merge with HS 08/11

RevathiJambunathan · Aug 11, 2024 · cf92850 · cf92850
2 parents 74cbd90 + e7f3e21
commit cf92850
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diff --git a/.clang-tidy b/.clang-tidy
@@ -7,6 +7,11 @@ Checks: '
         -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,
@@ -30,8 +35,6 @@ Checks: '
         -modernize-use-trailing-return-type,
     mpi-*,
     performance-*,
-        -performance-unnecessary-copy-initialization,
-        -performance-unnecessary-value-param,
     portability-*,
     readability-*,
         -readability-convert-member-functions-to-static,

diff --git a/.github/workflows/clang_tidy.yml b/.github/workflows/clang_tidy.yml
@@ -13,6 +13,7 @@ jobs:
         dim: [1, 2, RZ, 3]
     name: clang-tidy-${{ matrix.dim }}D
     runs-on: ubuntu-22.04
+    timeout-minutes: 120
     if: github.event.pull_request.draft == false
     steps:
     - uses: actions/checkout@v4
@@ -43,7 +44,7 @@ jobs:
           -DWarpX_DIMS="${{ matrix.dim }}"  \
           -DWarpX_MPI=ON                    \
           -DWarpX_COMPUTE=OMP               \
-          -DWarpX_PSATD=ON                  \
+          -DWarpX_FFT=ON                    \
           -DWarpX_QED=ON                    \
           -DWarpX_QED_TABLE_GEN=ON          \
           -DWarpX_OPENPMD=ON                \

diff --git a/.github/workflows/cuda.yml b/.github/workflows/cuda.yml
@@ -70,7 +70,7 @@ jobs:
           -DWarpX_OPENPMD=ON           \
           -DWarpX_openpmd_internal=OFF \
           -DWarpX_PRECISION=SINGLE     \
-          -DWarpX_PSATD=ON             \
+          -DWarpX_FFT=ON               \
           -DAMReX_CUDA_ERROR_CROSS_EXECUTION_SPACE_CALL=ON \
           -DAMReX_CUDA_ERROR_CAPTURE_THIS=ON
         cmake --build build_sp -j 4
@@ -115,8 +115,8 @@ jobs:
         which nvcc || echo "nvcc not in PATH!"
 
         git clone https://github.com/AMReX-Codes/amrex.git ../amrex
-        cd ../amrex && git checkout --detach 155f1f4c3f4fa03528d38d2769beb4b35b38042c && cd -
-        make COMP=gcc QED=FALSE USE_MPI=TRUE USE_GPU=TRUE USE_OMP=FALSE USE_PSATD=TRUE USE_CCACHE=TRUE -j 4
+        cd ../amrex && git checkout --detach 20e6f2eadf0c297517588ba38973ec7c7084fa31 && cd -
+        make COMP=gcc QED=FALSE USE_MPI=TRUE USE_GPU=TRUE USE_OMP=FALSE USE_FFT=TRUE USE_CCACHE=TRUE -j 4
 
         ccache -s
         du -hs ~/.cache/ccache
@@ -168,7 +168,7 @@ jobs:
           -DWarpX_PYTHON=OFF           \
           -DAMReX_CUDA_ARCH=8.0        \
           -DWarpX_OPENPMD=ON           \
-          -DWarpX_PSATD=ON             \
+          -DWarpX_FFT=ON               \
           -DAMReX_CUDA_ERROR_CROSS_EXECUTION_SPACE_CALL=ON \
           -DAMReX_CUDA_ERROR_CAPTURE_THIS=ON
         cmake --build build -j 4

diff --git a/.github/workflows/dependencies/hip.sh b/.github/workflows/dependencies/hip.sh
@@ -12,12 +12,24 @@ set -eu -o pipefail
 #   failed files the given number of times.
 echo 'Acquire::Retries "3";' | sudo tee /etc/apt/apt.conf.d/80-retries
 
-# Ref.: https://rocmdocs.amd.com/en/latest/Installation_Guide/Installation-Guide.html#ubuntu
-wget -q -O - https://repo.radeon.com/rocm/rocm.gpg.key \
-  | sudo apt-key add -
-echo 'deb [arch=amd64] https://repo.radeon.com/rocm/apt/debian/ ubuntu main' \
-  | sudo tee /etc/apt/sources.list.d/rocm.list
+# Ref.: https://rocm.docs.amd.com/projects/install-on-linux/en/latest/how-to/native-install/ubuntu.html
+
+# Make the directory if it doesn't exist yet.
+# This location is recommended by the distribution maintainers.
+sudo mkdir --parents --mode=0755 /etc/apt/keyrings
+
+# Download the key, convert the signing-key to a full
+# keyring required by apt and store in the keyring directory
+wget https://repo.radeon.com/rocm/rocm.gpg.key -O - | \
+    gpg --dearmor | sudo tee /etc/apt/keyrings/rocm.gpg > /dev/null
 
