Improve code portability

.github/workflows/push_pull.yml

@@ -9,7 +9,7 @@ permissions:
 
 jobs:
   macos:
-    runs-on: macos-15
+    runs-on: macos-26
     if: ${{ github.repository == 'espressomd/espresso' }}
     steps:
       - name: Checkout
@@ -24,19 +24,13 @@ jobs:
       - name: Install dependencies
         run: |
          echo '' > Brewfile
-         for dep in boost boost-mpi fftw gsl ccache ninja; do echo "brew \"${dep}\"" >> Brewfile; done
+         for dep in boost boost-mpi libomp fftw gsl ccache ninja; do echo "brew \"${dep}\"" >> Brewfile; done
          brew bundle check >/dev/null 2>&1 || brew bundle --verbose --no-upgrade
          # set up Xcode compiler
          echo "::group::List available Xcode compilers"
          ls /Applications | grep Xcode
          echo "::endgroup::"
-         sudo xcode-select -switch /Applications/Xcode_16.4.app
-         echo "::group::Install OpenMP (https://mac.r-project.org/openmp/)"
-         curl -s -o ${{ runner.temp }}/openmp.tar.gz https://mac.r-project.org/openmp/openmp-19.1.0-darwin20-Release.tar.gz
-         sudo tar fvxz ${{ runner.temp }}/openmp.tar.gz -C /
-         rm ${{ runner.temp }}/openmp.tar.gz
-         codesign -d -vv /usr/local/lib/libomp.dylib
-         echo "::endgroup::"
+         sudo xcode-select -switch /Applications/Xcode_26.2.0.app
          # Python dependencies
          python -m venv venv
          . venv/bin/activate
@@ -59,7 +53,7 @@ jobs:
   debian:
     runs-on: ubuntu-latest
     container:
-      image: ghcr.io/espressomd/docker/debian:3388b293a5e8a9b613b1bfa4220e54dfb4bff245-base-layer
+      image: ghcr.io/espressomd/docker/debian:4d3e236db5ae334ddcc9c3c82aae7637faa5dabc-base-layer
       credentials:
          username: ${{ github.actor }}
          password: ${{ secrets.github_token }}
@@ -101,7 +95,7 @@ jobs:
     runs-on: ubuntu-latest
     if: ${{ github.repository == 'espressomd/espresso' }}
     container:
-      image: ghcr.io/espressomd/docker/ubuntu-wo-dependencies:3388b293a5e8a9b613b1bfa4220e54dfb4bff245-base-layer
+      image: ghcr.io/espressomd/docker/ubuntu-wo-dependencies:4d3e236db5ae334ddcc9c3c82aae7637faa5dabc-base-layer
       credentials:
          username: ${{ github.actor }}
          password: ${{ secrets.github_token }}
@@ -143,7 +137,7 @@ jobs:
     runs-on: ubuntu-latest
     if: ${{ github.repository == 'espressomd/espresso' }}
     container:
-      image: ghcr.io/espressomd/docker/fedora:3388b293a5e8a9b613b1bfa4220e54dfb4bff245-base-layer
+      image: ghcr.io/espressomd/docker/fedora:4d3e236db5ae334ddcc9c3c82aae7637faa5dabc-base-layer
       credentials:
          username: ${{ github.actor }}
          password: ${{ secrets.github_token }}

.gitlab-ci.yml

@@ -1,4 +1,4 @@
-image: ghcr.io/espressomd/docker/ubuntu:3388b293a5e8a9b613b1bfa4220e54dfb4bff245
+image: ghcr.io/espressomd/docker/ubuntu:4d3e236db5ae334ddcc9c3c82aae7637faa5dabc
 
 stages:
   - prepare
@@ -16,11 +16,11 @@ stages:
 
 .notification_job_template: &notification_job_definition
   <<: *global_job_definition
-  image: ghcr.io/espressomd/docker/alpine:3388b293a5e8a9b613b1bfa4220e54dfb4bff245
+  image: ghcr.io/espressomd/docker/alpine:4d3e236db5ae334ddcc9c3c82aae7637faa5dabc
   variables:
     GET_SOURCES_ATTEMPTS: 3
   dependencies: []
-  timeout: 40m
+  timeout: 20m
   interruptible: false
   tags:
     - espresso

