Merge branch 'master' into fix-newmac-arm-issues

.github/workflows/ci.yml

@@ -33,4 +33,4 @@ jobs:
 
   conda:
     uses: ./.github/workflows/condaWF.yml
-    secrets: inherit
+    secrets: inherit

.github/workflows/codecheckWF.yml

@@ -18,7 +18,7 @@ jobs:
   codecheck:
     runs-on: ubuntu-20.04
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set path
       run: |
          echo "$HOME/opt/bin" >> $GITHUB_PATH

.github/workflows/codeql.yml

@@ -24,7 +24,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Packages (cpp)
         if: ${{ matrix.language == 'cpp' }}

.github/workflows/condaWF.yml

@@ -21,7 +21,7 @@ jobs:
         os: [ubuntu-20.04 , macos-11]
     runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Install conda
       run: |
         curl -LO https://raw.githubusercontent.com/GiovanniBussi/conda-ci/master/conda-ci

.github/workflows/dockerWF.yml

@@ -19,15 +19,13 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        # centos7 (gcc 4.8)
-        # fedora38 (gcc 13)
+        # fedora39 (gcc 13)
         # rockylinux8
         variant:
-        - centos7
-        - fedora38
+        - fedora39
         - rocky8
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Build and run tests
       run: |
         make -C docker ${{ matrix.variant }}

.github/workflows/linuxWF.yml

@@ -24,9 +24,11 @@ jobs:
         - -coverage-mpi-
         - -debug-
         - -debug-mpi-
-        - -intel-
+# temporarily commented out
+# see https://github.com/plumed/plumed2/issues/976
+#        - -intel-
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: actions/cache@v3
       with:
         path: ~/.ccache
@@ -35,7 +37,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.7
+        python-version: 3.9
     - name: Set paths
       run: |
         echo "$HOME/opt/bin" >> $GITHUB_PATH
@@ -46,8 +48,6 @@ jobs:
         echo "LIBRARY_PATH=$HOME/opt/lib:$LIBRARY_PATH" >> $GITHUB_ENV
         echo "LD_LIBRARY_PATH=$HOME/opt/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
         echo "PYTHONPATH=$HOME/opt/lib/plumed/python:$PYTHONPATH" >> $GITHUB_ENV
-        # this is to avoid errors on ubuntu 22. this is overridden in intel build
-        echo "FC=gfortran -fallow-argument-mismatch" >> $GITHUB_ENV
     - name: Install generic packages
       run: |
         sudo apt-get update -qq
@@ -82,8 +82,8 @@ jobs:
         # added by luigibonati
         mkdir -p $HOME/opt/
         cd $HOME/opt/ # GB: install in $HOME/opt/libtorch
-        wget --no-check-certificate https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-1.13.1%2Bcpu.zip ;
-        unzip libtorch-cxx11-abi-shared-with-deps-1.13.1+cpu.zip ;
+        wget --no-check-certificate https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-2.0.0%2Bcpu.zip ;
+        unzip libtorch-cxx11-abi-shared-with-deps-2.0.0+cpu.zip ;
         echo "LIBRARY_PATH=$PWD/libtorch/lib:$LIBRARY_PATH" >> $GITHUB_ENV
         echo "LD_LIBRARY_PATH=$PWD/libtorch/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
         echo "CPATH=$PWD/libtorch/include/torch/csrc/api/include/:$PWD/libtorch/include/:$PWD/libtorch/include/torch:$CPATH" >> $GITHUB_ENV

.github/workflows/macWF.yml

@@ -22,9 +22,9 @@ jobs:
         variant: [ "" , "+allmodules" ]
         # see https://github.community/t/how-to-conditionally-include-exclude-items-in-matrix-eg-based-on-branch/16853/6 for possible exclusions
     env:
-      PYVERS: "py37 py38 py39 py310"
+      PYVERS: "py39 py310"
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: actions/cache@v3
       with:
         path: ~/.macports-ci-ccache
@@ -59,7 +59,7 @@ jobs:
   macsimple:
     runs-on: macos-11
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set paths
       run: |
         echo "$HOME/opt/bin" >> $GITHUB_PATH

