Merge branch 'development' into use_openpmd-api

guj · Mar 28, 2024 · a129a8f · a129a8f
2 parents 963dcac + dffdeac
commit a129a8f
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diff --git a/.clang-tidy b/.clang-tidy
@@ -10,6 +10,7 @@ Checks: >
      clang-diagnostic-*,
      cppcoreguidelines-*,
        -cppcoreguidelines-avoid-c-arrays,
+       -cppcoreguidelines-avoid-do-while,
        -cppcoreguidelines-avoid-magic-numbers,
        -cppcoreguidelines-avoid-non-const-global-variables,
        -cppcoreguidelines-init-variables,
@@ -24,6 +25,7 @@ Checks: >
      google-global-names-in-headers,
      misc-*,
        -misc-const-correctness,
+       -misc-include-cleaner,
        -misc-non-private-member-variables-in-classes,
        -misc-no-recursion,
      modernize-*,
@@ -34,6 +36,7 @@ Checks: >
      performance-*,
      portability-*,
      readability-*,
+       -readability-avoid-unconditional-preprocessor-if,
        -readability-else-after-return,
        -readability-function-cognitive-complexity,
        -readability-function-size,

diff --git a/.github/workflows/dependencies/dependencies_clang-tidy-apt-llvm.sh b/.github/workflows/dependencies/dependencies_clang-tidy-apt-llvm.sh
@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+
+set -eu -o pipefail
+
+# `man apt.conf`:
+#   Number of retries to perform. If this is non-zero APT will retry
+#   failed files the given number of times.
+echo 'Acquire::Retries "3";' | sudo tee /etc/apt/apt.conf.d/80-retries
+
+if [[ ! -f /etc/apt/trusted.gpg.d/apt.llvm.org.asc ]]; then
+    wget -qO- https://apt.llvm.org/llvm-snapshot.gpg.key | sudo tee /etc/apt/trusted.gpg.d/apt.llvm.org.asc
+fi
+
+source /etc/os-release # set UBUNTU_CODENAME
+
+sudo add-apt-repository "deb http://apt.llvm.org/${UBUNTU_CODENAME}/ llvm-toolchain-${UBUNTU_CODENAME} main"
+sudo add-apt-repository "deb http://apt.llvm.org/${UBUNTU_CODENAME}/ llvm-toolchain-${UBUNTU_CODENAME}-$1 main"
+
+sudo apt-get update
+
+sudo apt-get install -y --no-install-recommends \
+    clang-tidy-$1 libomp-$1-dev
diff --git a/.github/workflows/gcc.yml b/.github/workflows/gcc.yml
@@ -20,7 +20,7 @@ jobs:
     - name: Dependencies
       run: |
         .github/workflows/dependencies/dependencies_gcc.sh 8
-        .github/workflows/dependencies/dependencies_clang-tidy.sh 12
+        .github/workflows/dependencies/dependencies_clang-tidy-apt-llvm.sh 17
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
       uses: actions/cache@v4
@@ -56,7 +56,7 @@ jobs:
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
         make -j4 -k -f clang-tidy-ccache-misses.mak \
-            CLANG_TIDY=clang-tidy-12 \
+            CLANG_TIDY=clang-tidy-17 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
         export PATH=/tmp/my-amrex/bin:$PATH
@@ -76,7 +76,7 @@ jobs:
     - name: Dependencies
       run: |
         .github/workflows/dependencies/dependencies.sh
-        .github/workflows/dependencies/dependencies_clang-tidy.sh 12
+        .github/workflows/dependencies/dependencies_clang-tidy-apt-llvm.sh 17
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
       uses: actions/cache@v4
@@ -108,7 +108,7 @@ jobs:
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
         make -j4 -k -f clang-tidy-ccache-misses.mak \
-            CLANG_TIDY=clang-tidy-12 \
+            CLANG_TIDY=clang-tidy-17 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
         ctest --test-dir build --output-on-failure
@@ -124,7 +124,7 @@ jobs:
     - name: Dependencies
       run: |
         .github/workflows/dependencies/dependencies.sh
-        .github/workflows/dependencies/dependencies_clang-tidy.sh 12
+        .github/workflows/dependencies/dependencies_clang-tidy-apt-llvm.sh 17
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
       uses: actions/cache@v4
@@ -156,7 +156,7 @@ jobs:
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
         make -j4 -k -f clang-tidy-ccache-misses.mak \
-            CLANG_TIDY=clang-tidy-12 \
+            CLANG_TIDY=clang-tidy-17 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
         ctest --test-dir build --output-on-failure
@@ -172,7 +172,7 @@ jobs:
     - name: Dependencies
       run: |
         .github/workflows/dependencies/dependencies.sh
-        .github/workflows/dependencies/dependencies_clang-tidy.sh 12
+        .github/workflows/dependencies/dependencies_clang-tidy-apt-llvm.sh 17
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
       uses: actions/cache@v4
@@ -205,7 +205,7 @@ jobs:
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
         make -j4 -k -f clang-tidy-ccache-misses.mak \
-            CLANG_TIDY=clang-tidy-12 \
+            CLANG_TIDY=clang-tidy-17 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
         ctest --test-dir build --output-on-failure
@@ -222,7 +222,7 @@ jobs:
     - name: Dependencies
       run: |
         .github/workflows/dependencies/dependencies_gcc.sh 10
-        .github/workflows/dependencies/dependencies_clang-tidy.sh 12
+        .github/workflows/dependencies/dependencies_clang-tidy-apt-llvm.sh 17
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
       uses: actions/cache@v4
@@ -264,7 +264,7 @@ jobs:
         # Let's not use clang-tidy for this test because it wants to use C++20.
         # ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
         # make -j4 -k -f clang-tidy-ccache-misses.mak \
-        #     CLANG_TIDY=clang-tidy-12 \
+        #     CLANG_TIDY=clang-tidy-17 \
         #     CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
