Support recent Linux distributions (#4526)

Description of changes: - fix compiler warnings and diagnostics from recent GCC/Clang releases - fix CMake 3.22 warnings and Python 3.10 numpy warnings - update installation instructions for Ubuntu 22.04 and macOS - check Fedora 36 and Ubuntu 22.04 in CI - add support for Sphinx 5.0.0
espressomd · Jun 21, 2022 · 8a92c36 · 8a92c36
2 parents e9f8e53 + 285e451
commit 8a92c36
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Showing 22 changed files with 171 additions and 135 deletions.
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -1,4 +1,4 @@
-image: ghcr.io/espressomd/docker/ubuntu-20.04:285fee33c6cdc3b617745a75bd28aec331a53365
+image: ghcr.io/espressomd/docker/ubuntu-20.04:7ec021ab4af6f89d65121db2eb24acb1ed452e02
 
 stages:
   - prepare
@@ -26,7 +26,6 @@ stages:
   timeout: 40m
   interruptible: false
   tags:
-    - docker
     - espresso
     - no-cuda
 
@@ -51,7 +50,6 @@ style:
   script:
     - sh maintainer/CI/fix_style.sh
   tags:
-    - docker
     - espresso
     - no-cuda
   variables:
@@ -73,7 +71,6 @@ style_doxygen:
     - cmake .. -DWITH_CUDA=ON -DWITH_SCAFACOS=ON
     - sh ../maintainer/CI/dox_warnings.sh
   tags:
-    - docker
     - espresso
     - no-cuda
 
@@ -94,7 +91,6 @@ default:
   script:
     - bash maintainer/CI/build_cmake.sh
   tags:
-    - docker
     - espresso
     - no-cuda
 
@@ -115,7 +111,6 @@ maxset:
   script:
     - bash maintainer/CI/build_cmake.sh
   tags:
-    - docker
     - espresso
     - no-cuda
     - numa
@@ -134,15 +129,14 @@ no_rotation:
   script:
     - bash maintainer/CI/build_cmake.sh
   tags:
-    - docker
     - espresso
     - no-cuda
     - numa
 
 ubuntu:wo-dependencies:
   <<: *global_job_definition
   stage: build
-  image: ghcr.io/espressomd/docker/ubuntu-wo-dependencies:285fee33c6cdc3b617745a75bd28aec331a53365
+  image: ghcr.io/espressomd/docker/ubuntu-wo-dependencies:7ec021ab4af6f89d65121db2eb24acb1ed452e02
   variables:
      myconfig: 'maxset'
      with_cuda: 'false'
@@ -152,7 +146,6 @@ ubuntu:wo-dependencies:
   script:
     - bash maintainer/CI/build_cmake.sh
   tags:
-    - docker
     - espresso
     - no-cuda
 
@@ -161,7 +154,7 @@ ubuntu:wo-dependencies:
 debian:10:
   <<: *global_job_definition
   stage: build
-  image: ghcr.io/espressomd/docker/debian:285fee33c6cdc3b617745a75bd28aec331a53365
+  image: ghcr.io/espressomd/docker/debian:7ec021ab4af6f89d65121db2eb24acb1ed452e02
   variables:
      with_cuda: 'false'
      myconfig: 'maxset'
@@ -170,14 +163,13 @@ debian:10:
   script:
     - bash maintainer/CI/build_cmake.sh
   tags:
-    - docker
     - espresso
     - no-cuda
 
-fedora:34:
+fedora:36:
   <<: *global_job_definition
   stage: build
-  image: ghcr.io/espressomd/docker/fedora:285fee33c6cdc3b617745a75bd28aec331a53365
+  image: ghcr.io/espressomd/docker/fedora:7ec021ab4af6f89d65121db2eb24acb1ed452e02
   variables:
      with_cuda: 'false'
      myconfig: 'maxset'
@@ -186,7 +178,6 @@ fedora:34:
   script:
     - bash maintainer/CI/build_cmake.sh
   tags:
-    - docker
     - espresso
     - no-cuda
 
