Merge ECP-WarpX:development into EZoni:psatd_secondorder

EZoni · Aug 24, 2023 · 4885bb3 · 4885bb3
2 parents f5e0c62 + b88db16
commit 4885bb3
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diff --git a/.azure-pipelines.yml b/.azure-pipelines.yml
@@ -41,7 +41,7 @@ jobs:
         WARPX_CI_EB: 'TRUE'
 
   # default: 60; maximum: 360
-  timeoutInMinutes: 120
+  timeoutInMinutes: 180
 
   steps:
   # set up caches:

diff --git a/.clang-tidy b/.clang-tidy
@@ -1,10 +1,78 @@
 Checks: '-*,
+    bugprone-*
+    -bugprone-easily-swappable-parameters,
+    -bugprone-implicit-widening-of-multiplication-result,
+    -bugprone-misplaced-widening-cast,
+    cert-*
+    -cert-err58-cpp,
     cppcoreguidelines-avoid-goto,
+    cppcoreguidelines-interfaces-global-init,
+    -cppcoreguidelines-avoid-non-const-global-variables,
+    -cppcoreguidelines-init-variables,
+    -cppcoreguidelines-macro-usage,
+    -cppcoreguidelines-narrowing-conversions,
+    -cppcoreguidelines-no-malloc,
+    -cppcoreguidelines-owning-memory,
     misc-const-correctness,
+    misc-misleading-bidirectional,
+    misc-misleading-identifier,
+    misc-misplaced-const,
+    misc-uniqueptr-reset-release,
+    misc-unused-alias-decls,
+    misc-unused-parameters,
+    misc-unused-using-decls,
+    -misc-definitions-in-headers,
+    modernize-avoid-bind,
+    modernize-concat-nested-namespaces,
+    modernize-deprecated-headers,
+    modernize-deprecated-ios-base-aliases,
+    modernize-loop-convert,
+    modernize-make-shared,
+    modernize-make-unique,
+    modernize-pass-by-value,
+    modernize-raw-string-literal,
+    modernize-redundant-void-arg,
+    modernize-replace-auto-ptr,
+    modernize-replace-disallow-copy-and-assign-macro,
+    modernize-replace-random-shuffle,
+    modernize-return-braced-init-list,
+    modernize-shrink-to-fit,
+    modernize-unary-static-assert,
     modernize-use-nullptr,
+    mpi-*,
     performance-faster-string-find,
     performance-for-range-copy,
+    performance-implicit-conversion-in-loop,
+    performance-inefficient-algorithm,
+    performance-inefficient-string-concatenation,
+    performance-inefficient-vector-operation,
+    performance-move-const-arg,
+    performance-move-constructor-init,
+    performance-no-automatic-move,
+    performance-no-int-to-ptr,
+    readability-non-const-parameter,
+    readability-redundant-control-flow,
+    readability-redundant-declaration,
+    readability-redundant-function-ptr-dereference,
+    readability-redundant-member-init,
+    readability-redundant-preprocessor,
+    readability-redundant-smartptr-get,
+    readability-redundant-string-cstr,
+    readability-redundant-string-init,
+    readability-simplify-boolean-expr,
+    readability-simplify-subscript-expr,
+    readability-static-accessed-through-instance,
+    readability-static-definition-in-anonymous-namespace,
+    readability-string-compare,
+    readability-suspicious-call-argument,
+    readability-uniqueptr-delete-release,
+    -readability-uppercase-literal-suffix,
+    readability-use-anyofallof,
     readability-non-const-parameter
     '
 
+CheckOptions:
+- key:          modernize-pass-by-value.ValuesOnly
+  value:        'true'
+
 HeaderFilterRegex: 'Source[a-z_A-Z0-9\/]+\.H$'
diff --git a/.github/workflows/cuda.yml b/.github/workflows/cuda.yml
@@ -12,7 +12,7 @@ jobs:
 #   https://github.com/ComputationalRadiationPhysics/picongpu/blob/0.5.0/share/picongpu/dockerfiles/ubuntu-1604/Dockerfile
 #   https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/
   build_nvcc:
-    name: NVCC 11.0.3 SP
+    name: NVCC 11.3 SP
     runs-on: ubuntu-20.04
     if: github.event.pull_request.draft == false
     env:
@@ -30,7 +30,7 @@ jobs:
         python-version: '3.x'
     - name: install dependencies
       run: |
-        .github/workflows/dependencies/nvcc11-0.sh
+        .github/workflows/dependencies/nvcc11-3.sh
     - name: CCache Cache
       uses: actions/cache@v3
       # - once stored under a key, they become immutable (even if local cache path content changes)
@@ -65,7 +65,7 @@ jobs:
           -DCMAKE_VERBOSE_MAKEFILE=ON  \
           -DWarpX_COMPUTE=CUDA         \
           -DWarpX_EB=ON                \
-          -DWarpX_LIB=ON               \
+          -DWarpX_PYTHON=ON            \
           -DAMReX_CUDA_ARCH=6.0        \
           -DWarpX_OPENPMD=ON           \
           -DWarpX_openpmd_internal=OFF \
@@ -77,7 +77,8 @@ jobs:
 
