bond-refactoring: resolve merge conflict with python branch

.clang-tidy

@@ -3,6 +3,7 @@ Checks: |
    clang-diagnostic-*,
    clang-analyzer-*,
    -clang-analyzer-core.NullDereference,
+   -clang-analyzer-core.uninitialized.UndefReturn,
    -clang-analyzer-optin.mpi.MPI-Checker,
    -clang-analyzer-security.FloatLoopCounter,
    bugprone-*,

.github/actions/build_and_check/action.yml

@@ -0,0 +1,31 @@
+name: 'Build and check'
+description: 'Build espresso and run checks'
+inputs:
+  asan:  # id of input
+    description: 'Whether to build with address sanitizer'
+    required: true
+    default: 'false'
+  ubsan:
+    description: 'Whether to build with undefined behavior sanitizer'
+    required: true
+    default: 'false'
+  check_skip_long:  # id of input
+    description: 'Whether to skip long python tests'
+    required: true
+    default: 'false'
+runs:
+  using: "composite"
+  steps:
+    - run: |
+       brew install boost boost-mpi fftw
+       brew install hdf5-mpi
+       pip3 install numpy cython h5py scipy
+      shell: bash
+    - run: |
+        export myconfig=maxset with_cuda=false test_timeout=600 with_asan=${{ inputs.asan }} with_ubsan=${{ inputs.ubsan }} check_skip_long=${{ inputs.check_skip_long }}
+        bash maintainer/CI/build_cmake.sh
+      shell: bash
+      # This is a workaround for the unfortunate interaction of MacOS and OpenMPI 4
+      # See https://github.com/open-mpi/ompi/issues/6518
+      env:
+        OMPI_MCA_btl: "self,tcp"

.github/workflows/push_pull.yml

@@ -0,0 +1,52 @@
+name: run tests on mac
+
+on:
+  push:
+  pull_request:
+  schedule:
+    - cron: '0 3 * * *'
+
+jobs:
+  regular_check:
+    runs-on: macos-latest
+    if: github.event_name != 'schedule'
+    steps:
+      - name: Checkout
+        uses: actions/checkout@main
+      - name: Setup Python environment
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.7'
+      - name: Check without sanitizer
+        uses: ./.github/actions/build_and_check
+        with:
+          asan: false
+          ubsan: false
+          check_skip_long: false
+
+  sanitizer_check:
+    runs-on: macos-latest
+    if: github.event_name == 'schedule'
+    steps:
+      - name: Checkout
+        uses: actions/checkout@main
+      - name: Setup Python environment
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.7'
+      - name: Check with sanitizer
+        uses: ./.github/actions/build_and_check
+        with:
+          asan: true
+          ubsan: true
+          check_skip_long: true
+      - name: Setting job link variable
+        if: ${{ failure() }}
+        run: |
+          echo "job_link=${GITHUB_SERVER_URL}/${GITHUB_REPOSITORY}/actions/runs/${GITHUB_RUN_ID}" >> $GITHUB_ENV
+      - uses: alialaa/issue-action@v1
+        if: ${{ failure() }}
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          title: Scheduled CI job has failed
+          body: ${{ env.job_link }}

.gitlab-ci.yml

@@ -1,4 +1,4 @@
-image: docker.pkg.github.com/espressomd/docker/ubuntu-20.04:e583d4b2eb8eedd10068957f952bd67008475ee5
+image: docker.pkg.github.com/espressomd/docker/ubuntu-20.04:063f945eb434f6900402fd412f28a4486288c82b
 
 stages:
   - prepare
@@ -100,6 +100,7 @@ maxset:
      with_scafacos: 'true'
      with_stokesian_dynamics: 'true'
      check_skip_long: 'true'
+     cmake_params: '-DTEST_NP=8'
   script:
     - bash maintainer/CI/build_cmake.sh
   tags:
@@ -130,6 +131,7 @@ ubuntu:wo-dependencies:
   variables:
      myconfig: 'maxset'
      with_cuda: 'false'
+     with_hdf5: 'false'
      make_check_unit_tests: 'false'
      make_check_python: 'false'
   script:

CMakeLists.txt

@@ -41,7 +41,6 @@ include(FeatureSummary)
 include(GNUInstallDirs)
 project(ESPResSo)
 include(option_enum)
-include(option_if_available)
 if(POLICY CMP0074)
   # make find_package() use <PackageName>_ROOT variables
   cmake_policy(SET CMP0074 NEW)
@@ -69,12 +68,12 @@ set(CMAKE_FIND_FRAMEWORK LAST)
 # ##############################################################################
 
 option(WITH_PYTHON "Build with Python bindings" ON)
-option_if_available(WITH_GSL "Build with GSL support" ON)
+option(WITH_GSL "Build with GSL support" OFF)
 option(WITH_CUDA "Build with GPU support" OFF)
-option_if_available(WITH_HDF5 "Build with HDF5 support" ON)
+option(WITH_HDF5 "Build with HDF5 support" OFF)
 option(WITH_TESTS "Enable tests" ON)
-option_if_available(WITH_SCAFACOS "Build with ScaFaCoS support" OFF)
-option_if_available(WITH_STOKESIAN_DYNAMICS "Build with Stokesian Dynamics" ON)
+option(WITH_SCAFACOS "Build with ScaFaCoS support" OFF)
+option(WITH_STOKESIAN_DYNAMICS "Build with Stokesian Dynamics" OFF)
 option(WITH_BENCHMARKS "Enable benchmarks" OFF)
 option(WITH_VALGRIND_INSTRUMENTATION
        "Build with valgrind instrumentation markers" OFF)
@@ -192,25 +191,16 @@ if(WITH_HDF5)
   # who are not familiar with the way hdf5 is distributed in Linux package
   # repositories (libhdf5-dev is the serial version).
   set(HDF5_PREFER_PARALLEL 1)
-  find_package(HDF5 "1.8" COMPONENTS C)
+  find_package(HDF5 "1.8" REQUIRED COMPONENTS C)
   if(HDF5_FOUND)
     if(HDF5_IS_PARALLEL)
       set(H5MD 1)
       add_feature_info(HDF5 ON "parallel")
     else()
       unset(H5MD)
       set(HDF5_FOUND FALSE)
-      if(NOT WITH_HDF5_IS_DEFAULT_VALUE)
-        message(
-          FATAL_ERROR
-            "Optional dependency HDF5 explicitly requested, but parallel version not found."
-        )
-      endif()
+      message(FATAL_ERROR "HDF5 parallel version not found.")
     endif(HDF5_IS_PARALLEL)
-  elseif(NOT WITH_HDF5_IS_DEFAULT_VALUE)
-    message(
-      FATAL_ERROR
-        "Optional dependency HDF5 explicitly requested, but not found.")
   endif(HDF5_FOUND)
 endif(WITH_HDF5)
 
@@ -231,50 +221,24 @@ if(WITH_HDF5 AND EXISTS "${CMAKE_SOURCE_DIR}/.git")
 endif()
 
 if(WITH_SCAFACOS)
-  find_package(PkgConfig)
-  pkg_check_modules(SCAFACOS scafacos)
+  find_package(PkgConfig REQUIRED)
+  pkg_check_modules(SCAFACOS scafacos REQUIRED)
   if(SCAFACOS_FOUND)
     set(SCAFACOS 1)
-  elseif(NOT WITH_SCAFACOS_IS_DEFAULT_VALUE)
-    message(
-      FATAL_ERROR
-        "Optional dependency ScaFaCoS explicitly requested, but not found.")
   endif(SCAFACOS_FOUND)
 endif(WITH_SCAFACOS)
 
 if(WITH_GSL)
+  find_package(GSL REQUIRED)
+else()
   find_package(GSL)
-  if(GSL_FOUND)
-    set(GSL 1)
-  elseif(NOT WITH_GSL_IS_DEFAULT_VALUE)
-    message(
-      FATAL_ERROR "Optional dependency GSL explicitly requested, but not found."
-    )
-  endif(GSL_FOUND)
 endif(WITH_GSL)
 