CMakeLists.txt

@@ -316,7 +316,7 @@ endif()
 # Python interpreter and Cython interface library
 if(ESPRESSO_BUILD_WITH_PYTHON)
   find_package(Python 3.11 REQUIRED COMPONENTS Interpreter Development NumPy)
-  find_package(Cython 3.0.4...<3.2.0 REQUIRED)
+  find_package(Cython 3.0.4...<4.0.0 REQUIRED)
   if(CYTHON_VERSION VERSION_LESS 3.0.8)
     message(WARNING "We strongly recommend using Cython 3.0.8 or later")
   endif()
@@ -633,14 +633,14 @@ if(ESPRESSO_BUILD_WITH_SHARED_MEMORY_PARALLELISM)
   find_package(OpenMP REQUIRED COMPONENTS CXX)
 
   if(NOT EXISTS ${FETCHCONTENT_BASE_DIR}/kokkos-src)
-    find_package(Kokkos 4.3 QUIET)
+    find_package(Kokkos 5.0 QUIET)
   endif()
   if(NOT DEFINED Kokkos_FOUND OR NOT ${Kokkos_FOUND})
     # cmake-format: off
     FetchContent_Declare(
       kokkos
       GIT_REPOSITORY https://github.com/kokkos/kokkos.git
-      GIT_TAG        18b830e # version 4.6.1 with patches
+      GIT_TAG        5.0.2
       OVERRIDE_FIND_PACKAGE
     )
     # cmake-format: on
@@ -652,6 +652,7 @@ if(ESPRESSO_BUILD_WITH_SHARED_MEMORY_PARALLELISM)
     set(Kokkos_ENABLE_COMPLEX_ALIGN ON CACHE BOOL "")
     set(Kokkos_ENABLE_AGGRESSIVE_VECTORIZATION ON CACHE BOOL "")
     set(Kokkos_ENABLE_HWLOC ON CACHE BOOL "")
+    set(Kokkos_ENABLE_DEPRECATED_CODE_5 OFF CACHE BOOL "")
     set(Kokkos_ARCH_NATIVE ON CACHE BOOL "")
     FetchContent_MakeAvailable(kokkos)
     set(BUILD_SHARED_LIBS ${ESPRESSO_BUILD_SHARED_LIBS_DEFAULT})
@@ -711,7 +712,7 @@ if(ESPRESSO_BUILD_WITH_HDF5)
   FetchContent_Declare(
     HighFive
     GIT_REPOSITORY https://github.com/highfive-devs/highfive.git
-    GIT_TAG        v3.2.0
+    GIT_TAG        v3.3.0
   )
   # cmake-format: on
   FetchContent_MakeAvailable(HighFive)
@@ -923,13 +924,14 @@ if(ESPRESSO_BUILD_WITH_WALBERLA)
   FetchContent_Declare(
     walberla
     GIT_REPOSITORY https://i10git.cs.fau.de/walberla/walberla.git
-    GIT_TAG        17fc54c8 # v7.2 with patches
+    GIT_TAG        3247aa73 # v7.2 with patches
   )
   # cmake-format: on
   string(REGEX REPLACE "([/\\]walberla)-src$" "\\1-build" walberla_BINARY_DIR
                        "${walberla_SOURCE_DIR}")
   set(WALBERLA_BUILD_TESTS off CACHE BOOL "")
   set(WALBERLA_BUILD_TOOLS off CACHE BOOL "")
+  set(WALBERLA_BUILD_LEGACY_LBM off CACHE BOOL "")
   set(WALBERLA_BUILD_BENCHMARKS off CACHE BOOL "")
   set(WALBERLA_BUILD_TUTORIALS off CACHE BOOL "")
   set(WALBERLA_BUILD_SHOWCASES off CACHE BOOL "")
@@ -979,7 +981,7 @@ if(ESPRESSO_BUILD_WITH_CALIPER)
   FetchContent_Declare(
     caliper
     GIT_REPOSITORY https://github.com/LLNL/Caliper.git
-    GIT_TAG        v2.13.0
+    GIT_TAG        v2.14.0
   )
   # cmake-format: on
   set(CALIPER_OPTION_PREFIX on CACHE BOOL "")
@@ -995,10 +997,14 @@ if(ESPRESSO_BUILD_WITH_CALIPER)
   set(BUILD_SHARED_LIBS ${ESPRESSO_BUILD_SHARED_LIBS_DEFAULT})
   set(CMAKE_INSTALL_LIBDIR "${ESPRESSO_OLD_CMAKE_INSTALL_LIBDIR}")
   set(CMAKE_SHARED_LIBRARY_PREFIX "${ESPRESSO_SHARED_LIBRARY_PREFIX}")
+  add_library(espresso_caliper_compiler_flags INTERFACE)
   target_compile_options(
-    caliper-common
-    PRIVATE $<$<COMPILE_LANG_AND_ID:CXX,GNU>:-Wno-free-nonheap-object
-            -Wno-deprecated-enum-enum-conversion -Wno-volatile>)
+    espresso_caliper_compiler_flags
+    INTERFACE $<$<COMPILE_LANG_AND_ID:CXX,GNU>:-Wno-free-nonheap-object
+              -Wno-deprecated-enum-enum-conversion -Wno-volatile
+              -Wno-maybe-uninitialized>)
+  target_link_libraries(caliper-common PRIVATE espresso_caliper_compiler_flags)
+  target_link_libraries(caliper-runtime PRIVATE espresso_caliper_compiler_flags)
 endif()
 
