Merge branch 'development' into use_openpmd-api

guj · Jan 4, 2024 · 52bb537 · 52bb537
2 parents ea95312 + f1ec8df
commit 52bb537
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Showing 78 changed files with 738 additions and 349 deletions.
diff --git a/.github/workflows/bittree.yml b/.github/workflows/bittree.yml
@@ -52,7 +52,7 @@ jobs:
         mpiexec -n 2 ./main2d.gnu.TEST.MPI.ex inputs_bittree amr.plot_int=1000
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
-        make -j2 -f clang-tidy-ccache-misses.mak \
+        make -j2 -k -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-15 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
@@ -104,7 +104,7 @@ jobs:
         mpiexec -n 2 ./main3d.gnu.TEST.MPI.ex inputs_bittree max_step=10
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
-        make -j2 -f clang-tidy-ccache-misses.mak \
+        make -j2 -k -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-15 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 

diff --git a/.github/workflows/clang.yml b/.github/workflows/clang.yml
@@ -59,7 +59,7 @@ jobs:
         make test_install
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
-        make -j2 -f clang-tidy-ccache-misses.mak \
+        make -j2 -k -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-12 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
@@ -117,7 +117,7 @@ jobs:
         make -j 2
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
-        make -j2 -f clang-tidy-ccache-misses.mak \
+        make -j2 -k -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-14 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
@@ -159,7 +159,7 @@ jobs:
         make install
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
-        make -j2 -f clang-tidy-ccache-misses.mak \
+        make -j2 -k -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-14 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 

diff --git a/.github/workflows/dependencies/dependencies_codeplay.sh b/.github/workflows/dependencies/dependencies_codeplay.sh
@@ -6,10 +6,24 @@
 
 set -eu -o pipefail
 
-curl -o oneapi_nvidia.sh -L "https://developer.codeplay.com/api/v1/products/download?product=oneapi&variant=nvidia&filters[]=linux&aat=$1"
-chmod +x oneapi_nvidia.sh
-sudo ./oneapi_nvidia.sh --yes
+# `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
 
-curl -o oneapi_amd.sh -L "https://developer.codeplay.com/api/v1/products/download?product=oneapi&variant=amd&filters[]=linux&aat=$1"
-chmod +x oneapi_amd.sh
-sudo ./oneapi_amd.sh --yes
+# https://developer.codeplay.com/apt/index.html
+sudo wget -qO - https://developer.codeplay.com/apt/public.key | gpg --dearmor | sudo tee /usr/share/keyrings/codeplay-keyring.gpg > /dev/null
+echo "deb [signed-by=/usr/share/keyrings/codeplay-keyring.gpg] https://developer.codeplay.com/apt all main" | sudo tee /etc/apt/sources.list.d/codeplay.list
+
+sudo apt-get update
+
+# try apt install up to five times, to avoid connection splits
+status=1
+for itry in {1..5}
+do
+    sudo apt-get install -y --no-install-recommends \
+        $1 \
+        && { sudo apt-get clean; status=0; break; }  \
+        || { sleep 10; }
+done
+if [[ ${status} -ne 0 ]]; then exit 1; fi
diff --git a/.github/workflows/dependencies/dependencies_hip.sh b/.github/workflows/dependencies/dependencies_hip.sh
@@ -45,6 +45,9 @@ sudo apt-get install -y --no-install-recommends \
     rocrand-dev     \
     rocprim-dev
 
+# hiprand-dev is a new package that does not exist in old versions
+sudo apt-get install -y --no-install-recommends hiprand-dev || true
+
 # activate
 #
 source /etc/profile.d/rocm.sh

