conflict resolve

.github/workflows/backend-template.yml

@@ -81,14 +81,6 @@ jobs:
           restore-keys: |
             ${{ runner.os }}-build-${{ inputs.backend_name }}-
 
-      # Using an exact key to forgo saving it in case of a match (tarring up
-      # is expensive); also including a date to allow a force-update.
-      - name: Load containers cache
-        uses: actions/cache@v3
-        with:
-          path: ~/.apptainer
-          key: Linux-x86_64-containers-build-2023-09-05
-
       - name: Checkout OpenMM (for Lepton library)
         uses: actions/checkout@v3
         with:
@@ -132,12 +124,8 @@ jobs:
         shell: bash
         working-directory: devel-tools
         run: |
-          # 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
+          apptainer pull CentOS7-devel.sif oras://ghcr.io/Colvars/devel-containers:CentOS7-devel
+          apptainer pull CentOS9-devel.sif oras://ghcr.io/Colvars/devel-containers:CentOS9-devel
 
       - name: Update and build ${{ inputs.backend_name }}
         shell: bash
@@ -162,10 +150,34 @@ jobs:
           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: ${{ github.workspace }}/${{ 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 ${{github.workspace}}/devel-tools/${{ 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: ${{ github.workspace }}/${{ inputs.test_interface_directory }}/*/*.diff
+
+      - name: Run regression tests for library code with ${{ inputs.backend_name }} (binary restarts)
+        if: ${{ inputs.test_lib_directory }}
+        shell: bash
+        working-directory: ${{ inputs.test_lib_directory }}
+        env:
+          COLVARS_BINARY_RESTART: 1
+        run: |
+          apptainer exec ${{github.workspace}}/devel-tools/${{ inputs.container_name }}.sif \
+          ./run_tests.sh ${{github.workspace}}/${{ inputs.backend_name }}-source/${{ inputs.rpath_exe }} 0??_*

.github/workflows/test-backends.yml

@@ -99,19 +99,6 @@ jobs:
       private_key: ${{ secrets.PULL_VMD_KEY }}
       private_key_vmd_plugins: ${{ secrets.PULL_VMD_PLUGINS_KEY }}
 
-  gromacs-2021:
-    name: GROMACS 2021
-    if: github.event_name == 'pull_request' || contains(github.event.head_commit.message, 'test-gromacs-2021')
-    uses: ./.github/workflows/backend-template.yml
-    with:
-      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
-
   gromacs-2022:
     name: GROMACS 2022
     if: github.event_name == 'pull_request' || contains(github.event.head_commit.message, 'test-gromacs-2022')
@@ -137,3 +124,16 @@ jobs:
       path_compile_script: devel-tools/compile-gromacs.sh
       test_lib_directory: gromacs/tests/library
       rpath_exe: install/bin/gmx_d
+
+  gromacs-devel:
+    name: GROMACS (MDModules)
+    if: github.event_name == 'pull_request' || contains(github.event.head_commit.message, 'test-gromacs-devel')
+    uses: ./.github/workflows/backend-template.yml
+    with:
+      backend_name: GROMACS-devel
+      backend_repo: gromacs/gromacs
+      backend_repo_ref: main
+      container_name: CentOS9-devel
+      path_compile_script: devel-tools/compile-gromacs.sh
+      test_lib_directory: gromacs/tests/library
+      rpath_exe: install/bin/gmx_d

.github/workflows/test-library.yml

@@ -93,12 +93,6 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - name: Load containers cache
-        uses: actions/cache@v3
-        with:
-          path: ~/.apptainer
-          key: Linux-x86_64-containers-build-doc-2023-07-19
-
       - name: Install Apptainer
         shell: bash
         run: |
@@ -110,9 +104,7 @@ jobs:
         shell: bash
         working-directory: devel-tools
         run: |
-          apptainer remote status SylabsCloud || apptainer remote add --no-login SylabsCloud cloud.sylabs.io
-          apptainer remote use SylabsCloud
-          apptainer pull texlive.sif library://giacomofiorin/default/colvars_development:texlive
+          apptainer pull texlive.sif oras://ghcr.io/Colvars/devel-containers:texlive
 
