Rename project build options and bump all requirements (#4612)

Fixes #4618 We have concrete plans to integrate more external libraries into ESPResSo, such as waLBerla for hydrodynamics and librepa+kdpart for MD load balancing. We opted for the CMake `FetchContent` method, which allows us to finely tune the way these libraries are compiled and integrated into ESPResSo. However, our build system has imperfections that makes it difficult to integrate new libraries, or to use ESPResSo as a library in a parent project. In particular, CMake flags such as `WITH_FFTW` are inherited by included projects, which sometimes cause them to build components that are not needed in ESPResSo. This unnecessarily increases build times, and in a few cases, forces users to install extra dependencies to complete the build. It is good practice to put a project-specific prefix on all CMake options to avoid this kind of name conflict. While we worked with external libraries maintainers to rename their CMake options, we obviously need to rename ESPResSo CMake options too. As such, this PR adds a prefix `ESPRESSO_BUILD_` to all options that control compilation, and a prefix `ESPRESSO_` to the other options. The new option names can be found in the user guide, section 2.4.4. "Options and Variables". Since the waLBerla project requires C++17, and CUDA versions 10.x only support C++14, we will be migrating to C++17 and CUDA 11.x. This change is also motivated by the `thrust` library, which generates compiler warnings for certain containers until CUDA 11.5, and Cython which now uses C++17 by default in Ubuntu 22.04. Description of changes: - rename ESPResSo-specific CMake options and functions - e.g. for build options: `-D WITH_CUDA=ON` becomes `-D ESPRESSO_BUILD_WITH_CUDA=ON` - e.g. for other options: `-D CTEST_ARGS=-j16` becomes `-D ESPRESSO_CTEST_ARGS=-j16` - require a C++17-capable compiler - replace 400 lines of code in the core by equivalent STL functions - reduce usage of Boost algorithms - check the project builds without external dependencies in C++20 mode - bump all version requirements - CMake >= 3.18, Python >= 3.9, Cython >= 0.29.21, Boost >= 1.74, CUDA >= 11.0, OpenMPI >= 4.0, MPICH >= 3.4.1, GCC >= 8.0, Clang >= 9.0.0, AppleClang >= 11.0.0, Intel Classic >= 18.0, Intel oneAPI >= 2021.0 - Python package version requirements are based on versions available in Ubuntu 22.04 and Debian 11 - `FindCython` now stops CMake generation when Cython was not found
espressomd · Dec 5, 2022 · 1970f48 · 1970f48
2 parents e1d0e49 + d91bb12
commit 1970f48
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diff --git a/.github/actions/build_and_check/action.yml b/.github/actions/build_and_check/action.yml
@@ -18,7 +18,7 @@ runs:
        pip3 install numpy cython h5py scipy
       shell: bash
     - run: |
-        export myconfig=maxset with_cuda=false test_timeout=800 with_asan=${{ inputs.asan }} with_ubsan=${{ inputs.ubsan }} check_skip_long=true build_procs=2 check_procs=2
+        export myconfig=maxset with_cuda=false with_gsl=false test_timeout=800 with_asan=${{ inputs.asan }} with_ubsan=${{ inputs.ubsan }} check_skip_long=true build_procs=2 check_procs=2
         bash maintainer/CI/build_cmake.sh
       shell: bash
       # This is a workaround for the unfortunate interaction of MacOS and OpenMPI 4

diff --git a/.github/workflows/push_pull.yml b/.github/workflows/push_pull.yml
@@ -19,7 +19,7 @@ jobs:
       - name: Setup Python environment
         uses: actions/setup-python@v2
         with:
-          python-version: '3.8'
+          python-version: '3.9'
       - name: Check without sanitizer
         uses: ./.github/actions/build_and_check
         with:
@@ -39,7 +39,7 @@ jobs:
       - name: Setup Python environment
         uses: actions/setup-python@v2
         with:
-          python-version: '3.8'
+          python-version: '3.9'
       - name: Check with sanitizer
         uses: ./.github/actions/build_and_check
         with:

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -1,4 +1,4 @@
-image: ghcr.io/espressomd/docker/ubuntu-20.04:efd89c5f66b8a65f579a7807d0059939fcb4b12f
+image: ghcr.io/espressomd/docker/ubuntu-22.04:3fd42369f84239b8c4f5d77067d404789c55ff44
 
 stages:
   - prepare
@@ -68,7 +68,7 @@ style_doxygen:
     - mkdir build
     - cd build
     - cp ../maintainer/configs/maxset.hpp myconfig.hpp
-    - cmake .. -DWITH_CUDA=ON -DWITH_SCAFACOS=ON
+    - cmake .. -D ESPRESSO_BUILD_WITH_CUDA=ON -D ESPRESSO_BUILD_WITH_GSL=ON -D ESPRESSO_BUILD_WITH_HDF5=ON -D ESPRESSO_BUILD_WITH_SCAFACOS=ON -D ESPRESSO_BUILD_WITH_STOKESIAN_DYNAMICS=ON
     - sh ../maintainer/CI/dox_warnings.sh
   tags:
     - espresso
@@ -80,8 +80,9 @@ default:
   <<: *global_job_definition
   stage: build
   variables:
-     CC: 'gcc-9'
-     CXX: 'g++-9'
+     CC: 'gcc-10'
+     CXX: 'g++-10'
+     GCOV: 'gcov-10'
      with_cuda: 'false'
      myconfig: 'default'
      with_coverage: 'true'
@@ -98,16 +99,17 @@ maxset:
   <<: *global_job_definition
   stage: build
   variables:
-     CC: 'gcc-9'
-     CXX: 'g++-9'
+     CC: 'gcc-10'
+     CXX: 'g++-10'
+     GCOV: 'gcov-10'
      with_cuda: 'false'
-     with_cxx_standard: '17'
+     with_cxx_standard: '20'
      myconfig: 'maxset'
      with_coverage: 'true'
      with_scafacos: 'true'
      with_stokesian_dynamics: 'true'
      check_skip_long: 'true'
-     cmake_params: '-DTEST_NP=8'
+     cmake_params: '-D ESPRESSO_TEST_NP=8'
   script:
     - bash maintainer/CI/build_cmake.sh
   tags:
@@ -119,8 +121,9 @@ no_rotation:
   <<: *global_job_definition
   stage: build
   variables:
-     CC: 'gcc-9'
-     CXX: 'g++-9'
+     CC: 'gcc-10'
+     CXX: 'g++-10'
+     GCOV: 'gcov-10'
      with_cuda: 'false'
      myconfig: 'no_rotation'
      with_coverage: 'true'
@@ -136,11 +139,13 @@ no_rotation:
 ubuntu:wo-dependencies:
   <<: *global_job_definition
   stage: build
-  image: ghcr.io/espressomd/docker/ubuntu-wo-dependencies:efd89c5f66b8a65f579a7807d0059939fcb4b12f
+  image: ghcr.io/espressomd/docker/ubuntu-wo-dependencies:3fd42369f84239b8c4f5d77067d404789c55ff44
   variables:
      myconfig: 'maxset'
      with_cuda: 'false'
      with_hdf5: 'false'
+     with_fftw: 'false'
+     with_gsl: 'false'
      make_check_unit_tests: 'false'
      make_check_python: 'false'
   script:
@@ -154,9 +159,10 @@ ubuntu:wo-dependencies:
 debian:10:
   <<: *global_job_definition
   stage: build
-  image: ghcr.io/espressomd/docker/debian:efd89c5f66b8a65f579a7807d0059939fcb4b12f
+  image: ghcr.io/espressomd/docker/debian:3fd42369f84239b8c4f5d77067d404789c55ff44
   variables:
      with_cuda: 'false'
+     with_gsl: 'false'
      myconfig: 'maxset'
      make_check_python: 'false'
      with_stokesian_dynamics: 'true'
@@ -169,9 +175,10 @@ debian:10:
 fedora:36:
   <<: *global_job_definition
   stage: build
-  image: ghcr.io/espressomd/docker/fedora:efd89c5f66b8a65f579a7807d0059939fcb4b12f
+  image: ghcr.io/espressomd/docker/fedora:3fd42369f84239b8c4f5d77067d404789c55ff44
   variables:
      with_cuda: 'false'
+     with_gsl: 'false'
      myconfig: 'maxset'
      make_check_python: 'true'
      with_stokesian_dynamics: 'true'
@@ -187,8 +194,8 @@ clang-sanitizer:
   <<: *global_job_definition
   stage: build
   variables:
-     CC: 'clang-9'
-     CXX: 'clang++-9'
+     CC: 'clang-14'
+     CXX: 'clang++-14'
      myconfig: 'maxset'
      with_cuda: 'true'
      with_cuda_compiler: 'clang'
@@ -210,10 +217,10 @@ clang-sanitizer:
 fast_math:
   <<: *global_job_definition
   stage: build
-  image: ghcr.io/espressomd/docker/cuda:efd89c5f66b8a65f579a7807d0059939fcb4b12f
   variables:
-     CC: 'gcc-9'
-     CXX: 'g++-9'
+     CC: 'gcc-10'
+     CXX: 'g++-10'
+     GCOV: 'gcov-10'
      myconfig: 'maxset'
      with_cuda: 'true'
      with_coverage: 'false'
@@ -227,31 +234,9 @@ fast_math:
     - cuda
   when: manual
 