-find_package(BLAS)
-if(BLAS_FOUND)
-  set(BLAS 1)
-endif()
-find_package(LAPACK)
-if(LAPACK_FOUND)
-  set(LAPACK 1)
-endif()
+if(GSL_FOUND)
+  set(GSL 1)
+endif(GSL_FOUND)
 
 if(WITH_STOKESIAN_DYNAMICS)
-  if(BLAS AND LAPACK)
-    set(STOKESIAN_DYNAMICS 1)
-  endif()
-  if(NOT STOKESIAN_DYNAMICS AND NOT WITH_STOKESIAN_DYNAMICS_IS_DEFAULT_VALUE)
-    message(
-      FATAL_ERROR
-        "Optional feature Stokesian Dynamics explicitly requested, but dependencies not found."
-    )
-  endif()
-endif(WITH_STOKESIAN_DYNAMICS)
-
-if(STOKESIAN_DYNAMICS)
   set(CMAKE_INSTALL_LIBDIR
       "${CMAKE_INSTALL_PREFIX}/${PYTHON_INSTDIR}/espressomd")
   include(FetchContent)
@@ -283,16 +247,17 @@ if(STOKESIAN_DYNAMICS)
     GIT_REPOSITORY https://github.com/hmenke/espresso-stokesian-dynamics.git
     GIT_TAG c14e57655e929)
   FetchContent_GetProperties(stokesian_dynamics)
+  set(STOKESIAN_DYNAMICS 1)
   if(NOT stokesian_dynamics_POPULATED)
     FetchContent_Populate(stokesian_dynamics)
     add_subdirectory(${stokesian_dynamics_SOURCE_DIR}
                      ${stokesian_dynamics_BINARY_DIR})
   endif()
-endif(STOKESIAN_DYNAMICS)
+endif(WITH_STOKESIAN_DYNAMICS)
 
 if(WITH_VALGRIND_INSTRUMENTATION)
-  find_package(PkgConfig)
-  pkg_check_modules(VALGRIND valgrind)
+  find_package(PkgConfig REQUIRED)
+  pkg_check_modules(VALGRIND valgrind REQUIRED)
   if(VALGRIND_FOUND)
     set(VALGRIND_INSTRUMENTATION 1)
     message(STATUS ${VALGRIND_INCLUDE_DIRS})
@@ -306,9 +271,9 @@ endif(WITH_VALGRIND_INSTRUMENTATION)
 
 find_package(MPI 3.0 REQUIRED)
 
-# ##############################################################################
+#
 # Boost
-# ##############################################################################
+#
 
 list(APPEND BOOST_COMPONENTS mpi serialization filesystem system)
 
@@ -423,6 +388,10 @@ target_compile_options(
 
 set(CMAKE_MACOSX_RPATH TRUE)
 
+#
+# Sanitizers
+#
+
 if(WITH_ASAN AND WITH_MSAN)
   message(
     FATAL_ERROR
@@ -448,14 +417,18 @@ endif()
 target_link_libraries(cxx_interface INTERFACE coverage_interface)
 
 #
-# Testing
-# ##############################################################################
+# Static analysis
+#
 
 if(WITH_CLANG_TIDY)
   find_package(ClangTidy "${CMAKE_CXX_COMPILER_VERSION}" EXACT REQUIRED)
   set(CMAKE_CXX_CLANG_TIDY "${CLANG_TIDY_EXE};--extra-arg=--cuda-host-only")
 endif()
 
+#
+# Testing
+#
+
 if(WITH_TESTS)
   enable_testing()
   add_custom_target(check)
@@ -480,6 +453,7 @@ endif(WITH_BENCHMARKS)
 add_subdirectory(doc)
 add_subdirectory(src)
 add_subdirectory(libs)
+
 #
 # Feature summary
 #

cmake/FindCUDACompilerClang.cmake

@@ -77,7 +77,6 @@ function(find_gpu_library)
   endif()
 endfunction(find_gpu_library)
 
-find_gpu_library(VARNAME CUDA_LIBRARY NAMES cuda REQUIRED)
 find_gpu_library(VARNAME CUDART_LIBRARY NAMES cudart REQUIRED)
 find_gpu_library(VARNAME CUFFT_LIBRARY NAMES cufft REQUIRED)
 

cmake/FindCUDACompilerNVCC.cmake

@@ -71,7 +71,6 @@ function(find_gpu_library)
   endif()
 endfunction(find_gpu_library)
 
-find_gpu_library(VARNAME CUDA_LIBRARY NAMES cuda REQUIRED)
 find_gpu_library(VARNAME CUDART_LIBRARY NAMES cudart REQUIRED)
 find_gpu_library(VARNAME CUDA_CUFFT_LIBRARIES NAMES cufft REQUIRED)