Merge branch 'development' of https://github.com/ECP-WarpX/WarpX into…

… AllocateFewerGuardCells

.azure-pipelines.yml

@@ -9,39 +9,40 @@ pr:
 
 jobs:
 - job:
+  # FIXME remove unused variables
   variables:
     BLASPP_HOME: '/usr/local'
     CEI_SUDO: 'sudo'
     CEI_TMP: '/tmp/cei'
     CMAKE_GENERATOR: 'Ninja'
     FFTW_HOME: '/usr'
     LAPACKPP_HOME: '/usr/local'
-    OMP_NUM_THREADS: 1
     WARPX_CI_CCACHE: 'TRUE'
-    WARPX_CI_NUM_MAKE_JOBS: 2
-    WARPX_CI_OPENPMD: 'TRUE'
-    WARPX_CI_TMP: '/tmp/ci'
+    #WARPX_OPENPMD: 'TRUE'
 
   strategy:
     matrix:
-      cartesian1d:
-        WARPX_CI_REGULAR_CARTESIAN_1D: 'TRUE'
-        WARPX_CI_PSATD: 'FALSE'
-      cartesian2d:
-        WARPX_CI_REGULAR_CARTESIAN_2D: 'TRUE'
-      cartesian3d:
-        WARPX_CI_REGULAR_CARTESIAN_3D: 'TRUE'
-      single_precision:
-        WARPX_CI_SINGLE_PRECISION: 'TRUE'
-      rz_or_nompi:
-        WARPX_CI_RZ_OR_NOMPI: 'TRUE'
-      qed:
-        WARPX_CI_QED: 'TRUE'
-      embedded_boundary:
-        WARPX_CI_EB: 'TRUE'
+      # Cartesian 1D
+      cartesian_1d:
+        WARPX_CMAKE_FLAGS: -DWarpX_DIMS=1 -DWarpX_FFT=ON -DWarpX_PYTHON=ON
+      # Cartesian 2D
+      cartesian_2d:
+        WARPX_CMAKE_FLAGS: -DWarpX_DIMS=2 -DWarpX_FFT=ON -DWarpX_PYTHON=ON
+      # Cartesian 3D
+      cartesian_3d:
+        WARPX_CMAKE_FLAGS: -DWarpX_DIMS=3 -DWarpX_FFT=ON -DWarpX_PYTHON=ON
+        WARPX_HEFFTE: 'TRUE'
+      # Cylindrical RZ
+      cylindrical_rz:
+        WARPX_CMAKE_FLAGS: -DWarpX_DIMS=RZ -DWarpX_FFT=ON -DWarpX_PYTHON=ON
+        WARPX_RZ_FFT: 'TRUE'
+      # single precision
+      #single_precision:
+      #  WARPX_CMAKE_FLAGS: -DWarpX_DIMS='1;2;3;RZ' -DWarpX_FFT=ON -DWarpX_PYTHON=ON -DWarpX_PRECISION=SINGLE
+      #  WARPX_RZ_FFT: 'TRUE'
 
