NaI analytic potential for FSSH (#178) #1032

Workflow file for this run

.github/workflows/gfortran.yml at 46e61e5

	name: GFortran CI

	# WARNING: When updating the OS version of the Github Actions runner,
	# e.g. from Ubuntu 20.04 to 22.04, you need to manually update the cache keys!
	# This is because there's no easy way to get the OS version from within this workflow file.

	on:
	push:
	branches: [ master ]
	pull_request:

	env:
	# FFLAGS for building ABIN, applicable for most jobs
	ABIN_FFLAGS: -O0 -fopenmp --coverage -fprofile-abs-path -ffpe-trap=invalid,zero,overflow,denormal -fimplicit-none -Wall -Wno-integer-division -Wno-maybe-uninitialized
	ABIN_LDLIBS: --coverage
	OPTIMIZED_FFLAGS: -O3 -fopenmp -fimplicit-none -Wall -Wno-integer-division
	# NOTE: It would be safer to only pass the secret token to the codecov-upload action,
	# but the impact of this token leaking is small anyway.
	# NOTE: It appears that even with this token there are issues,
	# so for now we let the CI succeed even if the upload fails.
	# Reported by many people also at:
	# https://github.com/codecov/codecov-action/issues/926
	CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

	jobs:

	format:
	name: Code format check
	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v4
	- uses: actions/setup-python@v5
	with:
	python-version: '3.11'

	- name: Install fprettify dependencies
	run: pip install configargparse

	- name: Run fprettify
	run: \|
	./autoformat.py
	f=`git ls-files -m`; if [[ -n $f ]];then echo -e "ERROR: Detected unformatted files:\n$f";exit 1;fi

	basic_build:
	name: Basic build
	runs-on: ubuntu-20.04
	strategy:
	fail-fast: false
	matrix:
	gcc_v: [7, 9, 10]
	env:
	FC: gfortran
	GCC_V: ${{ matrix.gcc_v}}
	CODECOV_NAME: ${{format('{0} GCC-{1}', github.job, matrix.gcc_v)}}

	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 2

	- name: Install GCC-7
	if: matrix.gcc_v == 7
	run: \|
	sudo apt install gcc-7 gfortran-7 g++-7
	echo "ABIN_FFLAGS=${ABIN_FFLAGS/-fprofile-abs-path/}" >> $GITHUB_ENV

	- name: Enable runtime checks
	# It looks like this messes up the code coverage, so enabling only some builds
	if: matrix.gcc_v != 7
	run: \|
	echo "ABIN_FFLAGS=${ABIN_FFLAGS} -fcheck=all -fsanitize=address,undefined,leak" >> $GITHUB_ENV
	echo "ABIN_LDLIBS=${ABIN_LDLIBS} -fsanitize=address,undefined,leak" >> $GITHUB_ENV

	- name: Set GFortran version
	run: \|
	sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-${GCC_V} 100 \
	--slave /usr/bin/gfortran gfortran /usr/bin/gfortran-${GCC_V} \
	--slave /usr/bin/gcov gcov /usr/bin/gcov-${GCC_V}

	# pFUnit library is used to build and run unit tests
	- name: pFUnit build Cache
	id: pfunit-cache
	uses: actions/cache@v4
	with:
	path: ~/pfunit/build/installed
	# To force a pFUnit rebuild (bust the cache), make a change to install_pfunit.sh
	key: ${{ runner.os }}-ubuntu20.04-pfunit-gfortran${{ env.GCC_V }}-${{ hashFiles('dev_scripts/install_pfunit.sh') }}
	save-always: true

	- name: Download and build pFUnit
	if: steps.pfunit-cache.outputs.cache-hit != 'true'
	run: ./dev_scripts/install_pfunit.sh ${HOME}/pfunit

	- name: Build ABIN
	run: ./configure --pfunit ${HOME}/pfunit/build/installed/ && make
	env:
	FFLAGS: ${{ env.ABIN_FFLAGS }}
	LDLIBS: ${{ env.ABIN_LDLIBS }}

	- name: Run Unit tests
	run: make unittest

	- name: Codecov upload unit tests
	uses: codecov/codecov-action@v4
	with:
	name: ${{env.CODECOV_NAME}}
	flags: unittests
	fail_ci_if_error: true