         ctest --output-on-failure
@@ -281,7 +281,7 @@ jobs:
     - name: Dependencies
       run: |
         .github/workflows/dependencies/dependencies_gcc.sh 8
-        .github/workflows/dependencies/dependencies_clang-tidy.sh 12
+        .github/workflows/dependencies/dependencies_clang-tidy-apt-llvm.sh 17
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
       uses: actions/cache@v4
@@ -305,6 +305,7 @@ jobs:
         cmake ..                        \
             -DCMAKE_BUILD_TYPE=Release  \
             -DCMAKE_VERBOSE_MAKEFILE=ON \
+            -DAMReX_FLATTEN_FOR=OFF     \
             -DAMReX_ASSERTIONS=ON       \
             -DAMReX_TESTING=ON          \
             -DAMReX_BOUND_CHECK=ON      \
@@ -321,7 +322,7 @@ jobs:
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
         make -j4 -k -f clang-tidy-ccache-misses.mak \
-            CLANG_TIDY=clang-tidy-12 \
+            CLANG_TIDY=clang-tidy-17 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
         ctest --output-on-failure
@@ -338,7 +339,7 @@ jobs:
     - name: Dependencies
       run: |
         .github/workflows/dependencies/dependencies_gcc.sh 12
-        .github/workflows/dependencies/dependencies_clang-tidy.sh 14
+        .github/workflows/dependencies/dependencies_clang-tidy-apt-llvm.sh 17
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
       uses: actions/cache@v4
@@ -385,7 +386,7 @@ jobs:
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
         make -j4 -k -f clang-tidy-ccache-misses.mak \
-            CLANG_TIDY=clang-tidy-14 \
+            CLANG_TIDY=clang-tidy-17 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
         ctest --output-on-failure
@@ -402,7 +403,7 @@ jobs:
     - name: Dependencies
       run: |
         .github/workflows/dependencies/dependencies.sh
-        .github/workflows/dependencies/dependencies_clang-tidy.sh 12
+        .github/workflows/dependencies/dependencies_clang-tidy-apt-llvm.sh 17
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
       uses: actions/cache@v4
@@ -427,7 +428,7 @@ jobs:
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
         make -j4 -k -f clang-tidy-ccache-misses.mak \
-            CLANG_TIDY=clang-tidy-12 \
+            CLANG_TIDY=clang-tidy-17 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
         ccache -s
@@ -442,7 +443,7 @@ jobs:
     - name: Dependencies
       run: |
         .github/workflows/dependencies/dependencies.sh
-        .github/workflows/dependencies/dependencies_clang-tidy.sh 15
+        .github/workflows/dependencies/dependencies_clang-tidy-apt-llvm.sh 17
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
       uses: actions/cache@v4
@@ -467,7 +468,7 @@ jobs:
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
         make -j4 -k -f clang-tidy-ccache-misses.mak \
-            CLANG_TIDY=clang-tidy-15 \
+            CLANG_TIDY=clang-tidy-17 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
         ccache -s
@@ -482,7 +483,7 @@ jobs:
     - name: Dependencies
       run: |
         .github/workflows/dependencies/dependencies.sh
-        .github/workflows/dependencies/dependencies_clang-tidy.sh 12
+        .github/workflows/dependencies/dependencies_clang-tidy-apt-llvm.sh 17
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
       uses: actions/cache@v4
@@ -507,7 +508,7 @@ jobs:
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
         make -j4 -k -f clang-tidy-ccache-misses.mak \
-            CLANG_TIDY=clang-tidy-12 \
+            CLANG_TIDY=clang-tidy-17 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
         ccache -s
@@ -522,7 +523,7 @@ jobs:
     - name: Dependencies
       run: |
         .github/workflows/dependencies/dependencies.sh
-        .github/workflows/dependencies/dependencies_clang-tidy.sh 12
+        .github/workflows/dependencies/dependencies_clang-tidy-apt-llvm.sh 17
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
       uses: actions/cache@v4
@@ -547,7 +548,7 @@ jobs:
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
         make -j4 -k -f clang-tidy-ccache-misses.mak \
-            CLANG_TIDY=clang-tidy-12 \
+            CLANG_TIDY=clang-tidy-17 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
         ccache -s
@@ -562,7 +563,7 @@ jobs:
     - name: Dependencies
       run: |
         .github/workflows/dependencies/dependencies.sh
-        .github/workflows/dependencies/dependencies_clang-tidy.sh 12
+        .github/workflows/dependencies/dependencies_clang-tidy-apt-llvm.sh 17
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
       uses: actions/cache@v4
@@ -586,7 +587,7 @@ jobs:
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
         make -j4 -k -f clang-tidy-ccache-misses.mak \
-            CLANG_TIDY=clang-tidy-12 \
+            CLANG_TIDY=clang-tidy-17 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
         ccache -s
@@ -601,7 +602,7 @@ jobs:
     - name: Dependencies
       run: |
         .github/workflows/dependencies/dependencies.sh
-        .github/workflows/dependencies/dependencies_clang-tidy.sh 12
+        .github/workflows/dependencies/dependencies_clang-tidy-apt-llvm.sh 17
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
       uses: actions/cache@v4
@@ -631,7 +632,7 @@ jobs:
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
         make -j4 -k -f clang-tidy-ccache-misses.mak \
-            CLANG_TIDY=clang-tidy-12 \
+            CLANG_TIDY=clang-tidy-17 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
         ccache -s

