From 0e5a4f6ac32d33c7e12ee36d5ca0a9751087765e Mon Sep 17 00:00:00 2001 From: Jon Rood Date: Thu, 14 Sep 2023 15:42:24 -0600 Subject: [PATCH] Updates. --- .github/workflows/ci.yml | 2 +- .../{old => }/convergenceTesting.yml | 0 .github/workflows/{old => }/cuda.yml | 0 .../{old => }/dependencies/dependencies.sh | 0 .../dependencies/dependencies_clang6.sh | 0 .../dependencies/dependencies_dpcpp.sh | 0 .../dependencies/dependencies_gcc10.sh | 0 .../dependencies/dependencies_hip.sh | 0 .../dependencies/dependencies_mac.sh | 0 .../dependencies/dependencies_nofortran.sh | 0 .../dependencies/dependencies_nvcc.sh | 0 .github/workflows/docs.yml | 12 ++-- .github/workflows/{old => }/hip.yml | 0 .github/workflows/{old => }/intel.yml | 0 .github/workflows/{old => }/linux.yml | 0 .github/workflows/{old => }/nightlyTest.yml | 0 .github/workflows/old/codeql.yml | 61 ------------------- .github/workflows/old/docs.yml | 51 ---------------- .github/workflows/{old => }/style.yml | 0 .../workflows/{old => }/style/check_tabs.sh | 0 .../style/check_trailing_whitespaces.sh | 0 .github/workflows/{old => }/unitTest.yml | 0 CMake/SetAmrexOptions.cmake | 2 +- CMakeLists.txt | 3 +- Exec/Cases/ChallengeProblem/GNUmakefile | 1 - Exec/Cases/CounterFlow/GNUmakefile | 1 - Exec/Cases/CounterFlowSpray/GNUmakefile | 1 - Exec/Cases/DiffBunsen2D/GNUmakefile | 1 - Exec/Cases/JetInCrossflow/GNUmakefile | 1 - Exec/Cases/NormalJet_OpenDomain/GNUmakefile | 1 - Exec/Cases/PremBunsen2D/GNUmakefile | 1 - Exec/Cases/PremBunsen3D/GNUmakefile | 1 - .../SwirlFlowWallInteractions/GNUmakefile | 1 - Exec/Cases/TripleFlame/GNUmakefile | 1 - Exec/Efield/FlameSheetIons/GNUmakefile | 1 - Exec/Efield/IonizedAirWave/GNUmakefile | 1 - Exec/Efield/PremBunsen3DKuhl/GNUmakefile | 1 - .../RegTests/EB_BackwardStepFlame/GNUmakefile | 1 - Exec/RegTests/EB_EnclosedFlame/GNUmakefile | 1 - Exec/RegTests/EB_EnclosedVortex/GNUmakefile | 1 - Exec/RegTests/EB_FlowPastCylinder/GNUmakefile | 1 - Exec/RegTests/EB_PipeFlow/GNUmakefile | 1 - Exec/RegTests/EnclosedFlame/GNUmakefile | 1 - Exec/RegTests/EnclosedInjection/GNUmakefile | 1 - Exec/RegTests/FlameSheet/CMakeLists.txt | 1 - Exec/RegTests/FlameSheet/GNUmakefile | 1 - Exec/RegTests/HITDecay/GNUmakefile | 1 - Exec/RegTests/HotBubble/GNUmakefile | 1 - Exec/RegTests/PeriodicCases/GNUmakefile | 1 - Exec/RegTests/SprayTest/GNUmakefile | 1 - Exec/RegTests/TaylorGreen/GNUmakefile | 1 - Exec/RegTests/TripleFlame/GNUmakefile | 1 - Exec/RegTests/TurbInflow/GNUmakefile | 1 - .../TurbInflow/TurbFileHIT/GNUmakefile | 1 - Exec/RegTests/Unit/GNUmakefile | 1 - Exec/UnitTests/DodecaneLu/GNUmakefile | 1 - Exec/UnitTests/EB_SphericalFlame/GNUmakefile | 1 - Source/main.cpp | 18 ++++++ Tests/CMakeLists.txt | 2 +- 59 files changed, 30 insertions(+), 154 deletions(-) rename .github/workflows/{old => }/convergenceTesting.yml (100%) rename .github/workflows/{old => }/cuda.yml (100%) rename .github/workflows/{old => }/dependencies/dependencies.sh (100%) rename .github/workflows/{old => }/dependencies/dependencies_clang6.sh (100%) rename .github/workflows/{old => }/dependencies/dependencies_dpcpp.sh (100%) rename .github/workflows/{old => }/dependencies/dependencies_gcc10.sh (100%) rename .github/workflows/{old => }/dependencies/dependencies_hip.sh (100%) rename .github/workflows/{old => }/dependencies/dependencies_mac.sh (100%) rename .github/workflows/{old => }/dependencies/dependencies_nofortran.sh (100%) rename .github/workflows/{old => }/dependencies/dependencies_nvcc.sh (100%) rename .github/workflows/{old => }/hip.yml (100%) rename .github/workflows/{old => }/intel.yml (100%) rename .github/workflows/{old => }/linux.yml (100%) rename .github/workflows/{old => }/nightlyTest.yml (100%) delete mode 100644 .github/workflows/old/codeql.yml delete mode 100644 .github/workflows/old/docs.yml rename .github/workflows/{old => }/style.yml (100%) rename .github/workflows/{old => }/style/check_tabs.sh (100%) rename .github/workflows/{old => }/style/check_trailing_whitespaces.sh (100%) rename .github/workflows/{old => }/unitTest.yml (100%) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7aa05c7d..6145b6d7 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -69,7 +69,7 @@ jobs: du -hs ${HOME}/.cache/ccache - name: FlameSheet debug test working-directory: ./Exec/RegTests/FlameSheet - run: ./PeleLMeX3d.gnu.DEBUG.ex flamesheet-drm19.inp max_step=2 amr.plot_files_output=0 amr.checkpoint_files_output=0 + run: ./PeleLMeX3d.gnu.DEBUG.ex flamesheet-drm19.inp amr.max_step=1 amr.plot_int=-1 amr.check_int=-1 - name: FlameSheet debug report working-directory: ./Exec/RegTests/FlameSheet run: | diff --git a/.github/workflows/old/convergenceTesting.yml b/.github/workflows/convergenceTesting.yml similarity index 100% rename from .github/workflows/old/convergenceTesting.yml rename to .github/workflows/convergenceTesting.yml diff --git a/.github/workflows/old/cuda.yml b/.github/workflows/cuda.yml similarity index 100% rename from .github/workflows/old/cuda.yml rename to .github/workflows/cuda.yml diff --git a/.github/workflows/old/dependencies/dependencies.sh b/.github/workflows/dependencies/dependencies.sh similarity index 100% rename from .github/workflows/old/dependencies/dependencies.sh rename to .github/workflows/dependencies/dependencies.sh diff --git a/.github/workflows/old/dependencies/dependencies_clang6.sh b/.github/workflows/dependencies/dependencies_clang6.sh similarity index 100% rename from .github/workflows/old/dependencies/dependencies_clang6.sh rename to .github/workflows/dependencies/dependencies_clang6.sh diff --git a/.github/workflows/old/dependencies/dependencies_dpcpp.sh b/.github/workflows/dependencies/dependencies_dpcpp.sh similarity index 100% rename from .github/workflows/old/dependencies/dependencies_dpcpp.sh rename to .github/workflows/dependencies/dependencies_dpcpp.sh diff --git a/.github/workflows/old/dependencies/dependencies_gcc10.sh b/.github/workflows/dependencies/dependencies_gcc10.sh similarity index 100% rename from .github/workflows/old/dependencies/dependencies_gcc10.sh rename to .github/workflows/dependencies/dependencies_gcc10.sh diff --git a/.github/workflows/old/dependencies/dependencies_hip.sh b/.github/workflows/dependencies/dependencies_hip.sh similarity index 100% rename from .github/workflows/old/dependencies/dependencies_hip.sh rename to .github/workflows/dependencies/dependencies_hip.sh diff --git a/.github/workflows/old/dependencies/dependencies_mac.sh b/.github/workflows/dependencies/dependencies_mac.sh similarity index 100% rename from .github/workflows/old/dependencies/dependencies_mac.sh