@@ -212,15 +203,14 @@ clang-sanitizer:
     - bash maintainer/CI/build_cmake.sh
   timeout: 2h
   tags:
-    - docker
     - espresso
     - cuda
     - numa
 
 fast_math:
   <<: *global_job_definition
   stage: build
-  image: ghcr.io/espressomd/docker/cuda:285fee33c6cdc3b617745a75bd28aec331a53365
+  image: ghcr.io/espressomd/docker/cuda:7ec021ab4af6f89d65121db2eb24acb1ed452e02
   variables:
      CC: 'gcc-9'
      CXX: 'g++-9'
@@ -233,15 +223,14 @@ fast_math:
   script:
     - bash maintainer/CI/build_cmake.sh
   tags:
-    - docker
     - espresso
     - cuda
   when: manual
 
-cuda11-maxset:
+cuda11-maxset-ubuntu20.04:
   <<: *global_job_definition
   stage: build
-  image: ghcr.io/espressomd/docker/cuda:285fee33c6cdc3b617745a75bd28aec331a53365
+  image: ghcr.io/espressomd/docker/cuda:7ec021ab4af6f89d65121db2eb24acb1ed452e02
   variables:
      CC: 'gcc-9'
      CXX: 'g++-9'
@@ -250,13 +239,32 @@ cuda11-maxset:
      with_cuda: 'true'
      with_coverage: 'true'
      check_skip_long: 'true'
-     srcdir: '${CI_PROJECT_DIR}'
      with_scafacos: 'true'
      with_stokesian_dynamics: 'true'
   script:
     - bash maintainer/CI/build_cmake.sh
   tags:
-    - docker
+    - espresso
+    - cuda
+    - numa
+
+cuda11-maxset-ubuntu22.04:
+  <<: *global_job_definition
+  stage: build
+  image: ghcr.io/espressomd/docker/ubuntu-22.04:7ec021ab4af6f89d65121db2eb24acb1ed452e02
+  variables:
+     CC: 'gcc-10'
+     CXX: 'g++-10'
+     GCOV: 'gcov-10'
+     myconfig: 'maxset'
+     with_cuda: 'true'
+     with_coverage: 'true'
+     check_skip_long: 'true'
+     with_scafacos: 'true'
+     with_stokesian_dynamics: 'true'
+  script:
+    - bash maintainer/CI/build_cmake.sh
+  tags:
     - espresso
     - cuda
     - numa
@@ -282,7 +290,6 @@ cuda10-maxset:
     - build/
     expire_in: 1 week
   tags:
-    - docker
     - espresso
     - cuda
     - numa
@@ -307,7 +314,6 @@ tutorials-samples-maxset:
   script:
     - bash maintainer/CI/build_cmake.sh
   tags:
-    - docker
     - espresso
     - cuda
 