diff --git a/.github/workflows/gcc.yml b/.github/workflows/gcc.yml
@@ -55,7 +55,7 @@ jobs:
         make test_install
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
-        make -j2 -f clang-tidy-ccache-misses.mak \
+        make -j2 -k -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-12 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
@@ -107,7 +107,7 @@ jobs:
         cmake --build build -j 2
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
-        make -j2 -f clang-tidy-ccache-misses.mak \
+        make -j2 -k -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-12 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
@@ -155,7 +155,7 @@ jobs:
         cmake --build build -j 2
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
-        make -j2 -f clang-tidy-ccache-misses.mak \
+        make -j2 -k -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-12 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
@@ -204,7 +204,7 @@ jobs:
         cmake --build build -j 2
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
-        make -j2 -f clang-tidy-ccache-misses.mak \
+        make -j2 -k -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-12 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
@@ -263,7 +263,7 @@ 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 ${{github.workspace}}/ccache.log.txt
-        # make -j2 -f clang-tidy-ccache-misses.mak \
+        # make -j2 -k -f clang-tidy-ccache-misses.mak \
         #     CLANG_TIDY=clang-tidy-12 \
         #     CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
@@ -320,7 +320,7 @@ jobs:
         make -j 2
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
-        make -j2 -f clang-tidy-ccache-misses.mak \
+        make -j2 -k -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-12 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
@@ -384,7 +384,7 @@ jobs:
         make -j 2
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
-        make -j2 -f clang-tidy-ccache-misses.mak \
+        make -j2 -k -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-14 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
@@ -426,7 +426,7 @@ jobs:
         make install
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
-        make -j2 -f clang-tidy-ccache-misses.mak \
+        make -j2 -k -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-12 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
@@ -466,7 +466,7 @@ jobs:
         make install
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
-        make -j2 -f clang-tidy-ccache-misses.mak \
+        make -j2 -k -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-15 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
@@ -506,7 +506,7 @@ jobs:
         make install
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
-        make -j2 -f clang-tidy-ccache-misses.mak \
+        make -j2 -k -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-12 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
@@ -546,7 +546,7 @@ jobs:
         make install
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
-        make -j2 -f clang-tidy-ccache-misses.mak \
+        make -j2 -k -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-12 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
@@ -585,7 +585,7 @@ jobs:
             CCACHE=ccache
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
-        make -j2 -f clang-tidy-ccache-misses.mak \
+        make -j2 -k -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-12 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
@@ -630,7 +630,7 @@ jobs:
         make -j 2
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
-        make -j2 -f clang-tidy-ccache-misses.mak \
+        make -j2 -k -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-12 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 

diff --git a/.github/workflows/hypre.yml b/.github/workflows/hypre.yml
@@ -100,7 +100,7 @@ jobs:
         mpiexec -n 2 ./main3d.gnu.MPI.ex inputs.hypre
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
-        make -j2 -f clang-tidy-ccache-misses.mak \
+        make -j2 -k -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-14 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
@@ -148,7 +148,7 @@ jobs:
         mpiexec -n 2 ./main2d.gnu.MPI.ex inputs.2d
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
-        make -j2 -f clang-tidy-ccache-misses.mak \
+        make -j2 -k -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-14 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 

diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
@@ -44,7 +44,8 @@ jobs:
             -DCMAKE_C_COMPILER=$(which icx)                \
             -DCMAKE_CXX_COMPILER=$(which icpx)             \
             -DCMAKE_Fortran_COMPILER=$(which ifx)          \
-            -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
+            -DCMAKE_CXX_COMPILER_LAUNCHER=ccache           \
+            -DAMReX_PARALLEL_LINK_JOBS=2
         cmake --build build --parallel 2
 
         ccache -s
@@ -86,7 +87,8 @@ jobs:
             -DAMReX_GPU_BACKEND=SYCL                       \
             -DCMAKE_C_COMPILER=$(which icx)                \
             -DCMAKE_CXX_COMPILER=$(which icpx)             \
-            -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
+            -DCMAKE_CXX_COMPILER_LAUNCHER=ccache           \
+            -DAMReX_PARALLEL_LINK_JOBS=2
         cmake --build build --parallel 2
 
         ccache -s
@@ -95,29 +97,24 @@ jobs:
   tests-oneapi-sycl-eb-nvidia:
     name: oneAPI SYCL for Nvidia GPUs [tests w/ EB]
     runs-on: ubuntu-latest
-    env:
-      CODEPLAYTOKEN: ${{ secrets.CODEPLAYTOKEN }}
     steps:
     - uses: actions/checkout@v3
     - name: Dependencies
-      if: ${{ env.CODEPLAYTOKEN != '' }}
       run: |
-        .github/workflows/dependencies/dependencies_nvcc.sh
+        .github/workflows/dependencies/ubuntu_free_disk_space.sh
         .github/workflows/dependencies/dependencies_dpcpp.sh
-        .github/workflows/dependencies/dependencies_codeplay.sh ${{ env.CODEPLAYTOKEN }}
+        .github/workflows/dependencies/dependencies_nvcc.sh 12.0
+        .github/workflows/dependencies/dependencies_codeplay.sh oneapi-nvidia-12.0
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
-      if: ${{ env.CODEPLAYTOKEN != '' }}
       uses: actions/cache@v3
       with:
         path: ~/.cache/ccache
         key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
         restore-keys: |
              ccache-${{ github.workflow }}-${{ github.job }}-git-
     - name: Build & Install
-      if: ${{ env.CODEPLAYTOKEN != '' }}
-      # clang currently supports CUDA up to version 11.5 and a warning is issued with newer versions
-      env: {CXXFLAGS: "-fsycl -fsycl-targets=nvptx64-nvidia-cuda -fno-operator-names -Werror -Wall -Wextra -Wpedantic -Wnull-dereference -Wfloat-conversion -Wshadow -Woverloaded-virtual -Wextra-semi -Wunreachable-code -Wnon-virtual-dtor -Wno-unknown-cuda-version"}
+      env: {CXXFLAGS: "-fsycl -fsycl-targets=nvptx64-nvidia-cuda -Xsycl-target-backend --offload-arch=sm_80 -fno-operator-names -Werror -Wall -Wextra -Wpedantic -Wnull-dereference -Wfloat-conversion -Wshadow -Woverloaded-virtual -Wextra-semi -Wunreachable-code -Wnon-virtual-dtor"}
       run: |
         export CCACHE_COMPRESS=1
         export CCACHE_COMPRESSLEVEL=10
@@ -136,7 +133,8 @@ jobs:
             -DAMReX_GPU_BACKEND=SYCL                       \
             -DCMAKE_C_COMPILER=$(which icx)                \
             -DCMAKE_CXX_COMPILER=$(which clang++)          \
-            -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
+            -DCMAKE_CXX_COMPILER_LAUNCHER=ccache           \
+            -DAMReX_PARALLEL_LINK_JOBS=2
         cmake --build build --parallel 2
 