 #
@@ -1028,6 +1034,17 @@ function(espresso_set_common_target_properties)
       elseif(CMAKE_CUDA_COMPILER_ID STREQUAL "Clang")
         set_target_properties(${TARGET_NAME} PROPERTIES LINKER_LANGUAGE "CXX")
       endif()
+      # handle builds with different GCC versions for C++ and CUDA
+      # (https://github.com/espressomd/espresso/issues/5256)
+      if(CMAKE_CUDA_COMPILER_ID STREQUAL "NVIDIA" AND CMAKE_CXX_COMPILER_ID
+                                                      STREQUAL "GNU"
+         AND NOT "$ENV{CUDAHOSTCXX}" STREQUAL "$ENV{CXX}"
+         AND "$ENV{CMAKE_CXX_IMPLICIT_LINK_DIRECTORIES_EXCLUDE}" MATCHES
+             "^/usr/lib/gcc/[^/]+/1[4-9]\$")
+        target_link_directories(
+          ${TARGET_NAME} BEFORE PUBLIC
+          "$ENV{CMAKE_CXX_IMPLICIT_LINK_DIRECTORIES_EXCLUDE}")
+      endif()
     endif()
   endif()
 endfunction()

doc/sphinx/conf.py.in

@@ -41,6 +41,7 @@ extensions = [
     'sphinx.ext.doctest',
     'sphinxcontrib.bibtex',
     'sphinx_toggleprompt',
+    'sphinx_tabs.tabs',
     'sphinx.ext.napoleon'
 ]
 

doc/sphinx/installation.rst

@@ -191,12 +191,20 @@ paths before building the project, for example via environment variables:
 
 .. code-block:: bash
 
-    export CUDA_TOOLKIT_ROOT_DIR="/usr/local/cuda-12.0"
+    export CUDA_TOOLKIT_ROOT_DIR="/usr/local/cuda-12.8"
     export PATH="${CUDA_TOOLKIT_ROOT_DIR}/bin${PATH:+:$PATH}"
     export LD_LIBRARY_PATH="${CUDA_TOOLKIT_ROOT_DIR}/lib64${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}"
 
+or alternatively via CMake-specific environment variables
+(e.g. `ENV{CUDACXX} <https://cmake.org/cmake/help/v4.0/envvar/CUDACXX.html>`__,
+`ENV{CUDAARCHS} <https://cmake.org/cmake/help/v4.0/envvar/CUDAARCHS.html>`__,
+`ENV{CUDAHOSTCXX} <https://cmake.org/cmake/help/v4.0/envvar/CUDAHOSTCXX.html>`__)
+or options (e.g. `-D CUDAToolkit_ROOT <https://cmake.org/cmake/help/v4.0/module/FindCUDAToolkit.html>`__,
+`-D CMAKE_CUDA_HOST_COMPILER <https://cmake.org/cmake/help/v4.0/variable/CMAKE_CUDA_HOST_COMPILER.html>`__).
+
 Later in the installation instructions, you will see CMake commands of the form
-``cmake ..`` with optional arguments, such as ``cmake .. -D ESPRESSO_BUILD_WITH_CUDA=ON``
+``cmake ..`` with optional CUDA-related options and environment variables,
+such as ``CUDACXX=/usr/lib/nvidia-cuda-toolkit/bin/nvcc cmake .. -D ESPRESSO_BUILD_WITH_CUDA=ON``
 to activate CUDA. These commands may need to be adapted depending on which
 operating system and CUDA version you are using.
 