         python3 -m pip install --upgrade pip setuptools wheel
         export WARPX_MPI=ON
-        PYWARPX_LIB_DIR=$PWD/build_sp/lib python3 -m pip wheel .
+        export PYWARPX_LIB_DIR=$PWD/build_sp/lib/site-packages/pywarpx/
+        python3 -m pip wheel .
         python3 -m pip install *.whl
 
   # make sure legacy build system continues to build, i.e., that we don't forget
@@ -110,7 +111,7 @@ jobs:
         which nvcc || echo "nvcc not in PATH!"
 
         git clone https://github.com/AMReX-Codes/amrex.git ../amrex
-        cd ../amrex && git checkout --detach d28b9ab1cd64e648372ae679a6be01c733899525 && cd -
+        cd ../amrex && git checkout --detach dda0d979ca2ec912f7dd2eb630399f33ee7990e0 && cd -
         make COMP=gcc QED=FALSE USE_MPI=TRUE USE_GPU=TRUE USE_OMP=FALSE USE_PSATD=TRUE USE_CCACHE=TRUE -j 2
 
   build_nvhpc21-11-nvcc:
@@ -161,7 +162,7 @@ jobs:
           -DCMAKE_VERBOSE_MAKEFILE=ON  \
           -DWarpX_COMPUTE=CUDA         \
           -DWarpX_EB=ON                \
-          -DWarpX_LIB=ON               \
+          -DWarpX_PYTHON=ON            \
           -DAMReX_CUDA_ARCH=8.0        \
           -DWarpX_OPENPMD=ON           \
           -DWarpX_PSATD=ON             \
@@ -176,5 +177,6 @@ jobs:
 
         python3 -m pip install --upgrade pip setuptools wheel
         export WARPX_MPI=ON
-        PYWARPX_LIB_DIR=$PWD/build/lib python3 -m pip wheel .
+        export PYWARPX_LIB_DIR=$PWD/build/lib/site-packages/pywarpx/
+        python3 -m pip wheel .
         python3 -m pip install *.whl
diff --git a/.github/workflows/dependencies/dpcpp.sh b/.github/workflows/dependencies/dpcpp.sh
@@ -14,10 +14,13 @@ echo 'Acquire::Retries "3";' | sudo tee /etc/apt/apt.conf.d/80-retries
 
 # Ref.: https://github.com/rscohn2/oneapi-ci
 # intel-basekit intel-hpckit are too large in size
-wget -q -O - https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB \
-  | sudo apt-key add -
-echo "deb https://apt.repos.intel.com/oneapi all main" \
-  | sudo tee /etc/apt/sources.list.d/oneAPI.list
+
+# download the key to system keyring
+wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB \
+| gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null
+
+# add signed entry to apt sources and configure the APT client to use Intel repository:
+echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
 
 sudo apt-get update
 
@@ -33,7 +36,7 @@ do
         build-essential \
         ccache          \
         cmake           \
-        intel-oneapi-dpcpp-cpp-compiler intel-oneapi-mkl-devel \
+        intel-oneapi-compiler-dpcpp-cpp intel-oneapi-mkl-devel \
         g++ gfortran    \
         libopenmpi-dev  \
         openmpi-bin     \

diff --git a/.github/workflows/dependencies/nvcc11-0.sh → .github/workflows/dependencies/nvcc11-3.sh b/.github/workflows/dependencies/nvcc11-0.sh → .github/workflows/dependencies/nvcc11-3.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 #
-# Copyright 2020-2022 The WarpX Community
+# Copyright 2020-2023 The WarpX Community
 #
 # License: BSD-3-Clause-LBNL
 # Authors: Axel Huebl
@@ -26,30 +26,27 @@ sudo apt-get install -y \
     pkg-config          \
     wget
 
-wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-ubuntu2004.pin
-sudo mv cuda-ubuntu2004.pin /etc/apt/preferences.d/cuda-repository-pin-600
-sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/3bf863cc.pub
-echo "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/ /" \
-    | sudo tee /etc/apt/sources.list.d/cuda.list
+wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-keyring_1.0-1_all.deb
+sudo dpkg -i cuda-keyring_1.0-1_all.deb
 
 sudo apt-get update
 sudo apt-get install -y          \
-    cuda-command-line-tools-11-0 \
-    cuda-compiler-11-0           \
-    cuda-cupti-dev-11-0          \
-    cuda-minimal-build-11-0      \
-    cuda-nvml-dev-11-0           \
-    cuda-nvtx-11-0               \
-    libcufft-dev-11-0            \
-    libcurand-dev-11-0
-sudo ln -s cuda-11.0 /usr/local/cuda
+    cuda-command-line-tools-11-3 \
+    cuda-compiler-11-3           \
+    cuda-cupti-dev-11-3          \
+    cuda-minimal-build-11-3      \
+    cuda-nvml-dev-11-3           \
+    cuda-nvtx-11-3               \
+    libcufft-dev-11-3            \
+    libcurand-dev-11-3
+sudo ln -s cuda-11.3 /usr/local/cuda
 
 # if we run out of temporary storage in CI:
-#du -sh /usr/local/cuda-11.0
+#du -sh /usr/local/cuda-11.3
 #echo "+++ REDUCING CUDA Toolkit install size +++"
-#sudo rm -rf /usr/local/cuda-11.0/targets/x86_64-linux/lib/libcu{fft,pti,rand}_static.a
-#sudo rm -rf /usr/local/cuda-11.0/targets/x86_64-linux/lib/libnvperf_host_static.a
-#du -sh /usr/local/cuda-11.0/
+#sudo rm -rf /usr/local/cuda-11.3/targets/x86_64-linux/lib/libcu{fft,pti,rand}_static.a
+#sudo rm -rf /usr/local/cuda-11.3/targets/x86_64-linux/lib/libnvperf_host_static.a
+#du -sh /usr/local/cuda-11.3/
 #df -h
 
 # cmake-easyinstall

diff --git a/.github/workflows/hip.yml b/.github/workflows/hip.yml
@@ -51,15 +51,16 @@ jobs:
           -DAMReX_AMD_ARCH=gfx900     \
           -DWarpX_COMPUTE=HIP         \
           -DWarpX_EB=ON               \
-          -DWarpX_LIB=ON              \
+          -DWarpX_PYTHON=ON           \
           -DWarpX_MPI=ON              \
           -DWarpX_OPENPMD=ON          \
           -DWarpX_PRECISION=SINGLE    \
           -DWarpX_PSATD=ON
         cmake --build build_sp -j 2
 
         export WARPX_MPI=OFF
-        PYWARPX_LIB_DIR=$PWD/build_sp/lib python3 -m pip wheel .
+        export PYWARPX_LIB_DIR=$PWD/build_sp/lib/site-packages/pywarpx/
+        python3 -m pip wheel .
         python3 -m pip install *.whl
 
   build_hip_2d_dp:
@@ -107,13 +108,14 @@ jobs:
           -DWarpX_DIMS=2              \
           -DWarpX_COMPUTE=HIP         \
           -DWarpX_EB=ON               \
-          -DWarpX_LIB=ON              \
+          -DWarpX_PYTHON=ON           \
           -DWarpX_MPI=ON              \
           -DWarpX_OPENPMD=ON          \
           -DWarpX_PRECISION=DOUBLE    \
           -DWarpX_PSATD=ON
         cmake --build build_2d -j 2
 
         export WARPX_MPI=OFF
-        PYWARPX_LIB_DIR=$PWD/build_2d/lib python3 -m pip wheel .
+        export PYWARPX_LIB_DIR=$PWD/build_2d/lib/site-packages/pywarpx/
+        python3 -m pip wheel .
         python3 -m pip install *.whl
diff --git a/.github/workflows/insitu.yml b/.github/workflows/insitu.yml
@@ -39,7 +39,7 @@ jobs:
       CC: gcc
       CMAKE_PREFIX_PATH: /ascent/install/lib/cmake/
     container:
-      image: alpinedav/ascent:0.9.1
+      image: alpinedav/ascent:0.9.2
     steps:
     - uses: actions/checkout@v3
     - name: Configure

diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
@@ -41,25 +41,29 @@ jobs:
         export CXX=$(which icpc)
         export CC=$(which icc)
 
