Merge branch 'master' into naming_cleanup

.github/backup/test_libclouphxx.yml

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+#    - name: Install Nvidia driver
+#      if: ${{!matrix.disable_cuda}}
+#      run: sudo apt install --no-install-recommends nvidia-driver-470
+#    
+#    - name: Install Singularity
+#      #when installed from this action, .SIF is always converted to sandbox (could be related to: https://githubmemory.com/repo/hpcng/singularity/issues/6065)
+#      uses: eWaterCycle/setup-singularity@v6
+#      with:
+#        singularity-version: 3.7.1
+#      #apt installation following https://sylabs.io/guides/3.0/user-guide/installation.html, but this is a too old version and uninstalls python-is-python3
+##      run: |
+##        wget -O- http://neuro.debian.net/lists/focal.de-fzj.libre | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
+##        sudo apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
+##        sudo apt-get update
+##        sudo apt-get install -y singularity-container
+#            
+#    - name: Cache UWLCM Singularity image
+#      id: cache_singularity
+#      uses: actions/cache@v2
+#      with:
+#        path: '${{ github.workspace }}/singularity_images/uwlcm_ubuntu_20_04_cuda_11_4.sif'
+#        key: 'sng_ubuntu_20_04_cuda_11_4'
+#        
+#    - name: Download UWLCM Singularity image
+#      if: steps.cache_singularity.outputs.cache-hit != 'true'
+#      run: |
+#        mkdir '${{ github.workspace }}/singularity_images'
+#        singularity pull --disable_cache --dir '${{ github.workspace }}/singularity_images' library://pdziekan/default/uwlcm:ubuntu_20_04_cuda_11_4
+#      # disable Singularity cache, we cache manually
+#
+#    - name: Set friendly Singularity image name
+#      uses: allenevans/[email protected]
+#      with:
+#        SI: '${{ github.workspace }}/singularity_images/uwlcm_ubuntu_20_04_cuda_11_4.sif'
+#      
+#    - name: Configure CMake
+#      # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
+#      # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
+#      run: singularity exec $SI cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{matrix.build_type}} -DLIBCLOUDPHXX_FORCE_MULTI_CUDA=True -DLIBCLOUDPHXX_DISABLE_CUDA=${{matrix.disable_cuda}}
+##
+#    - name: Build libcloudph++
+#      # Build your program with the given configuration
+#      run: VERBOSE=1 singularity exec $SI cmake --build ${{github.workspace}}/build --config ${{matrix.build_type}} -j${{matrix.threads}}
+
+
+ #   - name: Run Singularity shell
+ #     run: singularity shell '${{ github.workspace }}/singularity_images/uwlcm_ubuntu_20_04_cuda_11_1_1.0.sif'
+
+#    - name: Download UWLCM Singularity container
+#      run: wget https://github.com/igfuw/UWLCM/blob/0fc77ec68053936e36eea4b49f11b3dd2cb1a827/singularity/sng_ubuntu_20_04_cuda_11_1
+
+#    - name: Build UWLCM Singularity container
+#      run: singularity build sng_ubuntu_20_04_cuda_11_1.sif sng_ubuntu_20_04_cuda_11_1
+
+    # TODO: cache cuda-toolki
+
+    #- name: Install cuda-toolkit
+    #  id: cuda-toolkit
+    #  uses: Jimver/[email protected]
+    #  with:
+    #    linux-local-args: '["--toolkit"]'
+
+  #  - name: Install boost
+  #    uses: MarkusJx/[email protected]
+  #    id: install-boost
+  #    with:
+  #      # REQUIRED: Specify the required boost version
+  #      # A list of supported versions can be found here: 