-cuda11-maxset-ubuntu20.04:
+cuda11-coverage:
   <<: *global_job_definition
   stage: build
-  image: ghcr.io/espressomd/docker/cuda:efd89c5f66b8a65f579a7807d0059939fcb4b12f
-  variables:
-     CC: 'gcc-9'
-     CXX: 'g++-9'
-     GCOV: 'gcov-9'
-     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
-
-cuda11-maxset-ubuntu22.04:
-  <<: *global_job_definition
-  stage: build
-  image: ghcr.io/espressomd/docker/ubuntu-22.04:efd89c5f66b8a65f579a7807d0059939fcb4b12f
   variables:
      CC: 'gcc-10'
      CXX: 'g++-10'
@@ -269,12 +254,13 @@ cuda11-maxset-ubuntu22.04:
     - cuda
     - numa
 
-cuda10-maxset:
+cuda11-maxset:
   <<: *global_job_definition
   stage: build
   variables:
-     CC: 'gcc-8'
-     CXX: 'g++-8'
+     CC: 'gcc-10'
+     CXX: 'g++-10'
+     GCOV: 'gcov-10'
      myconfig: 'maxset'
      with_cuda: 'true'
      with_coverage: 'false'
@@ -298,8 +284,9 @@ tutorials-samples-maxset:
   <<: *global_job_definition
   stage: build
   variables:
-     CC: 'gcc-8'
-     CXX: 'g++-8'
+     CC: 'gcc-10'
+     CXX: 'g++-10'
+     GCOV: 'gcov-10'
      myconfig: 'maxset'
      with_cuda: 'true'
      with_coverage: 'false'
@@ -316,13 +303,15 @@ tutorials-samples-maxset:
   tags:
     - espresso
     - cuda
+    - numa
 
 tutorials-samples-default:
   <<: *global_job_definition
   stage: build
   variables:
-     CC: 'gcc-8'
-     CXX: 'g++-8'
+     CC: 'gcc-10'
+     CXX: 'g++-10'
+     GCOV: 'gcov-10'
      myconfig: 'default'
      with_cuda: 'true'
      with_coverage: 'false'
@@ -338,15 +327,17 @@ tutorials-samples-default:
   tags:
     - espresso
     - cuda
+    - numa
   only:
     - schedules
 