       - name: Checkout website repository
         uses: actions/checkout@v3
@@ -228,14 +220,6 @@ jobs:
           key: ${{ runner.os }}-build-multiple-${{ github.sha }}
           restore-keys: ${{ runner.os }}-build-multiple-
 
-      # Using an exact key to forgo saving it in case of a match (tarring up
-      # is expensive); also including a date to allow a force-update.
-      - name: Load containers cache
-        uses: actions/cache@v3
-        with:
-          path: ~/.apptainer
-          key: Linux-x86_64-containers-build-2023-09-05
-
       - name: Get small downloadable packages
         uses: actions/checkout@v3
         with:
@@ -250,14 +234,12 @@ jobs:
           sudo apt update
           sudo apt install -y apptainer-suid
 
-      - name: Get container image
+      - name: Get container images for build dependencies
         shell: bash
         working-directory: devel-tools
         run: |
-          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
+          apptainer pull CentOS7-devel.sif oras://ghcr.io/Colvars/devel-containers:CentOS7-devel
+          apptainer pull CentOS9-devel.sif oras://ghcr.io/Colvars/devel-containers:CentOS9-devel
 
       - name: GCC 4.8, C++11 (CentOS 7)
         env:
@@ -384,12 +366,6 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - name: Load containers cache
-        uses: actions/cache@v3
-        with:
-          path: ~/.apptainer
-          key: Linux-x86_64-containers-build-2023-09-05
-
       - name: Checkout Sun compiler (Oracle Developer Studio)
         uses: actions/checkout@v3
         with:
@@ -412,14 +388,11 @@ jobs:
           sudo apt update
           sudo apt install -y apptainer-suid
 
-      - name: Get container image
+      - name: Get container images for build dependencies
         shell: bash
         working-directory: devel-tools
         run: |
-          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
+          apptainer pull CentOS7-devel.sif oras://ghcr.io/Colvars/devel-containers:CentOS7-devel
 
       - name: Build library with Sun compiler (Oracle Developer Studio)
         shell: bash

cmake/CMakeLists.txt

@@ -142,7 +142,7 @@ if(COLVARS_DEBUG)
 endif()
 
 option(ENABLE_COVERAGE "Enable code coverage reporting" ON)
-if(ENABLE_COVERAGE AND (NOT CMAKE_CXX_COMPILER_ID STREQUAL "SunPro"))
+if(ENABLE_COVERAGE AND (NOT CMAKE_CXX_COMPILER_ID STREQUAL "SunPro") AND (NOT CMAKE_CXX_COMPILER_ID STREQUAL "MSVC"))
   target_compile_options(colvars PUBLIC --coverage)
   target_link_options(colvars PUBLIC --coverage)
 endif()

colvartools/plot_colvars_traj.py

@@ -26,6 +26,7 @@ def __init__(self, name):
         self._name = name
         self._step = np.zeros(shape=(0), dtype=np.int64)
         self._colvar = np.zeros(shape=(0), dtype=np.float64)
+        self._warned_dimensions = False
 
     def __len__(self):
         """Returns the length of the trajectory"""
@@ -40,11 +41,12 @@ def __str__(self):
 
     def _set_num_dimensions(self, n_d):
         """Set the number of components of the collective variable"""
-        if (len(self) > 0):
+        if len(self) > 0 and not self._warned_dimensions:
             print("Warning: changing the number of dimensions "
-                  "of collective variable \""+self._name+
+                  "of collective variable \""+self._name +
                   "\" after it has already been read.")
-        if (n_d > 1):
+            self._warned_dimensions = True
+        if n_d > 1:
             self._colvar.resize((len(self), n_d))
         else:
             self._colvar.resize((len(self)))

colvartools/poisson_integrator.cpp

@@ -1,3 +1,4 @@
+#include <iostream>
 #include <fstream>
 
 #include "colvargrid.h"