+  #      # https://github.com/actions/boost-versions/blob/main/versions-manifest.json
+  #      boost_version: 1.73.0
+  #      # OPTIONAL: Specify a platform version
+  #      #platform_version: 18.04
+  #      # OPTIONAL: Specify a custom install location
+  #      #boost_install_dir: /home/runner/some_directory
+
+#    - name: Install Thrust
+#      #run: sudo apt-get install libthrust-dev
+#      run: |
+#        git clone --depth=1 git://github.com/thrust/thrust.git --branch 1.9.10-1
+#        sudo ln -s `pwd`/thrust/thrust /usr/local/include/thrust
+
+#    - name: Cache Boost
+#      uses: actions/cache@v2
+#      with:
+#        path: '${{ runner.workspace }}/boost_*.tar.gz'
+#        key: 'boost-1.72.0'
+
+ #   - name: Build Boost
+ #     id: boost
+ #     # This won't re-download the archive unnecessarily:
+ #     uses: egor-tensin/build-boost@v1
+ #     with:
+ #       version: 1.72.0
+ #       libraries: date_time # in fact we don't need any compiled libs, only header libs, but when nothing is passed all libs are built
+ #       platform: x64
+ #       configuration: RelWithDebInfo
+
+    #- name: Install hdf5 (Linux)
+    #  run: sudo apt-get install libhdf5-dev
+    #  #if: matrix.os == 'ubuntu-latest'
+

.github/workflows/test_libclouphxx.yml

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+name: Test libcloudph++
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build_CUDA:
+    runs-on: ubuntu-20.04
+    strategy:
+      matrix:
+        name: ["CUDA"]
+        build_type: ["Debug", "RelWithDebInfoPortable"]
+        include:
+        - name: "CUDA"
+          disable_cuda: false
+          # not enough RAM to compile Debug CUDA on 4 threads
+          threads: 1
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: build libcloudph++
+      uses: igfuw/[email protected]
+      with:
+        disable_cuda: ${{matrix.disable_cuda}}
+        build_type: ${{matrix.build_type}}
+        threads: ${{matrix.threads}}
+        path: ${{ github.workspace }}
+
+  build:
+    runs-on: ubuntu-20.04
+    strategy:
+      matrix:
+        name: ["no_CUDA"]
+        build_type: ["Debug", "RelWithDebInfoPortable"]
+        mpi: ["none", "mvapich2"]
+        #mpi: ["none"]
+        include:
+        - name: "no_CUDA"
+          disable_cuda: true
+          threads: 4
+        - mpi: "none"
+          tag: "ubuntu_20_04_cuda_11_4"
+          cxx: "g++"
+        - mpi: "mvapich2"
+          tag: "ubuntu_20_04_cuda_11_4_mvapich2"
+          cxx: "mpic++"
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: build libcloudph++
+      uses: igfuw/[email protected]
+      with:
+        disable_cuda: ${{matrix.disable_cuda}}
+        build_type: ${{matrix.build_type}}
+        threads: ${{matrix.threads}}
+        path: ${{ github.workspace }}
+        install_prefix: ${{ github.workspace }}/installed 
+        tag: ${{ matrix.tag }}
+        cxx: ${{ matrix.cxx }}
+
+    # tar build dir before upload as artifact to retain permission and case-sensitive names
+    - name: Compress libcloudph++ build
+      run: tar -cvf build.tar build
+
+    - name: Upload libcloudph++ build
+      uses: actions/upload-artifact@v2
+      with:
+        name: libcloud_build_${{matrix.build_type}}_mpi_${{matrix.mpi}}_tar
+        path: build.tar
+
+  # test jobs
+  unit_test:
+    needs: build
+    runs-on: ubuntu-20.04
+
+    strategy:
+      matrix:
+        build_type: ["RelWithDebInfoPortable", "Debug"]
+        mpi: ["none", "mvapich2"]