         ccache -s
@@ -145,28 +143,23 @@ jobs:
   no-tests-oneapi-sycl-amd:
     name: oneAPI SYCL for AMD GPUs
     runs-on: ubuntu-20.04
-    env:
-      CODEPLAYTOKEN: ${{ secrets.CODEPLAYTOKEN }}
     steps:
     - uses: actions/checkout@v3
     - name: Dependencies
-      if: ${{ env.CODEPLAYTOKEN != '' }}
       run: |
         .github/workflows/dependencies/ubuntu_free_disk_space.sh
-        .github/workflows/dependencies/dependencies_hip.sh 5.4.6
         .github/workflows/dependencies/dependencies_dpcpp.sh
-        .github/workflows/dependencies/dependencies_codeplay.sh ${{ env.CODEPLAYTOKEN }}
+        .github/workflows/dependencies/dependencies_hip.sh 5.4.3
+        .github/workflows/dependencies/dependencies_codeplay.sh oneapi-amd-5.4.3
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
-      if: ${{ env.CODEPLAYTOKEN != '' }}
       uses: actions/cache@v3
       with:
         path: ~/.cache/ccache
         key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
         restore-keys: |
              ccache-${{ github.workflow }}-${{ github.job }}-git-
     - name: Build & Install
-      if: ${{ env.CODEPLAYTOKEN != '' }}
       env: {CXXFLAGS: "-fsycl -fsycl-targets=amdgcn-amd-amdhsa -Xsycl-target-backend --offload-arch=gfx90a -fno-operator-names -Werror -Wall -Wextra -Wpedantic -Wnull-dereference -Wfloat-conversion -Wshadow -Woverloaded-virtual -Wextra-semi -Wunreachable-code -Wnon-virtual-dtor"}
       run: |
         export CCACHE_COMPRESS=1
@@ -186,7 +179,8 @@ jobs:
             -DAMReX_SYCL_SUB_GROUP_SIZE=64                 \
             -DCMAKE_C_COMPILER=$(which icx)                \
             -DCMAKE_CXX_COMPILER=$(which clang++)          \
-            -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
+            -DCMAKE_CXX_COMPILER_LAUNCHER=ccache           \
+            -DAMReX_PARALLEL_LINK_JOBS=2
         cmake --build build --parallel 2
 
         ccache -s

diff --git a/.github/workflows/petsc.yml b/.github/workflows/petsc.yml
@@ -50,7 +50,7 @@ jobs:
         mpiexec -n 2 ./main2d.gnu.TEST.MPI.ex inputs.rt.2d.petsc
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
-        make -j2 -f clang-tidy-ccache-misses.mak \
+        make -j2 -k -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-14 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 

diff --git a/.github/workflows/smoke.yml b/.github/workflows/smoke.yml
@@ -47,7 +47,7 @@ jobs:
         make test_install
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
-        make -j2 -f clang-tidy-ccache-misses.mak \
+        make -j2 -k -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-15 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 

diff --git a/.github/workflows/sundials.yml b/.github/workflows/sundials.yml
@@ -60,7 +60,7 @@ jobs:
         cmake --build build -j 2
 
         ${{github.workspace}}/Tools/C_scripts/mmclt.py --input ${{github.workspace}}/ccache.log.txt
-        make -j2 -f clang-tidy-ccache-misses.mak \
+        make -j2 -k -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-14 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"