@@ -330,7 +336,6 @@ tutorials-samples-default:
   script:
     - bash maintainer/CI/build_cmake.sh
   tags:
-    - docker
     - espresso
     - cuda
   only:
@@ -356,7 +361,6 @@ tutorials-samples-empty:
   script:
     - bash maintainer/CI/build_cmake.sh
   tags:
-    - docker
     - espresso
     - cuda
   only:
@@ -382,7 +386,6 @@ tutorials-samples-no-gpu:
   script:
     - bash maintainer/CI/build_cmake.sh
   tags:
-    - docker
     - espresso
     - no-cuda
   only:
@@ -410,15 +413,15 @@ installation:
     # get path of installed files
     - CI_INSTALL_DIR="/tmp/espresso-unit-tests"
     - CI_INSTALL_PYTHON_PATH=$(dirname $(find "${CI_INSTALL_DIR}/lib" -name espressomd))
+    - CI_CORES=$(cmake -L . | grep CTEST_ARGS | grep --color=never -Po '(?<=-j)[0-9]+')
     # deploy object-in-fluid module
     - cp -r "src/python/object_in_fluid" "${CI_INSTALL_PYTHON_PATH}/object_in_fluid"
     # run all tests with the installed files
     - sed -i "s|$(pwd)/pypresso|${CI_INSTALL_DIR}/bin/pypresso|" testsuite/{python,scripts/samples,scripts/tutorials}/CTestTestfile.cmake
-    - make -j2 check_python
-    - make -j2 check_samples
-    - make -j2 check_tutorials
+    - make -j ${CI_CORES} check_python_skip_long
+    - make -j ${CI_CORES} check_samples
+    - make -j 2 check_tutorials
   tags:
-    - docker
     - espresso
     - cuda
   when: manual
@@ -438,7 +441,6 @@ empty:
   script:
     - bash maintainer/CI/build_cmake.sh
   tags:
-    - docker
     - espresso
     - cuda
     - numa
@@ -461,7 +463,6 @@ check_sphinx:
     - build/doc/sphinx
     expire_in: 1 week
   tags:
-    - docker
     - espresso
     - cuda
     - numa
@@ -486,7 +487,6 @@ run_tutorials:
     - build/doc/tutorials
     expire_in: 1 week
   tags:
-    - docker
     - espresso
     - cuda
     - numa
@@ -509,7 +509,6 @@ run_doxygen:
     - build/doc/doxygen
     expire_in: 1 week
   tags:
-    - docker
     - espresso
     - no-cuda
     - numa
@@ -525,7 +524,6 @@ maxset_no_gpu:
     - cd ${CI_PROJECT_DIR}/build
     - make -t && make check
   tags:
-    - docker
     - espresso
     - no-cuda
     - numa
@@ -541,7 +539,6 @@ maxset_3_cores:
     - cmake -DTEST_NP=3 .
     - make -t && make check_unit_tests && make check_python_parallel_odd
   tags:
-    - docker
     - espresso
     - cuda
     - numa

diff --git a/cmake/FindCUDACompilerClang.cmake b/cmake/FindCUDACompilerClang.cmake
@@ -64,6 +64,12 @@ set(gpu_interface_flags "${CUDA_NVCC_FLAGS} ${CUDA_NVCC_FLAGS_${CMAKE_BUILD_TYPE
 if(CMAKE_CUDA_COMPILER_VERSION VERSION_LESS 11)
   set(gpu_interface_flags "${gpu_interface_flags} --cuda-gpu-arch=sm_30")
 endif()
+if(CMAKE_CUDA_COMPILER_VERSION VERSION_GREATER_EQUAL "12.0.0" AND
+   CMAKE_CUDA_COMPILER_VERSION VERSION_LESS "13.0.0" AND
+   CUDA_VERSION VERSION_GREATER_EQUAL "11.0" AND
+   CUDA_VERSION VERSION_LESS "12.0")
+  set(gpu_interface_flags "${gpu_interface_flags} -Wno-unknown-cuda-version")
+endif()
 
 function(find_gpu_library)
   cmake_parse_arguments(LIBRARY "REQUIRED" "NAMES;VARNAME" "" ${ARGN})

diff --git a/doc/sphinx/_static/custom.css b/doc/sphinx/_static/custom.css
@@ -1,4 +1,6 @@
+/*****************************************/
 /* customization for the alabaster theme */
+/*****************************************/
 
 /* color links to python objects */
 div.bodywrapper a.reference.internal code {
@@ -31,3 +33,15 @@ div.admonition p {
 div.document {
   padding-right: 260px;
 }
+
+/*************************************/
+/* customization for the basic theme */
+/*************************************/
+
+/* remove automatic hyphenation */
+div.body p, div.body dd, div.body li, div.body blockquote {
+    -moz-hyphens: manual;
+    -ms-hyphens: manual;
+    -webkit-hyphens: manual;
+    hyphens: manual;
+}
diff --git a/doc/sphinx/conf.py.in b/doc/sphinx/conf.py.in
@@ -75,7 +75,7 @@ release = '@PROJECT_VERSION@'
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used: