Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update pelephysics submodule #715

Merged
merged 15 commits into from
Dec 13, 2023
Merged
Changes from 1 commit
Commits
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Next Next commit
Take into account reorg of pelephysics files
marchdf committed Dec 11, 2023
commit e050d1930b91efc9aca9e2aa2f5326466f988f8f
1 change: 0 additions & 1 deletion .github/dependabot.yml
Original file line number Diff line number Diff line change
@@ -6,5 +6,4 @@ updates:
interval: "weekly"
directory: /
allow:
- dependency-name: "Submodules/AMReX"
- dependency-name: "Submodules/PelePhysics"
49 changes: 23 additions & 26 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
@@ -30,7 +30,7 @@ jobs:
- name: Clone
uses: actions/checkout@v3
with:
submodules: true
submodules: 'recursive'
- name: Setup
working-directory: ./Exec/RegTests/PMF
run: |
@@ -39,8 +39,6 @@ jobs:
echo "CCACHE_COMPRESSLEVEL=1" >> $GITHUB_ENV
echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV
echo "CCACHE_MAXSIZE=350M" >> $GITHUB_ENV
#printf "CC=gcc-10\nCXX=g++-10\nFC=gfortran-10\nF90=gfortran-10" \
# >> ${{github.workspace}}/Submodules/AMReX/Tools/GNUMake/Make.local
make COMP=gnu USE_MPI=FALSE DEBUG=TRUE TPL
make COMP=llvm USE_MPI=FALSE DEBUG=TRUE PRECISION=FLOAT TPL
- name: Install Ccache
@@ -74,7 +72,7 @@ jobs:
working-directory: ./Exec/RegTests/PMF
run: |
egrep "warning:|error:" build-output.txt \
| egrep -v "Submodules/AMReX|Submodules/sundials|GNUmakefile" \
| egrep -v "Submodules/amrex|Submodules/sundials|GNUmakefile" \
| egrep -v "ld: warning:" | sort | uniq \
| awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' > warnings.txt
cat warnings.txt
@@ -99,7 +97,7 @@ jobs:
working-directory: ./Exec/RegTests/EB-C10
run: |
egrep "warning:|error:" build-output.txt \
| egrep -v "Submodules/AMReX|Submodules/sundials|GNUmakefile" \
| egrep -v "Submodules/amrex|Submodules/sundials|GNUmakefile" \
| egrep -v "ld: warning:" | sort | uniq \
| awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' > warnings.txt
cat warnings.txt
@@ -124,7 +122,7 @@ jobs:
working-directory: ./Exec/RegTests/TG
run: |
egrep "warning:|error:" build-output.txt \
| egrep -v "Submodules/AMReX|Submodules/sundials|GNUmakefile" \
| egrep -v "Submodules/amrex|Submodules/sundials|GNUmakefile" \
| egrep -v "ld: warning:" | sort | uniq \
| awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' > warnings.txt
cat warnings.txt
@@ -146,8 +144,8 @@ jobs:
working-directory: ./Exec/RegTests/Soot-Flame
run: |
egrep "warning:|error:" build-output.txt \
| egrep -v "Submodules/AMReX|Submodules/sundials|GNUmakefile|Submodules/PeleMP" \
| egrep -v "Submodules/PelePhysics/Support/Mechanism/Models" | sort | uniq \
| egrep -v "Submodules/amrex|Submodules/sundials|GNUmakefile" \
| egrep -v "Submodules/PelePhysics/Mechanisms" | sort | uniq \
| awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' > warnings.txt
cat warnings.txt
export return=$(tail -n 1 warnings.txt | awk '{print $2}')
@@ -168,8 +166,8 @@ jobs:
working-directory: ./Exec/RegTests/Spray-Conv
run: |
egrep "warning:|error:" build-output.txt \
| egrep -v "Submodules/AMReX|Submodules/sundials|GNUmakefile|Submodules/PeleMP" \
| egrep -v "Submodules/PelePhysics/Support/Mechanism/Models" | sort | uniq \