diff --git a/.github/workflows/sundials.yml b/.github/workflows/sundials.yml
@@ -68,7 +68,7 @@ jobs:
         du -hs ~/.cache/ccache
 
   sundials-cuda:
-    name: CUDA SUNDIALS@6.5.0
+    name: CUDA SUNDIALS@7.0.0
     runs-on: ubuntu-22.04
     env:
        CCACHE_COMPRESS: 1
@@ -97,9 +97,9 @@ jobs:
         export LD_LIBRARY_PATH=/usr/local/nvidia/lib:/usr/local/nvidia/lib64:/usr/local/cuda/lib64:${LD_LIBRARY_PATH}
         which nvcc || echo "nvcc not in PATH!"
 
-        wget -q https://github.com/LLNL/sundials/archive/refs/tags/v6.5.0.tar.gz
-        tar xfz v6.5.0.tar.gz
-        cd sundials-6.5.0
+        wget -q https://github.com/LLNL/sundials/archive/refs/tags/v7.0.0.tar.gz
+        tar xfz v7.0.0.tar.gz
+        cd sundials-7.0.0
         mkdir instdir builddir
         cd builddir
         cmake ..                                     \
@@ -126,7 +126,7 @@ jobs:
             -DAMReX_GPU_BACKEND=CUDA    \
             -DAMReX_CUDA_ARCH=8.0       \
             -DAMReX_SUNDIALS=ON         \
-            -DSUNDIALS_ROOT=${PWD}/sundials-6.5.0/instdir \
+            -DSUNDIALS_ROOT=${PWD}/sundials-7.0.0/instdir \
             -DCMAKE_CXX_COMPILER_LAUNCHER=ccache  \
             -DCMAKE_CUDA_COMPILER_LAUNCHER=ccache
         cmake --build build -j 4