 tutorials-samples-empty:
   <<: *global_job_definition
   stage: build
   variables:
-     CC: 'gcc-8'
-     CXX: 'g++-8'
+     CC: 'gcc-10'
+     CXX: 'g++-10'
+     GCOV: 'gcov-10'
      myconfig: 'empty'
      with_cuda: 'true'
      with_coverage: 'false'
@@ -363,15 +354,17 @@ tutorials-samples-empty:
   tags:
     - espresso
     - cuda
+    - numa
   only:
     - schedules
 
 tutorials-samples-no-gpu:
   <<: *global_job_definition
   stage: build
   variables:
-     CC: 'gcc-8'
-     CXX: 'g++-8'
+     CC: 'gcc-10'
+     CXX: 'g++-10'
+     GCOV: 'gcov-10'
      myconfig: 'maxset'
      with_cuda: 'true'
      with_coverage: 'false'
@@ -395,8 +388,9 @@ installation:
   <<: *global_job_definition
   stage: build
   variables:
-     CC: 'gcc-8'
-     CXX: 'g++-8'
+     CC: 'gcc-10'
+     CXX: 'g++-10'
+     GCOV: 'gcov-10'
      myconfig: 'maxset'
      with_cuda: 'true'
      with_coverage: 'false'
@@ -413,7 +407,7 @@ 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=$(cmake -L . | grep CTEST_ARGS | grep --color=never -Po '(?<=-j)[0-9]+')
+    - CI_CORES=$(cmake -L . | grep ESPRESSO_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
@@ -430,8 +424,8 @@ empty:
   <<: *global_job_definition
   stage: build
   variables:
-     CC: 'clang-9'
-     CXX: 'clang++-9'
+     CC: 'clang-14'
+     CXX: 'clang++-14'
      myconfig: 'empty'
      with_cuda: 'true'
      with_cuda_compiler: 'clang'
@@ -451,7 +445,7 @@ check_sphinx:
   <<: *global_job_definition
   stage: additional_checks
   needs:
-    - cuda10-maxset
+    - cuda11-maxset
   when: on_success
   script:
     - cd ${CI_PROJECT_DIR}/build
@@ -473,7 +467,7 @@ run_tutorials:
   <<: *global_job_definition
   stage: additional_checks
   needs:
-    - cuda10-maxset
+    - cuda11-maxset
   when: on_success
   script:
     - cd ${CI_PROJECT_DIR}/build
@@ -499,7 +493,7 @@ run_doxygen:
   <<: *global_job_definition
   stage: additional_checks
   needs:
-    - cuda10-maxset
+    - cuda11-maxset
   when: on_success
   only:
     - python
@@ -520,7 +514,7 @@ maxset_no_gpu:
   stage: additional_checks
   when: on_success
   needs:
-    - cuda10-maxset
+    - cuda11-maxset
   script:
     - export CUDA_VISIBLE_DEVICES=""
     - cd ${CI_PROJECT_DIR}/build
@@ -535,10 +529,10 @@ maxset_3_cores:
   stage: additional_checks
   when: on_success
   needs:
-    - cuda10-maxset
+    - cuda11-maxset
   script:
     - cd ${CI_PROJECT_DIR}/build
-    - cmake -DTEST_NP=3 .
+    - cmake -D ESPRESSO_TEST_NP=3 .
     - make -t && make check_unit_tests && make check_python_parallel_odd
   tags:
     - espresso

diff --git a/.gitpod.yml b/.gitpod.yml
@@ -18,7 +18,7 @@ tasks:
     command: |
        mkdir build
        cd build
-       cmake .. -D WITH_GSL=ON
+       cmake .. -D ESPRESSO_BUILD_WITH_GSL=ON
        make
        make tutorials
        for f in doc/tutorials/*/*.ipynb; do echo "configuring ${f}"; ./pypresso doc/tutorials/convert.py exercise2 --to-vscode-jupyter ${f}; done