Merge branch 'master' into fix-link-cells-nopbc

.astyle.options

@@ -1 +1,13 @@
--n --indent=spaces=2 --keep-one-line-statements --keep-one-line-blocks
+# long options can be written without the preceding '--'
+suffix=none #equivalent to "-n"
+style=attach
+add-braces
+indent=spaces=2
+break-one-line-headers
+
+# old options
+#suffix=none
+#indent=spaces=2
+#keep-one-line-statements
+#keep-one-line-blocks
+# end old options

.ci/install.boost

@@ -12,8 +12,9 @@ version_=${version//./_}
 
 echo $version $version_
 
-wget https://boostorg.jfrog.io/artifactory/main/release/$version/source/boost_${version_}.tar.gz > /dev/null 2> /dev/null
-tar xzf boost_${version_}.tar.gz
+#wget https://boostorg.jfrog.io/artifactory/main/release/$version/source/boost_${version_}.tar.gz > /dev/null 2> /dev/null
+wget https://sourceforge.net/projects/boost/files/boost/$version/boost_${version_}.tar.bz2 > /dev/null 2> /dev/null
+tar xjf boost_${version_}.tar.bz2
 
 cd boost_${version_}
 

.git-blame-ignore-revs

@@ -0,0 +1,9 @@
+# .git-blame-ignore-revs
+# https://docs.github.com/en/repositories/working-with-files/using-files/viewing-a-file#ignore-commits-in-the-blame-view
+# please comment the hashes that you add to this
+# new astyle applied to v2.9.3
+2cd41d16623b7a062b2a716eaf5c91a741cc19ea
+# new astyle applied to v2.10
+df781b48652d8cdde2994dae1197cdb623f3f3fa
+# new astyle applied to v2.11
+380bb46eea1bc2a38fba94f3f72af2d8d6e41669

.github/workflows/condaWF.yml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-20.04 , macos-12 , macos-14 ]
+        os: [ubuntu-20.04 , macos-13 , macos-14 ]
     runs-on: ${{ matrix.os }}
     steps:
     - uses: actions/checkout@v4

.github/workflows/linuxWF.yml

@@ -28,6 +28,8 @@ jobs:
 # see https://github.com/plumed/plumed2/issues/976
         - -intel-
         - -pycv-mpi-
+#this does not install mpi but uses the internal one
+        - -nvhpc-mpi-
     steps:
     - uses: actions/checkout@v4
     - uses: actions/cache@v4
@@ -136,6 +138,18 @@ jobs:
         echo "CXX=icpx" >> $GITHUB_ENV
         echo "CC=icx" >> $GITHUB_ENV
         echo "FC=ifx" >> $GITHUB_ENV
+    - name: Install NVHPC compiler
+      if: contains( matrix.variant, '-nvhpc-' )
+      # use this if it does not work
+      # wget https://developer.download.nvidia.com/hpc-sdk/24.3/nvhpc_2024_243_Linux_x86_64_cuda_12.3.tar.gz
+      # tar xpzf nvhpc_2024_243_Linux_x86_64_cuda_12.3.tar.gz
+      # nvhpc_2024_243_Linux_x86_64_cuda_12.3/install
+      run: |
+        curl https://developer.download.nvidia.com/hpc-sdk/ubuntu/DEB-GPG-KEY-NVIDIA-HPC-SDK | sudo gpg --dearmor -o /usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg
+        echo 'deb [signed-by=/usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg] https://developer.download.nvidia.com/hpc-sdk/ubuntu/amd64 /' | sudo tee /etc/apt/sources.list.d/nvhpc.list
+        sudo apt-get update -y
+        sudo apt-get install -y nvhpc-24-3
+      # nvhpcinstalls his own mpi compilers
     - name: Install MPI
       # install MPI at last since it modifies CC and CXX
       if: contains( matrix.variant, '-mpi-' )