| egrep -v "Submodules/amrex|Submodules/sundials|GNUmakefile" \
| egrep -v "Submodules/PelePhysics/Mechanisms" | sort | uniq \
| awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' > warnings.txt
cat warnings.txt
export return=$(tail -n 1 warnings.txt | awk '{print $2}')
@@ -205,7 +203,7 @@ jobs:
- name: Clone
uses: actions/checkout@v3
with:
submodules: true
submodules: 'recursive'
- name: Python
uses: actions/setup-python@v4
with:
@@ -219,7 +217,7 @@ jobs:
echo "CCACHE_MAXSIZE=${{matrix.ccache_size}}" >> $GITHUB_ENV
cmake -E make_directory ${{runner.workspace}}/deps
if [ "${RUNNER_OS}" != "macOS" ]; then
${{github.workspace}}/Submodules/AMReX/.github/workflows/dependencies/ubuntu_free_disk_space.sh
${{github.workspace}}/Submodules/PelePhysics/Submodules/amrex/.github/workflows/dependencies/ubuntu_free_disk_space.sh
fi
- name: Dependencies
run: |
@@ -296,7 +294,7 @@ jobs:
run: |
echo "::add-matcher::.github/problem-matchers/gcc.json"
egrep "warning:|error:" ${{runner.workspace}}/build-output.txt \
| egrep -v "Submodules/AMReX|Submodules/sundials" \
| egrep -v "Submodules/amrex|Submodules/sundials" \
| egrep -v "ld: warning:" | egrep -v "lto-wrapper: warning:" | sort | uniq \
| awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' > ${{runner.workspace}}/build-output-warnings.txt
cat ${{runner.workspace}}/build-output-warnings.txt
@@ -324,7 +322,7 @@ jobs:
- name: Clone
uses: actions/checkout@v3
with:
submodules: true
submodules: 'recursive'
- name: Setup
run: |
echo "NPROCS=$(nproc)" >> $GITHUB_ENV
@@ -334,7 +332,7 @@ jobs:
echo "CCACHE_MAXSIZE=500M" >> $GITHUB_ENV
- name: Dependencies
run: |
${{github.workspace}}/Submodules/AMReX/.github/workflows/dependencies/ubuntu_free_disk_space.sh
${{github.workspace}}/Submodules/PelePhysics/Submodules/amrex/.github/workflows/dependencies/ubuntu_free_disk_space.sh
curl -O https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-keyring_1.0-1_all.deb
sudo dpkg -i cuda-keyring_1.0-1_all.deb
sudo apt-get update
@@ -387,7 +385,7 @@ jobs:
- name: Clone
uses: actions/checkout@v3
with:
submodules: true
submodules: 'recursive'
- name: Setup
run: |
echo "NPROCS=$(nproc)" >> $GITHUB_ENV
@@ -397,7 +395,7 @@ jobs:
echo "CCACHE_MAXSIZE=100M" >> $GITHUB_ENV
- name: Dependencies
run: |
${{github.workspace}}/Submodules/AMReX/.github/workflows/dependencies/ubuntu_free_disk_space.sh
${{github.workspace}}/Submodules/PelePhysics/Submodules/amrex/.github/workflows/dependencies/ubuntu_free_disk_space.sh
curl -O https://repo.radeon.com/rocm/rocm.gpg.key
sudo apt-key add rocm.gpg.key
echo 'deb [arch=amd64] https://repo.radeon.com/rocm/apt/5.6.1 ubuntu main' \
@@ -458,7 +456,7 @@ jobs:
- name: Clone
uses: actions/checkout@v3
with:
submodules: true
submodules: 'recursive'
- name: Setup
run: |
echo "NPROCS=$(nproc)" >> $GITHUB_ENV
@@ -469,7 +467,7 @@ jobs:
echo "CCACHE_DEPEND=1" >> $GITHUB_ENV
- name: Dependencies
run: |
${{github.workspace}}/Submodules/AMReX/.github/workflows/dependencies/ubuntu_free_disk_space.sh
${{github.workspace}}/Submodules/PelePhysics/Submodules/amrex/.github/workflows/dependencies/ubuntu_free_disk_space.sh
sudo wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
echo "deb https://apt.repos.intel.com/oneapi all main" \
@@ -523,7 +521,7 @@ jobs:
# - name: Clone
# uses: actions/checkout@v3
# with:
# submodules: true
# submodules: 'recursive'
# - name: Dependencies
# run: |
# export HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=TRUE
@@ -558,15 +556,15 @@ jobs:
- name: Clone
uses: actions/checkout@v3
with:
submodules: true
submodules: 'recursive'
- name: Setup
run: |
echo "NPROCS=$(nproc)" >> $GITHUB_ENV
echo "CCACHE_COMPRESS=1" >> $GITHUB_ENV
echo "CCACHE_COMPRESSLEVEL=1" >> $GITHUB_ENV
echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV
echo "CCACHE_MAXSIZE=500M" >> $GITHUB_ENV
${{github.workspace}}/Submodules/AMReX/.github/workflows/dependencies/ubuntu_free_disk_space.sh
${{github.workspace}}/Submodules/PelePhysics/Submodules/amrex/.github/workflows/dependencies/ubuntu_free_disk_space.sh
- name: Install Ccache
run: |
wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
@@ -598,7 +596,7 @@ jobs:
#set -eu -o pipefail
cmake --build . --parallel ${{env.NPROCS}} 2>&1 | tee -a clang-tidy-full-report.txt
egrep "warning:|error:" clang-tidy-full-report.txt \
| egrep -v "Submodules/AMReX|Submodules/sundials" \
| egrep -v "Submodules/amrex|Submodules/sundials" \
| egrep -v "ld: warning:" | sort | uniq \
| awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' > clang-tidy-warnings.txt
- name: Ccache Report
@@ -622,7 +620,7 @@ jobs:
- name: Clone
uses: actions/checkout@v3
with:
submodules: true
submodules: 'recursive'
- name: Initialize CodeQL
uses: github/codeql-action/init@v2
with:
@@ -655,8 +653,7 @@ jobs:
with:
patterns: |
-**/Submodules/sundials/**
-**/Submodules/AMReX/**
-**/Submodules/AMReX-Hydro/**
-**/Submodules/amrex/**
input: sarif-results/cpp.sarif
output: sarif-results/cpp.sarif
- name: Upload CodeQL sarif
11 changes: 1 addition & 10 deletions .gitmodules
Original file line number Diff line number Diff line change
@@ -1,12 +1,3 @@
[submodule "Submodules/AMReX"]
path = Submodules/AMReX
url = https://github.com/AMReX-Codes/amrex.git
[submodule "Submodules/PelePhysics"]
path = Submodules/PelePhysics
url = https://github.com/AMReX-Combustion/PelePhysics.git
[submodule "Submodules/PeleMP"]
path = Submodules/PeleMP
url = https://github.com/AMReX-Combustion/PeleMP.git
[submodule "Submodules/sundials"]
path = Submodules/sundials
url = https://github.com/LLNL/sundials.git
url = https://github.com/AMReX-Combustion/PelePhysics.git
76 changes: 35 additions & 41 deletions CMake/BuildPeleCExe.cmake
Original file line number Diff line number Diff line change
@@ -22,50 +22,38 @@ function(build_pelec_exe pelec_exe_name pelec_lib_name)
target_include_directories(${pelec_exe_name} PRIVATE ${CMAKE_BINARY_DIR})
target_include_directories(${pelec_exe_name} PRIVATE ${CMAKE_SOURCE_DIR}/Source/Params/param_includes)

# Set PeleMP flags
set(PELEMP_SRC_DIR ${CMAKE_SOURCE_DIR}/Submodules/PeleMP/Source)
if(PELEC_ENABLE_AMREX_PARTICLES AND PELEMP_SPRAY_FUEL_NUM GREATER 0)
# Spray
set(PELE_PHYSICS_SPRAY_DIR ${CMAKE_SOURCE_DIR}/Submodules/PelePhysics/Source/Spray)
if(PELEC_ENABLE_AMREX_PARTICLES AND PELE_SPRAY_FUEL_NUM GREATER 0)
target_compile_definitions(${pelec_exe_name} PRIVATE PELEC_USE_SPRAY)
target_compile_definitions(${pelec_exe_name} PRIVATE SPRAY_FUEL_NUM=${PELEMP_SPRAY_FUEL_NUM})
target_compile_definitions(${pelec_exe_name} PRIVATE SPRAY_FUEL_NUM=${PELE_SPRAY_FUEL_NUM})
target_sources(${pelec_exe_name} PRIVATE
SprayParticlesInitInsert.cpp
