Fixed conflicts

zwpku · Dec 11, 2023 · a244537 · a244537
2 parents ba18c36 + f8ed169
commit a244537
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diff --git a/.github/workflows/backend-template.yml b/.github/workflows/backend-template.yml
@@ -63,9 +63,10 @@ jobs:
   test_backends:
     runs-on: ubuntu-latest
     env:
-      CCACHE_DIR: ${{ github.workspace }}/ccache_${{ inputs.container_name }}
-      # Silence OpenMPI warnings
-      PSM3_MULTI_EP: 1
+      CCACHE_DIR: ~/ccache_${{ inputs.container_name }}
+      # OpenMPI transport settings suitable for GH VMs
+      OMPI_MCA_mtl: "^ofi"
+      OMPI_MCA_btl: "vader,self"
 
     steps:
       - name: Checkout Colvars
@@ -78,7 +79,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: |
-            ${{ github.workspace }}/ccache_${{ inputs.container_name }}
+            ~/ccache_${{ inputs.container_name }}
           key: ${{ runner.os }}-build-${{ inputs.backend_name }}-${{ github.sha }}
           restore-keys: |
             ${{ runner.os }}-build-${{ inputs.backend_name }}-
@@ -126,18 +127,19 @@ jobs:
         shell: bash
         working-directory: devel-tools
         run: |
-          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
+          apptainer pull ${{ inputs.container_name }}.sif oras://ghcr.io/Colvars/devel-containers:${{ inputs.container_name }}
 
       - name: Update and build ${{ inputs.backend_name }}
         shell: bash
         env:
           OPENMM_SOURCE: ${{ github.workspace }}/openmm-source
           CMAKE_GENERATOR: Ninja
         run: |
-          apptainer exec devel-tools/${{ 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
+              ./update-colvars-code.sh -f ${{ inputs.backend_name }}-source
+          mkdir -p ${CCACHE_DIR}
+          apptainer exec devel-tools/${{ inputs.container_name }}.sif \
+              bash ${{ inputs.path_compile_script }} ${{ inputs.backend_name }}-source
 
 
       # 2 types of tests can be performed with the MD engine: library & interface

diff --git a/.github/workflows/test-backends.yml b/.github/workflows/test-backends.yml
@@ -1,6 +1,8 @@
 name: "Backends"
 
-on: [push, pull_request]
+on:
+  push:
+
 
 # These jobs call a template workflow `backend-template.yml`, which performs
 # all the necessary steps to run the regression tests of the backend.
@@ -18,11 +20,8 @@ env:
 
 jobs:
 
-  lammps:
-    name: LAMMPS
-    if: |
-      (github.event_name == 'pull_request') ||
-      (github.event_name == 'push' && (contains(github.event.head_commit.message, 'test-lammps') || github.event.base_ref == 'refs/heads/master'))
+  lammps-develop:
+    name: LAMMPS (develop)
     uses: ./.github/workflows/backend-template.yml
     with:
       backend_name: LAMMPS
@@ -34,56 +33,28 @@ jobs:
       test_interface_directory: lammps/tests/interface
       rpath_exe: install/bin/lmp
 
-  namd:
-    name: NAMD
+  namd-devel:
+    name: NAMD (devel)
     # Prevent running this job on PRs across different accounts, because
     # secrets wouldn't be shared
-    if: |
-      (github.event_name == 'pull_request' && github.repository_owner == github.event.pull_request.head.repo.owner.login) ||
-      (github.event_name == 'push' && (contains(github.event.head_commit.message, 'test-namd') || github.event.base_ref == 'refs/heads/master'))
     uses: ./.github/workflows/backend-template.yml
     with:
       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
-      rpath_exe: Linux-x86_64-g++.mpi/namd2
-    secrets:
-      # Choice of license by UIUC prevents sharing the code, hence the secret
-      private_key: ${{ secrets.PULL_NAMD_KEY }}
-
-  namd3:
-    name: NAMD3 (no CUDA)
-    # Prevent running this job on PRs across different accounts, because
-    # secrets wouldn't be shared
-    if: |
-      (github.event_name == 'pull_request' && github.repository_owner == github.event.pull_request.head.repo.owner.login) ||
-      (github.event_name == 'push' && (contains(github.event.head_commit.message, 'test-namd') || github.event.base_ref == 'refs/heads/master'))
-    uses: ./.github/workflows/backend-template.yml
-    with:
-      backend_name: NAMD3
-      backend_repo: Colvars/namd
       backend_repo_ref: devel
       path_compile_script: devel-tools/compile-namd.sh
       test_lib_directory: namd/tests/library
-      # Interface tests disabled until map variables are merged into NAMD3
-      # test_interface_directory: namd/tests/interface
+      test_interface_directory: namd/tests/interface
       rpath_exe: Linux-x86_64-g++.mpi/namd3
       container_name: CentOS7-devel
     secrets:
       # Choice of license by UIUC prevents sharing the code, hence the secret
       private_key: ${{ secrets.PULL_NAMD_KEY }}
 