.github/workflows/macWF.yml

@@ -21,7 +21,10 @@ jobs:
       matrix:
         variant: [ "" , "+allmodules" ]
         # this is to test both intel and arm64 macs
-        os: [ macos-12 , macos-14 ]
+        # note: macos-14 has a problem in fetching the git repository of plumed, namely a
+        # "fatal: detected dubious ownership in repository" error
+        # I didn't find any solution, so for the moment I keep macos-14 off
+        os: [ macos-13 ]
         exclude:
         # many tests on contributed modules are still failing for numerical reasons on arm64, see https://github.com/plumed/plumed2/pull/950
         # once fixed we could introduce this back:
@@ -68,7 +71,7 @@ jobs:
       fail-fast: false
       matrix:
         # this is to test both intel and arm64 macs
-        os: [ macos-12 , macos-14 ]
+        os: [ macos-13 , macos-14 ]
     runs-on: ${{ matrix.os }}
     steps:
     - uses: actions/checkout@v4

CHANGES/v2.10.md

@@ -71,3 +71,4 @@ Before switching to version 2.10, users are invited to carefully read the follow
   - You can use ActionShortcut to create complex inputs from a simpler initial input.  The nest will then allow users to explore these more complex inputs.
   - You can use \ref show_graph to create diagrams showing how values and forces are passed between the various actions in your input files.
   - Complete refactor of SwitchingFunction.cpp and SwitchingFunction.h, now adding new switching function is more straightforward and all the "book-keeping" can be done within a single class
+  - Python (cython) wrappers now use `nogil`. This should facilitate integration with Python. See https://github.com/plumed/plumed2/pull/1129#issuecomment-2410867829 (thanks to Guillaume Fraux).

CHANGES/v2.9.md

@@ -58,7 +58,14 @@ Changes from version 2.8 which are relevant for users:
 - Includes all fixes up to 2.8.4
 - Fixed a size check in python interface when passing native arrays.
 
-## Version 2.9.2 (tba)
+## Version 2.9.2 (Sep 3, 2024)
   - Patch for GROMACS 2023 updated to the latest version
   - new patch for GROMACS 2024 
+  - Small optimization of \ref COORDINATION and related collective variables (\issue{1096}).
 
+## Version 2.9.3 (Jan 15, 2025)
+  - Patch for GROMACS 2024 was updated to fix a big issue preventing its use
+
+## Version 2.9.4 (in progress)
+  - Fixed an issue that might lead to a crash when using multicolvars implemented with linked cells and no PBCs, apparently
+    only showing up with Intel Mac. See \issue{1181}.

README.md

@@ -45,16 +45,17 @@ Below you find the status on [GitHub Actions](https://github.com/plumed/plumed2/
 
 | Branch   |      Status   | First stable release (year) | Still supported |
 |:--------:|:-------------:|:--------:|:------:|
-| master   | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=master)](https://github.com/plumed/plumed2/actions) | 2024 (expected) | / |
-| v2.9     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.9)](https://github.com/plumed/plumed2/actions)   | 2023 | yes |
-| v2.8     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.8)](https://github.com/plumed/plumed2/actions)   | 2022 | yes |
-| v2.7     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.7)](https://github.com/plumed/plumed2/actions)   | 2020 | no |
-| v2.6     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.6)](https://github.com/plumed/plumed2/actions)   | 2019 | no |
-| v2.5     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.5)](https://github.com/plumed/plumed2/actions)   | 2018 | no |
-| v2.4     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.4)](https://github.com/plumed/plumed2/actions)   | 2017 | no |
-| v2.3     | [![Build Status](https://travis-ci.org/plumed/plumed2.svg?branch=v2.3)](https://travis-ci.org/plumed/plumed2)   | 2016 | no |
-| v2.2     | [![Build Status](https://travis-ci.org/plumed/plumed2.svg?branch=v2.2)](https://travis-ci.org/plumed/plumed2)   | 2015 | no |
-| v2.1     | [![Build Status](https://travis-ci.org/plumed/plumed2.svg?branch=v2.1)](https://travis-ci.org/plumed/plumed2)   | 2014 | no |
+| master   | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=master)](https://github.com/plumed/plumed2/actions) | 2025 (expected) | / |
+| v2.10b   | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.10)](https://github.com/plumed/plumed2/actions) | 2024 (expected) | yes |
+| v2.9     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.9)](https://github.com/plumed/plumed2/actions) | 2023 | yes |
+| v2.8     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.8)](https://github.com/plumed/plumed2/actions) | 2022 | no |
+| v2.7     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.7)](https://github.com/plumed/plumed2/actions) | 2020 | no |
+| v2.6     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.6)](https://github.com/plumed/plumed2/actions) | 2019 | no |
+| v2.5     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.5)](https://github.com/plumed/plumed2/actions) | 2018 | no |
+| v2.4     | [![CI](https://github.com/plumed/plumed2/workflows/CI/badge.svg?branch=v2.4)](https://github.com/plumed/plumed2/actions) | 2017 | no |
+| v2.3     | Not available | 2016 | no |
+| v2.2     | Not available | 2015 | no |
+| v2.1     | Not available | 2014 | no |
 | v2.0     | Not available | 2013 | no |
 