+curl -O https://repo.radeon.com/rocm/rocm.gpg.key
+sudo apt-key add rocm.gpg.key
+
+source /etc/os-release # set UBUNTU_CODENAME: focal or jammy or ...
+
+echo "deb [arch=amd64] https://repo.radeon.com/rocm/apt/${1-latest} ${UBUNTU_CODENAME} main" \
+  | sudo tee /etc/apt/sources.list.d/rocm.list
 echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' \
   | sudo tee -a /etc/profile.d/rocm.sh
 

diff --git a/.github/workflows/dependencies/icc.sh b/.github/workflows/dependencies/icc.sh
@@ -58,7 +58,7 @@ export CEI_TMP="/tmp/cei"
 CXX=$(which icpc) CC=$(which icc) \
   cmake-easyinstall               \
   --prefix=/usr/local             \
-  git+https://github.com/openPMD/[email protected].1 \
+  git+https://github.com/openPMD/[email protected].2 \
   -DopenPMD_USE_PYTHON=OFF \
   -DBUILD_TESTING=OFF      \
   -DBUILD_EXAMPLES=OFF     \

diff --git a/.github/workflows/hip.yml b/.github/workflows/hip.yml
@@ -55,7 +55,7 @@ jobs:
           -DWarpX_MPI=ON              \
           -DWarpX_OPENPMD=ON          \
           -DWarpX_PRECISION=SINGLE    \
-          -DWarpX_PSATD=ON
+          -DWarpX_FFT=ON
         cmake --build build_sp -j 4
 
         export WARPX_MPI=OFF
@@ -115,7 +115,7 @@ jobs:
           -DWarpX_MPI=ON              \
           -DWarpX_OPENPMD=ON          \
           -DWarpX_PRECISION=DOUBLE    \
-          -DWarpX_PSATD=ON
+          -DWarpX_FFT=ON
         cmake --build build_2d -j 4
 
         export WARPX_MPI=OFF

diff --git a/.github/workflows/macos.yml b/.github/workflows/macos.yml
@@ -36,9 +36,6 @@ jobs:
         brew tap openpmd/openpmd
         brew install openpmd-api
 
-        python3 -m pip install --upgrade pip
-        python3 -m pip install --upgrade virtualenv
-
         python3 -m venv py-venv
         source py-venv/bin/activate
         python3 -m pip install --upgrade pip
@@ -47,7 +44,7 @@ jobs:
     - name: CCache Cache
       uses: actions/cache@v4
       with:
-        path: /Users/runner/Library/Caches/ccache
+        path: ~/Library/Caches/ccache
         key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
         restore-keys: |
              ccache-${{ github.workflow }}-${{ github.job }}-git-
@@ -56,7 +53,7 @@ jobs:
         export CCACHE_COMPRESS=1
         export CCACHE_COMPRESSLEVEL=10
         export CCACHE_MAXSIZE=100M
-        export CCACHE_DEPEND=1
+        export CCACHE_SLOPPINESS=time_macros
         ccache -z
 
         source py-venv/bin/activate
@@ -79,6 +76,7 @@ jobs:
         cmake --build build_sp -j 3
         cmake --build build_sp --target pip_install
 
+        du -hs ~/Library/Caches/ccache
         ccache -s
 
     - name: run pywarpx

diff --git a/.github/workflows/ubuntu.yml b/.github/workflows/ubuntu.yml
@@ -77,7 +77,7 @@ jobs:
           -DCMAKE_VERBOSE_MAKEFILE=ON  \
           -DWarpX_DIMS="1;2"           \
           -DWarpX_EB=OFF               \
-          -DWarpX_PSATD=ON             \
+          -DWarpX_FFT=ON               \
           -DWarpX_QED_TABLE_GEN=ON     \
           -DWarpX_QED_TOOLS=ON
 
@@ -127,7 +127,7 @@ jobs:
           -DCMAKE_VERBOSE_MAKEFILE=ON       \
           -DWarpX_DIMS="RZ;3"               \
           -DWarpX_EB=OFF                    \
-          -DWarpX_PSATD=ON                  \
+          -DWarpX_FFT=ON                    \
           -DWarpX_PRECISION=SINGLE          \
           -DWarpX_PARTICLE_PRECISION=SINGLE \
           -DWarpX_QED_TABLE_GEN=ON
@@ -211,7 +211,7 @@ jobs:
         cmake -S . -B build            \
           -DCMAKE_VERBOSE_MAKEFILE=ON  \
           -DWarpX_APP=OFF              \
-          -DWarpX_PSATD=ON             \
+          -DWarpX_FFT=ON               \
           -DWarpX_PYTHON=ON            \
           -DWarpX_QED_TABLE_GEN=ON
         cmake --build build -j 4 --target pip_install
@@ -260,7 +260,7 @@ jobs:
           -GNinja                           \
           -DCMAKE_VERBOSE_MAKEFILE=ON       \
           -DWarpX_DIMS="RZ;1;2;3"           \
-          -DWarpX_PSATD=ON                  \
+          -DWarpX_FFT=ON                    \
           -DWarpX_QED=ON                    \
           -DWarpX_QED_TABLE_GEN=ON          \
           -DWarpX_OPENPMD=ON                \

diff --git a/.gitignore b/.gitignore
@@ -4,7 +4,7 @@ Python/pywarpx/libwarpx*.so
 d/
 f/
 o/
-build/
+build*/
 tmp_build_dir/
 test_dir
 test_dir/

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -18,7 +18,7 @@ exclude: '^share/openPMD/thirdParty'
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
     - id: trailing-whitespace
       args: [--markdown-linebreak-ext=md]

diff --git a/.zenodo.json b/.zenodo.json
@@ -98,6 +98,11 @@
         "name": "Gu, Junmin",
         "orcid": "0000-0002-1521-8534"
       },
+      {
+        "affiliation": "Lawrence Berkeley National Laboratory",
+        "name": "Haseeb, Muhammad",
+        "orcid": "0000-0002-0697-6894"
+      },
       {
         "affiliation": "Lawrence Berkeley National Laboratory",
         "name": "Jambunathan, Revathi",
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,7 +4,7 @@ Python/pywarpx/libwarpx*.so @@
     d/
     f/
     o/
-    build/
+    build*/
     tmp_build_dir/
     test_dir
     test_dir/
@@ Expand Down @@