-  vmd:
+  vmd-cvs:
     name: VMD
     # Prevent running this job on PRs across different accounts, because
     # secrets wouldn't be shared
-    if: |
-      (github.event_name == 'pull_request' && github.repository_owner == github.event.pull_request.head.repo.owner.login) ||
-      (github.event_name == 'push' && (contains(github.event.head_commit.message, 'test-vmd') || github.event.base_ref == 'refs/heads/master'))
     uses: ./.github/workflows/backend-template.yml
     with:
       backend_name: VMD
@@ -102,10 +73,7 @@ jobs:
       private_key_vmd_plugins: ${{ secrets.PULL_VMD_PLUGINS_KEY }}
 
   gromacs-2022:
-    name: GROMACS 2022
-    if: |
-      (github.event_name == 'pull_request') ||
-      (github.event_name == 'push' && (contains(github.event.head_commit.message, 'test-gromacs') || github.event.base_ref == 'refs/heads/master'))
+    name: GROMACS (release-2022)
     uses: ./.github/workflows/backend-template.yml
     with:
       backend_name: GROMACS-2022
@@ -117,10 +85,7 @@ jobs:
       rpath_exe: install/bin/gmx_d
 
   gromacs-2023:
-    name: GROMACS 2023
-    if: |
-      (github.event_name == 'pull_request') ||
-      (github.event_name == 'push' && (contains(github.event.head_commit.message, 'test-gromacs') || github.event.base_ref == 'refs/heads/master'))
+    name: GROMACS (release-2023)
     uses: ./.github/workflows/backend-template.yml
     with:
       backend_name: GROMACS-2023
@@ -131,14 +96,11 @@ jobs:
       test_lib_directory: gromacs/tests/library
       rpath_exe: install/bin/gmx_d
 
-  gromacs-devel:
-    name: GROMACS (MDModules)
-    if: |
-      (github.event_name == 'pull_request') ||
-      (github.event_name == 'push' && (contains(github.event.head_commit.message, 'test-gromacs') || github.event.base_ref == 'refs/heads/master'))
+  gromacs-main:
+    name: GROMACS (main)
     uses: ./.github/workflows/backend-template.yml
     with:
-      backend_name: GROMACS-devel
+      backend_name: GROMACS-main
       backend_repo: gromacs/gromacs
       backend_repo_ref: main
       container_name: CentOS9-devel

diff --git a/.github/workflows/test-library.yml b/.github/workflows/test-library.yml
@@ -1,6 +1,7 @@
 name: "Library"
 
-on: [push, pull_request]
+on:
+  push:
 
 
 jobs:
@@ -9,7 +10,6 @@ jobs:
 
     name: Basic checks
     runs-on: ubuntu-latest
-    if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
     outputs:
       hassecrets: ${{ steps.checksecrets.outputs.hassecrets }}
     env:
@@ -84,6 +84,13 @@ jobs:
       - name: Print ccache stats
         run: ccache -s -v
 
+      - name: Keep only one cache besides the one from this job
+        shell: bash
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          bash ${{ github.workspace }}/devel-tools/cleanup-gh-cache.sh ${{ runner.os }}-build-basic-
+
 
   build-doc:
     name: Build documentation
@@ -109,12 +116,36 @@ jobs:
       - name: Checkout website repository
         uses: actions/checkout@v4
         with:
+          ssh-key: ${{ secrets.PULL_PUSH_COLVARS_GITHUB_IO }}
           repository: 'Colvars/colvars.github.io'
           path: 'website'
 
-      - name: Build doc
+      - name: Build doc for current branch
+        working-directory: doc
+        run: |
+          make clean-all
+          apptainer exec ${{ github.workspace }}/devel-tools/texlive.sif make
+
+      - name: Install SSH key for access to website repository
+        if: contains(github.event.head_commit.message, '[update-doc]')
+        env:
+          WEBSITE_SSH_KEY: ${{ secrets.PULL_PUSH_COLVARS_GITHUB_IO }}
+        run: |
+          mkdir -p -m 700 ~/.ssh
+          echo "${WEBSITE_SSH_KEY}" > ~/.ssh/website
+          chmod 600 ~/.ssh/website
+
+      - name: Push updated doc to website repository
         working-directory: doc
-        run: apptainer exec ${{ github.workspace }}/devel-tools/texlive.sif make
+        if: contains(github.event.head_commit.message, '[update-doc]')
+        env:
+          COLVARS_WEBSITE_TREE: ${{ github.workspace }}/website
+        run: |
+          apptainer exec ${{ github.workspace }}/devel-tools/texlive.sif make install
+          export GIT_SSH="ssh -i ~/.ssh/website"
+          git config --global user.email "[email protected]"
+          git config --global user.name "CI runner"
+          bash update_website.sh ${{ github.workspace }}/website
 
 
   codeql:
@@ -267,7 +298,6 @@ jobs:
     name: Linux x86_64 (GCC, Clang)
     runs-on: ubuntu-latest
     needs: basicchecks
-    if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
     env:
       CCACHE: ccache
       CMAKE_GENERATOR: Ninja
@@ -478,7 +508,6 @@ jobs:
     name: Windows x86_64 (MSVC)
     runs-on: windows-latest
     needs: basicchecks
-    if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
 
     steps:
 
