Merge branch 'development' into add_subch_base_input

zhichen3 · Feb 4, 2024 · 3cc04bd · 3cc04bd
2 parents 6e9fe26 + cff7393
commit 3cc04bd
Show file tree

Hide file tree

Showing 135 changed files with 138,034 additions and 51,624 deletions.
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
@@ -6,7 +6,7 @@ jobs:
   cpp-linter:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -30,7 +30,7 @@ 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 ../../
 
@@ -56,7 +56,7 @@ jobs:
           -run-linter
 
       - name: Archive clang tidy report
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: clang-tidy-report
           path: clang-tidy-report.txt
diff --git a/.github/workflows/check-ifdefs.yml b/.github/workflows/check-ifdefs.yml
@@ -14,23 +14,14 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
-
-      - name: Cache pip
-        uses: actions/cache@v3
-        with:
-          # this path is specific to Ubuntu
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
+          python-version: '3.11'
 
       - name: Run check-ifdefs
         run: |

diff --git a/.github/workflows/check-makefiles.yml b/.github/workflows/check-makefiles.yml
@@ -19,18 +19,9 @@ jobs:
           fetch-depth: 0
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
-
-      - name: Cache pip
-        uses: actions/cache@v3
-        with:
-          # this path is specific to Ubuntu
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
+          python-version: '3.11'
 
       - name: Run check-ifdefs
         run: |

diff --git a/.github/workflows/check-params.yml b/.github/workflows/check-params.yml
@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -28,19 +28,10 @@ jobs:
           cd ../..
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 
-      - name: Cache pip
-        uses: actions/cache@v3
-        with:
-          # this path is specific to Ubuntu
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-
       - name: Run check-params
         run: |
           PYTHONPATH=external/Microphysics/util/build_scripts python .github/workflows/check_params.py .
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -14,23 +14,15 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.10'
-
-      - name: Cache pip
-        uses: actions/cache@v3
-        with:
-          # this path is specific to Ubuntu
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
+          cache: "pip"
 
       - name: Install dependencies
         run: pip install -r ./requirements.txt

diff --git a/.github/workflows/compiler-warnings.yml b/.github/workflows/compiler-warnings.yml
@@ -5,7 +5,7 @@ jobs:
   compiler_warnings:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -26,14 +26,14 @@ 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/create_release.yml b/.github/workflows/create_release.yml
@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Get the version
         id: get_version
@@ -33,4 +33,4 @@ jobs:
           release_name: Release ${{ github.ref }}
           body: ${{ env.RELEASE_TXT }}
           draft: false
-          prerelease: false
+          prerelease: false
diff --git a/.github/workflows/dependencies_hip.sh b/.github/workflows/dependencies_hip.sh
@@ -1,17 +1,26 @@
 #!/usr/bin/env bash
 #
-# Copyright 2020-2022 The AMReX Community
+# Copyright 2020 The AMReX Community
 #
 # License: BSD-3-Clause-LBNL
 # Authors: Axel Huebl
 
+# search recursive inside a folder if a file contains tabs
+#
+# @result 0 if no files are found, else 1
+#
+
 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
 
 # Ref.: https://rocmdocs.amd.com/en/latest/Installation_Guide/Installation-Guide.html#ubuntu
 curl -O https://repo.radeon.com/rocm/rocm.gpg.key
 sudo apt-key add rocm.gpg.key
-echo 'deb [arch=amd64] https://repo.radeon.com/rocm/apt/debian/ ubuntu main' \
+echo "deb [arch=amd64] https://repo.radeon.com/rocm/apt/${1-debian}/ ubuntu main" \
   | sudo tee /etc/apt/sources.list.d/rocm.list
 echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' \
   | sudo tee -a /etc/profile.d/rocm.sh
@@ -34,12 +43,14 @@ sudo apt-get install -y --no-install-recommends \
     roctracer-dev   \
     rocprofiler-dev \
     rocrand-dev     \
-    rocprim-dev
+    rocprim-dev     \
+    hiprand-dev
 
 # activate
 #
 source /etc/profile.d/rocm.sh
 hipcc --version
+hipconfig --full
 which clang
 which clang++
 which flang
diff --git a/.github/workflows/detonation-sdc-compare.yml b/.github/workflows/detonation-sdc-compare.yml
@@ -5,7 +5,7 @@ jobs:
   detonation-sdc:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -26,7 +26,7 @@ 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 +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/docs-test.yml b/.github/workflows/docs-test.yml
@@ -14,26 +14,18 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Install pandoc and doxygen
         run: |
           sudo apt install pandoc doxygen
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
-
-      - name: Cache pip
-        uses: actions/cache@v3
-        with:
-          # this path is specific to Ubuntu
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
+          python-version: '3.11'
+          cache: "pip"
 
       - name: Install dependencies
         run: pip install -r ./requirements.txt

diff --git a/.github/workflows/exact_riemann.yml b/.github/workflows/exact_riemann.yml
@@ -5,7 +5,7 @@ jobs:
   exact_riemann:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

diff --git a/.github/workflows/flame_wave-compare.yml b/.github/workflows/flame_wave-compare.yml
@@ -5,7 +5,7 @@ jobs:
   flame_wave-2d:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yml
@@ -10,35 +10,24 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Install pandoc and doxygen
         run: |
           sudo apt update
           sudo apt install pandoc doxygen
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: '3.11'
+          cache: "pip"
 
       - name: Upgrade pip
         run: |
           # install pip=>20.1 to use "pip cache dir"
           python3 -m pip install --upgrade pip
 
-      - name: Get pip cache dir
-        id: pip-cache
-        run: echo "::set-output name=dir::$(pip cache dir)"
-
-      - name: Cache dependencies
-        uses: actions/cache@v3
-        with:
-          path: ${{ steps.pip-cache.outputs.dir }}
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-
       - name: Install dependencies
         run: python3 -m pip install -r ./requirements.txt
 
@@ -48,7 +37,7 @@ jobs:
           GITHUB_BRANCH: 'main'
         run: ./deploy_docs_action.sh
 
-      - name: Build docs 
+      - name: Build docs
         if: ${{ endsWith(github.ref, 'development') }}
         env:
           GITHUB_BRANCH: 'development'
@@ -59,4 +48,4 @@ jobs:
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./out
-          keep_files: true
+          keep_files: true
diff --git a/.github/workflows/gpu_action.yml b/.github/workflows/gpu_action.yml
@@ -5,7 +5,7 @@ jobs:
   gpu-compilation:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -39,7 +39,7 @@ 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
@@ -10,7 +10,7 @@ jobs:
   hip-compile:
     runs-on: ubuntu-20.04
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -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