devel-tools/build_test_library.cmake

@@ -31,8 +31,8 @@ if(DEFINED CMAKE_SYSTEM_NAME AND COLVARS_TCL)
 
   if(EXISTS "${COLVARS_SOURCE_DIR}/devel-tools/packages")
     if(${CMAKE_SYSTEM_NAME} STREQUAL "Linux")
-      set(TCL_DIR "${COLVARS_SOURCE_DIR}/devel-tools/packages/tcl8.5.9-linux-x86_64")
-      set(TCL_LIBRARY "libtcl8.5.a")
+      set(TCL_DIR "${COLVARS_SOURCE_DIR}/devel-tools/packages/tcl8.6.13-linux-x86_64-threaded")
+      set(TCL_LIBRARY "libtcl8.6.a")
     endif()
 
     if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")

devel-tools/compile-gromacs.sh

@@ -9,6 +9,10 @@ source $(dirname $0)/set-ccache.sh
 
 compile_gromacs_target() {
 
+    if [ -n "${GROMACS_REGRESSION_TESTS}" ] ; then
+        export GROMACS_BUILD_TESTS=1
+    fi
+
     local CMAKE=cmake CTEST=ctest
     if hash cmake3 >& /dev/null ; then
         CMAKE=cmake3
@@ -68,8 +72,9 @@ compile_gromacs_target() {
         fi
     fi
 
-    # When on GitHub Actions, download the tests as well
+    # When on GitHub Actions, build the tests as well
     if [ -n "${GITHUB_ACTION}" ] ; then
+        export GROMACS_BUILD_TESTS=1
         GMX_BUILD_OPTS+=(-DREGRESSIONTEST_DOWNLOAD=ON)
     fi
 
@@ -98,25 +103,22 @@ compile_gromacs_target() {
         ${CMAKE} --build "${GMX_BUILD_DIR}" --parallel $(nproc --all)
     ret_code=$?
 
-    if [ -n "${GROMACS_REGRESSION_TESTS}" ] ; then
+    if [ -n "${GROMACS_BUILD_TESTS}" ] ; then
         # Build the tests as well
         ${CMAKE} --build "${GMX_BUILD_DIR}" --target tests --parallel $(nproc --all)
         ret_code=$((${ret_code} || $?))
     fi
 
     if [ ${ret_code} = 0 ] ; then
-        pushd "${GMX_BUILD_DIR}"
-        ${CTEST} --output-on-failure
-        retcode=$?
-        if [ -n "${GMX_INSTALL_DIR}" ] ; then
-            if hash ninja >& /dev/null ; then
-                ninja install
-            else
-                make install
-            fi
-            ret_code=$((${ret_code} || $?))
+        if [ -n "${GROMACS_BUILD_TESTS}" ] && [ -z "${GITHUB_ACTION}" ] ; then
+            # Some GROMACS tests are extremely long, we run them only offline
+            pushd "${GMX_BUILD_DIR}"
+            ${CTEST} --output-on-failure
+            retcode=$((${ret_code} || $?))
+            popd
         fi
-        popd
+        ${CMAKE} --install "${GMX_BUILD_DIR}"
+        ret_code=$((${ret_code} || $?))
     fi
 
     popd

devel-tools/compile-namd.sh

@@ -4,6 +4,9 @@ source $(dirname $0)/load-recent-git.sh
 
 source $(dirname $0)/set-ccache.sh
 
+# Save path to be used later
+devel_tools_folder=$(realpath $(dirname $0))
+
 
 compile_namd_target() {
 
@@ -64,13 +67,28 @@ EOF
         cmd+=(--charm-arch netlrts-linux-x86_64)
     fi
 
