WIP

.github/actions/build_and_check/action.yml

@@ -3,13 +3,9 @@ description: 'Build espresso and run checks'
 runs:
   using: "composite"
   steps:
-    - run: |
-       brew install boost boost-mpi fftw
-       pip3 install -c requirements.txt "cython<3.0" numpy scipy packaging
-      shell: bash
-      if: runner.os == 'macOS'
     - run: |
         export myconfig=maxset with_cuda=false with_gsl=false with_hdf5=false test_timeout=800 check_skip_long=true
+        if test -d venv; then . venv/bin/activate; fi
         bash maintainer/CI/build_cmake.sh
       shell: bash
       # This is a workaround for the unfortunate interaction of MacOS and OpenMPI 4

.github/workflows/push_pull.yml

@@ -9,7 +9,7 @@ permissions:
 
 jobs:
   macos:
-    runs-on: macos-14
+    runs-on: macos-15
     if: ${{ github.repository == 'espressomd/espresso' }}
     steps:
       - name: Checkout
@@ -19,12 +19,15 @@ jobs:
         with:
           key: macos
           save: ${{ github.ref == 'refs/heads/python' }}
-      - name: Setup Python environment
-        uses: actions/[email protected]
-        with:
-          python-version: '3.12'
       - name: Get runner specifications
         run: system_profiler SPHardwareDataType
+      - run: |
+         brew install boost boost-mpi fftw
+         python3 -m venv venv
+         . venv/bin/activate
+         pip3 install -c requirements.txt "cython<3.0.10" numpy scipy packaging
+         deactivate
+        shell: bash
       - name: Build and check
         uses: ./.github/actions/build_and_check
         env:
@@ -35,7 +38,7 @@ jobs:
   debian:
     runs-on: ubuntu-latest
     container:
-      image: ghcr.io/espressomd/docker/debian:f7f8ef2c0ca93c67aa16b9f91785492fb04ecc1b-base-layer
+      image: ghcr.io/jngrad/espresso-docker/debian:b65fb07658b6217546a1da19cde4fcbf89e2ecee-base-layer
       credentials:
          username: ${{ github.actor }}
          password: ${{ secrets.github_token }}
@@ -57,6 +60,8 @@ jobs:
         env:
           build_procs: 4
           check_procs: 4
+          CC: 'gcc-12'
+          CXX: 'g++-12'
           myconfig: 'maxset'
           with_ccache: 'true'
           with_cuda: 'false'
@@ -74,7 +79,7 @@ jobs:
     runs-on: ubuntu-latest
     if: ${{ github.repository == 'espressomd/espresso' }}
     container:
-      image: ghcr.io/espressomd/docker/ubuntu-wo-dependencies:f7f8ef2c0ca93c67aa16b9f91785492fb04ecc1b-base-layer
+      image: ghcr.io/jngrad/espresso-docker/ubuntu-wo-dependencies:b65fb07658b6217546a1da19cde4fcbf89e2ecee-base-layer
       credentials:
          username: ${{ github.actor }}
          password: ${{ secrets.github_token }}
@@ -96,6 +101,8 @@ jobs:
         env:
           build_procs: 4
           check_procs: 4
+          CC: 'gcc-13'
+          CXX: 'g++-13'
           myconfig: 'maxset'
           with_ccache: 'true'
           with_cuda: 'false'

.gitlab-ci.yml

@@ -1,4 +1,4 @@
-image: ghcr.io/espressomd/docker/ubuntu:f7f8ef2c0ca93c67aa16b9f91785492fb04ecc1b
+image: ghcr.io/jngrad/espresso-docker/ubuntu:b65fb07658b6217546a1da19cde4fcbf89e2ecee
 
 stages:
   - prepare
@@ -17,7 +17,7 @@ stages:
 
 .notification_job_template: &notification_job_definition
   <<: *global_job_definition
-  image: ghcr.io/espressomd/docker/fedora:f7f8ef2c0ca93c67aa16b9f91785492fb04ecc1b
+  image: ghcr.io/jngrad/espresso-docker/fedora:b65fb07658b6217546a1da19cde4fcbf89e2ecee
   variables:
     GET_SOURCES_ATTEMPTS: 3
   before_script:
@@ -77,9 +77,9 @@ default:
   <<: *global_job_definition
   stage: build
   variables:
-     CC: 'gcc-13'
-     CXX: 'g++-13'
-     GCOV: 'gcov-13'
+     CC: 'gcc-14'
+     CXX: 'g++-14'
+     GCOV: 'gcov-14'
      with_cuda: 'false'
      myconfig: 'default'
      with_coverage: 'true'
@@ -98,9 +98,9 @@ maxset:
   <<: *global_job_definition
   stage: build
   variables:
-     CC: 'gcc-13'
-     CXX: 'g++-13'
-     GCOV: 'gcov-13'
+     CC: 'gcc-14'
+     CXX: 'g++-14'
+     GCOV: 'gcov-14'
      with_cuda: 'false'
      myconfig: 'maxset'
      with_coverage: 'true'
@@ -122,9 +122,9 @@ no_rotation:
   <<: *global_job_definition
   stage: build
   variables:
-     CC: 'gcc-13'
-     CXX: 'g++-13'
-     GCOV: 'gcov-13'
+     CC: 'gcc-14'
+     CXX: 'g++-14'
+     GCOV: 'gcov-14'
      with_cuda: 'false'
      myconfig: 'no_rotation'
      with_coverage: 'true'
@@ -138,10 +138,10 @@ no_rotation:
     - no-cuda
     - numa
 
