Deploying to gh-pages from @ 4157d7a 🚀

.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: ba84d17926dce8878d80a0691be1baf6
+tags: 645f666f9bcd5a90fca523b33c5a78b7

.github/problem-matchers/gcc.json

@@ -0,0 +1,18 @@
+{
+     "__comment": "Taken from vscode-cpptools's Extension/package.json gcc rule",
+     "problemMatcher": [
+         {
+             "owner": "gcc-problem-matcher",
+             "pattern": [
+                 {
+                     "regexp": "^(.*):(\\d+):(\\d+):\\s+(?:fatal\\s+)?(warning|error):\\s+(.*)$",
+                     "file": 1,
+                     "line": 2,
+                     "column": 3,
+                     "severity": 4,
+                     "message": 5
+                 }
+             ]
+         }
+     ]
+} 

.github/problem-matchers/sphinx.json

@@ -0,0 +1,40 @@
+{
+     "problemMatcher": [
+         {
+             "owner": "sphinx-problem-matcher",
+             "pattern": [
+                 {
+                     "regexp": "^(.*):(\\d+):\\s+(\\w*):\\s+(.*)$",
+                     "file": 1,
+                     "line": 2,
+                     "severity": 3,
+                     "message": 4
+                 }
+             ]
+         },
+         {
+             "owner": "sphinx-problem-matcher-loose",
+             "pattern": [
+                 {
+                     "_comment": "A bit of a looser pattern, doesn't look for line numbers, just looks for file names relying on them to start with / and end with .rst",
+                     "regexp": "(\/.*\\.rst):\\s+(\\w*):\\s+(.*)$",
+                     "file": 1,
+                     "severity": 2,
+                     "message": 3
+                 }
+             ]
+         },
+         {
+             "owner": "sphinx-problem-matcher-loose-no-severity",
+             "pattern": [
+                 {
+                     "_comment": "Looks for file names ending with .rst and line numbers but without severity",
+                     "regexp": "^(.*\\.rst):(\\d+):(.*)$",
+                     "file": 1,
+                     "line": 2,
+                     "message": 3
+                 }
+             ]           
+         }
+     ]
+} 

