Merge branch 'development' into job_info_check

AMReX-Astro · Mar 27, 2024 · 7269f6d · 7269f6d
2 parents ceb7fde + 6b90dd1
commit 7269f6d
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diff --git a/.clang-tidy b/.clang-tidy
@@ -7,7 +7,7 @@ Checks: >
      clang-diagnostic-*,
      cppcoreguidelines-*,
        -cppcoreguidelines-avoid-c-arrays,
-       -cppcoreguidelines-avoid-goto,
+       -cppcoreguidelines-avoid-do-while,
        -cppcoreguidelines-avoid-magic-numbers,
        -cppcoreguidelines-avoid-non-const-global-variables,
        -cppcoreguidelines-init-variables,
@@ -17,11 +17,18 @@ Checks: >
        -cppcoreguidelines-non-private-member-variables-in-classes,
        -cppcoreguidelines-owning-memory,
        -cppcoreguidelines-pro-*,
+     misc-*,
+       -misc-const-correctness,
+       -misc-include-cleaner,
+       -misc-non-private-member-variables-in-classes,
+       -misc-no-recursion,
      modernize-*,
        -modernize-avoid-c-arrays,
        -modernize-use-trailing-return-type,
        -modernize-use-using,
      performance-*,
+       -performance-avoid-endl,
+     portability-*,
      readability-*,
        -readability-avoid-const-params-in-decls,
        -readability-braces-around-statements,

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,9 @@
+# Dependabot configuration
+# ref: https://docs.github.com/en/code-security/supply-chain-security/keeping-your-dependencies-updated-automatically/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    target-branch: "development"
diff --git a/.github/workflows/c-linter.yml b/.github/workflows/c-linter.yml
@@ -2,6 +2,10 @@ name: cpp-linter
 
 on: [pull_request]
 
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   cpp-linter:
     runs-on: ubuntu-latest
@@ -30,7 +34,7 @@ jobs:
           tar xfz v2.28.0.tar.gz
           cd hypre-2.28.0/src
           ./configure --with-cxxstandard=17 --without-MPI
-          make -j 2
+          make -j 4
           make install
           cd ../../
 

diff --git a/.github/workflows/check-ifdefs.yml b/.github/workflows/check-ifdefs.yml
@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

diff --git a/.github/workflows/clang-tidy.yml b/.github/workflows/clang-tidy.yml
@@ -0,0 +1,36 @@
+name: "clang-tidy"
+
+on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
+jobs:
+  clang_tidy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Get submodules
+        run: |
+          git submodule update --init
+          cd external/Microphysics
+          git fetch; git checkout development
+          echo "MICROPHYSICS_HOME=$(pwd)" >> $GITHUB_ENV
+          cd ../amrex
+          git fetch; git checkout development
+          echo "AMREX_HOME=$(pwd)" >> $GITHUB_ENV
+          cd ../..
+
+      - name: Install dependencies
+        run: |
+          .github/workflows/dependencies_clang-tidy-apt-llvm.sh 17
+
+      - name: Compile flame_wave
+        run: |
+          echo $AMREX_HOME
+          echo $MICROPHYSICS_HOME
+          cd Exec/science/subchandra
+          make USE_MPI=FALSE USE_CLANG_TIDY=TRUE CLANG_TIDY=clang-tidy-17 CLANG_TIDY_WARN_ERROR=TRUE -j 4
+
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -19,7 +19,7 @@ jobs:
           fetch-depth: 0
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.10'
           cache: "pip"

diff --git a/.github/workflows/compiler-warnings.yml b/.github/workflows/compiler-warnings.yml
@@ -1,6 +1,11 @@
 name: "compiler warnings"
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   compiler_warnings:
     runs-on: ubuntu-latest
@@ -26,14 +31,14 @@ jobs:
       - name: Compile Detonation
         run: |
           cd Exec/science/Detonation
-          make USE_MPI=FALSE USE_OMP=FALSE DEBUG=TRUE WARN_ALL=TRUE WARN_ERROR=TRUE -j 2
+          make USE_MPI=FALSE USE_OMP=FALSE DEBUG=TRUE WARN_ALL=TRUE WARN_ERROR=TRUE -j 4
 