-fedora:40:
+fedora:41:
   <<: *global_job_definition
   stage: build
-  image: ghcr.io/espressomd/docker/fedora:f7f8ef2c0ca93c67aa16b9f91785492fb04ecc1b
+  image: ghcr.io/jngrad/espresso-docker/fedora:b65fb07658b6217546a1da19cde4fcbf89e2ecee
   variables:
      with_cuda: 'false'
      with_gsl: 'false'
@@ -163,9 +163,9 @@ clang-sanitizer:
   <<: *global_job_definition
   stage: build
   variables:
-     CC: 'clang-18'
-     CXX: 'clang++-18'
-     CUDACXX: 'clang++-18'
+     CC: 'clang-19'
+     CXX: 'clang++-19'
+     CUDACXX: 'clang++-19'
      myconfig: 'maxset'
      with_cuda: 'true'
      with_cuda_compiler: 'clang'
@@ -411,9 +411,9 @@ empty:
   <<: *global_job_definition
   stage: build
   variables:
-     CC: 'clang-18'
-     CXX: 'clang++-18'
-     CUDACXX: 'clang++-18'
+     CC: 'clang-19'
+     CXX: 'clang++-19'
+     CUDACXX: 'clang++-19'
      myconfig: 'empty'
      with_cuda: 'true'
      with_cuda_compiler: 'clang'

CMakeLists.txt

@@ -25,6 +25,10 @@ if(POLICY CMP0167)
   # use BoostConfig.cmake shipped with Boost 1.70+ instead of the one in CMake
   cmake_policy(SET CMP0167 NEW)
 endif()
+if(POLICY CMP0169)
+  # use deprecated FetchContent_Populate function for h5xx dependency
+  cmake_policy(SET CMP0169 OLD)
+endif()
 message(STATUS "CMake version: ${CMAKE_VERSION}")
 # CMake modules/macros are in a subdirectory to keep this file cleaner
 set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
@@ -48,9 +52,9 @@ macro(espresso_minimal_compiler_version)
   endif()
 endmacro()
 
-espresso_minimal_compiler_version("GNU" 10.5.0)
-espresso_minimal_compiler_version("Clang" 14.0.0)
-espresso_minimal_compiler_version("AppleClang" 14.0.0)
+espresso_minimal_compiler_version("GNU" 12.2.0)
+espresso_minimal_compiler_version("Clang" 18.1.0)
+espresso_minimal_compiler_version("AppleClang" 16.0.0)
 espresso_minimal_compiler_version("IntelLLVM" 2023.1)
 
 set(UNSUPPORTED_COMPILERS "Intel;MSVC")
@@ -117,7 +121,7 @@ FetchContent_Declare(
 FetchContent_Declare(
   caliper
   GIT_REPOSITORY https://github.com/LLNL/Caliper.git
-  GIT_TAG        v2.12.0
+  GIT_TAG        v2.12.1
 )
 # cmake-format: on
 
