Update isooctane_lu mechanism to allow it to be generated (#431) #1038
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| name: PelePhysics-CI | |
| on: | |
| push: | |
| branches: [development] | |
| pull_request: | |
| branches: [development] | |
| concurrency: | |
| group: ${{github.ref}}-${{github.head_ref}}-ci | |
| cancel-in-progress: true | |
| jobs: | |
| Formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Clone | |
| uses: actions/checkout@v3 | |
| - name: Check formatting | |
| uses: DoozyX/[email protected] | |
| with: | |
| source: './Eos ./Transport ./Reactions ./Source ./Utility ./Testing ./Support/Mechanism/Models' | |
| exclude: '.' | |
| extensions: 'H,h,cpp' | |
| clangFormatVersion: 16 | |
| Codespell: | |
| needs: Formatting | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Clone | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: false | |
| - name: Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - name: Dependencies | |
| run: | | |
| # Install Python packages | |
| python -m pip install --upgrade pip | |
| pip install codespell | |
| - name: Run codespell | |
| run: codespell | |
| CEPTR: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ['3.10'] | |
| poetry-version: ['1.4.2'] | |
| defaults: | |
| run: | |
| working-directory: ${{github.workspace}}/Support/ceptr | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| 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: Lint with flake8 | |
| run: poetry run flake8 . | |
| - name: Run tests | |
| run: poetry run pytest | |
| - name: Convert air mechanism | |
| run: poetry run convert -f ${{github.workspace}}/Support/Mechanism/Models/air/mechanism.yaml | |
| - name: Convert LiDryer mechanism | |
| run: poetry run convert -f ${{github.workspace}}/Support/Mechanism/Models/LiDryer/mechanism.yaml | |
| Transport-EOS-Reactions: | |
| needs: Formatting | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| matrix: | |
| comp: [gnu, llvm, cuda, hip, sycl] | |
| python-version: ['3.10'] | |
| poetry-version: ['1.4.2'] | |
| 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=gfx90a LIBRARY_LOCATIONS=/opt/rocm/lib' | |
| dependency_cmds: '.github/workflows/dependencies/dependencies_hip.sh' | |
| - comp: sycl | |
| amrex_build_args: 'USE_SYCL=TRUE' | |
| dependency_cmds: '.github/workflows/dependencies/dependencies_dpcpp.sh' | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{matrix.python-version}} | |
| - name: Run image | |
| uses: abatilo/[email protected] | |
| with: | |
| poetry-version: ${{matrix.poetry-version}} | |
| - name: Clone PelePhysics | |
| uses: actions/checkout@v3 | |
| with: | |
| path: PelePhysics-${{matrix.comp}} | |
| - name: Clone SUNDIALS | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: LLNL/sundials | |
| ref: 'v6.6.1' | |
| path: sundials-${{matrix.comp}} | |
| - name: Clone AMReX | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: AMReX-Codes/amrex | |
| path: AMReX-${{matrix.comp}} | |
| - name: Set Environment Variables | |
| run: | | |
| echo "AMREX_HOME=${{github.workspace}}/AMReX-${{matrix.comp}}" >> $GITHUB_ENV | |
| echo "SUNDIALS_HOME=${{github.workspace}}/sundials-${{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" >> $GITHUB_ENV | |
| echo "JAC_WORKING_DIRECTORY=${{github.workspace}}/PelePhysics-${{matrix.comp}}/Testing/Exec/Jacobian" >> $GITHUB_ENV | |
| echo "NPROCS=$(nproc)" >> $GITHUB_ENV | |
| echo "CCACHE_COMPRESS=1" >> $GITHUB_ENV | |
| echo "CCACHE_COMPRESSLEVEL=5" >> $GITHUB_ENV | |
| echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV | |
| echo "CCACHE_MAXSIZE=1G" >> $GITHUB_ENV | |
| if [ "${{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" >> $GITHUB_PATH; \ | |
| fi | |
| - name: Install Ccache | |
| run: | | |
| wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz | |
| tar xvf ccache-4.8-linux-x86_64.tar.xz | |
| sudo cp -f ccache-4.8-linux-x86_64/ccache /usr/local/bin/ | |
| - name: Set Up Ccache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/ccache | |
| key: ccache-${{github.workflow}}-${{github.job}}-${{matrix.comp}}-git-${{github.sha}} | |
| restore-keys: | | |
| ccache-${{github.workflow}}-${{github.job}}-${{matrix.comp}}-git- | |
| - 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}}" == 'sycl' ]; then \ | |
| ${{github.workspace}}/PelePhysics-${{matrix.comp}}/${{matrix.dependency_cmds}}; \ | |
| source /opt/intel/oneapi/setvars.sh || true | |
| which icpx || echo "icpx not in PATH!"; \ | |
