Merge pull request #275 from psci2195/bd-pr1842

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bogdan-tanygin · Oct 26, 2019 · 4dbe052 · 4dbe052
2 parents 2b11644 + 032ee9d
commit 4dbe052
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diff --git a/.clang-tidy b/.clang-tidy
@@ -32,7 +32,6 @@ Checks: |
    readability-redundant-control-flow,
    readability-simplify-boolean-expr,
    readability-simplify-subscript-expr,
-   readability-static-accessed-through-instance,
    readability-static-definition-in-anonymous-namespace,
    readability-string-compare,
    readability-uniqueptr-delete-release,

diff --git a/.gitignore b/.gitignore
@@ -58,3 +58,4 @@ doc/dg/background_errors.unsorted
 *.pyc
 
 .ycm_extra_conf.py
+.ipynb_checkpoints
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -12,12 +12,16 @@ stages:
   except:
     - staging.tmp
     - trying.tmp
+  timeout: 1h
+  interruptible: true
 
 .notification_job_template: &notification_job_definition
   <<: *global_job_definition
   variables:
     GIT_SUBMODULE_STRATEGY: none
   dependencies: []
+  timeout: 15m
+  interruptible: false
   tags:
     - linux
 
@@ -45,7 +49,7 @@ status_pending:
 style:
   <<: *global_job_definition
   stage: prepare
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/clang:6.0
+  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/clang-python3:6.0
   dependencies: []
   before_script:
     - git submodule deinit .
@@ -68,7 +72,7 @@ style:
 style_doxygen:
   <<: *global_job_definition
   stage: prepare
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/cuda:9.0
+  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-9.0
   dependencies: []
   script:
     - mkdir build
@@ -123,24 +127,12 @@ no_rotation:
     - docker
     - linux
 
-nocheckmaxset:
-  <<: *global_job_definition
-  stage: build
-  script:
-    - export with_cuda=false myconfig=nocheck-maxset make_check=false
-    - bash maintainer/CI/build_cmake.sh
-  tags:
-    - docker
-    - linux
-
 ### Builds with different Distributions
 
-#debian:8 removed: similar to ubuntu:1404
-
-debian:9:
+debian:10:
   <<: *global_job_definition
   stage: build
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/debian-python3:9
+  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/debian-python3:10
   script:
     - export with_cuda=false
     - export myconfig=maxset make_check=false
@@ -182,7 +174,7 @@ fedora:
     - docker
     - linux
 
-#ubuntu:1604 not needed: used in cuda:9.0
+#ubuntu:1604 not needed: used in ubuntu-python3:cuda-9.0
 #ubuntu:1804 not needed: default used in non-CUDA builds
 #ubuntu:1904 not needed: base image for builds on different architectures
 
@@ -191,7 +183,7 @@ fedora:
 cuda10-maxset:
   <<: *global_job_definition
   stage: build
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/cuda:10.1
+  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-10.1
   script:
     - export myconfig=maxset with_coverage=false test_timeout=900 srcdir=${CI_PROJECT_DIR}
     - export cmake_params="-DIPYTHON_EXECUTABLE=$(which jupyter)"
@@ -205,10 +197,10 @@ cuda10-maxset:
     - linux
     - cuda
 
-cuda-maxset:
+cuda9-maxset:
   <<: *global_job_definition
   stage: build
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/cuda:9.0
+  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-9.0
   script:
     - export myconfig=maxset 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
@@ -217,6 +209,7 @@ cuda-maxset:
     paths:
     - build/
     expire_in: 1 week
+  when: on_success
   tags:
     - docker
     - linux
@@ -225,7 +218,7 @@ cuda-maxset:
 tutorials-samples-maxset:
   <<: *global_job_definition
   stage: build
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/cuda:tutorials
+  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-10.1
   script:
     - export myconfig=maxset with_coverage=false make_check=false
     - export make_check_tutorials=true make_check_samples=true make_check_benchmarks=true test_timeout=1200
@@ -238,7 +231,7 @@ tutorials-samples-maxset:
 tutorials-samples-default:
   <<: *global_job_definition
   stage: build
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/cuda:tutorials
+  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-10.1
   script:
     - export myconfig=default with_coverage=false make_check=false
     - export make_check_tutorials=true make_check_samples=true make_check_benchmarks=true test_timeout=1200
@@ -253,10 +246,10 @@ tutorials-samples-default:
 tutorials-samples-empty:
   <<: *global_job_definition
   stage: build
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/cuda:tutorials
+  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-10.1
   script:
     - export myconfig=empty with_coverage=false make_check=false
-    - export make_check_tutorials=true make_check_samples=true make_check_benchmarks=true test_timeout=1200
+    - export make_check_tutorials=true make_check_samples=true make_check_benchmarks=true test_timeout=1200 with_scafacos=false
     - bash maintainer/CI/build_cmake.sh
   tags:
     - docker
@@ -268,7 +261,7 @@ tutorials-samples-empty:
 tutorials-samples-no-gpu:
   <<: *global_job_definition
   stage: build
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/cuda:tutorials
+  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-10.1
   script:
     - export myconfig=maxset with_coverage=false make_check=false
     - export make_check_tutorials=true make_check_samples=true make_check_benchmarks=true test_timeout=1200 hide_gpu=true
@@ -279,12 +272,43 @@ tutorials-samples-no-gpu:
   only:
     - schedules
 