.github/workflows/ci.yml

@@ -0,0 +1,189 @@
+name: PelePhysics
+on:
+   push:
+     branches: [development]
+   pull_request:
+     branches: [development]
+
+jobs:
+  Formatting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: DoozyX/[email protected]
+        with:
+          source: './Eos ./Transport ./Reactions ./Source ./Utility ./Testing ./Support/Fuego/Mechanism/Models'
+          exclude: '.'
+          extensions: 'H,h,cpp'
+          clangFormatVersion: 13
+
+  Pythia:
+    needs: Formatting
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.8]
+        poetry-version: [1.1.7]
+    defaults:
+      run:
+        working-directory: ${{github.workspace}}/Support/Fuego/Pythia
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{matrix.python-version}}
+      - name: Run image
+        uses: abatilo/[email protected]
+        with:
+          poetry-version: ${{matrix.poetry-version}}
+      - name: Install Dependencies using Poetry
+        run: poetry install
+      - name: Formatting with black
+        run: poetry run black --check .
+      - name: Sort imports with isort
+        run: poetry run isort --check-only --diff .
+      - name: Run tests
+        run: poetry run bash -c "cd ../Mechanism/Models/air && ./make-mechanism.sh"
+
+  Transport-EOS-Reactions:
+    needs: Formatting
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        comp: [gnu, llvm, cuda, hip, dpcpp]
+        include:
+          - comp: gnu
+            amrex_build_args: 'COMP=gnu'
+            dependency_cmds:
+          - comp: llvm
+            amrex_build_args: 'COMP=llvm'
+            dependency_cmds:
+          - comp: cuda
+            amrex_build_args: 'COMP=gnu USE_CUDA=TRUE'
+            dependency_cmds: '.github/workflows/dependencies/dependencies_cuda.sh'
+          - comp: hip
+            amrex_build_args: 'USE_HIP=TRUE AMD_ARCH=gfx908 LIBRARY_LOCATIONS=/opt/rocm/lib'
+            dependency_cmds: '.github/workflows/dependencies/dependencies_hip.sh'
+          - comp: dpcpp
+            amrex_build_args: 'USE_DPCPP=TRUE'
+            dependency_cmds: '.github/workflows/dependencies/dependencies_dpcpp.sh'
+    steps:
+      - name: Cancel previous runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{github.token}}
+      - name: Checkout PelePhysics
+        uses: actions/checkout@v2
+        with:
+          path: PelePhysics-${{matrix.comp}}
+      - name: Checkout AMReX
+        uses: actions/checkout@v2
+        with:
+          repository: AMReX-Codes/amrex
+          path: AMReX-${{matrix.comp}}
+      - name: Set Environment Variables
+        run: |
+          echo "AMREX_HOME=${{github.workspace}}/AMReX-${{matrix.comp}}" >> $GITHUB_ENV
+          echo "PELE_PHYSICS_HOME=${{github.workspace}}/PelePhysics-${{matrix.comp}}" >> $GITHUB_ENV
+          echo "TRANSPORT_WORKING_DIRECTORY=${{github.workspace}}/PelePhysics-${{matrix.comp}}/Testing/Exec/TranEval" >> $GITHUB_ENV
+          echo "EOS_WORKING_DIRECTORY=${{github.workspace}}/PelePhysics-${{matrix.comp}}/Testing/Exec/EosEval" >> $GITHUB_ENV
+          echo "REACT_WORKING_DIRECTORY=${{github.workspace}}/PelePhysics-${{matrix.comp}}/Testing/Exec/ReactEval" >> $GITHUB_ENV
+          echo "IGNDELAY_WORKING_DIRECTORY=${{github.workspace}}/PelePhysics-${{matrix.comp}}/Testing/Exec/IgnitionDelay" >> $GITHUB_ENV
+          echo "NPROCS=$(nproc)" >> $GITHUB_ENV
+          if [ "${{matrix.comp}}" == 'cuda' ]; then \
+            echo "CUDA_HOME=/usr/local/cuda-11.2" >> $GITHUB_ENV; \
+            echo "LD_LIBRARY_PATH=/usr/local/cuda-11.2/lib64:${LD_LIBRARY_PATH}" >> $GITHUB_ENV; \
+            echo "/usr/local/cuda-11.2/bin" >> $GITHUB_PATH; \
+          fi
+      - name: Dependencies
+        working-directory: ${{env.TRANSPORT_WORKING_DIRECTORY}}
+        run: |
+          if [ "${{matrix.comp}}" == 'cuda' ]; then \
+            ${{github.workspace}}/PelePhysics-${{matrix.comp}}/${{matrix.dependency_cmds}}; \
+            echo "CUDA_HOME=${CUDA_HOME}"; \
+            ls ${CUDA_HOME} > /dev/null; \
+            which nvcc || echo "nvcc not in PATH!"; \
+          fi
+          if [ "${{matrix.comp}}" == 'hip' ]; then \
+            ${{github.workspace}}/PelePhysics-${{matrix.comp}}/${{matrix.dependency_cmds}}; \
+            source /etc/profile.d/rocm.sh
+            which hipcc || echo "hipcc not in PATH!"; \
+          fi
+          if [ "${{matrix.comp}}" == 'dpcpp' ]; then \
+            ${{github.workspace}}/PelePhysics-${{matrix.comp}}/${{matrix.dependency_cmds}}; \
+            source /opt/intel/oneapi/setvars.sh || true
