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debug multiple fault partition #17

debug multiple fault partition

debug multiple fault partition #17

Workflow file for this run

# Github Actions workflow
#
# runs compilation tests on Linux Ubuntu and Mac platforms
name: CI
on: [push, pull_request]
jobs:
changesCheck:
name: Check file changes
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Check for changes
id: diff
run: |
if [ $GITHUB_BASE_REF ]; then
# Pull Request
echo "Pull request:"
git fetch origin $GITHUB_BASE_REF --depth=1
export DIFF=$( git diff --name-only origin/$GITHUB_BASE_REF $GITHUB_SHA )
echo " diff between origin/$GITHUB_BASE_REF and $GITHUB_SHA"
else
# Push
echo "Push request:"
git fetch origin ${{ github.event.before }} --depth=1
export DIFF=$( git diff --name-only ${{ github.event.before }} $GITHUB_SHA )
echo " diff between ${{ github.event.before }} and $GITHUB_SHA"
fi
echo "***"; echo "$DIFF"; echo "***"
# Escape newlines (replace \n with %0A)
# deprecated:
#echo "::set-output name=diff::$( echo "$DIFF" | sed ':a;N;$!ba;s/\n/%0A/g' )"
# new:
# replace new line with %0A - will result finding only one file with a very long name...
#echo "diff=$( echo "$DIFF" | sed ':a;N;$!ba;s/\n/%0A/g' )" >> $GITHUB_OUTPUT
# doesn't work...
#echo "diff=\"$DIFF\"" >> "$GITHUB_OUTPUT"
# new multi-line format:
# (https://docs.github.com/en/actions/using-workflows/workflow-commands-for-github-actions#multiline-strings)
echo "diff<<EOF" >> $GITHUB_OUTPUT
echo "$DIFF" >> $GITHUB_OUTPUT
echo "EOF" >> $GITHUB_OUTPUT
- name: Output changes
run: echo "${{ steps.diff.outputs.diff }}"
- name: Check files
run: |
RUN_CHECKS=0
DIFF="${{ steps.diff.outputs.diff }}"
# Loop by lines
while read path; do
# Set $directory to substring before /
directory="$( echo $path | cut -d'/' -f1 -s )"
echo "file: $path - directory: $directory"
if [ -z "$directory" ]; then
# root directory
RUN_CHECKS=1
elif [ "$directory" == src ]; then
# src/ directory
RUN_CHECKS=1
elif [ "$directory" == setup ]; then
# setup/ directory
RUN_CHECKS=1
elif [ "$directory" == EXAMPLES ]; then
# EXAMPLES/ directory
RUN_CHECKS=1
elif [ "$directory" == tests ]; then
# tests/ directory
RUN_CHECKS=1
elif [ "$directory" == .github ]; then
# .github/ directory
RUN_CHECKS=1
fi
done <<< "$DIFF"
echo
echo "run checks: ${RUN_CHECKS}"
if [[ ${RUN_CHECKS} -eq 0 ]]; then echo "nothing to check, exiting..."; exit 1; fi
macosCheck:
name: Test on Mac
runs-on: macos-latest
needs: changesCheck
steps:
- uses: actions/checkout@v3
- name: Install dependencies
run: |
brew cleanup
brew reinstall gcc # need gfortran (symlink to gfortran-10)
brew install hwloc openmpi
echo ""
echo "compiler versions:"
echo "gcc --version"
gcc --version
echo "gfortran --version"
gfortran --version
echo "mpif90 --version"
mpif90 --version
echo ""
## avoids sed -i '' issue on MacOS, using gnu sed to have the same sed command lines as in linux
brew install gnu-sed
echo "PATH=/usr/local/opt/gnu-sed/libexec/gnubin:$PATH" >> $GITHUB_ENV
## OpenMP
echo "OMP_NUM_THREADS=2" >> $GITHUB_ENV
## avoids MPI issue with number of slots
echo "OMPI_MCA_rmaps_base_oversubscribe=1" >> $GITHUB_ENV
echo "OMPI_MCA_rmaps_base_inherit=1" >> $GITHUB_ENV
## avoids MPI issue when running in MacOS
echo "OMPI_MCA_btl=self,tcp" >> $GITHUB_ENV
# exports for xterm output (for make tests)
echo "TERM=xterm" >> $GITHUB_ENV
echo ""
echo "exports:"
export
echo ""
