add plots to test incident wave frequency content #9

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@v2

	- 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 $GITHUB_SHA"
	fi
	echo "$DIFF"
	# Escape newlines (replace \n with %0A)
	echo "::set-output name=diff::$( echo "$DIFF" \| sed ':a;N;$!ba;s/\n/%0A/g' )"

	- 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@v2

	- 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-18.04]

	steps:
	- uses: actions/checkout@v2

	- 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@v2

	- name: Cache Intel oneapi packages
	id: cache-intel-oneapi
	uses: actions/cache@v2
	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@v2

	- 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@v2

	- 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@v2

	- 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@v2

	- 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@v2

	- 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@v2

	- 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@v2

	- 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@v2

	- 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@v2

	- 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@v2

	- 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@v2

	- 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@v2

	- 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@v2

	- 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@v2

	- 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@v2

	- 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@v2

	- 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@v2

	- 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@v2

	- 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

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add plots to test incident wave frequency content #9

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add plots to test incident wave frequency content #9

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Workflow file for this run