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fix: Python script to read MPI meshes #769

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fix: Python script to read MPI meshes

fix: Python script to read MPI meshes #769

Workflow file for this run

.github/workflows/ci.yml at cbde6f1
name: samurai CI
on: [pull_request]
jobs:
#
# Check samurai with pre-commit
#
#########################################################
pre-commit:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
- uses: pre-commit/[email protected]
#
# Check samurai with cppcheck
#
#########################################################
cppcheck:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Cache
uses: actions/cache@v4
with:
path: |
~/.cache/ccache
~/micromamba/envs/samurai-env
key: cppcheck
- name: Mamba and samurai env installation
uses: mamba-org/setup-micromamba@v1
with:
environment-file: conda/environment.yml
environment-name: samurai-env
cache-environment: true
- name: cppcheck installation
shell: bash -el {0}
run: |
conda install -y cppcheck=2.12 python=3.12 cxx-compiler
- name: Configure
shell: bash -el {0}
run: |
cmake . -Bbuild -DCMAKE_EXPORT_COMPILE_COMMANDS=ON -DCMAKE_BUILD_TYPE=Debug -DBUILD_DEMOS=ON
- name: Run cppcheck on samurai
shell: bash -el {0}
run: |
cppcheck --enable=all -q --project=./build/compile_commands.json --suppressions-list=.cppcheck --inline-suppr 2> cppcheck_err.txt
- name: Check for errors
run: |
if [[ -s cppcheck_err.txt ]];
then
cat cppcheck_err.txt
exit -1
fi
#
# Check linux build with mamba environment
#
#########################################################
linux-mamba:
needs: [pre-commit, cppcheck]
strategy:
fail-fast: false
matrix:
include:
- cpp-version: gcc-10
os: ubuntu-latest
compiler: "gcc"
package: "gcc-10 g++-10"
cc: "gcc-10"
cxx: "g++-10"
- cpp-version: gcc-11
os: ubuntu-latest
compiler: "gcc"
package: "gcc-11 g++-11"
cc: "gcc-11"
cxx: "g++-11"
- cpp-version: gcc-12
os: ubuntu-latest
compiler: "gcc"
package: "gcc-12 g++-12"
cc: "gcc-12"
cxx: "g++-12"
- cpp-version: gcc-13
os: ubuntu-latest
compiler: "gcc"
package: "gcc-13 g++-13"
cc: "gcc-13"
cxx: "g++-13"
- cpp-version: gcc-14
os: ubuntu-latest
compiler: "gcc"
package: "gcc-14 g++-14"
cc: "gcc-14"
cxx: "g++-14"
- cpp-version: clang-13
os: ubuntu-22.04
compiler: "clang"
package: "clang-13"
cc: "clang-13"
cxx: "clang++-13"
- cpp-version: clang-14
os: ubuntu-22.04
compiler: "clang"
package: "clang-14"
cc: "clang-14"
cxx: "clang++-14"
- cpp-version: clang-15
os: ubuntu-22.04
compiler: "clang"
package: "clang-15"
cc: "clang-15"
cxx: "clang++-15"
- cpp-version: clang-16
os: ubuntu-24.04
compiler: "clang"
package: "clang-16"
cc: "clang-16"
cxx: "clang++-16"
- cpp-version: clang-17
os: ubuntu-24.04
compiler: "clang"
package: "clang-17"
cc: "clang-17"
cxx: "clang++-17"
- cpp-version: clang-18
os: ubuntu-24.04
compiler: "clang"
package: "clang-18"
cc: "clang-18"
cxx: "clang++-18"
runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v4
- name: Cache
uses: actions/cache@v4
with:
path: |
~/.cache/ccache
~/micromamba-root/envs/samurai-env
key: linux-${{ matrix.cpp-version }}
restore-keys: |
linux-${{ matrix.cpp-version }}
- name: Compiler and dev tools installation
run: |
sudo apt update
sudo apt install ${{ matrix.package }}
# - name: Information about ccache
# run: |
# ccache -s -v
- name: Mamba and samurai env installation
uses: mamba-org/setup-micromamba@v1
with:
environment-file: conda/environment.yml
environment-name: samurai-env
cache-environment: true
# - name: Conda update
# shell: bash -l {0}
# run: |
# conda update --all
- name: Petsc installation
shell: bash -l {0}
run: |
conda install -y petsc pkg-config
- name: Conda informations
shell: bash -l {0}
run: |
conda info
conda list
- name: Configure
shell: bash -l {0}
run: |
export LDFLAGS="${LDFLAGS} -L$CONDA_PREFIX/lib"
CC=${{ matrix.cc }} CXX=${{ matrix.cxx }} cmake \
. \
-Bbuild \
-GNinja \
-DCMAKE_BUILD_TYPE=Release \
-DBUILD_DEMOS=ON \
-DBUILD_TESTS=ON
- name: Build
shell: bash -l {0}