+            which dpcpp || echo "dpcpp not in PATH!"; \
+          fi
+          cmake --version
+          make TPL ${{matrix.amrex_build_args}};
+      - name: Test Transport
+        working-directory: ${{env.TRANSPORT_WORKING_DIRECTORY}}
+        run: |
+          echo "::add-matcher::${{github.workspace}}/PelePhysics-${{matrix.comp}}/.github/problem-matchers/gcc.json"
+          if [ "${{matrix.comp}}" == 'hip' ]; then source /etc/profile.d/rocm.sh; fi;
+          if [ "${{matrix.comp}}" == 'dpcpp' ]; then source /opt/intel/oneapi/setvars.sh || true; fi;
+          for TYPE in Constant Simple Sutherland; do \
+            printf "\n-------- ${TYPE} --------\n"; \
+            make -j ${{env.NPROCS}} Transport_Model=${TYPE} TINY_PROFILE=TRUE ${{matrix.amrex_build_args}}; \
+            if [ "${{matrix.comp}}" == 'gnu' ] || [ "${{matrix.comp}}" == 'llvm' ]; then \
+              ./Pele2d.${{matrix.comp}}.TPROF.ex inputs.2d_${TYPE}; \
+            fi; \
+            make realclean; \
+            if [ $? -ne 0 ]; then exit 1; fi; \
+          done
+      - name: Test EOS
+        working-directory: ${{env.EOS_WORKING_DIRECTORY}}
+        run: |
+          echo "::add-matcher::${{github.workspace}}/PelePhysics-${{matrix.comp}}/.github/problem-matchers/gcc.json"
+          if [ "${{matrix.comp}}" == 'hip' ]; then source /etc/profile.d/rocm.sh; fi;
+          if [ "${{matrix.comp}}" == 'dpcpp' ]; then source /opt/intel/oneapi/setvars.sh || true; fi;
+          for TYPE in Fuego GammaLaw; do \
+            if [ "${TYPE}" == 'Fuego' ]; then CHEMISTRY=LiDryer; else CHEMISTRY=Null; fi; \
+            printf "\n-------- ${TYPE} --------\n"; \
+            make -j ${{env.NPROCS}} Eos_Model=${TYPE} Chemistry_Model=${CHEMISTRY} TINY_PROFILE=TRUE ${{matrix.amrex_build_args}}; \
+            if [ "${{matrix.comp}}" == 'gnu' ] || [ "${{matrix.comp}}" == 'llvm' ]; then \
+              ./Pele2d.${{matrix.comp}}.TPROF.ex inputs.2d; \
+            fi; \
+            make realclean; \
+            if [ $? -ne 0 ]; then exit 1; fi; \
+          done
+      - name: Test Reactions
+        working-directory: ${{env.REACT_WORKING_DIRECTORY}}
+        run: |
+          echo "::add-matcher::${{github.workspace}}/PelePhysics-${{matrix.comp}}/.github/problem-matchers/gcc.json"
+          if [ "${{matrix.comp}}" == 'hip' ]; then source /etc/profile.d/rocm.sh; fi;
+          if [ "${{matrix.comp}}" == 'dpcpp' ]; then source /opt/intel/oneapi/setvars.sh || true; fi;
+          make -j ${{env.NPROCS}} Eos_Model=Fuego Chemistry_Model=drm19 TINY_PROFILE=TRUE ${{matrix.amrex_build_args}}
+          if [ "${{matrix.comp}}" == 'gnu' ] || [ "${{matrix.comp}}" == 'llvm' ]; then \
+            for TYPE in Cvode Arkode RK64; do \
+              printf "\n-------- ${TYPE} --------\n"; \
+              ./Pele3d.${{matrix.comp}}.TPROF.ex inputs.3d_Array4 ode.dt=1.e-05 ode.ndt=100 chem_integrator="Reactor${TYPE}"; \
+              ./Pele3d.${{matrix.comp}}.TPROF.ex inputs.3d_1dArray ode.dt=1.e-05 ode.ndt=100 chem_integrator="Reactor${TYPE}"; \
+              if [ $? -ne 0 ]; then exit 1; fi; \
+            done \
+          fi;
+          make realclean
+          make -j ${{env.NPROCS}} Eos_Model=Fuego Chemistry_Model=LiDryer TINY_PROFILE=TRUE ${{matrix.amrex_build_args}}
+          if [ "${{matrix.comp}}" == 'gnu' ] || [ "${{matrix.comp}}" == 'llvm' ]; then \
+            for TYPE in Cvode Arkode RK64; do \
+              printf "\n-------- ${TYPE} --------\n"; \
+               ./Pele3d.${{matrix.comp}}.TPROF.ex inputs.3d_Array4 ode.dt=1.e-05 ode.ndt=100 chem_integrator="Reactor${TYPE}"; \
+               ./Pele3d.${{matrix.comp}}.TPROF.ex inputs.3d_1dArray ode.dt=1.e-05 ode.ndt=100 chem_integrator="Reactor${TYPE}"; \
+              if [ $? -ne 0 ]; then exit 1; fi; \
+            done \
+          fi
+          make realclean
+      - name: Test Ignition delay
+        working-directory: ${{env.IGNDELAY_WORKING_DIRECTORY}}
+        run: |
+          echo "::add-matcher::${{github.workspace}}/PelePhysics-${{matrix.comp}}/.github/problem-matchers/gcc.json"
+          if [ "${{matrix.comp}}" == 'gnu' ] || [ "${{matrix.comp}}" == 'llvm' ]; then \
+              python -m pip install --upgrade pip
+              pip install numpy
+              make -j ${{env.NPROCS}} Eos_Model=Fuego Chemistry_Model=dodecane_lu TINY_PROFILE=TRUE ${{matrix.amrex_build_args}}
+              bash exec_ignDelay.sh
+              python check_ignDelay.py
+              if [ $? -ne 0 ]; then exit 1; fi; \
+          fi;
+          make realclean