-    # Quick check for more recent Tcl using RH and Debian paths
-    if [ -f /usr/lib64/libtcl8.6.so ] || \
-        [ -f /usr/lib/x86_64-linux-gnu/libtcl8.6.so ] ; then
-        sed -i 's/-ltcl8.5/-ltcl8.6/' arch/Linux-x86_64.tcl
+    if grep -q -- -ltcl8.6 arch/Linux-x86_64.tcl ; then
+        if [ -d ${devel_tools_folder}/packages/tcl8.6.13-linux-x86_64-threaded ] ; then
+            export TCL_HOME=${devel_tools_folder}/packages/tcl8.6.13-linux-x86_64-threaded
+        fi
+    else
+        # Amend NAMD 2.x arch file for recent Tcl versions under RH and Debian paths
+        if [ -f /usr/lib64/libtcl8.6.so ] || \
+               [ -f /usr/lib/x86_64-linux-gnu/libtcl8.6.so ] ; then
+            sed -i 's/-ltcl8.5/-ltcl8.6/' arch/Linux-x86_64.tcl
+        fi
+    fi
+
+    if [ -z "${TCL_HOME}" ] ; then
+        if [ -f /usr/local/include/tcl.h ] ; then
+            export TCL_HOME=/usr/local
+        else
+            export TCL_HOME=/usr
+        fi
     fi
 
-    cmd+=(--tcl-prefix ${TCL_HOME:-/usr})
+    cmd+=(--tcl-prefix ${TCL_HOME})
+
     cmd+=(--with-fftw3 --fftw-prefix ${FFTW_HOME:-/usr})
 
     local python_version=$(python3 --version 2> /dev/null | cut -d' ' -f 2)
@@ -83,10 +101,10 @@ EOF
 
     eval ${cmd[@]}
 
-    if pushd ${dirname} ; then 
+    if pushd ${dirname} ; then
         make -j$(nproc --all)
         ret_code=$?
-        popd 
+        popd
     else
         ret_code=1
     fi

devel-tools/containers/CentOS7-devel.def

@@ -10,8 +10,9 @@ From: centos:7
     yum -y update
     yum -y install epel-release centos-release-scl
     yum -y install \
-        redhat-lsb-core "@Development Tools" \
-        ncurses which bc man-db vim emacs screen tmux \
+        redhat-lsb-core \
+        bc man-db vim emacs tcsh which bash-completion screen tmux \
+        "@Development Tools" \
         gcc gcc-c++ gcc-gfortran glibc-static libstdc++-static clang cppcheck \
         autoconf automake cvs git git-cvs cvsps subversion mercurial \
         rh-git227 devtoolset-{7..11} llvm-toolset-7 cmake3 ccache ninja-build \
@@ -55,3 +56,13 @@ EOF
     git clone https://github.com/jhenin/spiff /tmp/spiff && \
         make -C /tmp/spiff && \
         install /tmp/spiff/spiff /usr/local/bin/
+
+    # Install Tcl 8.6 to support newer NAMD versions
+    cd /tmp && \
+        rm -f tcl8.6.13-linux-x86_64-threaded.tar.gz && \
+        curl -O https://www.ks.uiuc.edu/Research/namd/libraries/tcl8.6.13-linux-x86_64-threaded.tar.gz && \
+        tar xzf tcl8.6.13-linux-x86_64-threaded.tar.gz && \
+        cd tcl8.6.13-linux-x86_64-threaded && \
+        find . -type f -exec install -v -D "{}" "/opt/tcl/8.6/{}" \; && \
+        cd && \
+        rm -fr /tmp/tcl8.6.13-linux-x86_64-threaded /tmp/tcl8.6.13-linux-x86_64-threaded.tar.gz

devel-tools/load-openmpi.sh

@@ -1,6 +1,12 @@
 if declare -f module >& /dev/null ; then
+    # Ensure that Lmod is properly initialized
+    source /etc/profile
     # Default modulefile in OpenMPI RPM package
     if module load mpi/openmpi-x86_64 >& /dev/null ; then
         echo "Loaded OpenMPI version $(mpirun --version | head -n 1 | rev | cut -d' ' -f1 | rev)"
+        if ompi_info --param btl vader | grep -q vader ; then
+            # Enforce intra-node communication on recent OpenMPI versions
+            export OMPI_MCA_btl="vader,self"
+        fi
     fi
 fi