Merge branch 'master' into BAOA

.github/workflows/backend-template.yml

@@ -25,6 +25,10 @@ on:
         description: "Name of the branch of the backend repository"
         required: true
         type: string
+      container_name:
+        description: "Name of the container used to build on"
+        required: true
+        type: string
       vmd_plugins_repo:
         description: "Name of the VMD plugins repository"
         required: false
@@ -71,7 +75,7 @@ jobs:
         with:
           path: |
             ~/.ccache
-            ~/ccache_CentOS7-devel
+            ~/ccache_${{ inputs.container_name }}
           key: ${{ runner.os }}-build-${{ inputs.backend_name }}-${{ github.sha }}
           restore-keys: |
             ${{ runner.os }}-build-${{ inputs.backend_name }}-
@@ -82,7 +86,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ~/.apptainer
-          key: Linux-x86_64-containers-build-2022-10-11
+          key: Linux-x86_64-containers-build-2023-07-20
 
       - name: Checkout OpenMM (for Lepton library)
         uses: actions/checkout@v3
@@ -122,29 +126,30 @@ jobs:
           wget https://github.com/apptainer/apptainer/releases/download/v1.0.3/apptainer_1.0.3_amd64.deb
           sudo apt-get -y install ./apptainer_1.0.3_amd64.deb
 
-      - name: Get container image of backends' dependencies
+      - name: Get container images for build dependencies
         shell: bash
         working-directory: devel-tools
         run: |
-          # Pull CentOS 7 container used to build backends
+          # Pull all containers used to build backends
           # (contains build tools, OpenMPI, FFTW, Tcl/Tk and Charm++)
           apptainer remote status SylabsCloud || apptainer remote add --no-login SylabsCloud cloud.sylabs.io
           apptainer remote use SylabsCloud
           apptainer pull CentOS7-devel.sif library://giacomofiorin/default/colvars_development:centos7
+          apptainer pull CentOS9-devel.sif library://giacomofiorin/default/colvars_development:centos9
 
       - name : Get spiff
         shell: bash
         working-directory: devel-tools
-        run: sudo cp -f $(apptainer exec CentOS7-devel.sif ./get_spiff) /usr/local/bin
+        run: sudo cp -f $(apptainer exec ${{ inputs.container_name }}.sif ./get_spiff) /usr/local/bin
 
       - name: Update and build ${{ inputs.backend_name }}
         shell: bash
         env:
           OPENMM_SOURCE: ${{ github.workspace }}/openmm-source
         run: |
-          apptainer exec devel-tools/CentOS7-devel.sif ./update-colvars-code.sh -f ${{ inputs.backend_name }}-source
-          CCACHE_DIR=~/ccache_CentOS7-devel \
-          apptainer exec devel-tools/CentOS7-devel.sif \
+          apptainer exec devel-tools/${{ inputs.container_name }}.sif ./update-colvars-code.sh -f ${{ inputs.backend_name }}-source
+          CCACHE_DIR=~/ccache_${{ inputs.container_name }} \
+          apptainer exec devel-tools/${{ inputs.container_name }}.sif \
           bash ${{ inputs.path_compile_script }} ${{ inputs.backend_name }}-source
 
 
@@ -157,7 +162,7 @@ jobs:
         shell: bash
         working-directory: ${{ inputs.test_lib_directory }}
         run: |
-          apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \
+          apptainer exec ${{github.workspace}}/devel-tools/${{ inputs.container_name }}.sif \
           ./run_tests.sh ${{github.workspace}}/${{ inputs.backend_name }}-source/${{ inputs.rpath_exe }} 0??_*
 
       - name: Save failed library test artifact
@@ -172,7 +177,7 @@ jobs:
         shell: bash
         working-directory: ${{ inputs.test_interface_directory }}
         run: |
-          apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \
+          apptainer exec ${{github.workspace}}/devel-tools/${{ inputs.container_name }}.sif \
           ./run_tests.sh ${{github.workspace}}/${{ inputs.backend_name }}-source/${{ inputs.rpath_exe }}
 
       - name: Save failed interface test artifact

.github/workflows/test-backends.yml

@@ -26,6 +26,7 @@ jobs:
       backend_name: LAMMPS
       backend_repo: lammps/lammps
       backend_repo_ref: develop
+      container_name: CentOS7-devel
       path_compile_script: devel-tools/compile-lammps.sh
       test_lib_directory: lammps/tests/library
       test_interface_directory: lammps/tests/interface
@@ -43,6 +44,7 @@ jobs:
       backend_name: NAMD
       backend_repo: Colvars/namd
       backend_repo_ref: master
+      container_name: CentOS7-devel
       path_compile_script: devel-tools/compile-namd.sh
       test_lib_directory: namd/tests/library
       test_interface_directory: namd/tests/interface
@@ -68,6 +70,7 @@ jobs:
       # Interface tests disabled until map variables are merged into NAMD3
       # test_interface_directory: namd/tests/interface
       rpath_exe: Linux-x86_64-g++.multicore/namd3
+      container_name: CentOS7-devel
     secrets:
       # Choice of license by UIUC prevents sharing the code, hence the secret
       private_key: ${{ secrets.PULL_NAMD_KEY }}
@@ -84,6 +87,7 @@ jobs:
       backend_name: VMD
       backend_repo: Colvars/vmd
       backend_repo_ref: master
+      container_name: CentOS7-devel
       # Special variable for VMD test case since it's the only one
       # which needs to checkout 2 repos
       vmd_plugins_repo: Colvars/vmd-plugins
@@ -103,6 +107,7 @@ jobs:
       backend_name: GROMACS-2020
       backend_repo: gromacs/gromacs
       backend_repo_ref: release-2020
+      container_name: CentOS7-devel
       path_compile_script: devel-tools/compile-gromacs.sh
       test_lib_directory: gromacs/tests/library
       # Gromacs need to be compiled in double precision to pass the tests
@@ -116,6 +121,7 @@ jobs:
       backend_name: GROMACS-2021
       backend_repo: gromacs/gromacs
       backend_repo_ref: release-2021
+      container_name: CentOS9-devel
       path_compile_script: devel-tools/compile-gromacs.sh
       test_lib_directory: gromacs/tests/library
       rpath_exe: install/bin/gmx_d
@@ -128,6 +134,7 @@ jobs:
       backend_name: GROMACS-2022
       backend_repo: gromacs/gromacs
       backend_repo_ref: release-2022
+      container_name: CentOS9-devel
       path_compile_script: devel-tools/compile-gromacs.sh
       test_lib_directory: gromacs/tests/library
       rpath_exe: install/bin/gmx_d