       - name: Compile subchandra
         run: |
           cd Exec/science/subchandra
-          make USE_MPI=FALSE USE_OMP=FALSE DEBUG=TRUE WARN_ALL=TRUE WARN_ERROR=TRUE -j 2
+          make USE_MPI=FALSE USE_OMP=FALSE DEBUG=TRUE WARN_ALL=TRUE WARN_ERROR=TRUE -j 4
 
       - name: Compile wdmerger
         run: |
           cd Exec/science/wdmerger
-          make USE_MPI=FALSE USE_OMP=FALSE DEBUG=TRUE WARN_ALL=TRUE WARN_ERROR=TRUE -j 2
+          make USE_MPI=FALSE USE_OMP=FALSE DEBUG=TRUE WARN_ALL=TRUE WARN_ERROR=TRUE -j 4
diff --git a/.github/workflows/dependencies_clang-tidy-apt-llvm.sh b/.github/workflows/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/detonation-sdc-compare.yml b/.github/workflows/detonation-sdc-compare.yml
@@ -1,6 +1,11 @@
 name: detonation-sdc
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   detonation-sdc:
     runs-on: ubuntu-latest
@@ -26,7 +31,7 @@ jobs:
       - name: Compile Detonation
         run: |
           cd Exec/science/Detonation
-          make DIM=1 USE_MPI=FALSE -j 2 USE_SIMPLIFIED_SDC=TRUE
+          make DIM=1 USE_MPI=FALSE -j 4 USE_SIMPLIFIED_SDC=TRUE
 
       - name: Run Detonation
         run: |
@@ -36,7 +41,7 @@ jobs:
       - name: Build the fextrema tool
         run: |
           cd external/amrex/Tools/Plotfile
-          make programs=fextrema -j 2
+          make programs=fextrema -j 4
 
       - name: Check the extrema
         run: |

diff --git a/.github/workflows/docs-test.yml b/.github/workflows/docs-test.yml
@@ -9,6 +9,10 @@ on:
     branches:
       - development
 
+env:
+  # enable color output from Sphinx
+  FORCE_COLOR: "1"
+
 jobs:
   docs:
     runs-on: ubuntu-latest
@@ -33,7 +37,10 @@ jobs:
       - name: Build docs
         run: |
           cd Docs/
-          make SPHINXOPTS=-v NO_DOXYGEN=TRUE html
+          # remove missing TOC entries that would otherwise be generated by
+          # doxygen to avoid warnings about missing references
+          sed -i -e 's/^   filelist$//; s/^   classlist$//' source/index.rst
+          make SPHINXOPTS='-v -W --keep-going' NO_DOXYGEN=TRUE html
 
       - name: Check links
         run: |

diff --git a/.github/workflows/flame_wave-compare.yml b/.github/workflows/flame_wave-compare.yml
@@ -1,6 +1,11 @@
 name: flame_wave
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   flame_wave-2d:
     runs-on: ubuntu-latest

diff --git a/.github/workflows/fsanitizer.yml b/.github/workflows/fsanitizer.yml
@@ -0,0 +1,37 @@
+name: fsanitizer
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-fsanitizer
+  cancel-in-progress: true
+
+jobs:
+  fsanitizer:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Get submodules
+        run: |
+          git submodule update --init
+          cd external/Microphysics
+          git fetch; git checkout development
+          cd ../amrex
+          git fetch; git checkout development
+          cd ../..
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update -y -qq
+          sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0
+
+      - name: Compile subchandra
+        run: |
+          cd Exec/science/subchandra
+          make FSANITIZER=TRUE USE_MPI=FALSE -j 4
+
+      - name: Run subchandra
+        run: |
+          cd Exec/science/subchandra
+          ./Castro2d.gnu.SMPLSDC.ex inputs_2d.N14.coarse amr.max_level=1 max_step=1 amr.n_cell=320 640
diff --git a/.github/workflows/get_release_txt.py b/.github/workflows/get_release_txt.py
@@ -26,9 +26,9 @@
                     txt = txt[m.end():].strip()
             else:
                 txt = ""
-                    
-            # we now need to substitute characters in the string so that 
-            # the action can deal with line breaks 
+
+            # we now need to substitute characters in the string so that
+            # the action can deal with line breaks
             txt = txt.replace('%', '%25')
             txt = txt.replace('\n', '%0A')
             txt = txt.replace('\r', '%0D')