 Content

VERSION.txt

@@ -5,4 +5,4 @@
 # (this is same as gromacs)
 # Notice that "plumed info --version" will return only 2.X
 # and "plumed info --long-version" will return the full string
-2.10.0-dev
+2.11.0-dev

conda/plumed/build.sh

@@ -19,6 +19,10 @@ export CXXFLAGS="${CXXFLAGS//-O2/-O3}"
 if [[ $(uname) == "Darwin" ]]; then
 # see https://conda-forge.org/docs/maintainer/knowledge_base.html#newer-c-features-with-old-sdk
   CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
+
+# for some unexpected reason, when building on MacOS plumed 2.10 (likely because of C++17) # we need to pass the arguments below.
+# if we do not do so, linking plumed-runtime fails because the destructor of std::bad_function_call is not found
+  export STATIC_LIBS="-Wl,-rpath,$PREFIX/lib -L$PREFIX/lib"
 fi
 
 # libraries are explicitly listed here due to --disable-libsearch

configure

@@ -2341,7 +2341,7 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
 
 
 # PLUMED_CHECK_LDFLAGS(flag)
-# use it to check if a flag is available on this compiler
+# use it to check if a flag is available for linking
 
 
 # PLUMED_SEARCH_LIBS(function,search-libs[,action-if-found][,action-if-not-found][,other-libraries])
@@ -9664,26 +9664,13 @@ fi
 if test $libtorch = true ; then
   # disable as-needed in linking libraries (both static and shared)
 
-  save_CXXFLAGS="$CXXFLAGS"
-  CXXFLAGS="$CXXFLAGS -Wl,--no-as-needed"
-  { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX accepts -Wl,--no-as-needed" >&5
-$as_echo_n "checking whether $CXX accepts -Wl,--no-as-needed... " >&6; }
+  save_LDFLAGS="$LDFLAGS"
+  LDFLAGS="$LDFLAGS -Wl,--no-as-needed"
+  { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether LDFLAGS can contain -Wl,--no-as-needed" >&5
+$as_echo_n "checking whether LDFLAGS can contain -Wl,--no-as-needed... " >&6; }
   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
 
-int
-main ()
-{
-
-  ;
-  return 0;
-}
-_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"; then :
-
-      cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-
 int
 main ()
 {
@@ -9696,20 +9683,12 @@ if ac_fn_cxx_try_link "$LINENO"; then :
   { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
 $as_echo "yes" >&6; }
 else
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: not linking" >&5
-$as_echo "not linking" >&6; }; CXXFLAGS="$save_CXXFLAGS"
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }; LDFLAGS="$save_LDFLAGS"
 fi
 rm -f core conftest.err conftest.$ac_objext \
     conftest$ac_exeext conftest.$ac_ext
 