	- name: Run End-to-End tests
	if: always()
	run: make e2etest

	- name: Codecov upload
	uses: codecov/codecov-action@v4
	with:
	name: ${{env.CODECOV_NAME}}
	fail_ci_if_error: true

	intel_build:
	name: Intel OneAPI build
	runs-on: ubuntu-20.04
	env:
	FC: mpiifort
	# Use GCC for C++ code to speed up the build
	#CC: icc
	#CXX: icpc
	APT_PACKAGES: >-
	intel-oneapi-compiler-fortran
	intel-oneapi-mpi
	intel-oneapi-mpi-devel
	# intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic

	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 2

	- name: Add Intel repository
	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
	rm GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
	echo "deb https://apt.repos.intel.com/oneapi all main" \| sudo tee /etc/apt/sources.list.d/oneAPI.list
	sudo apt-get update

	- name: Install Intel oneAPI compiler
	run: \|
	sudo apt-get install ${{ env.APT_PACKAGES }}
	source /opt/intel/oneapi/setvars.sh
	printenv >> $GITHUB_ENV

	- name: Build ABIN
	run: ./configure --mpi "" && make
	env:
	FFLAGS: -O0 -fopenmp -warn all,noextern

	- name: Run End-to-End tests
	run: make e2etest

	tcpb_build:
	name: TCPB build
	runs-on: ubuntu-20.04
	needs: basic_build
	env:
	FC: gfortran
	CODECOV_NAME: ${{format('{0}', github.job)}}
	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 2

	- name: Install protocol buffers library
	run: sudo apt install protobuf-compiler

	- name: TCBP build cache
	id: tcpb-cache
	uses: actions/cache@v4
	with:
	path: ~/tcpb-cpp/lib
	# To force a rebuild (bust the cache), make a change to install_tcpb.sh
	key: ${{ runner.os }}-ubuntu20.04-tcpb-gfortran-default-${{ hashFiles('dev_scripts/install_tcpb.sh') }}

	- name: Download and build tcpb_cpp
	if: steps.tcpb-cache.outputs.cache-hit != 'true'
	run: ./dev_scripts/install_tcpb.sh ${HOME}/tcpb-cpp

	- name: Build ABIN
	run: ./configure --tcpb ${HOME}/tcpb-cpp/lib && make
	env:
	FFLAGS: ${{ env.ABIN_FFLAGS }}
	LDLIBS: ${{ env.ABIN_LDLIBS }}

	- name: Run End-to-End tests
	run: make e2etest

	- name: Codecov upload
	uses: codecov/codecov-action@v4
	with:
	name: tcpb
	fail_ci_if_error: true


	optimized_build:
	name: Optimized build
	# NOTE: We use a more recent Ubuntu version here
	# so we can test more recent GCC versions.
	runs-on: ubuntu-22.04
	needs: basic_build
	strategy:
	fail-fast: false
	matrix:
	gcc_v: [9, 11, 12]
	env:
	FC: gfortran
	GCC_V: ${{ matrix.gcc_v}}

	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 2
	- name: Set GFortran version
	run: \|
	sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-${GCC_V} 100 \
	--slave /usr/bin/gfortran gfortran /usr/bin/gfortran-${GCC_V}

	- name: pFUnit build Cache
	id: pfunit-cache
	uses: actions/cache@v4
	with:
	path: ~/pfunit/build/installed
	key: ${{ runner.os }}-ubuntu22.04-pfunit-gfortran${{ env.GCC_V }}-${{ hashFiles('dev_scripts/install_pfunit.sh') }}
	save-always: true

	- name: Download and build pFUnit
	if: steps.pfunit-cache.outputs.cache-hit != 'true'
	run: ./dev_scripts/install_pfunit.sh ${HOME}/pfunit

	- name: build ABIN
	run: ./configure --pfunit ${HOME}/pfunit/build/installed/ && make
	env:
	FFLAGS: ${{ env.OPTIMIZED_FFLAGS }}

	- name: Run Unit tests
	run: make unittest

	- name: Run End-to-End tests
	run: make e2etest

	# Here we just take the defaults everywhere, except installing libfftw via apt
	# To use FFTW with other Gfortran versions, we would need to build it.
	fftw_build:
	runs-on: ubuntu-22.04
	name: FFTW build
	needs: basic_build
	env:
	CODECOV_NAME: ${{format('{0}', github.job)}}
	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 2

