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Merge branch 'SPECFEM:devel' into devel
2 parents 8ba40c5 + a5bb135 commit 3e7a2b9

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‎.github/scripts/run_build.sh‎

Lines changed: 14 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -29,13 +29,25 @@ echo "mpif90 --version"
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mpif90 --version
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echo
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32+
## ADIOS2
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if [ "${ADIOS2}" == "true" ]; then
34+
echo
35+
echo "enabling ADIOS2"
36+
echo
37+
ADIOS2_CONFIG="${ADIOS2_DIR}/bin/adios2-config"
38+
adios=(--with-adios2 ADIOS2_CONFIG="$ADIOS2_CONFIG" )
39+
else
40+
adios=()
41+
fi
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# configuration
3444
echo
35-
echo "configuration: default"
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echo "configuration:"
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echo
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38-
./configure FC=gfortran MPIFC=mpif90 CC=gcc ${TESTFLAGS}
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./configure \
49+
${adios[@]} \
50+
FC=gfortran MPIFC=mpif90 CC=gcc ${TESTFLAGS}
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# checks
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if [[ $? -ne 0 ]]; then echo "configuration failed:"; cat config.log; echo ""; echo "exiting..."; exit 1; fi

‎.github/scripts/run_install.sh‎

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Original file line numberDiff line numberDiff line change
@@ -38,6 +38,12 @@ fi
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if [[ $? -ne 0 ]]; then exit 1; fi
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echo
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# python3 pip upgrade might complain: "ERROR: launchpadlib 1.10.13 requires testresources"
42+
sudo apt-get install -yq --no-install-recommends python3-testresources
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# checks exit code
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if [[ $? -ne 0 ]]; then exit 1; fi
45+
echo
46+
4147
# python script needs numpy
4248
#sudo apt-get install -qq python-numpy # not working, likely installed on older python version
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pip install --user --upgrade pip setuptools wheel
@@ -68,6 +74,39 @@ echo "mpif90 --version"
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mpif90 --version
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echo
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## ADIOS2
78+
if [ "${ADIOS2}" == "true" ]; then
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echo
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echo "ADIOS2 installation:"
81+
echo
82+
# installs cmake wget
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sudo apt-get install -yq --no-install-recommends cmake wget
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# checks exit code
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if [[ $? -ne 0 ]]; then exit 1; fi
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# uses /opt as installation directory
87+
mkdir -p /opt; cd /opt
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# download source
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wget https://github.com/ornladios/ADIOS2/archive/refs/tags/v2.10.1.tar.gz
90+
tar zxf v2.10.1.tar.gz
91+
cd ADIOS2-2.10.1/
92+
# build source
93+
mkdir -p build; cd build/
94+
CC=gcc CXX=g++ FC=gfortran cmake -DADIOS2_USE_Fortran=ON \
95+
-DADIOS2_USE_HDF5=OFF -DADIOS2_BUILD_EXAMPLES=OFF -DBUILD_TESTING=OFF \
96+
-DCMAKE_INSTALL_PREFIX=/opt/ADIOS2 ../
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# checks exit code
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if [[ $? -ne 0 ]]; then exit 1; fi
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make -j4
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# checks exit code
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if [[ $? -ne 0 ]]; then exit 1; fi
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make install
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# checks exit code
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if [[ $? -ne 0 ]]; then exit 1; fi
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# environment for directory
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echo "ADIOS2_DIR=/opt/ADIOS2" >> $GITHUB_ENV
107+
echo; echo "done ADIOS2"; echo
108+
fi
109+
71110
# MPI
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# github actions uses for Linux virtual machines a 2-core CPU environment
73112
# see: https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources

‎.github/scripts/run_tests.sh‎

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Original file line numberDiff line numberDiff line change
@@ -117,6 +117,12 @@ if [[ "${TEST}" == *"with-hdf5"* ]]; then
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cp -v run_this_example_HDF5_IO_server.sh run_this_example.sh
118118
fi
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120+
# adios
121+
if [ "${ADIOS2}" == "true" ]; then
122+
# turns on ADIOS
123+
sed -i "s:^ADIOS_ENABLED .*:ADIOS_ENABLED = .true.:" DATA/Par_file
124+
fi
125+
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# default script
121127
./run_this_example.sh
122128