   # default: 60; maximum: 360
-  timeoutInMinutes: 120
+  timeoutInMinutes: 240
 
   steps:
   # set up caches:
@@ -50,9 +51,8 @@ jobs:
   - task: Cache@2
     continueOnError: true
     inputs:
-      key: 'Ccache | "$(System.JobName)" | .azure-pipelines.yml | cmake/dependencies/AMReX.cmake | run_test.sh'
+      key: 'Ccache | "$(System.JobName)" | .azure-pipelines.yml | cmake/dependencies/AMReX.cmake'
       restoreKeys: |
-         Ccache | "$(System.JobName)" | .azure-pipelines.yml | cmake/dependencies/AMReX.cmake | run_test.sh
          Ccache | "$(System.JobName)" | .azure-pipelines.yml | cmake/dependencies/AMReX.cmake
          Ccache | "$(System.JobName)" | .azure-pipelines.yml
       path: /home/vsts/.ccache
@@ -62,9 +62,8 @@ jobs:
   - task: Cache@2
     continueOnError: true
     inputs:
-      key: 'Python3 | "$(System.JobName)" | .azure-pipelines.yml | run_test.sh'
+      key: 'Python3 | "$(System.JobName)" | .azure-pipelines.yml'
       restoreKeys: |
-         Python3 | "$(System.JobName)" | .azure-pipelines.yml | run_test.sh
          Python3 | "$(System.JobName)" | .azure-pipelines.yml
       path: /home/vsts/.local/lib/python3.8
       cacheHitVar: PYTHON38_CACHE_RESTORED
@@ -74,48 +73,91 @@ jobs:
       set -eu -o pipefail
       cat /proc/cpuinfo | grep "model name" | sort -u
       df -h
+      echo 'Acquire::Retries "3";' | sudo tee /etc/apt/apt.conf.d/80-retries
       sudo apt update
       sudo apt install -y ccache curl gcc gfortran git g++ ninja-build \
         openmpi-bin libopenmpi-dev \
         libfftw3-dev libfftw3-mpi-dev libhdf5-openmpi-dev pkg-config make \
         python3 python3-pandas python3-pip python3-venv python3-setuptools libblas-dev liblapack-dev
       ccache --set-config=max_size=10.0G
       python3 -m pip install --upgrade pip
+      python3 -m pip install --upgrade build
+      python3 -m pip install --upgrade packaging
       python3 -m pip install --upgrade setuptools
       python3 -m pip install --upgrade wheel
       python3 -m pip install --upgrade virtualenv
       python3 -m pip install --upgrade pipx
       python3 -m pipx install cmake
       python3 -m pipx ensurepath
       export PATH="$HOME/.local/bin:$PATH"
-      sudo curl -L -o /usr/local/bin/cmake-easyinstall https://git.io/JvLxY
+      sudo curl -L -o /usr/local/bin/cmake-easyinstall https://raw.githubusercontent.com/ax3l/cmake-easyinstall/main/cmake-easyinstall
       sudo chmod a+x /usr/local/bin/cmake-easyinstall
-      if [ "${WARPX_CI_OPENPMD:-FALSE}" == "TRUE" ]; then
-        cmake-easyinstall --prefix=/usr/local                   \
-          git+https://github.com/openPMD/[email protected] \
-          -DCMAKE_CXX_COMPILER_LAUNCHER=$(which ccache)         \
-          -DCMAKE_VERBOSE_MAKEFILE=ON                           \
-          -DopenPMD_USE_PYTHON=OFF -DBUILD_TESTING=OFF -DBUILD_EXAMPLES=OFF -DBUILD_CLI_TOOLS=OFF
-        python3 -m pip install --upgrade openpmd-api
-      fi
-      if [[ "${WARPX_CI_RZ_OR_NOMPI:-FALSE}" == "TRUE" ]]; then
-        cmake-easyinstall --prefix=/usr/local git+https://bitbucket.org/icl/blaspp.git \
+      #if [ "${WARPX_OPENPMD:-FALSE}" == "TRUE" ]; then
+      #  cmake-easyinstall --prefix=/usr/local                   \
+      #    git+https://github.com/openPMD/[email protected] \
+      #    -DCMAKE_CXX_COMPILER_LAUNCHER=$(which ccache)         \
+      #    -DCMAKE_VERBOSE_MAKEFILE=ON                           \
+      #    -DopenPMD_USE_PYTHON=OFF -DBUILD_TESTING=OFF -DBUILD_EXAMPLES=OFF -DBUILD_CLI_TOOLS=OFF
+      #  #python3 -m pip install --upgrade openpmd-api
+      #fi
+      if [ "${WARPX_RZ_FFT:-FALSE}" == "TRUE" ]; then
+        # BLAS++
+        cmake-easyinstall --prefix=/usr/local           \
+          git+https://github.com/icl-utk-edu/blaspp.git \
           -DCMAKE_CXX_COMPILER_LAUNCHER=$(which ccache) \
           -DCMAKE_CXX_STANDARD=17                       \
           -Duse_openmp=OFF -Dbuild_tests=OFF -DCMAKE_VERBOSE_MAKEFILE=ON
-        cmake-easyinstall --prefix=/usr/local git+https://bitbucket.org/icl/lapackpp.git \
-          -DCMAKE_CXX_COMPILER_LAUNCHER=$(which ccache) \
-          -DCMAKE_CXX_STANDARD=17                       \
+        # LAPACK++
+        cmake-easyinstall --prefix=/usr/local             \
+          git+https://github.com/icl-utk-edu/lapackpp.git \
+          -DCMAKE_CXX_COMPILER_LAUNCHER=$(which ccache)   \
+          -DCMAKE_CXX_STANDARD=17                         \
           -Duse_cmake_find_lapack=ON -Dbuild_tests=OFF -DCMAKE_VERBOSE_MAKEFILE=ON
       fi
+      if [ "${WARPX_HEFFTE:-FALSE}" == "TRUE" ]; then
+        cmake-easyinstall --prefix=/usr/local git+https://github.com/icl-utk-edu/[email protected] \
+          -DCMAKE_CXX_COMPILER_LAUNCHER=$(which ccache)          \
+          -DCMAKE_CXX_STANDARD=17 -DHeffte_ENABLE_DOXYGEN=OFF    \
+          -DHeffte_ENABLE_FFTW=ON -DHeffte_ENABLE_TESTING=OFF    \
+          -DHeffte_ENABLE_CUDA=OFF -DHeffte_ENABLE_ROCM=OFF      \
+          -DHeffte_ENABLE_ONEAPI=OFF -DHeffte_ENABLE_MKL=OFF     \
+          -DHeffte_ENABLE_PYTHON=OFF -DHeffte_ENABLE_FORTRAN=OFF \
+          -DHeffte_ENABLE_MAGMA=OFF                              \
+          -DCMAKE_VERBOSE_MAKEFILE=ON
+      fi
+      # Python modules required for test analysis
+      python3 -m pip install --upgrade -r Regression/requirements.txt
+      python3 -m pip cache purge
+      # external repositories required for test analysis
+      cd ..
+      git clone --depth 1 https://github.com/ECP-WarpX/warpx-data.git
+      # TODO select only specific datasets?
+      git clone --depth 1 https://github.com/openPMD/openPMD-example-datasets.git
+      cd -
       rm -rf ${CEI_TMP}
       df -h
     displayName: 'Install dependencies'
 