@@ -500,7 +529,6 @@ jobs:
     name: macOS x86_64 (AppleClang)
     runs-on: macos-latest
     needs: basicchecks
-    if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
 
     steps:
 

diff --git a/README.md b/README.md
@@ -2,17 +2,16 @@
 
 A software module for molecular simulation and analysis that provides a high-performance implementation of sampling algorithms defined on a reduced space of continuously differentiable functions (aka collective variables).
 
-First released in 2008 as part of the standard distribution of [NAMD](https://www.ks.uiuc.edu/Research/namd/) version 2.7b1, Colvars has also been integrated in [LAMMPS](https://lammps.sandia.gov/download.html) and [VMD](https://www.ks.uiuc.edu/Research/vmd/).  In VMD, interactive use is possible both from the command line and through the [Dashboard](vmd/cv_dashboard/README.md) graphical user interface.
+First released in 2008 as part of the standard distribution of [NAMD](https://www.ks.uiuc.edu/Research/namd/) version 2.7b1, Colvars has also been integrated in [LAMMPS](https://lammps.sandia.gov/download.html), [VMD](https://www.ks.uiuc.edu/Research/vmd/), [GROMACS](http://www.gromacs.org/), and [Tinker-HP](https://tinker-hp.org/).  In VMD, interactive use is possible both from the command line and through the [Dashboard](vmd/cv_dashboard/README.md) graphical user interface.
 
-Patched [releases](https://github.com/Colvars/gromacs) of [GROMACS](http://www.gromacs.org/) that contain Colvars are also available ([see below](#gromacs-colvars-releases)).
-
-The functionality provided by the Colvars library includes a variety of functions and algorithms, including free-energy estimators based on thermodynamic forces, non-equilibrium work and probability distributions.
+The functionality provided to those packages by the Colvars library includes a variety of functions and algorithms, including free-energy estimators based on thermodynamic forces, non-equilibrium work and probability distributions.
 
 ## Obtaining and using
 
 The easiest way to obtain pre-compiled versions of Colvars is via one of following:
 - the molecular simulation program [LAMMPS](https://lammps.sandia.gov/download.html);
 - the molecular simulation program [NAMD](https://www.ks.uiuc.edu/Research/namd/);
+- the molecular simulation program [Tinker-HP](https://tinker-hp.org/);
 - the molecular visualization program [VMD](https://www.ks.uiuc.edu/Research/vmd/).
 
 Please check [here](https://github.com/Colvars/colvars/wiki/List-of-Colvars-versions-included-in-simulation-and-analysis-packages) to see which version of Colvars is included with the round-number or "stable" versions of each code.
@@ -21,9 +20,9 @@ For the molecular simulation program [GROMACS](http://www.gromacs.org/), code ma
 
 ## Documentation
 
-The [Colvars webpage](https://colvars.github.io/) includes user documentation for the four codes, as well as a Doxygen-based [developer documentation](https://colvars.github.io/doxygen/html/).
+The [Colvars webpage](https://colvars.github.io/) includes user documentation for all codes, as well as a Doxygen-based [developer documentation](https://colvars.github.io/doxygen/html/).
 
-To reflect the different availability of features in each engine, the Colvars reference manual comes in several flavors: [GROMACS](https://colvars.github.io/colvars-refman-gromacs/colvars-refman-gromacs.html) [LAMMPS](https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html) [NAMD](https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html) [VMD](https://colvars.github.io/colvars-refman-vmd/colvars-refman-vmd.html)
+To reflect the different availability of features in each engine, the Colvars reference manual comes in several flavors: [GROMACS](https://colvars.github.io/colvars-refman-gromacs/colvars-refman-gromacs.html) [LAMMPS](https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html) [NAMD](https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html) [Tinker-HP](https://colvars.github.io/colvars-refman-tinkerhp/colvars-refman-tinkerhp.html) [VMD](https://colvars.github.io/colvars-refman-vmd/colvars-refman-vmd.html)
 
 ## Citing
 
@@ -52,10 +51,13 @@ cv configfile <Colvars configuration file>
 ```
 fix Colvars all colvars configfile <Colvars configuration file>
 ```
-- In GROMACS:
+- In GROMACS 2024 and later (mdp file):
 ```
-gmx mdrun -s topol.tpr -deffnm topol -colvars <Colvars configuration file>
+colvars-active = yes
+colvars-configfile = my_config.colvars
 ```
+- In Tinker-HP:
+Create a Colvars configuration file with the same prefix as the `.key` file, and the extension `.colvars`.
 