‎.github/workflows/CI.yml‎

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@@ -11,7 +11,7 @@ jobs:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Check for changes
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id: diff
@@ -86,7 +86,7 @@ jobs:
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needs: changesCheck
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Install dependencies
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run: |
@@ -104,9 +104,16 @@ jobs:
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echo ""
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## avoids sed -i '' issue on MacOS, using gnu sed to have the same sed command lines as in linux
106106
brew install gnu-sed
107-
echo "PATH=/usr/local/opt/gnu-sed/libexec/gnubin:$PATH" >> $GITHUB_ENV
107+
echo "PATH=/opt/homebrew/opt/gnu-sed/libexec/gnubin:$PATH" >> $GITHUB_ENV
108108
## OpenMP
109109
echo "OMP_NUM_THREADS=2" >> $GITHUB_ENV
110+
## MPI
111+
echo
112+
echo "MPI environment:"
113+
echo "mpif90 on path: $(which mpif90)"
114+
echo
115+
# add OpenMPI path to have ./configure detect mpi.h
116+
echo "MPI_INC=/opt/homebrew/include" >> $GITHUB_ENV
110117
## avoids MPI issue with number of slots
111118
echo "OMPI_MCA_rmaps_base_oversubscribe=1" >> $GITHUB_ENV
112119
echo "OMPI_MCA_rmaps_base_inherit=1" >> $GITHUB_ENV
@@ -121,7 +128,8 @@ jobs:
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- name: configure
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run: |
124-
./configure
131+
./configure ; if [[ $? -ne 0 ]]; then cat config.log; exit 1; fi
132+
# changes SCOTCH Makefile for macOS
125133
echo "modifying external_libs/scotch/src/Makefile.inc"
126134
cp -v external_libs/scotch/src/Make.inc/Makefile.inc.i686_mac_darwin8 external_libs/scotch/src/Makefile.inc
127135
@@ -139,10 +147,10 @@ jobs:
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strategy:
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matrix:
142-
os: [ubuntu-latest,ubuntu-20.04]
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os: [ubuntu-latest,ubuntu-22.04]
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Install packages
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run: ./.github/scripts/run_install.sh
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linuxCheck-Intel:
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name: Test Intel on ubuntu-20.04
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runs-on: ubuntu-20.04
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name: Test Intel on ubuntu-22.04
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runs-on: ubuntu-22.04
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needs: changesCheck
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Cache Intel oneapi packages
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id: cache-intel-oneapi
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uses: actions/cache@v3
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uses: actions/cache@v4
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with:
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path: /opt/intel/oneapi
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key: install-${{ runner.os }}-all
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needs: [linuxCheck]
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- uses: actions/checkout@v3
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- name: Install packages
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needs: [linuxCheck]
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needs: [linuxCheck]
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needs: [linuxCheck]
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- uses: actions/checkout@v3
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- name: Install packages
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needs: [linuxCheck]
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- uses: actions/checkout@v3
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needs: [linuxCheck]
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needs: [linuxCheck]
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needs: [linuxCheck]
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needs: [linuxCheck]
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env:
@@ -751,3 +759,31 @@ jobs:
751759
run: ./.github/scripts/run_tests.sh
752760
shell: bash
753761

762+
linuxTest_19:
763+
name: Test run example 19 - meshfem3D simple model w/ ADIOS2
764+
runs-on: ubuntu-latest
765+
needs: [linuxCheck]
766+
767+
steps:
768+
- uses: actions/checkout@v4
769+
770+
- name: Install packages
771+
env:
772+
ADIOS2: true
773+
run: ./.github/scripts/run_install.sh
774+
shell: bash
775+
776+
- name: Run build
777+
env:
778+
TESTFLAGS: --with-mpi --enable-vectorization
779+
ADIOS2: true
780+
run: ./.github/scripts/run_build.sh
781+
shell: bash
782+
783+
- name: Run test
784+
env:
785+
TESTDIR: EXAMPLES/applications/meshfem3D_examples/simple_model/
786+
ADIOS2: true
787+
run: ./.github/scripts/run_tests.sh
788+
shell: bash
789+

‎.gitignore‎

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Original file line numberDiff line numberDiff line change
@@ -24,6 +24,7 @@ src/generate_databases/*.mod
2424
src/meshfem3D/*.mod
2525
src/specfem3D/*.mod
2626
*__genmod.f90
27+
my_mpi.mod
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2829
# documentation
2930
manual_SPECFEM3D_Cartesian.aux

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