Merge branch 'Colvars:master' into improve_rotation

.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
@@ -58,6 +62,8 @@ on:
 jobs:
   test_backends:
     runs-on: ubuntu-latest
+    env:
+      CCACHE_DIR: ${{ github.workspace }}/ccache_${{ inputs.container_name }}
 
     steps:
       - name: Checkout Colvars
@@ -70,8 +76,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: |
-            ~/.ccache
-            ~/ccache_CentOS7-devel
+            ${{ github.workspace }}/ccache_${{ inputs.container_name }}
           key: ${{ runner.os }}-build-${{ inputs.backend_name }}-${{ github.sha }}
           restore-keys: |
             ${{ runner.os }}-build-${{ inputs.backend_name }}-
@@ -82,7 +87,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ~/.apptainer
-          key: Linux-x86_64-containers-build-2022-10-11
+          key: Linux-x86_64-containers-build-2023-09-05
 
       - name: Checkout OpenMM (for Lepton library)
         uses: actions/checkout@v3
@@ -119,32 +124,29 @@ jobs:
       - name: Install Apptainer
         shell: bash
         run: |
-          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
+          sudo add-apt-repository -y ppa:apptainer/ppa
+          sudo apt update
+          sudo apt install -y apptainer-suid
 
-      - 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
-
-      - name : Get spiff
-        shell: bash
-        working-directory: devel-tools
-        run: sudo cp -f $(apptainer exec CentOS7-devel.sif ./get_spiff) /usr/local/bin
+          apptainer pull CentOS9-devel.sif library://giacomofiorin/default/colvars_development:centos9
 
       - name: Update and build ${{ inputs.backend_name }}
         shell: bash
         env:
           OPENMM_SOURCE: ${{ github.workspace }}/openmm-source
+          CMAKE_GENERATOR: Ninja
         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 ${{ inputs.backend_name }}-source
+          apptainer exec devel-tools/${{ inputs.container_name }}.sif \
           bash ${{ inputs.path_compile_script }} ${{ inputs.backend_name }}-source
 
 
@@ -157,13 +159,28 @@ 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
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v3
+        with:
+          name: failed-library-test-diffs-${{ inputs.backend_name }}
+          path: ${{ inputs.test_lib_directory }}/*/*.diff
+
       - name: Run regression tests for ${{ inputs.backend_name }} interface code
         if: ${{ inputs.test_interface_directory }}
         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
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v3
+        with:
+          name: failed-interface-test-diffs-${{ inputs.backend_name }}
+          path: ${{ inputs.test_interface_directory }}/*/*.diff
+

.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
@@ -95,19 +99,6 @@ jobs:
       private_key: ${{ secrets.PULL_VMD_KEY }}
       private_key_vmd_plugins: ${{ secrets.PULL_VMD_PLUGINS_KEY }}
 
-  gromacs-2020:
-    name: GROMACS 2020
-    if: github.event_name == 'pull_request' || contains(github.event.head_commit.message, 'test-gromacs-2020')
-    uses: ./.github/workflows/backend-template.yml
-    with:
-      backend_name: GROMACS-2020
-      backend_repo: gromacs/gromacs
-      backend_repo_ref: release-2020
-      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
-      rpath_exe: install/bin/gmx_d
-
   gromacs-2021:
     name: GROMACS 2021
     if: github.event_name == 'pull_request' || contains(github.event.head_commit.message, 'test-gromacs-2021')
@@ -116,6 +107,7 @@ 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 +120,20 @@ 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
+
+  gromacs-2023:
+    name: GROMACS 2023
+    if: github.event_name == 'pull_request' || contains(github.event.head_commit.message, 'test-gromacs-2023')
+    uses: ./.github/workflows/backend-template.yml
+    with:
+      backend_name: GROMACS-2023
+      backend_repo: gromacs/gromacs
+      backend_repo_ref: release-2023
+      container_name: CentOS9-devel
       path_compile_script: devel-tools/compile-gromacs.sh
       test_lib_directory: gromacs/tests/library
       rpath_exe: install/bin/gmx_d