 The contents of the configuration file are typically the same across all programs, for example:
 ```
@@ -100,7 +102,7 @@ and run the provided `update-colvars-code.sh` script against the unpacked source
 and recompile them.
 
 The `update-colvars-code.sh` script support patching the latest development version of each program:
-- [GROMACS](https://github.com/gromacs/gromacs);
+- [GROMACS](https://gitlab.com/gromacs/gromacs);
 - [LAMMPS](https://github.com/lammps/lammps);
 - [NAMD](https://gitlab.com/tcbgUIUC/namd);
 - [VMD and its plugins](https://www.ks.uiuc.edu/Research/vmd/doxygen/cvsget.html); note that starting from Colvars version 2023-06-23, some updates are needed to the VMD build script (see [here](https://colvars.github.io/README-c++11.html) for details).
@@ -126,7 +128,7 @@ If using a patched release, please also reference the Colvars version: this is i
 
 ## Which version of Colvars is recommended?
 
-The Git `master` branch is to be considered the "*stable*" release at any given time; any bugfixes are released through `master` first.  The input syntax is near-completely *backward-compatible* and output files are *forward-compatible*.  Feel free to download Colvars and update NAMD, VMD, LAMMPS or GROMACS as needed.
+The Git `master` branch is to be considered the "*stable*" release at any given time; any bugfixes are released through `master` first.  The input syntax is near-completely *backward-compatible* and output files are *forward-compatible*.  Feel free to download Colvars and update NAMD, VMD, LAMMPS, GROMACS, or Tinker-HP as needed.
 
 Other branches are dedicated to the development of specific features: please use them at your own discretion.
 

diff --git a/devel-tools/cleanup-gh-cache.sh b/devel-tools/cleanup-gh-cache.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-key=${1:-key Linux-build-}
+key=${1:-Linux-build-}
 
 if [ -z "${key}" ] ; then
     echo "Error: please specify a cache key as argument." >& 2
@@ -9,7 +9,7 @@ fi
 
 gh actions-cache --help >& /dev/null || gh extension install actions/gh-actions-cache
 
-# Keep at least one cache for each branch
+# Keep at most one cache for each branch
 branches=$(gh actions-cache list --key ${key} | cut -f 3 | uniq)
 for branch in ${branches} ; do
     caches=($(gh actions-cache list --key ${key} --branch ${branch} | cut -f 1))

diff --git a/devel-tools/compile-gromacs.sh b/devel-tools/compile-gromacs.sh
@@ -49,7 +49,7 @@ compile_gromacs_target() {
         if [ "${1,,}" = "debug" ]; then
             GMX_BUILD_TYPE=Debug
             GMX_BUILD_OPTS+=(-DCMAKE_BUILD_TYPE=Debug -DCMAKE_VERBOSE_MAKEFILE=yes)
-            GMX_BUILD_OPTS+=(-DCOLVARS_DEBUG)
+            GMX_BUILD_OPTS+=(-DCOLVARS_DEBUG=ON)
         else
             GMX_INSTALL_DIR=${1}
         fi
@@ -60,7 +60,7 @@ compile_gromacs_target() {
         GMX_BUILD_OPTS+=("-DGMX_MPI=ON")
     fi
 
-    # GMX_BUILD_OPTS+=("-DBUILD_OMP=yes")
+    GMX_BUILD_OPTS+=("-DGMX_OPENMP=yes")
 
     # Select FFT
     if [ "$(basename \"${CXX}\")" = "icpc" ] ; then

diff --git a/devel-tools/compile-lammps.sh b/devel-tools/compile-lammps.sh
@@ -1,11 +1,9 @@
 #!/bin/bash
 
-source $(dirname $0)/load-recent-git.sh
+source $(dirname $0)/load-openmpi.sh
 
 source $(dirname $0)/set-ccache.sh
 
-source $(dirname $0)/load-openmpi.sh
-
 
 compile_lammps_target() {
 
@@ -75,6 +73,10 @@ compile_lammps_target() {
 
     LAMMPS_BUILD_OPTS+=("-DPKG_PYTHON=on")
 
+    if hash ccache >& /dev/null ; then
+        LAMMPS_BUILD_OPTS+=(-DCMAKE_{CXX,CC}_COMPILER_LAUNCHER=ccache)
+    fi
+
     if hash ninja >& /dev/null ; then
         LAMMPS_BUILD_OPTS+=("-G" "Ninja")
     fi