.github/workflows/dependencies/dependencies_cuda.sh

@@ -0,0 +1,35 @@
+#!/usr/bin/env bash
+#
+# Copyright 2020 Axel Huebl
+#
+# License: BSD-3-Clause-LBNL
+
+# search recursive inside a folder if a file contains tabs
+#
+# @result 0 if no files are found, else 1
+#
+
+set -eu -o pipefail
+
+CUDA_VERSION=11-2
+
+sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub
+echo "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64 /" \
+    | sudo tee /etc/apt/sources.list.d/cuda.list
+sudo apt-get update
+sudo apt-get install -y \
+    cuda-command-line-tools-${CUDA_VERSION} \
+    cuda-compiler-${CUDA_VERSION}           \
+    cuda-cupti-dev-${CUDA_VERSION}          \
+    cuda-minimal-build-${CUDA_VERSION}      \
+    cuda-nvml-dev-${CUDA_VERSION}           \
+    cuda-nvtx-${CUDA_VERSION}               \
+    libcurand-dev-${CUDA_VERSION}           \
+    libcusolver-dev-${CUDA_VERSION}         \
+    libcusparse-dev-${CUDA_VERSION}         \
+    libcublas-dev-${CUDA_VERSION}           \
+    libcurand-dev-${CUDA_VERSION}
+
+export PATH=/usr/local/cuda-11.2/bin:${PATH}
+which nvcc
+nvcc --version

.github/workflows/dependencies/dependencies_dpcpp.sh

@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+#
+# Copyright 2020 The AMReX Community
+#
+# License: BSD-3-Clause-LBNL
+# Authors: Axel Huebl
+
+set -eu -o pipefail
+
+sudo wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
+sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
+echo "deb https://apt.repos.intel.com/oneapi all main" \
+  | sudo tee /etc/apt/sources.list.d/oneAPI.list
+
+sudo apt-get update
+sudo apt-get install -y \
+    intel-oneapi-dpcpp-cpp-compiler \
+    intel-oneapi-mkl-devel

.github/workflows/dependencies/dependencies_hip.sh

@@ -0,0 +1,36 @@
+#!/usr/bin/env bash
+#
+# 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
+
+sudo wget http://repo.radeon.com/rocm/rocm.gpg.key
+sudo apt-key add rocm.gpg.key
+echo 'deb [arch=amd64] http://repo.radeon.com/rocm/apt/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
+
+sudo apt-get update
+sudo apt-get install -y \
+    rocm-dev        \
+    roctracer-dev   \
+    rocprofiler-dev \
+    rocrand-dev     \
+    rocprim-dev     \
+    rocm-libs
+
+source /etc/profile.d/rocm.sh
+which hipcc
+which clang
+which clang++
+which flang
+hipcc --version

.github/workflows/docs.yml

@@ -0,0 +1,48 @@
+name: PelePhysics-Docs
+
+on:
+  push:
+    branches: [development]
+    paths:
+       - 'Docs/**'
+       - 'README.md'
+       - '.github/workflows/docs.yml'
+  pull_request:
+    branches: [development]
+    paths:
+       - 'Docs/**'
+       - 'README.md'
+       - '.github/workflows/docs.yml'
+
+jobs:
+  Docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.x'
+      - name: Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install sphinx sphinx_rtd_theme
+      - name: Configure
+        run: cmake -B${{runner.workspace}}/build-docs ${{github.workspace}}/Docs
+      - name: Build
+        working-directory: ${{runner.workspace}}/build-docs
+        run:  |
+           echo "::add-matcher::.github/problem-matchers/sphinx.json"
+           cmake --build ${{runner.workspace}}/build-docs
+           echo "::remove-matcher owner=sphinx-problem-matcher-loose-no-severity::"
+           echo "::remove-matcher owner=sphinx-problem-matcher-loose::"
+           echo "::remove-matcher owner=sphinx-problem-matcher::"
+           touch ${{runner.workspace}}/build-docs/sphinx/html/.nojekyll
+      - name: Deploy
+        if: github.event_name == 'push' && github.ref == 'refs/heads/development'
+        uses: JamesIves/github-pages-deploy-action@releases/v3
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          BRANCH: gh-pages
+          FOLDER: ${{runner.workspace}}/build-docs/sphinx/html
+          SINGLE_COMMIT: true