@@ -237,8 +241,6 @@ if(ESPRESSO_BUILD_WITH_CUDA)
   include(CheckLanguage)
   enable_language(CUDA)
   check_language(CUDA)
-  espresso_minimal_compiler_version("GNU" 11.4.0)
-  espresso_minimal_compiler_version("Clang" 17.0.0)
   set(CMAKE_CUDA_STANDARD 20)
   set(CMAKE_CUDA_STANDARD_REQUIRED ON)
   set(ESPRESSO_MINIMAL_CUDA_VERSION 12.0)
@@ -767,15 +769,21 @@ if(ESPRESSO_BUILD_WITH_WALBERLA)
     set(BUILD_SHARED_LIBS ${ESPRESSO_BUILD_SHARED_LIBS_DEFAULT})
     set(CMAKE_SHARED_LIBRARY_PREFIX "${ESPRESSO_SHARED_LIBRARY_PREFIX}")
   endif()
+  # patching
+  target_compile_options(
+    blockforest
+    PRIVATE
+      $<$<AND:$<CXX_COMPILER_ID:GNU>,$<VERSION_GREATER_EQUAL:$<CXX_COMPILER_VERSION>,14>>:-Wno-alloc-size>
+  )
   set(WALBERLA_LIBS
       walberla::core walberla::domain_decomposition walberla::blockforest
       walberla::boundary walberla::field walberla::lbm walberla::timeloop
       walberla::vtk)
   if(WALBERLA_BUILD_WITH_FFTW)
-    set(WALBERLA_LIBS ${WALBERLA_LIBS} walberla::fft)
+    list(APPEND WALBERLA_LIBS walberla::fft)
   endif()
   if(WALBERLA_BUILD_WITH_CUDA)
-    set(WALBERLA_LIBS ${WALBERLA_LIBS} walberla::gpu)
+    list(APPEND WALBERLA_LIBS walberla::gpu)
   endif()
   set(WALBERLA_LIBS_EXPORT
       ${WALBERLA_LIBS}

doc/sphinx/Readme.rst

@@ -5,7 +5,8 @@ How to get started with Sphinx
 
    .. code-block:: bash
 
-       pip3 install --user --upgrade 'sphinx>=2.3.0,!=3.0.0' 'sphinxcontrib-bibtex>=0.3.5'
+       python3 -m pip install -c requirements.txt \
+         sphinx sphinx-toggleprompt sphinxcontrib-bibtex numpydoc pybtex
 
 #. Compile the ``sphinx`` target in your build directory (that can take some
    time since we depend on finishing the build of the interface):

doc/sphinx/ek.rst

@@ -426,7 +426,7 @@ Start by installing the code generator dependencies:
 
 .. code-block:: bash
 
-    python3 -m pip install --user -c requirements.txt numpy sympy lbmpy pystencils islpy
+    python3 -m pip install -c requirements.txt numpy sympy lbmpy pystencils islpy
 
 Next, edit the code generator script to configure new kernels, then execute it:
 

doc/sphinx/installation.rst

@@ -132,7 +132,7 @@ To install the ZnDraw visualizer:
 
 .. code-block:: bash
 
-    python3 -m pip install --user -c requirements.txt 'zndraw==0.4.6'
+    python3 -m pip install -c requirements.txt 'zndraw==0.4.6'
 
 .. _Nvidia GPU acceleration:
 
@@ -207,7 +207,7 @@ To generate the Sphinx documentation, install the following packages:
 
 .. code-block:: bash
 
-    python3 -m pip install --user -c requirements.txt \
+    python3 -m pip install -c requirements.txt \
         sphinx sphinxcontrib-bibtex sphinx-toggleprompt
 
 To generate the Doxygen documentation, install the following packages:
@@ -250,15 +250,14 @@ to use, we recommend installing JupyterLab:
 
 .. code-block:: bash
 
-    python3 -m pip install --user -c requirements.txt \
-        nbformat nbconvert jupyterlab
+    python3 -m pip install -c requirements.txt \
+        jupyterlab>=4.3 nbformat nbconvert lxml[html_clean]
 
-If you prefer the look and feel of Jupyter Classic, install the following:
+If you prefer the look and feel of Jupyter Classic, install the following extra package:
 
 .. code-block:: bash
 
-    python3 -m pip install --user -c requirements.txt \
-        nbformat nbconvert jupyterlab nbclassic
+    python3 -m pip install -c requirements.txt nbclassic
 
 Alternatively, to use VS Code Jupyter, install the following extensions:
 

doc/sphinx/lb.rst

@@ -533,7 +533,7 @@ Start by installing the code generator dependencies:
 
 .. code-block:: bash
 
-    python3 -m pip install --user -c requirements.txt numpy sympy lbmpy pystencils islpy
+    python3 -m pip install -c requirements.txt numpy sympy lbmpy pystencils islpy
 
 Next, edit the code generator script to configure new kernels, then execute it:
 

doc/sphinx/running.rst

@@ -906,7 +906,7 @@ Valgrind
     .. code-block:: bash
 
         sudo apt install valgrind kcachegrind graphviz
-        python3 -m pip install --user gprof2dot
+        python3 -m pip install gprof2dot
 
 The Valgrind [2]_ :cite:`nethercote07a,nethercote03a` framework brings several
 tools to examine a program runtime performance.
@@ -1066,7 +1066,7 @@ kernprof
 
     .. code-block:: bash
 
-        python3 -m pip install --user line_profiler
+        python3 -m pip install line_profiler
 
 kernprof [8]_ :cite:`misc-kernprof` is a low-overhead Python profiler.
 It supports two instrumentation modes: ``line_profile`` and ``cProfile``.