+        python3 -m pip install --upgrade pip setuptools wheel
+
         cmake -S . -B build_dp \
           -DCMAKE_VERBOSE_MAKEFILE=ON \
-          -DWarpX_LIB=ON              \
+          -DpyAMReX_IPO=OFF           \
+          -DWarpX_PYTHON=ON           \
+          -DWarpX_PYTHON_IPO=OFF      \
           -DWarpX_MPI=OFF             \
           -DWarpX_OPENPMD=ON          \
           -DWarpX_openpmd_internal=OFF
         cmake --build build_dp -j 2
 
         cmake -S . -B build_sp \
           -DCMAKE_VERBOSE_MAKEFILE=ON  \
-          -DWarpX_LIB=ON               \
+          -DpyAMReX_IPO=OFF            \
+          -DWarpX_PYTHON=ON            \
+          -DWarpX_PYTHON_IPO=OFF       \
           -DWarpX_MPI=OFF              \
           -DWarpX_OPENPMD=ON           \
           -DWarpX_openpmd_internal=OFF \
           -DWarpX_PRECISION=SINGLE
         cmake --build build_sp -j 2
-
-        python3 -m pip install --upgrade pip setuptools wheel
-        PYWARPX_LIB_DIR=$PWD/build_sp/lib python3 -m pip install -v .
+        cmake --build build_sp --target pip_install
 
   build_icpx:
     name: oneAPI ICX SP
@@ -99,20 +103,19 @@ jobs:
         export CXX=$(which icpx)
         export CC=$(which icx)
 
+        python3 -m pip install --upgrade pip
+        python3 -m pip install --upgrade setuptools wheel
+
         cmake -S . -B build_sp         \
           -DCMAKE_CXX_FLAGS_RELEASE="-O1 -DNDEBUG" \
           -DCMAKE_VERBOSE_MAKEFILE=ON  \
           -DWarpX_EB=ON                \
-          -DWarpX_LIB=ON               \
+          -DWarpX_PYTHON=ON            \
           -DWarpX_MPI=OFF              \
           -DWarpX_OPENPMD=ON           \
           -DWarpX_PRECISION=SINGLE
         cmake --build build_sp -j 2
-
-        python3 -m pip install --upgrade pip
-        python3 -m pip install --upgrade setuptools wheel
-        PYWARPX_LIB_DIR=$PWD/build_sp/lib python3 -m pip wheel -v .
-        python3 -m pip install *.whl
+        cmake --build build_sp --target pip_install
 
     - name: run pywarpx
       run: |
@@ -167,7 +170,7 @@ jobs:
           -DCMAKE_VERBOSE_MAKEFILE=ON  \
           -DWarpX_COMPUTE=SYCL         \
           -DWarpX_EB=ON                \
-          -DWarpX_LIB=ON               \
+          -DWarpX_PYTHON=ON            \
           -DWarpX_MPI=OFF              \
           -DWarpX_OPENPMD=ON           \
           -DWarpX_PRECISION=SINGLE
@@ -176,5 +179,5 @@ jobs:
      # Skip this as it will copy the binary artifacts and we are tight on disk space
      #   python3 -m pip install --upgrade pip
      #   python3 -m pip install --upgrade setuptools wheel
-     #   PYWARPX_LIB_DIR=$PWD/build_sp/lib python3 -m pip wheel .
+     #   PYWARPX_LIB_DIR=$PWD/build_sp/lib/site-packages/pywarpx/ python3 -m pip wheel .
      #   python3 -m pip install *.whl
diff --git a/.github/workflows/macos.yml b/.github/workflows/macos.yml
@@ -63,6 +63,9 @@ jobs:
           ccache-macos-appleclang-
     - name: build WarpX
       run: |
+        python3 -m pip install --upgrade pip
+        python3 -m pip install --upgrade pip setuptools wheel
+
         cmake -S . -B build_dp         \
           -DCMAKE_VERBOSE_MAKEFILE=ON  \
           -DWarpX_EB=ON                \
@@ -72,17 +75,14 @@ jobs:
 
         cmake -S . -B build_sp         \
           -DCMAKE_VERBOSE_MAKEFILE=ON  \
+          -DPython_EXECUTABLE=$(which python3) \
           -DWarpX_EB=ON                \
-          -DWarpX_LIB=ON               \
+          -DWarpX_PYTHON=ON            \
           -DWarpX_OPENPMD=ON           \
           -DWarpX_openpmd_internal=OFF \
           -DWarpX_PRECISION=SINGLE
         cmake --build build_sp -j 3
-
-        python3 -m pip install --upgrade pip setuptools wheel
-        export WARPX_MPI=ON
-        PYWARPX_LIB_DIR=$PWD/build_sp/lib python3 -m pip wheel .
-        python3 -m pip install *.whl
+        cmake --build build_sp --target pip_install
 
     - name: run pywarpx
       run: |