@@ -210,39 +218,96 @@ The CMake option ``CMAKE_CUDA_ARCHITECTURES`` cannot be used to set CUDA
 architectures, because it has a default value that is too old for the
 minimally required CUDA version.
 
-On Ubuntu 24.04, the default GCC compiler may be too recent for nvcc.
-You can either use GCC 12:
+On Ubuntu 24.04, the default GCC compiler may be too recent for nvcc 12.0.
+You can either use GCC 12 or alternatively install Clang 19 as a replacement for nvcc and GCC.
 
-.. code-block:: bash
+.. tabs::
 
-    CC=gcc-12 CXX=g++-12 CUDACXX=/usr/local/cuda-12.0/bin/nvcc cmake .. \
-      -D ESPRESSO_BUILD_WITH_CUDA=ON \
-      -D CUDAToolkit_ROOT=/usr/local/cuda-12.0 \
-      -D CMAKE_CUDA_FLAGS="--compiler-bindir=/usr/bin/g++-12"
+   .. group-tab:: GCC on Ubuntu 24.04
 
-or alternatively install Clang 19 as a replacement for nvcc and GCC:
+      .. code-block:: bash
 
-.. code-block:: bash
+         CC=gcc-12 CXX=g++-12 CUDACXX=/usr/lib/nvidia-cuda-toolkit/bin/nvcc cmake .. \
+           -D ESPRESSO_BUILD_WITH_CUDA=ON \
+           -D CUDAToolkit_ROOT=/usr/lib/nvidia-cuda-toolkit \
+           -D CMAKE_CUDA_HOST_COMPILER=g++-12
+
+      with compiler dependencies:
+
+      .. code-block:: bash
+
+         sudo apt install gcc-12 g++-12 libstdc++-12-dev
+
+   .. group-tab:: Clang on Ubuntu 24.04
 
-    CC=clang-19 CXX=clang++-19 CUDACXX=clang++-19 cmake .. \
-      -D ESPRESSO_BUILD_WITH_CUDA=ON \
-      -D CUDAToolkit_ROOT=/usr/local/cuda-12.0 \
-      -D CMAKE_CXX_FLAGS="-I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12 --cuda-path=/usr/local/cuda-12.0" \
-      -D CMAKE_CUDA_FLAGS="-I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12 --cuda-path=/usr/local/cuda-12.0"
+      .. code-block:: bash
+
+         CC=clang-19 CXX=clang++-19 CUDACXX=clang++-19 cmake .. \
+           -D ESPRESSO_BUILD_WITH_CUDA=ON \
+           -D CUDAToolkit_ROOT=/usr/local/cuda-12.0 \
+           -D CMAKE_CXX_FLAGS="-I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12" \
+           -D CMAKE_CUDA_FLAGS="-I/usr/include/x86_64-linux-gnu/c++/12 -I/usr/include/c++/12 --cuda-path=/usr/local/cuda-12.0"
+
+      with compiler dependencies:
+
+      .. code-block:: bash
+
+         sudo apt install \
+            clang-19 clang-tidy-19 clang-format-19 llvm-19 libc++-19-dev \
+            libclang-rt-19-dev libomp-19-dev gcc-12 g++-12 libstdc++-12-dev
 
 Please note that all CMake options and compiler flags that involve
 ``/usr/local/cuda-*`` need to be adapted to your CUDA environment.
 But they are only necessary on systems with multiple CUDA releases installed,
 and can be safely removed if you have only one CUDA release installed.
 
-Please also note that with Clang, you still need the GCC 12 toolchain,
-which can be set up with ``apt install gcc-12 g++-12 libstdc++-12-dev``.
+Please also note that with Clang, you still need the GCC 12 toolchain.
 The extra compiler flags in the Clang CMake command above are needed to pin
 the search paths of Clang. By default, it searches trough the most recent
 GCC version, which is GCC 13 on Ubuntu 24.04. It is not possible to install
 the NVIDIA driver without GCC 13 due to a dependency resolution issue
 (``nvidia-dkms`` depends on ``dkms`` which depends on ``gcc-13``).
 