run: |
cmake --build build --target all --parallel 3
- name: Test with googletest
shell: bash -l {0}
run: |
export LD_LIBRARY_PATH="$CONDA_PREFIX/lib:$LD_LIBRARY_PATH"
cd build
./tests/test_samurai_lib
- name: Test with pytest
shell: bash -l {0}
run: |
export LD_LIBRARY_PATH="$CONDA_PREFIX/lib:$LD_LIBRARY_PATH"
cd tests
pytest -v -s --h5diff
#
# Check linux build with mamba environment
#
#########################################################
linux-mpi-mamba:
needs: [pre-commit, cppcheck]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Cache
uses: actions/cache@v4
with:
path: |
~/.cache/ccache
~/micromamba-root/envs/samurai-env
key: linux-mpi
restore-keys: |
linux-mpi
- name: Mamba and samurai env installation
uses: mamba-org/setup-micromamba@v1
with:
environment-file: conda/mpi-environment.yml
environment-name: samurai-env
cache-environment: true
# - name: Conda update
# shell: bash -l {0}
# run: |
# conda update --all
- name: Petsc installation
shell: bash -l {0}
run: |
conda install -y mpich petsc pkg-config cxx-compiler
- name: Conda informations
shell: bash -l {0}
run: |
conda info
conda list
- name: Configure
shell: bash -l {0}
run: |
cmake \
. \
-Bbuild \
-GNinja \
-DCMAKE_BUILD_TYPE=Release \
-DWITH_MPI=ON \
-DBUILD_DEMOS=ON \
-DBUILD_TESTS=ON
- name: Build
shell: bash -l {0}
run: |
cmake --build build --target finite-volume-advection-2d --parallel 4
cmake --build build --target finite-volume-burgers --parallel 4
- name: MPI test finite-volume-advection-2d
shell: bash -l {0}
run: |
cd build
set -e # Stop on first failure
mpiexec -n 1 ./demos/FiniteVolume/finite-volume-advection-2d --Tf 0.02
mpiexec -n 2 ./demos/FiniteVolume/finite-volume-advection-2d --Tf 0.02
mpiexec -n 3 ./demos/FiniteVolume/finite-volume-advection-2d --Tf 0.02
mpiexec -n 4 ./demos/FiniteVolume/finite-volume-advection-2d --Tf 0.02
mpiexec -n 9 ./demos/FiniteVolume/finite-volume-advection-2d --Tf 0.02
ls
python ../python/compare.py FV_advection_2d_size_1 FV_advection_2d_size_2
python ../python/compare.py FV_advection_2d_size_1 FV_advection_2d_size_3
python ../python/compare.py FV_advection_2d_size_1 FV_advection_2d_size_4
python ../python/compare.py FV_advection_2d_size_1 FV_advection_2d_size_9
- name: MPI test finite-volume-burgers
shell: bash -l {0}
run: |
cd build
set -e # Stop on first failure
mpiexec -n 1 ./demos/FiniteVolume/finite-volume-burgers --Tf 0.02 --nfiles 1 --max-level 7
mpiexec -n 2 ./demos/FiniteVolume/finite-volume-burgers --Tf 0.02 --nfiles 1 --max-level 7
mpiexec -n 3 ./demos/FiniteVolume/finite-volume-burgers --Tf 0.02 --nfiles 1 --max-level 7
mpiexec -n 4 ./demos/FiniteVolume/finite-volume-burgers --Tf 0.02 --nfiles 1 --max-level 7
mpiexec -n 9 ./demos/FiniteVolume/finite-volume-burgers --Tf 0.02 --nfiles 1 --max-level 7
ls
# Uncomment the following lines once mesh refinement is fixed
# python ../python/compare.py burgers_2D_size_1 burgers_2D_size_2
# python ../python/compare.py burgers_2D_size_1 burgers_2D_size_3
# python ../python/compare.py burgers_2D_size_1 burgers_2D_size_4
# python ../python/compare.py burgers_2D_size_1 burgers_2D_size_9
macos-mamba:
needs: [pre-commit, cppcheck]
runs-on: macos-14
steps:
- uses: actions/checkout@v4
- name: Mamba and samurai env installation
uses: mamba-org/setup-micromamba@v1
with:
environment-file: conda/environment.yml
environment-name: samurai-env
cache-environment: true
# - name: Petsc installation
# shell: bash -l {0}
# run: |
# micromamba install -y petsc=3.18 pkg-config
- name: Installl cxx compiler
shell: bash -l {0}
run: |
micromamba install -y cxx-compiler
- name: micromamba informations
shell: bash -l {0}
run: |
micromamba info
micromamba list
- name: Configure
shell: bash -l {0}
run: |
cmake \
. \
-Bbuild \
-GNinja \
-DCMAKE_BUILD_TYPE=Release \
-DBUILD_DEMOS=ON \
-DBUILD_TESTS=ON
- name: Build
shell: bash -l {0}
run: |
cmake --build ./build --config Release --parallel 3
- name: Run tests
shell: bash -l {0}
run: |
./build/tests/test_samurai_lib
cd tests; pytest --h5diff