rename to .github/workflows/dependencies/dependencies_mac.sh diff --git a/.github/workflows/old/dependencies/dependencies_nofortran.sh b/.github/workflows/dependencies/dependencies_nofortran.sh similarity index 100% rename from .github/workflows/old/dependencies/dependencies_nofortran.sh rename to .github/workflows/dependencies/dependencies_nofortran.sh diff --git a/.github/workflows/old/dependencies/dependencies_nvcc.sh b/.github/workflows/dependencies/dependencies_nvcc.sh similarity index 100% rename from .github/workflows/old/dependencies/dependencies_nvcc.sh rename to .github/workflows/dependencies/dependencies_nvcc.sh diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 5eb6a492..e919e891 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -1,31 +1,33 @@ name: PeleLMeX-Docs on: + workflow_dispatch: 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: - - name: Clone - uses: actions/checkout@v3 + - uses: actions/checkout@v3 - name: Python uses: actions/setup-python@v3 with: python-version: '3.x' - name: Dependencies run: | + #Currently ignoring doxygen + #export DEBIAN_FRONTEND=noninteractive + #sudo apt-get update + #sudo apt-get install -y --no-install-recommends doxygen graphviz python -m pip install --upgrade pip pip install sphinx sphinx_rtd_theme - name: Configure @@ -38,7 +40,7 @@ jobs: 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/html/.nojekyll + touch ${{runner.workspace}}/build-docs/html/manual/html/.nojekyll - name: Deploy if: github.event_name == 'push' && github.ref == 'refs/heads/development' uses: JamesIves/github-pages-deploy-action@releases/v4 diff --git a/.github/workflows/old/hip.yml b/.github/workflows/hip.yml similarity index 100% rename from .github/workflows/old/hip.yml rename to .github/workflows/hip.yml diff --git a/.github/workflows/old/intel.yml b/.github/workflows/intel.yml similarity index 100% rename from .github/workflows/old/intel.yml rename to .github/workflows/intel.yml diff --git a/.github/workflows/old/linux.yml b/.github/workflows/linux.yml similarity index 100% rename from .github/workflows/old/linux.yml rename to .github/workflows/linux.yml diff --git a/.github/workflows/old/nightlyTest.yml b/.github/workflows/nightlyTest.yml similarity index 100% rename from .github/workflows/old/nightlyTest.yml rename to .github/workflows/nightlyTest.yml diff --git a/.github/workflows/old/codeql.yml b/.github/workflows/old/codeql.yml deleted file mode 100644 index 50a5a58c..00000000 --- a/.github/workflows/old/codeql.yml +++ /dev/null @@ -1,61 +0,0 @@ -name: 🔍 CodeQL - -on: - push: - branches: [ "development" ] - pull_request: - branches: [ "development" ] - schedule: - - cron: "27 3 * * 0" - -concurrency: - group: ${{ github.ref }}-${{ github.head_ref }}-codeql - cancel-in-progress: true - -jobs: - analyze: - name: Analyze - runs-on: ubuntu-latest - permissions: - actions: read - contents: read - security-events: write - - steps: - - name: Checkout - uses: actions/checkout@v3 - with: - submodules: true - - name: System Dependencies - run: .github/workflows/dependencies/dependencies_gcc10.sh - - name: Initialize CodeQL - uses: github/codeql-action/init@v2 - with: - languages: cpp - queries: +security-and-quality - - name: Configure - run: | - cmake -S . -B build - - name: Build - run: | - cmake --build build --parallel 4 - - name: Perform CodeQL Analysis - uses: github/codeql-action/analyze@v2 - with: - category: "/language:cpp" - upload: False - output: sarif-results - - name: Filter CodeQL sarif - uses: advanced-security/filter-sarif@v1 - with: - patterns: | - -**/Submodules/sundials/** - -**/Submodules/amrex/** - -**/Submodules/AMReX-Hydro/** - -**/pelelmex/** - input: sarif-results/cpp.sarif - output: sarif-results/cpp.sarif - - name: Upload CodeQL sarif - uses: github/codeql-action/upload-sarif@v2 - with: - sarif_file: sarif-results/cpp.sarif diff --git a/.github/workflows/old/docs.yml b/.github/workflows/old/docs.yml deleted file mode 100644 index e919e891..00000000 --- a/.github/workflows/old/docs.yml +++ /dev/null @@ -1,51 +0,0 @@ -name: PeleLMeX-Docs - -on: - workflow_dispatch: - push: - branches: [development] - paths: - - 'Docs/**' - - '.github/workflows/docs.yml' - pull_request: - branches: [development] - paths: - - 'Docs/**' - - '.github/workflows/docs.yml' - -jobs: - Docs: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - name: Python - uses: actions/setup-python@v3 - with: - python-version: '3.x' - - name: Dependencies - run: | - #Currently ignoring doxygen - #export DEBIAN_FRONTEND=noninteractive - #sudo apt-get update - #sudo apt-get install -y --no-install-recommends doxygen graphviz - 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/html/manual/html/.nojekyll - - name: Deploy - if: github.event_name == 'push' && github.ref == 'refs/heads/development' - uses: JamesIves/github-pages-deploy-action@releases/v4 - with: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - BRANCH: gh-pages - FOLDER: ${{runner.workspace}}/build-docs/html - SINGLE_COMMIT: true diff --git a/.github/workflows/old/style.yml b/.github/workflows/style.yml similarity index 100% rename from .github/workflows/old/style.yml rename to .github/workflows/style.yml diff --git a/.github/workflows/old/style/check_tabs.sh b/.github/workflows/style/check_tabs.sh similarity index 100% rename from .github/workflows/old/style/check_tabs.sh rename to .github/workflows/style/check_tabs.sh diff --git a/.github/workflows/old/style/check_trailing_whitespaces.sh b/.github/workflows/style/check_trailing_whitespaces.sh similarity index 100% rename from .github/workflows/old/style/check_trailing_whitespaces.sh rename to .github/workflows/style/check_trailing_whitespaces.sh diff --git a/.github/workflows/old/unitTest.yml b/.github/workflows/unitTest.yml similarity index 100% rename from .github/workflows/old/unitTest.yml rename to .github/workflows/unitTest.yml diff --git a/CMake/SetAmrexOptions.cmake b/CMake/SetAmrexOptions.cmake index e14cce47..25e13f6e 100644 --- a/CMake/SetAmrexOptions.cmake +++ b/CMake/SetAmrexOptions.cmake @@ -2,7 +2,7 @@ set(USE_XSDK_DEFAULTS OFF) set(AMReX_SPACEDIM "${PELELMEX_DIM}" CACHE STRING "Number of physical dimensions" FORCE) set(AMReX_MPI ${PELELMEX_ENABLE_MPI}) set(AMReX_OMP ${PELELMEX_ENABLE_OPENMP}) -set(AMReX_EB ON) +set(AMReX_EB ${PELELMEX_ENABLE_EB}) set(AMReX_PARTICLES ${PELELMEX_ENABLE_AMREX_PARTICLES}) set(AMReX_PLOTFILE_TOOLS ${PELELMEX_ENABLE_FCOMPARE}) set(AMReX_SUNDIALS OFF) diff --git a/CMakeLists.txt b/CMakeLists.txt index 4fdadbed..0bea4f2a 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -25,9 +25,10 @@ option(PELELMEX_ENABLE_HYPRE "Enable Offload to Hypre" OFF) set(PELELMEX_PRECISION "DOUBLE" CACHE STRING "Floating point precision SINGLE or DOUBLE") # Physics options -option(PELELMEX_ENABLE_EB "Enable Embedded Boundary" ON) +option(PELELMEX_ENABLE_EB "Enable Embedded Boundary" OFF) option(PELELMEX_ENABLE_EFIELD "Enable Electric field module" OFF) option(PELELMEX_ENABLE_SOOT "Enable Soot module" OFF) +option(PELELMEX_ENABLE_PARTICLE "Enable particles" OFF) # HPC options option(PELELMEX_ENABLE_MPI "Enable MPI" OFF) diff --git a/Exec/Cases/ChallengeProblem/GNUmakefile b/Exec/Cases/ChallengeProblem/GNUmakefile index 02e900fa..eef1b5e7 100644 --- a/Exec/Cases/ChallengeProblem/GNUmakefile +++ b/Exec/Cases/ChallengeProblem/GNUmakefile @@ -2,7 +2,6 @@ DIM = 3 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = TRUE USE_HYPRE = FALSE diff --git a/Exec/Cases/CounterFlow/GNUmakefile b/Exec/Cases/CounterFlow/GNUmakefile index 8cdc30c4..0967fc37 100644 --- a/Exec/Cases/CounterFlow/GNUmakefile +++ b/Exec/Cases/CounterFlow/GNUmakefile @@ -2,7 +2,6 @@ DIM = 2 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = TRUE USE_HYPRE = FALSE diff --git a/Exec/Cases/CounterFlowSpray/GNUmakefile b/Exec/Cases/CounterFlowSpray/GNUmakefile index a8f25840..6b897267 100644 --- a/Exec/Cases/CounterFlowSpray/GNUmakefile +++ b/Exec/Cases/CounterFlowSpray/GNUmakefile @@ -2,7 +2,6 @@ DIM = 2 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = TRUE USE_HYPRE = FALSE diff --git a/Exec/Cases/DiffBunsen2D/GNUmakefile b/Exec/Cases/DiffBunsen2D/GNUmakefile index 8cdc30c4..0967fc37 100644 --- a/Exec/Cases/DiffBunsen2D/GNUmakefile +++ b/Exec/Cases/DiffBunsen2D/GNUmakefile @@ -2,7 +2,6 @@ DIM = 2 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = TRUE USE_HYPRE = FALSE diff --git a/Exec/Cases/JetInCrossflow/GNUmakefile b/Exec/Cases/JetInCrossflow/GNUmakefile index b03618cd..deb747c8 100644 --- a/Exec/Cases/JetInCrossflow/GNUmakefile +++ b/Exec/Cases/JetInCrossflow/GNUmakefile @@ -2,7 +2,6 @@ DIM = 3 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = TRUE USE_HYPRE = FALSE diff --git a/Exec/Cases/NormalJet_OpenDomain/GNUmakefile b/Exec/Cases/NormalJet_OpenDomain/GNUmakefile index 429e2d42..3a12ca53 100644 --- a/Exec/Cases/NormalJet_OpenDomain/GNUmakefile +++ b/Exec/Cases/NormalJet_OpenDomain/GNUmakefile @@ -2,7 +2,6 @@ DIM = 3 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = TRUE USE_HYPRE = FALSE diff --git a/Exec/Cases/PremBunsen2D/GNUmakefile b/Exec/Cases/PremBunsen2D/GNUmakefile index 8cdc30c4..0967fc37 100644 --- a/Exec/Cases/PremBunsen2D/GNUmakefile +++ b/Exec/Cases/PremBunsen2D/GNUmakefile @@ -2,7 +2,6 @@ DIM = 2 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = TRUE USE_HYPRE = FALSE diff --git a/Exec/Cases/PremBunsen3D/GNUmakefile b/Exec/Cases/PremBunsen3D/GNUmakefile index 05ecc97b..53bc5909 100644 --- a/Exec/Cases/PremBunsen3D/GNUmakefile +++ b/Exec/Cases/PremBunsen3D/GNUmakefile @@ -2,7 +2,6 @@ DIM = 3 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = TRUE USE_HYPRE = FALSE diff --git a/Exec/Cases/SwirlFlowWallInteractions/GNUmakefile b/Exec/Cases/SwirlFlowWallInteractions/GNUmakefile index bfbeff95..fb31b588 100644 --- a/Exec/Cases/SwirlFlowWallInteractions/GNUmakefile +++ b/Exec/Cases/SwirlFlowWallInteractions/GNUmakefile @@ -2,7 +2,6 @@ DIM = 3 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = TRUE USE_HYPRE = FALSE diff --git a/Exec/Cases/TripleFlame/GNUmakefile b/Exec/Cases/TripleFlame/GNUmakefile index 4339a720..89ba560c 100644 --- a/Exec/Cases/TripleFlame/GNUmakefile +++ b/Exec/Cases/TripleFlame/GNUmakefile @@ -2,7 +2,6 @@ DIM = 2 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = FALSE USE_HYPRE = FALSE diff --git a/Exec/Efield/FlameSheetIons/GNUmakefile b/Exec/Efield/FlameSheetIons/GNUmakefile index 3188006b..38a9ef31 100644 --- a/Exec/Efield/FlameSheetIons/GNUmakefile +++ b/Exec/Efield/FlameSheetIons/GNUmakefile @@ -2,7 +2,6 @@ DIM = 2 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = FALSE USE_HYPRE = FALSE diff --git a/Exec/Efield/IonizedAirWave/GNUmakefile b/Exec/Efield/IonizedAirWave/GNUmakefile index 4c75bef7..f729bcce 100644 --- a/Exec/Efield/IonizedAirWave/GNUmakefile +++ b/Exec/Efield/IonizedAirWave/GNUmakefile @@ -2,7 +2,6 @@ DIM = 2 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = FALSE USE_HYPRE = FALSE diff --git a/Exec/Efield/PremBunsen3DKuhl/GNUmakefile b/Exec/Efield/PremBunsen3DKuhl/GNUmakefile index 1c50075b..7fda7f66 100644 --- a/Exec/Efield/PremBunsen3DKuhl/GNUmakefile +++ b/Exec/Efield/PremBunsen3DKuhl/GNUmakefile @@ -2,7 +2,6 @@ DIM = 3 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = FALSE USE_HYPRE = FALSE diff --git a/Exec/RegTests/EB_BackwardStepFlame/GNUmakefile b/Exec/RegTests/EB_BackwardStepFlame/GNUmakefile index 1685996b..942b4631 100644 --- a/Exec/RegTests/EB_BackwardStepFlame/GNUmakefile +++ b/Exec/RegTests/EB_BackwardStepFlame/GNUmakefile @@ -2,7 +2,6 @@ DIM = 2 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = TRUE USE_HYPRE = FALSE diff --git a/Exec/RegTests/EB_EnclosedFlame/GNUmakefile b/Exec/RegTests/EB_EnclosedFlame/GNUmakefile index 01994bd9..b3e5dd47 100644 --- a/Exec/RegTests/EB_EnclosedFlame/GNUmakefile +++ b/Exec/RegTests/EB_EnclosedFlame/GNUmakefile @@ -2,7 +2,6 @@ DIM = 2 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = TRUE USE_HYPRE = FALSE diff --git a/Exec/RegTests/EB_EnclosedVortex/GNUmakefile b/Exec/RegTests/EB_EnclosedVortex/GNUmakefile index e1691c71..f45e17f9 100644 --- a/Exec/RegTests/EB_EnclosedVortex/GNUmakefile +++ b/Exec/RegTests/EB_EnclosedVortex/GNUmakefile @@ -2,7 +2,6 @@ DIM = 2 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = TRUE USE_HYPRE = FALSE diff --git a/Exec/RegTests/EB_FlowPastCylinder/GNUmakefile b/Exec/RegTests/EB_FlowPastCylinder/GNUmakefile index 22f36449..781b7a46 100644 --- a/Exec/RegTests/EB_FlowPastCylinder/GNUmakefile +++ b/Exec/RegTests/EB_FlowPastCylinder/GNUmakefile @@ -8,7 +8,6 @@ AMREX_HYDRO_HOME ?= ${PELELMEX_HOME}/Submodules/AMReX-Hydro DIM = 2 DEBUG = FALSE PRECISION = DOUBLE -VERBOSE = FALSE TINY_PROFILE = FALSE USE_EB = TRUE USE_HYPRE = FALSE diff --git a/Exec/RegTests/EB_PipeFlow/GNUmakefile b/Exec/RegTests/EB_PipeFlow/GNUmakefile index bf009add..655f2c9e 100644 --- a/Exec/RegTests/EB_PipeFlow/GNUmakefile +++ b/Exec/RegTests/EB_PipeFlow/GNUmakefile @@ -2,7 +2,6 @@ DIM = 3 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = TRUE USE_HYPRE = FALSE diff --git a/Exec/RegTests/EnclosedFlame/GNUmakefile b/Exec/RegTests/EnclosedFlame/GNUmakefile index 01994bd9..b3e5dd47 100644 --- a/Exec/RegTests/EnclosedFlame/GNUmakefile +++ b/Exec/RegTests/EnclosedFlame/GNUmakefile @@ -2,7 +2,6 @@ DIM = 2 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = TRUE USE_HYPRE = FALSE diff --git a/Exec/RegTests/EnclosedInjection/GNUmakefile b/Exec/RegTests/EnclosedInjection/GNUmakefile index 92e35ce5..598a7fa6 100644 --- a/Exec/RegTests/EnclosedInjection/GNUmakefile +++ b/Exec/RegTests/EnclosedInjection/GNUmakefile @@ -2,7 +2,6 @@ DIM = 3 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = FALSE USE_HYPRE = FALSE diff --git a/Exec/RegTests/FlameSheet/CMakeLists.txt b/Exec/RegTests/FlameSheet/CMakeLists.txt index d3ffc6d0..ae48d20f 100644 --- a/Exec/RegTests/FlameSheet/CMakeLists.txt +++ b/Exec/RegTests/FlameSheet/CMakeLists.txt @@ -1,4 +1,3 @@ -set(PELELMEX_ENABLE_PARTICLES OFF) set(PELELMEX_EOS_MODEL Fuego) set(PELELMEX_CHEMISTRY_MODEL drm19) set(PELELMEX_TRANSPORT_MODEL Simple) diff --git a/Exec/RegTests/FlameSheet/GNUmakefile b/Exec/RegTests/FlameSheet/GNUmakefile index cf1235d8..1050b9d2 100644 --- a/Exec/RegTests/FlameSheet/GNUmakefile +++ b/Exec/RegTests/FlameSheet/GNUmakefile @@ -2,7 +2,6 @@ DIM = 3 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = FALSE USE_HYPRE = FALSE diff --git a/Exec/RegTests/HITDecay/GNUmakefile b/Exec/RegTests/HITDecay/GNUmakefile index 111b6098..997ab426 100644 --- a/Exec/RegTests/HITDecay/GNUmakefile +++ b/Exec/RegTests/HITDecay/GNUmakefile @@ -2,7 +2,6 @@ DIM = 3 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = FALSE USE_HYPRE = FALSE diff --git a/Exec/RegTests/HotBubble/GNUmakefile b/Exec/RegTests/HotBubble/GNUmakefile index 406f242f..31b84e77 100644 --- a/Exec/RegTests/HotBubble/GNUmakefile +++ b/Exec/RegTests/HotBubble/GNUmakefile @@ -2,7 +2,6 @@ DIM = 2 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = FALSE USE_HYPRE = FALSE diff --git a/Exec/RegTests/PeriodicCases/GNUmakefile b/Exec/RegTests/PeriodicCases/GNUmakefile index 0a3e5413..1b9ac3c0 100644 --- a/Exec/RegTests/PeriodicCases/GNUmakefile +++ b/Exec/RegTests/PeriodicCases/GNUmakefile @@ -2,7 +2,6 @@ DIM = 2 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = FALSE USE_HYPRE = FALSE diff --git a/Exec/RegTests/SprayTest/GNUmakefile b/Exec/RegTests/SprayTest/GNUmakefile index c8cbd3d6..55920165 100644 --- a/Exec/RegTests/SprayTest/GNUmakefile +++ b/Exec/RegTests/SprayTest/GNUmakefile @@ -2,7 +2,6 @@ DIM = 2 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = FALSE USE_HYPRE = FALSE diff --git a/Exec/RegTests/TaylorGreen/GNUmakefile b/Exec/RegTests/TaylorGreen/GNUmakefile index f05c6c80..d1c0983e 100644 --- a/Exec/RegTests/TaylorGreen/GNUmakefile +++ b/Exec/RegTests/TaylorGreen/GNUmakefile @@ -2,7 +2,6 @@ DIM = 3 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = FALSE USE_HYPRE = FALSE diff --git a/Exec/RegTests/TripleFlame/GNUmakefile b/Exec/RegTests/TripleFlame/GNUmakefile index 1215a116..4f76ac19 100644 --- a/Exec/RegTests/TripleFlame/GNUmakefile +++ b/Exec/RegTests/TripleFlame/GNUmakefile @@ -2,7 +2,6 @@ DIM = 2 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = FALSE USE_HYPRE = FALSE diff --git a/Exec/RegTests/TurbInflow/GNUmakefile b/Exec/RegTests/TurbInflow/GNUmakefile index d754ab14..e481a461 100644 --- a/Exec/RegTests/TurbInflow/GNUmakefile +++ b/Exec/RegTests/TurbInflow/GNUmakefile @@ -2,7 +2,6 @@ DIM = 3 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = TRUE USE_HYPRE = FALSE diff --git a/Exec/RegTests/TurbInflow/TurbFileHIT/GNUmakefile b/Exec/RegTests/TurbInflow/TurbFileHIT/GNUmakefile index 18b31723..57cc1e91 100644 --- a/Exec/RegTests/TurbInflow/TurbFileHIT/GNUmakefile +++ b/Exec/RegTests/TurbInflow/TurbFileHIT/GNUmakefile @@ -8,7 +8,6 @@ EBASE = PeleTurb DIM = 3 DEBUG = FALSE PRECISION = DOUBLE -VERBOSE = FALSE TINY_PROFILE = FALSE # Compilation diff --git a/Exec/RegTests/Unit/GNUmakefile b/Exec/RegTests/Unit/GNUmakefile index d4c45ff4..dbe89520 100644 --- a/Exec/RegTests/Unit/GNUmakefile +++ b/Exec/RegTests/Unit/GNUmakefile @@ -2,7 +2,6 @@ DIM = 2 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = FALSE USE_HYPRE = FALSE diff --git a/Exec/UnitTests/DodecaneLu/GNUmakefile b/Exec/UnitTests/DodecaneLu/GNUmakefile index f3ecfff6..6b0c637b 100644 --- a/Exec/UnitTests/DodecaneLu/GNUmakefile +++ b/Exec/UnitTests/DodecaneLu/GNUmakefile @@ -2,7 +2,6 @@ DIM = 3 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = TRUE USE_HYPRE = FALSE diff --git a/Exec/UnitTests/EB_SphericalFlame/GNUmakefile b/Exec/UnitTests/EB_SphericalFlame/GNUmakefile index 5ac1d956..adbb160e 100644 --- a/Exec/UnitTests/EB_SphericalFlame/GNUmakefile +++ b/Exec/UnitTests/EB_SphericalFlame/GNUmakefile @@ -2,7 +2,6 @@ DIM = 3 COMP = clang PRECISION = DOUBLE -VERBOSE = FALSE USE_EB = TRUE USE_HYPRE = FALSE diff --git a/Source/main.cpp b/Source/main.cpp index f1f26c04..64778645 100644 --- a/Source/main.cpp +++ b/Source/main.cpp @@ -1,5 +1,11 @@ #include +// Defined and initialized when in gnumake, but not defined in cmake and +// initialization done manually +#ifndef AMREX_USE_SUNDIALS +#include +#endif + using namespace amrex; int @@ -19,6 +25,12 @@ main(int argc, char* argv[]) // in AMReX.cpp Initialize(argc, argv); +// Defined and initialized when in gnumake, but not defined in cmake and +// initialization done manually +#ifndef AMREX_USE_SUNDIALS + amrex::sundials::Initialize(amrex::OpenMP::get_max_threads()); +#endif + // Refuse to continue if we did not provide an inputs file. if (argc <= 1) { Abort("Error: no inputs file provided on command line."); @@ -68,6 +80,12 @@ main(int argc, char* argv[]) // destroy timer for profiling BL_PROFILE_VAR_STOP(main); +// Defined and finalized when in gnumake, but not defined in cmake and +// finalization done manually +#ifndef AMREX_USE_SUNDIALS + amrex::sundials::Finalize(); +#endif + // in AMReX.cpp Finalize(); } diff --git a/Tests/CMakeLists.txt b/Tests/CMakeLists.txt index 2b9feea5..604aac44 100644 --- a/Tests/CMakeLists.txt +++ b/Tests/CMakeLists.txt @@ -55,7 +55,7 @@ macro(setup_test) file(COPY ${CURRENT_TEST_SOURCE_DIR}/${TEST_NAME}.inp DESTINATION "${CURRENT_TEST_BINARY_DIR}/") file(COPY ${TEST_FILES} DESTINATION "${CURRENT_TEST_BINARY_DIR}/") # Set some default runtime options for all tests - set(RUNTIME_OPTIONS "amr.plot_file=plt amr.checkpoint_files_output=0 amr.plot_files_output=1 amrex.the_arena_is_managed=0") + set(RUNTIME_OPTIONS "amr.plot_file=plt amr.plot_int=-1 amr.check_int=-1 amrex.the_arena_is_managed=0") if(PELELMEX_ENABLE_FPE_TRAP_FOR_TESTS) set(RUNTIME_OPTIONS "${RUNTIME_OPTIONS} amrex.signal_handling=1 amrex.fpe_trap_invalid=1 amrex.fpe_trap_zero=1 amrex.fpe_trap_overflow=1") else()