+On Ubuntu 26.04, only GCC <= 13 can be used with nvcc 12.4.
+Alternatively, the Clang toolchain can be used.
+
+.. tabs::
+
+   .. group-tab:: GCC on Ubuntu 26.04
+
+      .. code-block:: bash
+
+         CC=gcc-15 CXX=g++-15 CUDAHOSTCXX=g++-13 CUDACXX=/usr/lib/nvidia-cuda-toolkit/bin/nvcc \
+           CMAKE_CXX_IMPLICIT_LINK_DIRECTORIES_EXCLUDE=/usr/lib/gcc/x86_64-linux-gnu/15 cmake .. \
+           -D ESPRESSO_BUILD_WITH_CUDA=ON \
+           -D CUDAToolkit_ROOT=/usr/lib/nvidia-cuda-toolkit
+
+      with compiler dependencies:
+
+      .. code-block:: bash
+
+         sudo apt install \
+            gcc-13 g++-13 libstdc++-13-dev \
+            gcc-15 g++-15 libstdc++-15-dev
+
+   .. group-tab:: Clang on Ubuntu 26.04
+
+      .. code-block:: bash
+
+         CC=clang-20 CXX=clang++-20 CUDACXX=clang++-20 cmake .. \
+           -D ESPRESSO_BUILD_WITH_CUDA=ON \
+           -D CUDAToolkit_ROOT=/usr/lib/cuda \
+           -D CMAKE_CXX_FLAGS="-I/usr/include/x86_64-linux-gnu/c++/15 -I/usr/include/c++/15" \
+           -D CMAKE_CUDA_FLAGS="-I/usr/include/x86_64-linux-gnu/c++/15 -I/usr/include/c++/15 --cuda-path=/usr/lib/cuda"
+
+      with compiler dependencies:
+
+      .. code-block:: bash
+
+         sudo apt install \
+            clang-20 clang-tidy-20 clang-format-20 llvm-20 libc++-20-dev \
+            libclang-rt-20-dev libomp-20-dev gcc-15 g++-15 libstdc++-15-dev
+
 .. _Setting up a Jupyter environment:
 
 Setting up a Jupyter environment
@@ -321,7 +386,7 @@ To generate the Sphinx documentation, install the following packages:
 .. code-block:: bash
 
     python3 -m pip install -c requirements.txt \
-        sphinx sphinxcontrib-bibtex sphinx-toggleprompt
+        sphinx sphinxcontrib-bibtex sphinx-toggleprompt sphinx-tabs
 
 To generate the Doxygen documentation, install the following packages:
 

maintainer/CI/build_cmake.sh

@@ -187,6 +187,19 @@ if [ "${with_cuda}" = true ]; then
     fi
 fi
 
+if [[ "${OSTYPE}" == "darwin"* ]]; then
+  # detect libomp on macOS (see https://gitlab.kitware.com/cmake/cmake/-/issues/24097)
+  cmake_param_list+=(
+    -D OpenMP_C_FLAG="-Xclang -fopenmp"
+    -D OpenMP_CXX_FLAG="-Xclang -fopenmp"
+    -D OpenMP_C_LIB_NAMES=libomp
+    -D OpenMP_CXX_LIB_NAMES=libomp
+    -D OpenMP_C_INCLUDE_DIR=/opt/homebrew/opt/libomp/include
+    -D OpenMP_CXX_INCLUDE_DIR=/opt/homebrew/opt/libomp/include
+    -D OpenMP_libomp_LIBRARY=/opt/homebrew/opt/libomp/lib/libomp.dylib
+  )
+fi
+
 # show system characteristics
 if test -x "$(command -v nvidia-smi)"; then
   nvidia-smi || echo "nvidia-smi returned an error"
@@ -236,6 +249,7 @@ if [ -f "/etc/os-release" ]; then
                                 --admindir "${HOME}/.local/var/lib/alternatives" \
                                 --install "${HOME}/.local/bin/gcov" "gcov" "${custom_gcov}" 10
         fi
+        export OMPI_MCA_mpi_abort_print_stack=enabled
     fi
 fi
 
@@ -386,7 +400,6 @@ if [ "${with_coverage}" = true ] || [ "${with_coverage_python}" = true ]; then
         echo "Running lcov and gcov..."
         codecov_opts="${codecov_opts} --gcov"
         "${srcdir}/maintainer/CI/run_lcov.sh" coverage.info
-        rm coverage.info
     fi
     if [ "${with_coverage_python}" = true ]; then
         echo "Running python3-coverage..."

requirements.txt

@@ -30,6 +30,7 @@ coverage>=7.4.4
 sphinx>=7.2.6
 sphinx-toggleprompt==0.5.2
 sphinxcontrib-bibtex>=2.6.2
+sphinx-tabs>=3.4.4
 numpydoc>=1.6.0
 pybtex>=0.24.0
 # jupyter dependencies