+        include:
+        - mpi: "none"
+          tag: "ubuntu_20_04_cuda_11_4"
+        - mpi: "mvapich2"
+          tag: "ubuntu_20_04_cuda_11_4_mvapich2"
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Download libcloudph++ build
+      uses: actions/download-artifact@v2
+      with:
+        name: libcloud_build_${{matrix.build_type}}_mpi_${{matrix.mpi}}_tar
+
+    - name: Decompress libcloudph++ build
+      run: tar -xvf build.tar
+
+    - name: load UWLCM Singularity image
+      uses: igfuw/[email protected]
+      with:
+        path: ${{ github.workspace }}/singularity_images
+        tag: ${{ matrix.tag }}
+
+    - name: Run unit tests
+      working-directory: ${{github.workspace}}/build
+      # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
+      run: OMP_NUM_THREADS=4 singularity exec $SI ctest -C ${{matrix.build_type}} || cat Testing/Temporary/LastTest.log / # "/" intentional! (just to make cat exit with an error code)
+
+
+  kinematic_2D_test:
+    needs: build
+    runs-on: ubuntu-20.04
+
+    strategy:
+      matrix:
+        build_type: ["RelWithDebInfoPortable"]
+        mpi: ["none"]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Download libcloudph++ build
+      uses: actions/download-artifact@v2
+      with:
+        name: libcloud_build_${{matrix.build_type}}_mpi_${{matrix.mpi}}_tar
+
+    - name: Decompress libcloudph++ build
+      run: tar -xvf build.tar
+
+    # Debugging with a ssh session
+#    - name: Setup tmate session
+#      uses: mxschmitt/action-tmate@v3
+
+    - name: Install libcloudph++
+      run: sudo cmake --install build
+
+    - name: checkout libmpdata++ repo
+      uses: actions/checkout@v2
+      with:
+        repository: igfuw/libmpdataxx
+        path: libmpdataxx
+
+    - name: Install libmpdata++
+      uses: igfuw/[email protected]
+      with:
+        build_type: ${{matrix.build_type}}
+        threads: 4
+        path: ${{ github.workspace }}/libmpdataxx/libmpdata++
+        install_prefix: ${{ github.workspace }}/installed
+
+    - name: Configure kinematic_2D CMake
+      working-directory: ${{github.workspace}}/models/kinematic_2D
+      run: singularity exec -B ${{ github.workspace }}/installed/ $SI cmake -B build -DCMAKE_BUILD_TYPE=${{matrix.build_type}} -Dlibcloudph++_DIR=${{ github.workspace }}/installed/share/libcloudph++ -Dlibmpdata++_DIR=${{ github.workspace }}/installed/share/libmpdata++
+
+
+    - name: Build kinematic_2D 
+      working-directory: ${{github.workspace}}/models/kinematic_2D
+      run: VERBOSE=1 singularity exec -B ${{ github.workspace }}/installed/ $SI cmake --build build --config ${{matrix.build_type}} 
+
+    - name: Run kinematic_2D tests
+      working-directory: ${{github.workspace}}/models/kinematic_2D/build
+      run: |
+        singularity exec -B ${{ github.workspace }}/installed/ $SI ctest -VV -R travis # compare icicle results against reference data (done for full simulation for bulk schemes and a couple of steps for lagrangian)
+        cat Testing/Temporary/LastTest.log
+
+    # Debugging with a ssh session on failure
+#    - name: Setup tmate session
+#      if: ${{ failure() }}
+#      uses: mxschmitt/action-tmate@v3
+
+
+  parcel_test:
+    needs: build
+# do after kinematic_2D_test, because otherwise we occasionally get "illegal instruction" errors, probably because libcloudphxx is installed simultaneously on the same runner at the same location by two different jobs (?)