-else
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-$as_echo "no" >&6; }; CXXFLAGS="$save_CXXFLAGS"
-
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-
-  LDSHARED="$LDSHARED -Wl,--no-as-needed "
 
   # CUDA and CPU libtorch libs have different libraries
   # first test CUDA program

configure.ac

@@ -79,7 +79,7 @@ AC_DEFUN([PLUMED_CHECK_CFLAG], [
 ])
 
 # PLUMED_CHECK_LDFLAGS(flag)
-# use it to check if a flag is available on this compiler
+# use it to check if a flag is available for linking
 AC_DEFUN([PLUMED_CHECK_LDFLAGS], [
   save_LDFLAGS="$LDFLAGS"
   LDFLAGS="$LDFLAGS $1"
@@ -935,8 +935,7 @@ fi
 #added by luigibonati
 if test $libtorch = true ; then 
   # disable as-needed in linking libraries (both static and shared)
-  PLUMED_CHECK_CXXFLAG([-Wl,--no-as-needed])
-  LDSHARED="$LDSHARED -Wl,--no-as-needed "
+  PLUMED_CHECK_LDFLAGS([-Wl,--no-as-needed])
 
   # CUDA and CPU libtorch libs have different libraries
   # first test CUDA program

developer-doc/.gitignore

@@ -5,5 +5,6 @@
 /*PP.txt
 /links-to-user-manual.md
 /plumedcheck.md
-/coverage
+/coverage*/
+/coverage*
 

developer-doc/AddingRegressionTests.md

@@ -49,18 +49,17 @@ extra_files="../../trajectories/diala_traj_nm.xyz  ../trajectories/path_msd/all.
 - The first line in this file - the one containing the string mpiprocs=2 - tells PLUMED that when this regtest should be run using MPI on two nodes.
 If mpiprocs is not specified then PLUMED will, by default, run the test one node.
 
-- The second line tells PLUMED that the test is to be performed using the command line tool <a href="../../user-doc/html/driver.html">driver</a>.  
-There are four options that you can use here:
-type=driver tells PLUMED to run the test by reading in a trajectory and analysing it using <a href="../../user-doc/html/driver.html">driver</a>, 
-type=simplemd tells PLUMED that the test will involve
-running some Lennard Jones MD using <a href="../../user-doc/html/simplemd.html">simplemd</a>, 
-type=sum_hills tells PLUMED that the test will involve summing gaussians using the 
-<a href="../../user-doc/html/sum_hills.html">sum_hills</a> untility
- and type=make tells PLUMED that a main function (called main.cpp) is included in the regtest directory and that the test should compile this function, link in
-the PLUMED library and run the resulting executible. The vast majority of features are best tested using type=driver here although the type=make function
-can be useful for testing tools that are used in many places in the code (see the code in regtest/basic/rt-make-4 for an example of how use type=make to test
-PLUMED's internal matrix class).  If you need to test PLUMED in a way that is not included in these various types please contact the PLUMED developers before
+- The second line tells PLUMED that the test is to be performed using the command line tool <a href="../../user-doc/html/driver.html">driver</a>.
+The vast majority of features are best tested using type=driver here although the type=make function can be useful for testing tools that are used in many places in the code (see the code in regtest/basic/rt-make-4 for an example of how use type=make to test PLUMED's internal matrix class).  If you need to test PLUMED in a way that is not included in these various types please contact the PLUMED developers before
 making any changes.
+There are four options that you can use here:
+    - type=driver tells PLUMED to run the test by reading in a trajectory and analysing it using <a href="../../user-doc/html/driver.html">driver</a>,
+    - type=simplemd tells PLUMED that the test will involve
+running some Lennard Jones MD using <a href="../../user-doc/html/simplemd.html">simplemd</a>,
+    - type=sum_hills tells PLUMED that the test will involve summing gaussians using the 
+<a href="../../user-doc/html/sum_hills.html">sum_hills</a> utility
+    - type=make tells PLUMED that a main function (called main.cpp) is included in the regtest directory and that the test should compile this function, link in
+the PLUMED library and run the resulting executible.
 