- name: configure
run: |
./configure
echo "modifying external_libs/scotch/src/Makefile.inc"
cp -v external_libs/scotch/src/Make.inc/Makefile.inc.i686_mac_darwin8 external_libs/scotch/src/Makefile.inc
# skipping - compilation check done as well in make tests
#- name: make
# run: make -j2 all
- name: make tests
run: make tests
linuxCheck:
name: Test on ${{ matrix.os }}
runs-on: ${{ matrix.os }}
needs: changesCheck
strategy:
matrix:
os: [ubuntu-latest,ubuntu-20.04]
steps:
- uses: actions/checkout@v3
- name: Install packages
run: ./.github/scripts/run_install.sh
shell: bash
- name: configure
run: ./configure
- name: make
run: make -j2 all
linuxCheck-Intel:
name: Test Intel on ubuntu-20.04
runs-on: ubuntu-20.04
needs: changesCheck
steps:
- uses: actions/checkout@v3
- name: Cache Intel oneapi packages
id: cache-intel-oneapi
uses: actions/cache@v3
with:
path: /opt/intel/oneapi
key: install-${{ runner.os }}-all
- name: Install packages
if: steps.cache-intel-oneapi.outputs.cache-hit != 'true'
run: |
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 ""
sudo echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
sudo apt-get update
echo ""
echo "packages intel oneapi:"
sudo apt-get install -y intel-oneapi-compiler-fortran intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic intel-oneapi-mpi intel-oneapi-mpi-devel
- name: compiler infos
run: |
echo ""
source /opt/intel/oneapi/setvars.sh
echo ""
echo "compiler versions:"
echo "icc --version"
icc --version
echo "ifort --version"
ifort --version
echo "mpiifort --version"
mpiifort --version
echo "mpif90 --version"
mpif90 --version
echo ""
export TERM=xterm
echo "exports:"
export
echo ""
which ifort
which icc
which mpiifort
echo ""
printenv >> $GITHUB_ENV
echo "CXX=icpc" >> $GITHUB_ENV
echo "CC=icc" >> $GITHUB_ENV
echo "FC=ifort" >> $GITHUB_ENV
echo ""
- name: configure serial debug
run: ./configure --enable-debug --without-mpi FC=ifort CC=icc
- name: make serial debug
run: |
make -j2 all
make -j2 all --always-make
make clean
- name: configure serial
run: ./configure --without-mpi FC=ifort CC=icc
- name: make serial
run: |
make -j2 all
make clean
- name: configure parallel debug
run: ./configure --enable-debug --with-mpi FC=ifort CC=icc MPIFC=mpiifort MPI_INC="${I_MPI_ROOT}/include"
- name: make parallel debug
run: |
make -j2 all
make -j2 all --always-make
make clean
- name: configure parallel
run: ./configure --with-mpi FC=ifort CC=icc MPIFC=mpiifort MPI_INC="${I_MPI_ROOT}/include"
- name: make parallel
run: |
make -j2 all
make clean
# check: fails due to intel MPI issue with mpif90 using gfortran as default on virtual nodes
#- name: make tests
# run: make tests
linuxTest_0:
name: Test run example 0 - make tests
runs-on: ubuntu-latest
needs: [linuxCheck]
steps:
- uses: actions/checkout@v3
- name: Install packages
run: ./.github/scripts/run_install.sh
shell: bash
- name: configure
run: ./configure
- name: make tests
run: make tests
linuxTest_1:
name: Test run example 1 - meshfem3D simple model
runs-on: ubuntu-latest
needs: [linuxCheck]
steps:
- uses: actions/checkout@v3
- name: Install packages
run: ./.github/scripts/run_install.sh
shell: bash
- name: Run build
env:
TESTFLAGS: --with-mpi # --enable-vectorization
run: ./.github/scripts/run_build.sh
shell: bash
- name: Run test
env:
TESTDIR: EXAMPLES/meshfem3D_examples/simple_model/
run: ./.github/scripts/run_tests.sh
shell: bash
linuxTest_2:
name: Test run example 2 - fault tpv5
runs-on: ubuntu-latest
needs: [linuxCheck]
steps:
- uses: actions/checkout@v3
- name: Install packages
run: ./.github/scripts/run_install.sh
shell: bash
- name: Run build
env:
TESTFLAGS: --with-mpi
run: ./.github/scripts/run_build.sh
shell: bash
- name: Run test
env:
TESTDIR: EXAMPLES/fault_examples/tpv5/
run: ./.github/scripts/run_tests.sh
shell: bash
linuxTest_3:
name: Test run example 3 - layered halfspace
runs-on: ubuntu-latest
needs: [linuxCheck]
steps:
- uses: actions/checkout@v3
- name: Install packages
run: ./.github/scripts/run_install.sh
shell: bash
- name: Run build
env:
TESTFLAGS: --with-mpi
TESTNGLL: 6
run: ./.github/scripts/run_build.sh
shell: bash
- name: Run test
env:
TESTDIR: EXAMPLES/layered_halfspace/
run: ./.github/scripts/run_tests.sh
shell: bash
linuxTest_4:
name: Test run example 4 - small adjoint
runs-on: ubuntu-latest
needs: [linuxCheck]
steps:
- uses: actions/checkout@v3
- name: Install packages
run: ./.github/scripts/run_install.sh
shell: bash
- name: Run build
env:
TESTFLAGS: --with-mpi
run: ./.github/scripts/run_build.sh
shell: bash
- name: Run test
env:
TESTDIR: EXAMPLES/small_adjoint_multiple_sources/
run: ./.github/scripts/run_tests.sh
shell: bash
linuxTest_5:
name: Test run example 5 - socal1D
runs-on: ubuntu-latest
needs: [linuxCheck]
steps:
- uses: actions/checkout@v3
- name: Install packages
run: ./.github/scripts/run_install.sh
shell: bash
- name: Run build
env:
TESTFLAGS: --with-mpi
run: ./.github/scripts/run_build.sh
shell: bash
- name: Run test
env:
TESTDIR: EXAMPLES/meshfem3D_examples/socal1D/
TESTID: 0
run: ./.github/scripts/run_tests.sh
shell: bash
linuxTest_6:
name: Test run example 6 - socal1D 1d_socal
runs-on: ubuntu-latest
needs: [linuxCheck]
steps:
- uses: actions/checkout@v3
- name: Install packages
run: ./.github/scripts/run_install.sh
shell: bash
- name: Run build
env:
TESTFLAGS: --with-mpi
run: ./.github/scripts/run_build.sh
shell: bash
- name: Run test
env:
TESTDIR: EXAMPLES/meshfem3D_examples/socal1D/
TESTID: 1
run: ./.github/scripts/run_tests.sh
shell: bash
linuxTest_7:
name: Test run example 7 - socal1D 1d_prem
runs-on: ubuntu-latest
needs: [linuxCheck]
steps:
- uses: actions/checkout@v3
- name: Install packages
run: ./.github/scripts/run_install.sh
shell: bash
- name: Run build
env:
TESTFLAGS: --with-mpi
run: ./.github/scripts/run_build.sh
shell: bash
- name: Run test
env:
TESTDIR: EXAMPLES/meshfem3D_examples/socal1D/
TESTID: 2
run: ./.github/scripts/run_tests.sh
shell: bash
linuxTest_8:
name: Test run example 8 - socal1D 1d_cascadia
runs-on: ubuntu-latest
needs: [linuxCheck]
steps:
- uses: actions/checkout@v3
- name: Install packages
run: ./.github/scripts/run_install.sh
shell: bash
- name: Run build
env:
TESTFLAGS: --with-mpi
run: ./.github/scripts/run_build.sh
shell: bash
- name: Run test
env:
TESTDIR: EXAMPLES/meshfem3D_examples/socal1D/
TESTID: 3
run: ./.github/scripts/run_tests.sh
shell: bash
linuxTest_9:
name: Test run example 9 - coupling FK
runs-on: ubuntu-latest
needs: [linuxCheck]
steps:
- uses: actions/checkout@v3
- name: Install packages
run: ./.github/scripts/run_install.sh
shell: bash
- name: Run build
env:
TESTFLAGS: --with-mpi
run: ./.github/scripts/run_build.sh
shell: bash
- name: Run test
env:
TESTDIR: EXAMPLES/small_example_coupling_FK_specfem/
run: ./.github/scripts/run_tests.sh
shell: bash
linuxTest_10:
name: Test run example 10 - homogeneous halfspace