   - bash: |
       set -eu -o pipefail
       df -h
-      ./run_test.sh
-      rm -rf ${WARPX_CI_TMP}
+
+      # configure
+      export AMReX_CMAKE_FLAGS="-DAMReX_ASSERTIONS=ON -DAMReX_TESTING=ON"
+      cmake -S . -B build       \
+        ${AMReX_CMAKE_FLAGS}    \
+        ${WARPX_CMAKE_FLAGS}    \
+        -DWarpX_TEST_CLEANUP=ON \
+        -DWarpX_TEST_FPETRAP=ON
+
+      # build
+      cmake --build build -j 2
       df -h
-    displayName: 'Build & test'
+    displayName: 'Build'
+
+  - bash: |
+      set -eu -o pipefail
+
+      # run tests (exclude pytest.AMReX when running Python tests)
+      ctest --test-dir build --output-on-failure -E AMReX
+    displayName: 'Test'

.clang-tidy

@@ -0,0 +1,60 @@
+Checks: '
+    -*,
+    bugprone-*,
+        -bugprone-easily-swappable-parameters,
+        -bugprone-implicit-widening-of-multiplication-result,
+        -bugprone-misplaced-widening-cast,
+        -bugprone-unchecked-optional-access,
+    cert-*,
+        -cert-err58-cpp,
+    clang-analyzer-*,
+        -clang-analyzer-optin.performance.Padding,
+        -clang-analyzer-optin.mpi.MPI-Checker,
+        -clang-analyzer-osx.*,
+        -clang-analyzer-optin.osx.*,
+    clang-diagnostic-*,
+    cppcoreguidelines-*,
+        -cppcoreguidelines-avoid-c-arrays,
+        -cppcoreguidelines-avoid-magic-numbers,
+        -cppcoreguidelines-avoid-non-const-global-variables,
+        -cppcoreguidelines-init-variables,
+        -cppcoreguidelines-macro-usage,
+        -cppcoreguidelines-narrowing-conversions,
+        -cppcoreguidelines-non-private-member-variables-in-classes,
+        -cppcoreguidelines-owning-memory,
+        -cppcoreguidelines-pro-*,
+    google-build-explicit-make-pair,
+    google-build-namespaces,
+    google-global-names-in-headers,
+    misc-*,
+        -misc-no-recursion,
+        -misc-non-private-member-variables-in-classes,
+    modernize-*,
+        -modernize-avoid-c-arrays,
+        -modernize-return-braced-init-list,
+        -modernize-use-trailing-return-type,
+    mpi-*,
+    performance-*,
+    portability-*,
+    readability-*,
+        -readability-convert-member-functions-to-static,
+        -readability-else-after-return,
+        -readability-function-cognitive-complexity,
+        -readability-identifier-length,
+        -readability-implicit-bool-conversion,
+        -readability-isolate-declaration,
+        -readability-magic-numbers,
+        -readability-named-parameter,
+        -readability-uppercase-literal-suffix
+    '
+
+CheckOptions:
+- key:          bugprone-narrowing-conversions.WarnOnIntegerToFloatingPointNarrowingConversion
+  value:        "false"
+- key:          misc-definitions-in-headers.HeaderFileExtensions
+  value:        "H,"
+- key:          modernize-pass-by-value.ValuesOnly
+  value:        "true"
+
+
+HeaderFilterRegex: 'Source[a-z_A-Z0-9\/]+\.H$'

.editorconfig

@@ -35,3 +35,7 @@ indent_size = unset
 [*.py]
 # isort config
 force_sort_within_sections = true
+known_first_party = amrex,impactx,picmistandard,pywarpx,warpx
+# same as the "black" multi-line import style
+multi_line_output = 3
+include_trailing_comma = True

.github/codeql/warpx-codeql.yml

@@ -0,0 +1,6 @@
+name: "WarpX CodeQL config"
+
+# ignore AMReX, pyAMReX, PICSAR, openPMD et al.
+# note: not yet suppored, thus doing post-analysis SARIF filtering
+paths-ignore:
+  - build/_deps