	- name: Install FFTW libraries
	run: sudo apt-get install libfftw3-dev

	- name: pFUnit build Cache
	id: pfunit-cache
	uses: actions/cache@v4
	with:
	path: ~/pfunit/build/installed
	key: ${{ runner.os }}-ubuntu22.04-pfunit-gfortran-default-${{ hashFiles('dev_scripts/install_pfunit.sh') }}
	save-always: true

	- name: Download and build pFUnit
	if: steps.pfunit-cache.outputs.cache-hit != 'true'
	run: ./dev_scripts/install_pfunit.sh ${HOME}/pfunit

	- name: Build ABIN
	run: ./configure --pfunit ${HOME}/pfunit/build/installed/ --fftw && make
	env:
	FFLAGS: ${{ env.ABIN_FFLAGS }}
	LDLIBS: ${{ env.ABIN_LDLIBS }}

	- name: Run Unit tests
	run: make unittest

	- name: Codecov upload unit tests
	uses: codecov/codecov-action@v4
	with:
	name: ${{env.CODECOV_NAME}}
	flags: unittests

	- name: Run End-to-End tests
	run: make e2etest

	- name: Codecov upload
	uses: codecov/codecov-action@v4
	with:
	name: ${{env.CODECOV_NAME}}
	fail_ci_if_error: true

	mpich_build:
	name: MPICH build
	runs-on: ubuntu-20.04
	timeout-minutes: 25
	needs: basic_build
	strategy:
	fail-fast: false
	matrix:
	gcc_v: [7, 10]
	mpich_v: ["3.4.3", "4.0.2"]
	env:
	# To speed-up MPICH build
	CFLAGS: -O0
	GCC_V: ${{ matrix.gcc_v}}
	MPICH_V: ${{matrix.mpich_v}}
	CODECOV_NAME: ${{format('{0} GCC-{1} MPICH-{2}', github.job, matrix.gcc_v, matrix.mpich_v)}}

	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 2

	- name: Install GCC-7
	if: matrix.gcc_v == 7
	run: \|
	sudo apt install gcc-7 gfortran-7 g++-7
	echo "ABIN_FFLAGS=${ABIN_FFLAGS/-fprofile-abs-path/}" >> $GITHUB_ENV

	- name: Set GFortran version
	run: \|
	sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-${GCC_V} 100 \
	--slave /usr/bin/gfortran gfortran /usr/bin/gfortran-${GCC_V} \
	--slave /usr/bin/gcov gcov /usr/bin/gcov-${GCC_V}
	- name: MPICH build Cache
	id: mpich-cache
	uses: actions/cache@v4
	with:
	path: ~/mpich/${{ env.MPICH_V }}/install
	key: ${{runner.os}}-ubuntu20.04-mpich${{ env.MPICH_V }}-gfortran${{ env.GCC_V }}-${{hashFiles('dev_scripts/install_mpich.sh')}}
	save-always: true

	- name: Build and Install MPICH
	if: steps.mpich-cache.outputs.cache-hit != 'true'
	# Without the extra "-fallow-argument-mismatch" FFLAG, configure with GFortran-10 fails with:
	# "The Fortran compiler gfortran does not accept programs
	# that call the same routine with arguments of different types"
	# Unfortunately, previous GCC versions do not have this flag
	# so we need to set it conditionally.
	# MPICH 4.0 also needs FCFLAGS set.
	# We also need to set it for ABIN compilation below.
	run: \|
	if [ $GCC_V -ge 10 ];then export FFLAGS="-fallow-argument-mismatch";export FCFLAGS="-fallow-argument-mismatch";fi && \
	./dev_scripts/install_mpich.sh ${HOME}/mpich ${MPICH_V}