diff --git a/.github/workflows/good_defines.txt b/.github/workflows/good_defines.txt
@@ -3,6 +3,7 @@ AMREX_PARTICLES
 AMREX_SPACEDIM
 AMREX_USE_CUDA
 AMREX_USE_GPU
+AMREX_USE_HIP
 AMREX_USE_OMP
 AUX_THERMO
 BL_FORT_USE_LOWERCASE

diff --git a/.github/workflows/gpu_action.yml b/.github/workflows/gpu_action.yml
@@ -1,6 +1,11 @@
 name: GPU compilation
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   gpu-compilation:
     runs-on: ubuntu-latest
@@ -39,7 +44,7 @@ jobs:
           tar xfz v2.28.0.tar.gz
           cd hypre-2.28.0/src
           CUDA_HOME=/usr/local/cuda HYPRE_CUDA_SM=60 ./configure --with-cxxstandard=17 --with-cuda --enable-unified-memory --without-MPI
-          make -j 2
+          make -j 4
           make install
           cd ../../
 

diff --git a/.github/workflows/hip.yml b/.github/workflows/hip.yml
@@ -29,4 +29,4 @@ jobs:
       - name: compile flame_wave
         run: |
           cd Exec/science/flame_wave
-          make COMP=gnu USE_HIP=TRUE USE_MPI=FALSE USE_OMP=FALSE USE_CUDA=FALSE -j 2
+          make COMP=gnu USE_HIP=TRUE USE_MPI=FALSE USE_OMP=FALSE USE_CUDA=FALSE -j 4
diff --git a/.github/workflows/mhd-compare.yml b/.github/workflows/mhd-compare.yml
@@ -26,7 +26,7 @@ jobs:
       - name: Compile OrszagTang
         run: |
           cd Exec/mhd_tests/OrszagTang
-          make USE_MPI=TRUE -j 2
+          make USE_MPI=TRUE -j 4
 
       - name: Run OrszagTang-3d
         run: |
@@ -36,7 +36,7 @@ jobs:
       - name: Build the fextrema tool
         run: |
           cd external/amrex/Tools/Plotfile
-          make programs=fextrema -j 2
+          make programs=fextrema -j 4
 
       - name: Check the extrema
         run: |

diff --git a/.github/workflows/rad-compare.yml b/.github/workflows/rad-compare.yml
@@ -29,7 +29,7 @@ jobs:
           tar xfz v2.26.0.tar.gz
           cd hypre-2.26.0/src
           ./configure --with-cxxstandard=17
-          make -j 2
+          make -j 4
           make install
           cd ../../
 
@@ -47,7 +47,7 @@ jobs:
       - name: Build the fextrema tool
         run: |
           cd external/amrex/Tools/Plotfile
-          make programs=fextrema -j 2
+          make programs=fextrema -j 4
 
       - name: Check the extrema
         run: |

diff --git a/.github/workflows/reacting-convergence-true-sdc.yml b/.github/workflows/reacting-convergence-true-sdc.yml
@@ -26,7 +26,7 @@ jobs:
       - name: Compile reacting_convergence
         run: |
           cd Exec/reacting_tests/reacting_convergence
-          make DIM=2 USE_MPI=FALSE -j 2 USE_TRUE_SDC=TRUE
+          make DIM=2 USE_MPI=FALSE -j 4 USE_TRUE_SDC=TRUE
 
       - name: Run reacting_convergence
         run: |
@@ -36,7 +36,7 @@ jobs:
       - name: Build the fextrema tool
         run: |
           cd external/amrex/Tools/Plotfile
-          make programs=fextrema -j 2
+          make programs=fextrema -j 4
 
       - name: Check the extrema
         run: |

diff --git a/.github/workflows/style.yml b/.github/workflows/style.yml
@@ -0,0 +1,22 @@
+name: Style
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-style
+  cancel-in-progress: true
+
+jobs:
+  tabs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Tabs
+        run: .github/workflows/style/check_tabs.sh
+
+  trailing_whitespaces:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Trailing Whitespaces
+        run: .github/workflows/style/check_trailing_whitespaces.sh