runs-on: ubuntu-latest
needs: [linuxCheck]
steps:
- uses: actions/checkout@v3
- name: Install packages
run: ./.github/scripts/run_install.sh
shell: bash
- name: Run build
env:
TESTFLAGS: --with-mpi
run: ./.github/scripts/run_build.sh
shell: bash
- name: Run test
env:
TESTDIR: EXAMPLES/homogeneous_halfspace_HEX8_elastic_no_absorbing/
run: ./.github/scripts/run_tests.sh
shell: bash
linuxTest_11:
name: Test run example 11 - poroelastic
runs-on: ubuntu-latest
needs: [linuxCheck]
steps:
- uses: actions/checkout@v3
- name: Install packages
run: ./.github/scripts/run_install.sh
shell: bash
- name: Run build
env:
TESTFLAGS: --with-mpi
run: ./.github/scripts/run_build.sh
shell: bash
- name: Run test
env:
TESTDIR: EXAMPLES/homogeneous_poroelastic/
run: ./.github/scripts/run_tests.sh
shell: bash
linuxTest_12:
name: Test run example 12 - PML elastic
runs-on: ubuntu-latest
needs: [linuxCheck]
steps:
- uses: actions/checkout@v3
- name: Install packages
run: ./.github/scripts/run_install.sh
shell: bash
- name: Run build
env:
TESTFLAGS: --with-mpi
run: ./.github/scripts/run_build.sh
shell: bash
- name: Run test
env:
TESTDIR: EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_elastic_absorbing_CPML_5sides/
run: ./.github/scripts/run_tests.sh
shell: bash
linuxTest_13:
name: Test run example 13 - PML acoustic
runs-on: ubuntu-latest
needs: [linuxCheck]
steps:
- uses: actions/checkout@v3
- name: Install packages
run: ./.github/scripts/run_install.sh
shell: bash
- name: Run build
env:
TESTFLAGS: --with-mpi
run: ./.github/scripts/run_build.sh
shell: bash
- name: Run test
env:
TESTDIR: EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_acoustic_absorbing_CPML_5sides/
run: ./.github/scripts/run_tests.sh
shell: bash
linuxTest_14:
name: Test run example 14 - waterlayered halfspace
runs-on: ubuntu-latest
needs: [linuxCheck]
steps:
- uses: actions/checkout@v3
- name: Install packages
run: ./.github/scripts/run_install.sh
shell: bash
- name: Run build
env:
TESTFLAGS: --with-mpi
run: ./.github/scripts/run_build.sh
shell: bash
- name: Run test
env:
TESTDIR: EXAMPLES/waterlayered_halfspace/
run: ./.github/scripts/run_tests.sh
shell: bash
linuxTest_15:
name: Test run example 15 - tomographic model
runs-on: ubuntu-latest
needs: [linuxCheck]
steps:
- uses: actions/checkout@v3
- name: Install packages
run: ./.github/scripts/run_install.sh
shell: bash
- name: Run build
env:
TESTFLAGS: --with-mpi
run: ./.github/scripts/run_build.sh
shell: bash
- name: Run test
env:
TESTDIR: EXAMPLES/tomographic_model/
run: ./.github/scripts/run_tests.sh
shell: bash
linuxTest_16:
name: Test run example 16 - cavity
runs-on: ubuntu-latest
needs: [linuxCheck]
steps:
- uses: actions/checkout@v3
- name: Install packages
run: ./.github/scripts/run_install.sh
shell: bash
- name: Run build
env:
TESTFLAGS: --with-mpi
run: ./.github/scripts/run_build.sh
shell: bash
- name: Run test
env:
TESTDIR: EXAMPLES/meshfem3D_examples/cavity/
run: ./.github/scripts/run_tests.sh
shell: bash
linuxTest_17:
name: Test run example 17 - sep bathymetry
runs-on: ubuntu-latest
needs: [linuxCheck]
steps:
- uses: actions/checkout@v3
- name: Install packages
run: ./.github/scripts/run_install.sh
shell: bash
- name: Run build
env:
TESTFLAGS: --with-mpi
run: ./.github/scripts/run_build.sh
shell: bash
- name: Run test
env:
TESTDIR: EXAMPLES/meshfem3D_examples/sep_bathymetry/
run: ./.github/scripts/run_tests.sh
shell: bash