	- name: build ABIN
	run: \|
	if [ $GCC_V -ge 10 ];then export FFLAGS="-fallow-argument-mismatch $FFLAGS";fi && \
	./configure --mpi ${HOME}/mpich/${MPICH_V}/install && make
	env:
	FFLAGS: ${{ env.ABIN_FFLAGS }} -g
	LDLIBS: ${{ env.ABIN_LDLIBS }}
	- name: test ABIN
	run: make test
	- name: Codecov upload
	uses: codecov/codecov-action@v4
	with:
	name: ${{env.CODECOV_NAME}}
	fail_ci_if_error: true

	openmpi_build:
	name: OpenMPI build
	runs-on: ubuntu-20.04
	timeout-minutes: 25
	needs: basic_build
	strategy:
	fail-fast: false
	env:
	# To speed-up OpenMPI build
	CFLAGS: -O0
	CODECOV_NAME: ${{format('{0} OpenMPI-4.0', github.job)}}
	OPENMPI_V: "4.1"
	OPENMPI_PATCH: "2"

	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 2
	- name: OpenMPI build cache
	id: openmpi-cache
	uses: actions/cache@v4
	with:
	path: ~/openmpi/${{ env.OPENMPI_V }}/install
	key: ${{runner.os}}-ubuntu20.04-openmpi${{ env.OPENMPI_V }}-gfortran-default-${{hashFiles('dev_scripts/install_openmpi.sh')}}
	save-always: true

	- name: Build and Install OpenMPI
	if: steps.openmpi-cache.outputs.cache-hit != 'true'
	run: ./dev_scripts/install_openmpi.sh ${HOME}/openmpi ${OPENMPI_V} ${OPENMPI_PATCH}

	- name: build ABIN
	run: ./configure --mpi "${HOME}/openmpi/${OPENMPI_V}/install" && make
	env:
	FFLAGS: ${{ env.ABIN_FFLAGS }}
	LDLIBS: ${{ env.ABIN_LDLIBS }}
	- name: test ABIN
	run: make test
	- name: Codecov upload
	uses: codecov/codecov-action@v4
	with:
	name: ${{env.CODECOV_NAME}}
	fail_ci_if_error: true

	plumed_build:
	name: PLUMED build
	runs-on: ubuntu-20.04
	needs: basic_build
	strategy:
	fail-fast: false
	matrix:
	plumed_v: [2.7.6, 2.8.2]

	env:
	PLUMED_V: ${{ matrix.plumed_v}}
	# Speeding up the Plumed build
	CFLAGS: -O0
	CXXLAGS: -O0
	CODECOV_NAME: ${{format('{0} PLUMED-{1}', github.job, matrix.plumed_v)}}

	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 2
	- name: Plumed build cache
	id: plumed-cache
	uses: actions/cache@v4
	with:
	path: ~/plumed/${{ env.PLUMED_V }}/install
	key: ${{runner.os}}-ubuntu20.04-plumed${{env.PLUMED_V}}-gcc-default-${{hashFiles('dev_scripts/install_plumed.sh')}}
	save-always: true

	- name: Build and Install PLUMED
	if: steps.plumed-cache.outputs.cache-hit != 'true'
	run: ./dev_scripts/install_plumed.sh ${HOME}/plumed ${PLUMED_V}

	- name: pFUnit build Cache
	id: pfunit-cache
	uses: actions/cache@v4
	with:
	path: ~/pfunit/build/installed
	key: ${{ runner.os }}-ubuntu20.04-pfunit-gfortran-default-${{ hashFiles('dev_scripts/install_pfunit.sh') }}

	- name: Download and build pFUnit
	if: steps.pfunit-cache.outputs.cache-hit != 'true'
	run: ./dev_scripts/install_pfunit.sh ${HOME}/pfunit

	- name: build ABIN
	run: \|
	./configure --plumed "${HOME}/plumed/${PLUMED_V}/install"\
	--pfunit ~/pfunit/build/installed/ &&\
	make
	env:
	FFLAGS: ${{ env.ABIN_FFLAGS }}
	LDLIBS: ${{ env.ABIN_LDLIBS }}

	- name: Run Unit tests
	run: make unittest

	- name: Codecov upload unit tests
	uses: codecov/codecov-action@v4
	with:
	name: ${{env.CODECOV_NAME}}
	flags: unittests

	- name: Run End-to-End tests
	run: make e2etest

	- name: Codecov upload
	uses: codecov/codecov-action@v4
	with:
	name: ${{env.CODECOV_NAME}}
	fail_ci_if_error: true

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NaI analytic potential for FSSH (#178) #1032

Workflow file

NaI analytic potential for FSSH (#178) #1032

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Workflow file for this run