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# 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 |
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{ | ||
"__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+(.*)$", | ||
"file": 1, | ||
"line": 2, | ||
"column": 3, | ||
"severity": 4, | ||
"message": 5 | ||
} | ||
] | ||
} | ||
] | ||
} |
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{ | ||
"problemMatcher": [ | ||
{ | ||
"owner": "sphinx-problem-matcher", | ||
"pattern": [ | ||
{ | ||
"regexp": "^(.*):(\\d+):\\s+(\\w*):\\s+(.*)$", | ||
"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 | ||
} | ||
] | ||
} | ||
] | ||
} |
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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 [ $? -ne 0 ]; then exit 1; fi; \ | ||
fi; | ||
make realclean |
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#!/usr/bin/env bash | ||
# | ||
# Copyright 2020 Axel Huebl | ||
# | ||
# License: BSD-3-Clause-LBNL | ||
|
||
# search recursive inside a folder if a file contains tabs | ||
# | ||
# @result 0 if no files are found, else 1 | ||
# | ||
|
||
set -eu -o pipefail | ||
|
||
CUDA_VERSION=11-2 | ||
|
||
sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub | ||
echo "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64 /" \ | ||
| sudo tee /etc/apt/sources.list.d/cuda.list | ||
sudo apt-get update | ||
sudo apt-get install -y \ | ||
cuda-command-line-tools-${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:${PATH} | ||
which nvcc | ||
nvcc --version |
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#!/usr/bin/env bash | ||
# | ||
# Copyright 2020 The AMReX Community | ||
# | ||
# License: BSD-3-Clause-LBNL | ||
# Authors: Axel Huebl | ||
|
||
set -eu -o pipefail | ||
|
||
sudo wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB | ||
sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB | ||
echo "deb https://apt.repos.intel.com/oneapi all main" \ | ||
| sudo tee /etc/apt/sources.list.d/oneAPI.list | ||
|
||
sudo apt-get update | ||
sudo apt-get install -y \ | ||
intel-oneapi-dpcpp-cpp-compiler \ | ||
intel-oneapi-mkl-devel |
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#!/usr/bin/env bash | ||
# | ||
# Copyright 2020 The AMReX Community | ||
# | ||
# License: BSD-3-Clause-LBNL | ||
# Authors: Axel Huebl | ||
|
||
# search recursive inside a folder if a file contains tabs | ||
# | ||
# @result 0 if no files are found, else 1 | ||
# | ||
|
||
set -eu -o pipefail | ||
|
||
sudo wget http://repo.radeon.com/rocm/rocm.gpg.key | ||
sudo apt-key add rocm.gpg.key | ||
echo 'deb [arch=amd64] http://repo.radeon.com/rocm/apt/debian/ ubuntu main' \ | ||
| sudo tee /etc/apt/sources.list.d/rocm.list | ||
echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$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 |
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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 |
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