| fi | |
| cmake --version | |
| make TPL ${{matrix.amrex_build_args}}; | |
| if [ "${{matrix.comp}}" == 'gnu' ] || [ "${{matrix.comp}}" == 'llvm' ]; then \ | |
| make TPL DEBUG=TRUE TINY_PROFILE=TRUE ${{matrix.amrex_build_args}}; | |
| cd ${{github.workspace}}/PelePhysics-${{matrix.comp}}/Support/ceptr | |
| poetry install | |
| fi | |
| - 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}}" == 'sycl' ]; then source /opt/intel/oneapi/setvars.sh || true; fi; | |
| ccache -z | |
| for TYPE in Constant Simple Sutherland; do \ | |
| printf "\n-------- ${TYPE} --------\n"; \ | |
| make -j ${{env.NPROCS}} Transport_Model=${TYPE} TINY_PROFILE=TRUE USE_CCACHE=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: Transport ccache report | |
| working-directory: ${{env.TRANSPORT_WORKING_DIRECTORY}} | |
| run: | | |
| ccache -s | |
| du -hs ${HOME}/.cache/ccache | |
| - 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 [ "${{matrix.comp}}" == 'sycl' ]; then source /opt/intel/oneapi/setvars.sh || true; fi; | |
| ccache -z | |
| for TYPE in Fuego GammaLaw Soave-Redlich-Kwong; do \ | |
| if [ "${TYPE}" == 'Fuego' ] || [ "${TYPE}" == 'Soave-Redlich-Kwong' ]; then CHEMISTRY=LiDryer; else CHEMISTRY=Null; fi; \ | |
| if [ "${TYPE}" == 'Soave-Redlich-Kwong' ]; then TRANSPORT=Simple; else TRANSPORT=Constant; fi; \ | |
| printf "\n-------- ${TYPE} --------\n"; \ | |
| make -j ${{env.NPROCS}} Eos_Model=${TYPE} Chemistry_Model=${CHEMISTRY} Transport_Model=${TRANSPORT} TINY_PROFILE=TRUE USE_CCACHE=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: EOS ccache report | |
| working-directory: ${{env.EOS_WORKING_DIRECTORY}} | |
| run: | | |
| ccache -s | |
| du -hs ${HOME}/.cache/ccache | |
| - name: Test Integration | |
| 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}}" == 'sycl' ]; then source /opt/intel/oneapi/setvars.sh || true; fi; | |
| ccache -z | |
| make -j ${{env.NPROCS}} Eos_Model=Fuego Chemistry_Model=drm19 TINY_PROFILE=TRUE USE_CCACHE=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 USE_CCACHE=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 fuel_name=H2 ode.dt=1.e-05 ode.ndt=100 chem_integrator="Reactor${TYPE}"; \ | |
| ./Pele3d.${{matrix.comp}}.TPROF.ex inputs.3d_1dArray fuel_name=H2 ode.dt=1.e-05 ode.ndt=100 chem_integrator="Reactor${TYPE}"; \ | |
| if [ $? -ne 0 ]; then exit 1; fi; \ | |
| done \ | |
| fi | |
| make realclean | |
| - name: Integration ccache report | |
| working-directory: ${{env.REACT_WORKING_DIRECTORY}} | |
| run: | | |
| ccache -s | |
| du -hs ${HOME}/.cache/ccache | |
| - 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 | |
| ccache -z | |
| make -j ${{env.NPROCS}} Eos_Model=Fuego Chemistry_Model=dodecane_lu TINY_PROFILE=TRUE USE_CCACHE=TRUE ${{matrix.amrex_build_args}} | |
| bash exec_ignDelay.sh | |
| python check_ignDelay.py | |
| if [ $? -ne 0 ]; then exit 1; fi; \ | |
| fi; | |
| make realclean | |
| - name: Ignition delay ccache report | |
| working-directory: ${{env.IGNDELAY_WORKING_DIRECTORY}} | |
| run: | | |
| ccache -s | |
| du -hs ${HOME}/.cache/ccache | |
| - name: Test Jacobian | |
| working-directory: ${{env.JAC_WORKING_DIRECTORY}} | |
| run: | | |
| echo "::add-matcher::${{github.workspace}}/PelePhysics-${{matrix.comp}}/.github/problem-matchers/gcc.json" | |
| if [ "${{matrix.comp}}" == 'gnu' ] || [ "${{matrix.comp}}" == 'llvm' ]; then \ | |
| ccache -z | |
| cd ${{github.workspace}}/PelePhysics-${{matrix.comp}}/Support/ceptr | |
| poetry run qssa -f ${{github.workspace}}/PelePhysics-${{matrix.comp}}/Support/Mechanism/Models/dodecane_lu_qss/skeletal.yaml -n ${{github.workspace}}/Support/Mechanism/Models/dodecane_lu_qss/non_qssa_list.yaml | |
| poetry run convert -f ${{github.workspace}}/PelePhysics-${{matrix.comp}}/Support/Mechanism/Models/dodecane_lu_qss/qssa.yaml --qss_format_input ${{github.workspace}}/PelePhysics-${{matrix.comp}}/Support/Mechanism/Models/dodecane_lu_qss/qssa_input_non_optimized.toml --qss_symbolic_jacobian | |
| cd ${{env.JAC_WORKING_DIRECTORY}} | |
| make -j ${{env.NPROCS}} Eos_Model=Fuego Chemistry_Model=dodecane_lu_qss DEBUG=TRUE TINY_PROFILE=TRUE USE_CCACHE=TRUE ${{matrix.amrex_build_args}} | |
| ./Pele3d.${{matrix.comp}}.DEBUG.TPROF.ex; \ | |
| if [ $? -ne 0 ]; then exit 1; fi; \ | |
| fi; | |
| make realclean | |
| - name: Jacobian ccache report | |
| working-directory: ${{env.JAC_WORKING_DIRECTORY}} | |
| run: | | |
| ccache -s | |
| du -hs ${HOME}/.cache/ccache |