SprayParticlesInitInsert.cpp
${SRC_DIR}/Particle.cpp
${PELEMP_SRC_DIR}/PP_Spray/SprayParticles.cpp
${PELEMP_SRC_DIR}/PP_Spray/SprayParticles.H
${PELEMP_SRC_DIR}/PP_Spray/SprayFuelData.H
${PELEMP_SRC_DIR}/PP_Spray/SprayInterpolation.H
${PELEMP_SRC_DIR}/PP_Spray/Drag.H
${PELEMP_SRC_DIR}/PP_Spray/SprayInjection.H
${PELEMP_SRC_DIR}/PP_Spray/SpraySetup.cpp
${PELEMP_SRC_DIR}/PP_Spray/SprayDerive.cpp
${PELEMP_SRC_DIR}/PP_Spray/SprayJet.H
${PELEMP_SRC_DIR}/PP_Spray/SprayJet.cpp
${PELEMP_SRC_DIR}/PP_Spray/SprayIO.cpp
${PELEMP_SRC_DIR}/PP_Spray/WallFunctions.H
${PELEMP_SRC_DIR}/PP_Spray/Distribution/DistBase.H
${PELEMP_SRC_DIR}/PP_Spray/Distribution/Distributions.H
${PELEMP_SRC_DIR}/PP_Spray/Distribution/Distributions.cpp)
target_include_directories(${pelec_exe_name} PRIVATE ${PELEMP_SRC_DIR}/PP_Spray)
target_include_directories(${pelec_exe_name} PRIVATE ${PELEMP_SRC_DIR}/PP_Spray/Distribution)
endif()
if(PELEC_ENABLE_SOOT)
target_compile_definitions(${pelec_exe_name} PRIVATE PELEC_USE_SOOT)
target_compile_definitions(${pelec_exe_name} PRIVATE NUM_SOOT_MOMENTS=${PELEMP_NUM_SOOT_MOMENTS})
set(SOOT_MOMENTS_VALUES 3 6)
if(NOT PELEMP_NUM_SOOT_MOMENTS IN_LIST SOOT_MOMENTS_VALUES)
message(FATAL_ERROR "NUM_SOOT_MOMENTS must be either 3 or 6")
endif()
target_sources(${pelec_exe_name} PRIVATE
${SRC_DIR}/Soot.cpp
${PELEMP_SRC_DIR}/Soot_Models/SootModel.cpp
${PELEMP_SRC_DIR}/Soot_Models/SootModel_react.cpp
${PELEMP_SRC_DIR}/Soot_Models/SootModel_derive.cpp
${PELEMP_SRC_DIR}/Soot_Models/Constants_Soot.H
${PELEMP_SRC_DIR}/Soot_Models/SootData.H
${PELEMP_SRC_DIR}/Soot_Models/SootReactions.H
${PELEMP_SRC_DIR}/Soot_Models/SootModel.H
${PELEMP_SRC_DIR}/Soot_Models/SootModel_derive.H)
target_include_directories(${pelec_exe_name} PRIVATE ${PELEMP_SRC_DIR}/Soot_Models)
${PELE_PHYSICS_SPRAY_DIR}/Drag.H
${PELE_PHYSICS_SPRAY_DIR}/SprayDerive.cpp
${PELE_PHYSICS_SPRAY_DIR}/SprayFuelData.H
${PELE_PHYSICS_SPRAY_DIR}/SprayIO.cpp
${PELE_PHYSICS_SPRAY_DIR}/SprayInjection.H
${PELE_PHYSICS_SPRAY_DIR}/SprayInterpolation.H
${PELE_PHYSICS_SPRAY_DIR}/SprayJet.H
${PELE_PHYSICS_SPRAY_DIR}/SprayJet.cpp
${PELE_PHYSICS_SPRAY_DIR}/SprayParticles.H
${PELE_PHYSICS_SPRAY_DIR}/SprayParticles.cpp
${PELE_PHYSICS_SPRAY_DIR}/SpraySB.cpp
${PELE_PHYSICS_SPRAY_DIR}/SpraySetup.cpp
${PELE_PHYSICS_SPRAY_DIR}/WallFunctions.H
${PELE_PHYSICS_SPRAY_DIR}/BreakupSplash/AhamedSplash.H
${PELE_PHYSICS_SPRAY_DIR}/BreakupSplash/ReitzKHRT.H
${PELE_PHYSICS_SPRAY_DIR}/BreakupSplash/SBData.H
${PELE_PHYSICS_SPRAY_DIR}/BreakupSplash/TABBreakup.H
${PELE_PHYSICS_SPRAY_DIR}/BreakupSplash/WallFilm.H
${PELE_PHYSICS_SPRAY_DIR}/Distribution/DistBase.H
${PELE_PHYSICS_SPRAY_DIR}/Distribution/Distributions.H
${PELE_PHYSICS_SPRAY_DIR}/Distribution/Distributions.cpp)
target_include_directories(${pelec_exe_name} PUBLIC ${PELE_PHYSICS_SPRAY_DIR})
target_include_directories(${pelec_exe_name} PUBLIC ${PELE_PHYSICS_SPRAY_DIR}/Distribution)
target_include_directories(${pelec_exe_name} PUBLIC ${PELE_PHYSICS_SPRAY_DIR}/BreakupSplash)
endif()

target_sources(${pelec_exe_name}
@@ -122,6 +110,12 @@ function(build_pelec_exe pelec_exe_name pelec_lib_name)
${SRC_DIR}/WENO.H
)

# Soot
if(PELEC_ENABLE_SOOT)
target_sources(${pelec_exe_name} PRIVATE
${SRC_DIR}/Soot.cpp)
endif()

if(PELEC_ENABLE_ASCENT)
target_sources(${pelec_exe_name}
PRIVATE
Loading