+#    needs: kinematic_2D_test
+    runs-on: ubuntu-20.04
+
+    strategy:
+      matrix:
+        build_type: ["RelWithDebInfoPortable", "Debug"]
+        mpi: ["none"]
+        include:
+        - build_type: "RelWithDebInfoPortable"
+          long_tests: true
+          debug_tests: false
+        - build_type: "Debug"
+          long_tests: false
+          debug_tests: true
+
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Download libcloudph++ build
+      uses: actions/download-artifact@v2
+      with:
+        name: libcloud_build_${{matrix.build_type}}_mpi_${{matrix.mpi}}_tar
+
+    - name: Decompress libcloudph++ build
+      run: tar -xvf build.tar
+
+    - name: load UWLCM Singularity image
+      uses: igfuw/[email protected]
+      with:
+        path: ${{ github.workspace }}/singularity_images
+
+    - name: Install libcloudph++
+      run: sudo cmake --install build
+
+    - name: checkout parcel repo
+      uses: actions/checkout@v2
+      with:
+        repository: igfuw/parcel
+        path: parcel
+
+    - run: mkdir parcel/plots/outputs
+
+    - name: run parcel unit_test
+      working-directory: ${{github.workspace}}/parcel
+      if: ${{matrix.long_tests}}
+      run: PYTHONPATH=${{ github.workspace }}/installed/usr/lib/python3/dist-packages singularity exec -B${{ github.workspace }}/installed $SI python3 -m pytest -s -v unit_test
+      #run: PYTHONPATH=${{ github.workspace }}/installed/usr/lib/python3/dist-packages singularity exec -B${{ github.workspace }}/installed,/usr/lib/python3/dist-packages/Gnuplot $SI python3 -m pytest -v unit_test
+
+    - name: run parcel long_test
+      working-directory: ${{github.workspace}}/parcel
+      if: ${{matrix.long_tests}}
+      run: PYTHONPATH=${{ github.workspace }}/installed/usr/lib/python3/dist-packages singularity exec -B${{ github.workspace }}/installed $SI python3 -m pytest -s -v long_test
+
+    - name: run parcel unit_test_debug
+      working-directory: ${{github.workspace}}/parcel
+      if: ${{matrix.debug_tests}}
+      run: PYTHONPATH=${{ github.workspace }}/installed/usr/lib/python3/dist-packages singularity exec -B${{ github.workspace }}/installed $SI python3 -m pytest -s -v unit_test_debug
+
+  build_and_test_KiD-A:
+    runs-on: ubuntu-20.04
+    strategy:
+      matrix:
+        name: ["no_CUDA"]
+        build_type: ["RelWithDebInfoPortable"]
+        mpi: ["none"]
+        include:
+        - name: "no_CUDA"
+          disable_cuda: true
+          threads: 4
+
+    steps:
+    - name: Checkout libcloudphxx PR
+      uses: actions/checkout@v2
+      with:
+        fetch-depth: 0 
+
+    - name: merge with the KiD-A branch
+      run: |
+        git config --global user.email "[email protected]"
+        git config --global user.name "Piotr Dziekan"
+        git fetch origin
+        git merge origin/kida-1d
+
+    - run: grep diag_accr include/libcloudph++/lgrngn/particles.hpp
+
+    - name: build libcloudph++
+      uses: igfuw/[email protected]
+      with:
+        disable_cuda: ${{matrix.disable_cuda}}
+        build_type: ${{matrix.build_type}}
+        threads: ${{matrix.threads}}
+        path: ${{ github.workspace }}
+        install_prefix: ${{ github.workspace }}/installed 
+
+    - name: Install libcloudph++
+      run: sudo cmake --install build
+
+    - name: checkout KiD-libcloud repo
+      uses: actions/checkout@v2
+      with:
+        repository: igfuw/kid-libcloud
+        path: kid-libcloud
+
+    - name: run KiD LWP test
+      working-directory: ${{github.workspace}}/kid-libcloud
+      run: PYTHONPATH=${{ github.workspace }}/installed/usr/lib/python3/dist-packages singularity exec -B${{ github.workspace }}/installed  $SI bash ./.travis_scripts/lwp_test.sh
+
+  call_test_uwlcm_hlpr:
+    uses: igfuw/UWLCM/.github/workflows/test_uwlcm_hlpr.yml@master
+    with:
+      UWLCM_sha: "master"
+      libcloudphxx_sha: ${{ github.sha }} # merge PR SHA
+      libmpdataxx_sha: "master"