+installation:
+  <<: *global_job_definition
+  stage: build
+  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-10.1
+  script:
+    - export myconfig=maxset with_coverage=false make_check=false
+    - export srcdir=${CI_PROJECT_DIR} test_timeout=1800
+    - bash maintainer/CI/build_cmake.sh
+    - cd build
+    # install ESPResSo (in CI, pypresso will run up to 5 times slower when
+    # located outside the build directory, hence the larger timeout value)
+    - make install
+    # get path of installed files
+    - CI_INSTALL_DIR="/tmp/espresso-unit-tests"
+    - CI_INSTALL_PYTHON_PATH=$(dirname $(find "${CI_INSTALL_DIR}/lib" -name espressomd))
+    # 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
+    # skip long tests
+    - sed -i "/tutorial_11-ferrofluid_3/d" testsuite/scripts/tutorials/CTestTestfile.cmake
+    - make -j2 check_python_skip_long
+    - make -j2 check_samples
+    - make -j2 check_tutorials
+  tags:
+    - docker
+    - linux
+    - cuda
+  timeout: 3h
+  when: manual
+
 empty:
   <<: *global_job_definition
   stage: build
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/cuda:9.0
+  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/clang-python3:6.0
   script:
-    - export myconfig=empty
+    - export myconfig=empty with_static_analysis=true
     - bash maintainer/CI/build_cmake.sh
   tags:
     - docker
@@ -325,6 +349,7 @@ rocm-maxset:
     - export OMPI_MCA_btl_vader_single_copy_mechanism=none
     - export myconfig=maxset
     - bash maintainer/CI/build_cmake.sh
+  timeout: 6h
   tags:
     - docker
     - linux
@@ -338,6 +363,7 @@ ubuntu:armhf:
 
 ubuntu:i386:
   <<: *arch_definition
+  timeout: 1h
   only:
     - branches
     - tags
@@ -379,6 +405,7 @@ clang:6.0:
   script:
     - export myconfig=maxset with_coverage=false with_static_analysis=true with_asan=true with_ubsan=true test_timeout=900
     - bash maintainer/CI/build_cmake.sh
+  timeout: 2h
   tags:
     - docker
     - linux
@@ -403,14 +430,14 @@ intel:18:
 check_sphinx:
   <<: *global_job_definition
   stage: additional_checks
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/cuda:9.0
+  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-10.1
   needs:
-    - cuda-maxset
+    - cuda10-maxset
   when: on_success
   script:
     - sed -i 's/ or "DISPLAY" in os.environ/ or True/' ${CI_PROJECT_DIR}/src/python/espressomd/visualization.pyx
     - cd ${CI_PROJECT_DIR}/build
-    - make -t && make sphinx
+    - make -t && rm src/python/espressomd/visualization.* && make sphinx
     - bash ../maintainer/CI/doc_warnings.sh
   artifacts:
     paths:
@@ -424,7 +451,7 @@ check_sphinx:
 run_tutorials:
   <<: *global_job_definition
   stage: additional_checks
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/cuda:10.1
+  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-10.1
   needs:
     - cuda10-maxset
   when: on_success
@@ -445,13 +472,15 @@ run_tutorials:
     - linux
     - cuda
 
-check_doxygen:
+run_doxygen:
   <<: *global_job_definition
   stage: additional_checks
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/cuda:9.0
+  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-9.0
   needs:
-    - cuda-maxset
+    - cuda9-maxset
   when: on_success
+  only:
+    - python
   script:
     - cd ${CI_PROJECT_DIR}/build
     - make -t && make doxygen
@@ -462,32 +491,30 @@ check_doxygen:
   tags:
     - docker
     - linux
-    - cuda
 
 check_cuda_maxset_no_gpu:
   <<: *global_job_definition
   stage: additional_checks
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/cuda:9.0
+  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-9.0
   when: on_success
   needs: 
-    - cuda-maxset
+    - cuda9-maxset
   script:
     - export CUDA_VISIBLE_DEVICES=""
     - cd ${CI_PROJECT_DIR}/build
     - make -t && make check
   tags:
     - docker
     - linux
-    - cuda
 
 
 check_with_odd_no_of_processors:
   <<: *global_job_definition
   stage: additional_checks 
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/cuda:9.0
+  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-9.0
   when: on_success
   needs: 
-    - cuda-maxset
+    - cuda9-maxset
   script:
     - cd ${CI_PROJECT_DIR}/build
     - cmake -DTEST_NP=3 .
@@ -501,7 +528,7 @@ check_with_odd_no_of_processors:
 .deploy_base:
   <<: *global_job_definition
   stage: deploy
-  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/cuda:9.0
+  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-9.0
   only:
     - python
   before_script:
@@ -512,6 +539,7 @@ check_with_odd_no_of_processors:
     - echo "$SSH_PRIVATE_KEY" > ${HOME}/.ssh/espresso_rsa && chmod 600 ${HOME}/.ssh/espresso_rsa
     - echo "$SSH_PUBLIC_KEY" > ${HOME}/.ssh/espresso_rsa.pub && chmod 600 ${HOME}/.ssh/espresso_rsa.pub
     - '[[ -f /.dockerenv ]] && echo -e "Host *\n\tStrictHostKeyChecking no\n\n" > ~/.ssh/config'
+  interruptible: false
   tags:
     - docker
     - linux
@@ -528,7 +556,7 @@ deploy_sphinx_documentation:
 deploy_doxygen_documentation:
   extends: .deploy_base
   dependencies:
-    - check_doxygen
+    - run_doxygen
   script:
     - cd ${CI_PROJECT_DIR}/build/doc/doxygen/html &&
       rsync -avz --delete -e "ssh -i ${HOME}/.ssh/espresso_rsa" ./ [email protected]:/home/espresso/public_html/html/dox