Simplify CI and bump version requirements (#3687)

Description of changes: - reduce number of CI images for CUDA jobs (partial fix for #3611) - test CUDA 9.1 and 10.1 using compatible compilers without patches (fixes #3654) - drop support for Ubuntu 16.04 - bump minimal Boost version to 1.65 (partial fix for #3093) - bump Python packages to the versions available in Ubuntu 18.04 (partial fix for #3421) - add missing lxml package (fixes #3686) - fix issues in docs revealed by the new Doxygen and Sphinx versions
espressomd · Apr 27, 2020 · 35e0865 · 35e0865
2 parents ed01bed + 7bcb911
commit 35e0865
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diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -1,4 +1,4 @@
-image: docker.pkg.github.com/espressomd/docker/ubuntu-18.04:a1192b35590a1a474c55fe1e9a1e6c25758454ea
+image: docker.pkg.github.com/espressomd/docker/ubuntu-20.04:06b6216c7aa3555bcf28c90734dbb84e7285c96f
 
 stages:
   - prepare
@@ -19,7 +19,7 @@ stages:
   variables:
     GIT_SUBMODULE_STRATEGY: none
   dependencies: []
-  timeout: 15m
+  timeout: 40m
   interruptible: false
   tags:
     - linux
@@ -38,7 +38,6 @@ status_pending:
 style:
   <<: *global_job_definition
   stage: prepare
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-20.04:b0de8c7df57d39edf72ad7d40c28bb67467dd7ec
   dependencies: []
   before_script:
     - git submodule deinit .
@@ -58,14 +57,13 @@ style:
 style_doxygen:
   <<: *global_job_definition
   stage: prepare
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:c9fe9d6d79ffd7e3e89ef282548e0b5278afde2c
   dependencies: []
   script:
     - mkdir build
     - cd build
     - cp ../maintainer/configs/maxset.hpp myconfig.hpp
-    - cmake .. -DWITH_CUDA=OFF
-    - bash ../maintainer/CI/dox_warnings.sh
+    - cmake .. -DWITH_CUDA=ON -DWITH_SCAFACOS=ON
+    - sh ../maintainer/CI/dox_warnings.sh
   tags:
     - docker
     - linux
@@ -75,6 +73,9 @@ style_doxygen:
 default:
   <<: *global_job_definition
   stage: build
+  variables:
+     CC: 'gcc-9'
+     CXX: 'g++-9'
   script:
     - export with_cuda=false myconfig=default with_coverage=true
     - bash maintainer/CI/build_cmake.sh
@@ -85,6 +86,9 @@ default:
 maxset:
   <<: *global_job_definition
   stage: build
+  variables:
+     CC: 'gcc-9'
+     CXX: 'g++-9'
   script:
     - export with_cuda=false myconfig=maxset with_coverage=true
     - bash maintainer/CI/build_cmake.sh
@@ -95,41 +99,35 @@ maxset:
 no_rotation:
   <<: *global_job_definition
   stage: build
+  variables:
+     CC: 'gcc-9'
+     CXX: 'g++-9'
   script:
     - export with_cuda=false myconfig=no_rotation with_coverage=true
     - bash maintainer/CI/build_cmake.sh
   tags:
     - docker
     - linux
 
-ubuntu-20.04-sanitizer:
+ubuntu:wo-dependencies:
   <<: *global_job_definition
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-20.04:b0de8c7df57d39edf72ad7d40c28bb67467dd7ec
   stage: build
-  variables:
-     CC: 'clang-9'
-     CXX: 'clang++-9'
+  image: docker.pkg.github.com/espressomd/docker/ubuntu-wo-dependencies:06b6216c7aa3555bcf28c90734dbb84e7285c96f
   script:
-    - export myconfig=maxset with_cuda=true with_cuda_compiler=clang with_coverage=false
-    - export with_static_analysis=true test_timeout=900
-    - export with_asan=true ASAN_OPTIONS="allocator_may_return_null=1"
-    - export with_ubsan=true UBSAN_OPTIONS=suppressions=${CI_PROJECT_DIR}/maintainer/CI/ubsan.supp
+    - export myconfig=maxset with_cuda=false make_check_unit_tests=false make_check_python=false
     - bash maintainer/CI/build_cmake.sh
-  timeout: 2h
   tags:
     - docker
     - linux
-    - cuda
 
-### Builds with different Distributions
+### Builds with different distributions
 
 debian:10:
   <<: *global_job_definition
   stage: build
   image: docker.pkg.github.com/espressomd/docker/debian:446ff604bbfa63f30ddb462697fa0d0dc2630460
   script:
-    - export with_cuda=false
-    - export myconfig=maxset make_check_python=false
+    - export with_cuda=false myconfig=maxset make_check_python=false
     - bash maintainer/CI/build_cmake.sh
   tags:
     - docker
@@ -182,13 +180,32 @@ fedora:latest:
 