 - The third line - the one containing the string plumed_modules=adjmat - tells PLUMED that this regtest needs the optional module adjmat to be installed in 
 order for it to be run.  Before trying to run this test PLUMED will thus check whether or not the module is installed.  If it is not installed then it will 

patches/gromacs-2024.2.diff/src/gromacs/mdrun/md.cpp → patches/gromacs-2024.3.diff/src/gromacs/mdrun/md.cpp

@@ -1089,6 +1089,13 @@ void gmx::LegacySimulator::do_md()
                                     do_verbose && !bPMETunePrinting);
                 upd.updateAfterPartition(state_->numAtoms(), md->cFREEZE, md->cTC, md->cACC);
                 fr_->longRangeNonbondeds->updateAfterPartition(*md);
+                /* PLUMED */
+                if(plumedswitch){
+                  int nat_home = dd_numHomeAtoms(*cr_->dd);
+                  plumed_cmd(plumedmain,"setAtomsNlocal",&nat_home);
+                  plumed_cmd(plumedmain,"setAtomsGatindex",cr_->dd->globalAtomIndices.data());
+                }
+                /* END PLUMED */
             }
         }
 
@@ -1721,7 +1728,6 @@ void gmx::LegacySimulator::do_md()
                 trotter_update(ir,
                                step,
                                ekind_,
-                               enerd_,
                                state_,
                                total_vir,
                                md->homenr,

patches/gromacs-2024.2.diff/src/gromacs/mdrun/md.cpp.preplumed → patches/gromacs-2024.3.diff/src/gromacs/mdrun/md.cpp.preplumed

@@ -1480,7 +1480,6 @@ void gmx::LegacySimulator::do_md()
                 trotter_update(ir,
                                step,
                                ekind_,
-                               enerd_,
                                state_,
                                total_vir,
                                md->homenr,

patches/gromacs-2024.2.diff/src/gromacs/mdrun/runner.cpp → patches/gromacs-2024.3.diff/src/gromacs/mdrun/runner.cpp

@@ -2248,11 +2248,15 @@ int Mdrunner::mdrunner()
                         deviceStreamManager->context(),
                         deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedLocal),
                         wcycle.get());
-                fr->gpuForceReduction[gmx::AtomLocality::NonLocal] =
-                        std::make_unique<gmx::GpuForceReduction>(
-                                deviceStreamManager->context(),
-                                deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedNonLocal),
-                                wcycle.get());
+
+                if (runScheduleWork.simulationWork.havePpDomainDecomposition)
+                {
+                    fr->gpuForceReduction[gmx::AtomLocality::NonLocal] =
+                            std::make_unique<gmx::GpuForceReduction>(
+                                    deviceStreamManager->context(),
+                                    deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedNonLocal),
+                                    wcycle.get());
+                }
 
                 if (runScheduleWork.simulationWork.useMdGpuGraph)
                 {

patches/gromacs-2024.2.diff/src/gromacs/mdrun/runner.cpp.preplumed → patches/gromacs-2024.3.diff/src/gromacs/mdrun/runner.cpp.preplumed

@@ -2234,11 +2234,15 @@ int Mdrunner::mdrunner()
                         deviceStreamManager->context(),
                         deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedLocal),
                         wcycle.get());
-                fr->gpuForceReduction[gmx::AtomLocality::NonLocal] =
-                        std::make_unique<gmx::GpuForceReduction>(
-                                deviceStreamManager->context(),
-                                deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedNonLocal),
-                                wcycle.get());
+
+                if (runScheduleWork.simulationWork.havePpDomainDecomposition)
+                {
+                    fr->gpuForceReduction[gmx::AtomLocality::NonLocal] =
+                            std::make_unique<gmx::GpuForceReduction>(
+                                    deviceStreamManager->context(),
+                                    deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedNonLocal),
+                                    wcycle.get());
+                }
 
                 if (runScheduleWork.simulationWork.useMdGpuGraph)
                 {