.github/workflows/nightly.yml

@@ -9,10 +9,10 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest , macos-latest]
-        branch: [v2.6, v2.7, master]
+        branch: [v2.8, v2.9, master]
     runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         ref: ${{ matrix.branch }}
     - name: Install conda

CHANGES/v2.10.md

@@ -4,5 +4,8 @@
 
 This page contains changes that will end up in 2.10
 
+- **PLUMED 2.10 requires a C++17 compatible compiler**.
+
 - Changes relevant for developers:
-  - Removed some shortcuts for `ActionRegister.h` (from the modules bias colvar function sasa and vatom) and `CLToolRegister.h` (from the module cltools), now the two headers can only be included with `#include "core/ActionRegister.h"` or `#include "core/CLToolRegister.h"`.
+  - Removed some shortcuts for `ActionRegister.h` (from the modules bias colvar function sasa and vatom) and `CLToolRegister.h` (from the module cltools), now the two headers can only be included with `#include "core/ActionRegister.h"` or `#include "core/CLToolRegister.h"`.
+  - `plumed mklib` can now process more than one cpp file. Files are combined in a single library.

CHANGES/v2.8.md

@@ -101,3 +101,7 @@ Changes from version 2.7 which are relevant for users:
 - Fixed a numerical instability in \ref OPES_EXPANDED that could cause `-inf` to appear in the DELTAFS file when biasing large systems
 - Small fixes in the test suite to make sure `plumed` is always invoked with `--no-mpi` when testing for features. This avoids
   problems that were appearing when testing with some specific versions of OpenMPI.
+
+## Version 2.8.4
+- Added the possibility to disable `RTLD_DEEPBIND` (see \issue{952}).
+- Fixed a bug in `switchingfunction` mode `Q` thanks to @nm3787, (see #951)

CHANGES/v2.9.md

@@ -7,6 +7,7 @@ Changes from version 2.8 which are relevant for users:
 - Changes leading to differences with previous versions:
   - Number of bins in \ref METAD, \ref PBMETAD and \ref sum_hills is now computed correctly
     when setting a spacing that divide exactly the range. See \issue{868}.
+  - \ref SAXS in the ISDB module does not have the `SCALEINT` keyword anymore and the default normalisation of the intensity is to set the intensity at q=0 to 1.
 
 - New contributed modules:
   - A new pytorch module by Luigi Bonati
@@ -52,4 +53,8 @@ Changes from version 2.8 which are relevant for users:
   - Plumed patch now accepts the `--include` option. Might become the default in a future version.
   - Python (cython) wrappers now only use plain C instead of C++. Plumed exceptions are mapped to python exceptions.
   - Step number is now stored as a `long long int`. Might facilitate Windows compatibility.
+
+## Version 2.9.1 (to be released)
+- Includes all fixes up to 2.8.4
+- Plumed now fetches the massses correctly from QEspresso 7.0
 

README.md

@@ -46,7 +46,7 @@ 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 (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 | 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 |
@@ -92,9 +92,8 @@ Required software
 Required software:
 
 * GNU make.
-* C/c++ compiler (c++11 support is required as of version 2.4).
+* C/c++ compiler (c++17 support is required as of version 2.10).
 * A modern version of the `patch` command line tool.
-* Support for POSIX library `dirent.h`.
 
 Suggested software (libraries are checked by `./configure` and enabled if available):
 

conda/plumed/build.sh

@@ -16,6 +16,11 @@ export CPPFLAGS="-D__PLUMED_DEFAULT_KERNEL=$PREFIX/lib/libplumedKernel$SHLIB_EXT
 # enable optimization
 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"
+fi
+
 # libraries are explicitly listed here due to --disable-libsearch
 export LIBS="-lfftw3 -lgsl -lgslcblas -llapack -lblas -lz $LIBS"
 

conda/py-plumed/build.sh

@@ -3,5 +3,7 @@
 cd python
 make pip
 export plumed_default_kernel=$PREFIX/lib/libplumedKernel$SHLIB_EXT
+export plumed_disable_rtld_deepbind=yes
+
 $PYTHON -m pip install . --no-deps -vv