 ### Builds with CUDA
 
+clang-sanitizer:
+  <<: *global_job_definition
+  stage: build
+  variables:
+     CC: 'clang-9'
+     CXX: 'clang++-9'
+  script:
+    - export myconfig=maxset with_cuda=true with_cuda_compiler=clang with_coverage=false
+    - export with_static_analysis=true test_timeout=900
+    - export with_asan=true ASAN_OPTIONS="allocator_may_return_null=1"
+    - export with_ubsan=true UBSAN_OPTIONS=suppressions=${CI_PROJECT_DIR}/maintainer/CI/ubsan.supp
+    - bash maintainer/CI/build_cmake.sh
+  timeout: 2h
+  tags:
+    - docker
+    - linux
+    - cuda
+
 cuda10-maxset:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:c9fe9d6d79ffd7e3e89ef282548e0b5278afde2c
+  variables:
+     CC: 'gcc-8'
+     CXX: 'g++-8'
   script:
     - export myconfig=maxset with_cuda=true with_coverage=false test_timeout=900 srcdir=${CI_PROJECT_DIR}
-    - export cmake_params="-DIPYTHON_EXECUTABLE=$(which jupyter)"
     - bash maintainer/CI/build_cmake.sh
   artifacts:
     paths:
@@ -202,10 +219,13 @@ cuda10-maxset:
 cuda9-maxset:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-9.0:c9fe9d6d79ffd7e3e89ef282548e0b5278afde2c
+  image: docker.pkg.github.com/espressomd/docker/ubuntu-18.04:06b6216c7aa3555bcf28c90734dbb84e7285c96f
+  variables:
+     CC: 'gcc-6'
+     CXX: 'g++-6'
+     GCOV: 'gcov-6'
   script:
     - export myconfig=maxset with_cuda=true with_coverage=true test_timeout=900 srcdir=${CI_PROJECT_DIR}
-    - sed -i 's/ or "DISPLAY" in os.environ/ or True/' src/python/espressomd/visualization.pyx
     - bash maintainer/CI/build_cmake.sh
   artifacts:
     paths:
@@ -220,7 +240,9 @@ cuda9-maxset:
 tutorials-samples-maxset:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:c9fe9d6d79ffd7e3e89ef282548e0b5278afde2c
+  variables:
+     CC: 'gcc-8'
+     CXX: 'g++-8'
   script:
     - export myconfig=maxset with_cuda=true with_coverage=false make_check_unit_tests=false make_check_python=false
     - export make_check_tutorials=true make_check_samples=true make_check_benchmarks=false test_timeout=1200
@@ -233,7 +255,9 @@ tutorials-samples-maxset:
 tutorials-samples-default:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:c9fe9d6d79ffd7e3e89ef282548e0b5278afde2c
+  variables:
+     CC: 'gcc-8'
+     CXX: 'g++-8'
   script:
     - export myconfig=default with_cuda=true with_coverage=false make_check_unit_tests=false make_check_python=false
     - export make_check_tutorials=true make_check_samples=true make_check_benchmarks=false test_timeout=1200
@@ -248,7 +272,9 @@ tutorials-samples-default:
 tutorials-samples-empty:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:c9fe9d6d79ffd7e3e89ef282548e0b5278afde2c
+  variables:
+     CC: 'gcc-8'
+     CXX: 'g++-8'
   script:
     - export myconfig=empty with_cuda=true with_coverage=false make_check_unit_tests=false make_check_python=false
     - export make_check_tutorials=true make_check_samples=true make_check_benchmarks=false test_timeout=1200 with_scafacos=false
@@ -263,7 +289,9 @@ tutorials-samples-empty:
 tutorials-samples-no-gpu:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:c9fe9d6d79ffd7e3e89ef282548e0b5278afde2c
+  variables:
+     CC: 'gcc-8'
+     CXX: 'g++-8'
   script:
     - export myconfig=maxset with_cuda=true with_coverage=false make_check_unit_tests=false make_check_python=false
     - export make_check_tutorials=true make_check_samples=true make_check_benchmarks=false test_timeout=1200 hide_gpu=true
@@ -277,10 +305,12 @@ tutorials-samples-no-gpu:
 installation:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:c9fe9d6d79ffd7e3e89ef282548e0b5278afde2c
+  variables:
+     CC: 'gcc-8'
+     CXX: 'g++-8'
   script:
     - export myconfig=maxset with_cuda=true with_coverage=false make_check_unit_tests=false make_check_python=false
-    - export srcdir=${CI_PROJECT_DIR} test_timeout=1800 build_type=Release
+    - export srcdir=${CI_PROJECT_DIR} build_type=Release
     - bash maintainer/CI/build_cmake.sh
     - cd build
     - make install
@@ -298,13 +328,11 @@ installation:
     - docker
     - linux
     - cuda
-  timeout: 2h
   when: manual
 
 empty:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-20.04:b0de8c7df57d39edf72ad7d40c28bb67467dd7ec
   variables:
      CC: 'clang-9'
      CXX: 'clang++-9'
@@ -316,23 +344,12 @@ empty:
     - linux
     - cuda
 
