7 @@ From: containers/basic/{{ BASE_CONTAINER }}.sif
         mawk \
         ninja-build \
         pkg-config \
-        python3 python3-dev python3-myst-parser \
+        python3 python3-dev python3-myst-parser python3-venv \
         sed \
         meson \
         zlib1g-dev
@@ -63,9 +63,10 @@ From: containers/basic/{{ BASE_CONTAINER }}.sif
     cd /opt/hpctoolkit
     git checkout {{ FRAMEWORK_VERSION }}
     # Create hpctoolkit-ci.ini configuration
+    mkdir -p /usr/share/meson/native
     t=/usr/share/meson/native/hpctoolkit-ci.ini
     rm -f "$t"
-    echo "[built-in options]" >> "$t"
+    echo "[built-in options]" > "$t"
     echo "wrap_mode = 'nofallback'" >> "$t"
     echo "force_fallback_for = ['dyninst', 'libunwind', 'xed']" >> "$t"
     echo "" >> "$t"
@@ -84,8 +85,9 @@ From: containers/basic/{{ BASE_CONTAINER }}.sif
     meson setup build
     meson compile -C build
     meson install -C build
-    echo "export JAVA_HOME=${JAVA_HOME} > /opt/hpctoolkit/bashrc"
-    echo "export PATH=${PATH}:${JAVA_HOME}/bin:/opt/hpcviewer >> /opt/hpctoolkit/bashrc"
+    echo "export JAVA_HOME=${JAVA_HOME}" > /opt/hpctoolkit/bashrc
+    echo "export PATH=${PATH}:${JAVA_HOME}/bin:/opt/hpcviewer" >> /opt/hpctoolkit/bashrc
+    echo "export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/local/lib64" >> /opt/hpctoolkit/bashrc
     jq --arg app hpctoolkit --arg commit {{ FRAMEWORK_GIT_REF }} \
         --arg branch {{ FRAMEWORK_GIT_REF }} \
         '.[$app] |= if . == null then

build.yaml

@@ -178,8 +178,6 @@
                 --build-arg BASE_CONTAINER={{ item.base_container }} \
                 --build-arg OS_VERSION={{ containers.basic[item.base_container].os.version }} \
                 --build-arg MPI_VERSION={{ containers.basic[item.base_container].mpi.version }} \
-                --build-arg FRAMEWORK_VERSION={{ containers.basic[item.base_container].framework.version }} \
-                --build-arg FRAMEWORK_GIT_REF={{ containers.basic[item.base_container].framework.git_ref | default('default') }} \
                 {{ original_dir }}/containers/projects/{{ item.name }}.sif \
                 {{ original_dir }}/{{ item.definition }} \
                 > {{ item.name }}.log 2>&1

projects/extend-test.def

@@ -23,8 +23,9 @@ From: {{ CONTAINERS_DIR }}/basic/{{ BASE_CONTAINER }}.sif
 
 %post
     echo "Testing OpenMPI implementation"
-    /bin/bash -c "cd /opt/OMPIFoam && mpicc -o ompiTest testOMPI.cpp"
-    /bin/bash -c "source /opt/foam/foam-extend-{{ OPENFOAM_VERSION }}/etc/bashrc && cd /opt/OMPIFoam && wmake"
+    source $(jq -r '.openfoam.source_script' /apps.json)
+    cd /opt/OMPIFoam && mpicc -o ompiTest testOMPI.cpp
+    cd /opt/OMPIFoam && wmake
     jq --arg app extend-test \
         '.[$app] |= if . == null then
         {
@@ -38,5 +39,26 @@ From: {{ CONTAINERS_DIR }}/basic/{{ BASE_CONTAINER }}.sif
         } end' /apps.json > /tmp/apps.json
     mv /tmp/apps.json /apps.json
 
+%environment
+    #!/bin/bash
+    jq -r '.. | .source_script? // empty' /apps.json | while read -r script; do
+      if [[ -f "$script" ]]; then
+        source "$script"
+      fi
+    done
+    jq -r '.. | .python_env? // empty' /apps.json | while read -r script; do
+      if [[ -f "$script" ]]; then
+        source "$script/bin/activate"
+      fi
+    done
+
+%runscript
+    #!/bin/bash
+    if [ $# -eq 0 ]; then
+        /bin/bash
+    else
+        /bin/bash -c "$@"
+    fi
+
 %labels
     Description Test applications for Foam-Extend

projects/test.def

@@ -26,7 +26,7 @@ From: {{ CONTAINERS_DIR }}/basic/{{ BASE_CONTAINER }}.sif
 
 %post -c /bin/bash
     echo "Testing OpenMPI implementation"
-    source /usr/lib/openfoam/openfoam{{ FRAMEWORK_VERSION }}/etc/bashrc
+    source $(jq -r '.openfoam.source_script' /apps.json)
     export LD_LIBRARY_PATH=/opt/{{ MPI_IMPLEMENTATION }}/lib:$LD_LIBRARY_PATH
     cd /opt/OMPIFoam && mpicc -o ompiTest testOMPI.cpp && wmake
     jq --arg app test --arg branch {{ BRANCH }} \
@@ -44,12 +44,25 @@ From: {{ CONTAINERS_DIR }}/basic/{{ BASE_CONTAINER }}.sif
         } end' /apps.json > /tmp/apps.json
     mv /tmp/apps.json /apps.json
 
+%environment
+    #!/bin/bash
+    jq -r '.. | .source_script? // empty' /apps.json | while read -r script; do
+      if [[ -f "$script" ]]; then
+        source "$script"
+      fi
+    done
+    jq -r '.. | .python_env? // empty' /apps.json | while read -r script; do
+      if [[ -f "$script" ]]; then
+        source "$script/bin/activate"
+      fi
+    done
+
 %runscript
-    /bin/bash -c 'cd /usr/lib/openfoam/openfoam{{ FRAMEWORK_VERSION }} && source etc/bashrc && mkdir -p $FOAM_USER_LIBBIN && mkdir -p $FOAM_USER_APPBIN'
+    #!/bin/bash
     if [ $# -eq 0 ]; then
-        /usr/bin/openfoam{{ FRAMEWORK_VERSION }}
+        /bin/bash
     else
-        /usr/bin/openfoam{{ FRAMEWORK_VERSION }} $@
+        /bin/bash -c "$@"
     fi
 
 %labels