Improve support for newer compilers

Bump all library requirements. Address compiler diagnostics for
GCC 13 to 16, Clang 19 to 21, CrayClang 19, IntelLLVM 2023.2.0,
nvcc 12.0 to 12.8. Add CMake options for packaging on Fedora.

Author: jngrad

.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
@@ -54,12 +48,12 @@ jobs:
           with_gsl: 'true'
           with_walberla: 'true'
           with_walberla_avx: 'false'
-          with_shared_memory_parallelism: 'false'
+          with_shared_memory_parallelism: 'true'
 
   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
@@ -98,7 +98,7 @@ maxset:
      with_nlopt: 'true'
      with_caliper: 'true'
      check_skip_long: 'true'
-     cmake_params: '-D CMAKE_CXX_STANDARD=23 -D CMAKE_CXX_EXTENSIONS=OFF -D ESPRESSO_TEST_NP=8'
+     cmake_params: '-D CMAKE_CXX_STANDARD=23 -D CMAKE_CXX_EXTENSIONS=OFF -D ESPRESSO_TEST_NP=8 -D ESPRESSO_TEST_NT=8'
   script:
     - bash maintainer/CI/build_cmake.sh
   tags:

CMakeLists.txt

@@ -142,6 +142,10 @@ option(ESPRESSO_INSIDE_DOCKER "Set this to ON when running inside Docker." OFF)
 mark_as_advanced(ESPRESSO_INSIDE_DOCKER)
 set(ESPRESSO_TEST_TIMEOUT "300"
     CACHE STRING "Timeout in seconds for each testsuite test")
+if(ESPRESSO_BUILD_WITH_PYTHON)
+  set(ESPRESSO_MODULE_INSTALL_PATH ""
+      CACHE PATH "Install ESPResSo Python module in a custom location")
+endif()
 
 if(ESPRESSO_BUILD_WITH_CCACHE)
   find_program(CCACHE_PROGRAM ccache REQUIRED)
@@ -316,7 +320,7 @@ 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()
@@ -358,7 +362,7 @@ set(ESPRESSO_INSTALL_LIBDIR "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}")
 
 set(ESPRESSO_OLD_CMAKE_INSTALL_LIBDIR "${CMAKE_INSTALL_LIBDIR}")
 
-# python site-packages, can be overriden with CMake options
+# python site-packages, can be overridden with CMake options
 if(ESPRESSO_BUILD_WITH_PYTHON)
   if(NOT ESPRESSO_INSTALL_PYTHON)
     if(CMAKE_INSTALL_PREFIX STREQUAL "/")
@@ -369,7 +373,10 @@ if(ESPRESSO_BUILD_WITH_PYTHON)
       )
     endif()
   endif()
-  # override: package C++, CUDA and Cython shared objects together
+  if(NOT ESPRESSO_MODULE_INSTALL_PATH STREQUAL "")
+    set(ESPRESSO_INSTALL_PYTHON "${ESPRESSO_MODULE_INSTALL_PATH}")
+  endif()
+  # install shared objects in the Python folder
   set(ESPRESSO_INSTALL_LIBDIR "${ESPRESSO_INSTALL_PYTHON}/espressomd")
   add_custom_target(espresso_packaging_dependencies)
 endif()
@@ -633,14 +640,14 @@ 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 4.6 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 +659,7 @@ 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 ${ESPRESSO_BUILD_SHARED_LIBS_DEFAULT})
@@ -711,7 +719,7 @@ if(ESPRESSO_BUILD_WITH_HDF5)
   FetchContent_Declare(
     HighFive
     GIT_REPOSITORY https://github.com/highfive-devs/highfive.git
-    GIT_TAG        v3.2.0
+    GIT_TAG        v3.3.0
   )
   # cmake-format: on
   FetchContent_MakeAvailable(HighFive)
@@ -893,6 +901,8 @@ if(ESPRESSO_BUILD_TESTS)
             "Extra arguments to give to ctest calls (separated by semicolons)")
   set(ESPRESSO_TEST_NP "4" CACHE STRING
                                  "Maximal number of MPI ranks to use per test")
+  set(ESPRESSO_TEST_NT "4"
+      CACHE STRING "Maximal number of OpenMP threads to use per test")
   add_library(espresso_tests_compiler_flags INTERFACE)
   add_library(espresso::tests::compiler_flags ALIAS
               espresso_tests_compiler_flags)
@@ -923,13 +933,14 @@ if(ESPRESSO_BUILD_WITH_WALBERLA)
   FetchContent_Declare(
     walberla
     GIT_REPOSITORY https://i10git.cs.fau.de/walberla/walberla.git
-    GIT_TAG        17fc54c8 # v7.2 with patches
+    GIT_TAG        3247aa73 # v7.2 with patches
   )
   # cmake-format: on
   string(REGEX REPLACE "([/\\]walberla)-src$" "\\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 "")
@@ -972,14 +983,21 @@ if(ESPRESSO_BUILD_WITH_WALBERLA)
     endfunction()
     espresso_enable_avx2_support(espresso_avx_flags_callback)
   endif()
+  add_library(espresso_walberla_sqlite_compiler_flags INTERFACE)
+  target_compile_options(
+    espresso_walberla_sqlite_compiler_flags
+    INTERFACE $<$<COMPILE_LANG_AND_ID:C,GNU>:-Wno-discarded-qualifiers>
+              -Wno-misleading-indentation -Wno-unused-but-set-variable)
+  target_link_libraries(walberla_sqlite
+                        PRIVATE espresso_walberla_sqlite_compiler_flags)
 endif()
 
 if(ESPRESSO_BUILD_WITH_CALIPER)
   # cmake-format: off
   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 +1013,14 @@ 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 +1050,17 @@ 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()

cmake/espresso_unit_test.cmake

@@ -80,6 +80,9 @@ function(espresso_unit_test_register)
   if(NOT DEFINED TEST_NUM_THREADS)
     set(TEST_NUM_THREADS 2)
   endif()
+  if(${TEST_NUM_THREADS} GREATER ${ESPRESSO_TEST_NT})
+    set(TEST_NUM_THREADS ${ESPRESSO_TEST_NT})
+  endif()
 
   if(ESPRESSO_WARNINGS_ARE_ERRORS)
     set(SANITIZERS_HALT_ON_ERROR "halt_on_error=1")

doc/sphinx/conf.py.in

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