-ubuntu:wo-dependencies:
-  <<: *global_job_definition
-  stage: build
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-wo-dependencies:446ff604bbfa63f30ddb462697fa0d0dc2630460
-  script:
-    - export myconfig=maxset with_cuda=false make_check_unit_tests=false make_check_python=false
-    - bash maintainer/CI/build_cmake.sh
-  tags:
-    - docker
-    - linux
-
 ### Builds with ROCm
 
 rocm-maxset:
   <<: *global_job_definition
   stage: build
-  image: docker.pkg.github.com/espressomd/docker/rocm:446ff604bbfa63f30ddb462697fa0d0dc2630460
+  image: docker.pkg.github.com/espressomd/docker/rocm:06b6216c7aa3555bcf28c90734dbb84e7285c96f
   script:
     - export myconfig=maxset with_cuda=true with_cuda_compiler=hip
     - bash maintainer/CI/build_cmake.sh
@@ -381,7 +398,6 @@ intel:19:
 check_sphinx:
   <<: *global_job_definition
   stage: additional_checks
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:c9fe9d6d79ffd7e3e89ef282548e0b5278afde2c
   needs:
     - cuda10-maxset
   when: on_success
@@ -402,7 +418,6 @@ check_sphinx:
 run_tutorials:
   <<: *global_job_definition
   stage: additional_checks
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:c9fe9d6d79ffd7e3e89ef282548e0b5278afde2c
   needs:
     - cuda10-maxset
   when: on_success
@@ -426,7 +441,6 @@ run_tutorials:
 run_doxygen:
   <<: *global_job_definition
   stage: additional_checks
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-10.1:c9fe9d6d79ffd7e3e89ef282548e0b5278afde2c
   needs:
     - cuda10-maxset
   when: on_success
@@ -446,10 +460,9 @@ run_doxygen:
 check_cuda_maxset_no_gpu:
   <<: *global_job_definition
   stage: additional_checks
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-9.0:c9fe9d6d79ffd7e3e89ef282548e0b5278afde2c
   when: on_success
   needs: 
-    - cuda9-maxset
+    - cuda10-maxset
   script:
     - export CUDA_VISIBLE_DEVICES=""
     - cd ${CI_PROJECT_DIR}/build
@@ -462,10 +475,9 @@ check_cuda_maxset_no_gpu:
 check_with_odd_no_of_processors:
   <<: *global_job_definition
   stage: additional_checks 
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-cuda-9.0:c9fe9d6d79ffd7e3e89ef282548e0b5278afde2c
   when: on_success
   needs: 
-    - cuda9-maxset
+    - cuda10-maxset
   script:
     - cd ${CI_PROJECT_DIR}/build
     - cmake -DTEST_NP=3 .
@@ -479,7 +491,6 @@ check_with_odd_no_of_processors:
 .deploy_base:
   <<: *global_job_definition
   stage: deploy
-  image: docker.pkg.github.com/espressomd/docker/ubuntu-20.04:e24415d47e2611662efe56b9946f1d0c1dda32d7
   only:
     - python
   before_script:

diff --git a/.travis.yml b/.travis.yml
@@ -11,7 +11,7 @@ matrix:
     - os: linux
       sudo: required
       services: docker
-      env: myconfig=maxset image=espressomd/docker-ubuntu-18.04:446ff604bbfa63f30ddb462697fa0d0dc2630460
+      env: myconfig=maxset image=espressomd/docker-ubuntu-20.04:06b6216c7aa3555bcf28c90734dbb84e7285c96f
 
 script:
   - maintainer/CI/build_docker.sh
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -279,13 +279,11 @@ if(WITH_TESTS)
   list(APPEND BOOST_COMPONENTS unit_test_framework)
 endif()
 
-if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-  set(BOOST_MINIMUM_VERSION "1.65.0")
-  if(CUDA_FOUND AND CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
-    set(BOOST_MINIMUM_VERSION "1.66.0")
-  endif()
-else()
-  set(BOOST_MINIMUM_VERSION "1.58.0")
+set(BOOST_MINIMUM_VERSION "1.65.0")
+
+if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel" AND CUDA_FOUND
+   AND CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
+  set(BOOST_MINIMUM_VERSION "1.66.0")
 endif()
 
 # old Boost.MPI versions contain a use-after-free bug that seems to only cause
@@ -296,18 +294,6 @@ endif()
 
 find_package(Boost ${BOOST_MINIMUM_VERSION} REQUIRED ${BOOST_COMPONENTS})
 
-if(Boost_VERSION VERSION_GREATER_EQUAL 106400 AND Boost_VERSION VERSION_LESS
-                                                  106500)
-  # Boost 1.64 has incompatible Serialization and MPI modules, see
-  # https://svn.boost.org/trac10/ticket/12723 . Some distributions, like Fedora,
-  # have backported the patch.
-  file(READ "${Boost_INCLUDE_DIR}/boost/mpi/detail/mpi_datatype_primitive.hpp"
-       boost_mpi_datatype_file)
-  if(boost_mpi_datatype_file MATCHES "boost::serialization::detail::get_data")
-    message(FATAL_ERROR "Boost 1.64 is unsupported")
-  endif()
-endif()
-
 #
 # Paths
 #