enable hwloc and HeFFTe support in GROMACS easyblock #5259

Workflow file for this run

.github/workflows/unit_tests.yml at 53a9a23

	name: easyblocks unit tests
	on: [push, pull_request]

	permissions:
	contents: read # to fetch code (actions/checkout)

	concurrency:
	group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}}
	cancel-in-progress: true

	jobs:
	build:
	runs-on: ubuntu-20.04
	strategy:
	matrix:
	python: [3.6, 3.7, 3.8, 3.9, '3.10', '3.11']
	modules_tool: [Lmod-6.6.3, Lmod-7.8.22, Lmod-8.1.14, modules-tcl-1.147, modules-3.2.10, modules-4.1.4]
	module_syntax: [Lua, Tcl]
	# exclude some configuration for non-Lmod modules tool:
	# - don't test with Lua module syntax (only supported in Lmod)
	# - don't test with Python 3.7+ (only with 3.6), to limit test configurations
	exclude:
	- modules_tool: modules-tcl-1.147
	module_syntax: Lua
	- modules_tool: modules-3.2.10
	module_syntax: Lua
	- modules_tool: modules-4.1.4
	module_syntax: Lua
	- modules_tool: modules-tcl-1.147
	python: 3.7
	- modules_tool: modules-tcl-1.147
	python: 3.8
	- modules_tool: modules-tcl-1.147
	python: 3.9
	- modules_tool: modules-tcl-1.147
	python: '3.10'
	- modules_tool: modules-tcl-1.147
	python: '3.11'
	- modules_tool: modules-3.2.10
	python: 3.7
	- modules_tool: modules-3.2.10
	python: 3.8
	- modules_tool: modules-3.2.10
	python: 3.9
	- modules_tool: modules-3.2.10
	python: '3.10'
	- modules_tool: modules-3.2.10
	python: '3.11'
	- modules_tool: modules-4.1.4
	python: 3.7
	- modules_tool: modules-4.1.4
	python: 3.8
	- modules_tool: modules-4.1.4
	python: 3.9
	- modules_tool: modules-4.1.4
	python: '3.10'
	- modules_tool: modules-4.1.4
	python: '3.11'
	fail-fast: false
	steps:
	- uses: actions/checkout@v2

	- name: set up Python
	uses: actions/setup-python@v2
	with:
	python-version: ${{matrix.python}}
	architecture: x64

	- name: install OS & Python packages
	run: \|
	# disable apt-get update, we don't really need it,
	# and it does more harm than good (it's fairly expensive, and it results in flaky test runs)
	# sudo apt-get update
	# for modules tool
	sudo apt-get install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev
	# fix for lua-posix packaging issue, see https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082
	# needed for Ubuntu 18.04, but not for Ubuntu 20.04, so skipping symlinking if posix.so already exists
	if [ ! -e /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so ] ; then
	sudo ln -s /usr/lib/x86_64-linux-gnu/lua/5.2/posix_c.so /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so
	fi
	# for testing OpenMPI-system*eb we need to have Open MPI installed
	sudo apt-get install libopenmpi-dev openmpi-bin

	- name: install EasyBuild framework
	run: \|
	# first determine which branch of easybuild-framework repo to install
	BRANCH=develop
	if [ "x$GITHUB_BASE_REF" = 'xmain' ]; then BRANCH=main; fi
	if [ "x$GITHUB_BASE_REF" = 'x4.x' ]; then BRANCH=4.x; fi
	echo "Using easybuild-framework branch $BRANCH (\$GITHUB_BASE_REF $GITHUB_BASE_REF)"
	git clone -b $BRANCH --depth 10 --single-branch https://github.com/easybuilders/easybuild-framework.git
	cd easybuild-framework; git log -n 1; cd -
	pip install $PWD/easybuild-framework

	- name: install modules tool
	run: \|
	cd $HOME
	# use install_eb_dep.sh script provided with easybuild-framework
	export INSTALL_DEP=$(which install_eb_dep.sh)
	echo "Found install_eb_dep.sh script: $INSTALL_DEP"

	# install modules tool
	source $INSTALL_DEP ${{matrix.modules_tool}} $HOME

	# changes in environment are not passed to other steps, so need to create files...
	echo $MOD_INIT > mod_init
	echo $PATH > path
	if [ ! -z $MODULESHOME ]; then echo $MODULESHOME > moduleshome; fi

	- name: install sources
	run: \|
	# install from source distribution tarball, to test release as published on PyPI
	python setup.py sdist
	ls dist
	export PREFIX=/tmp/$USER/$GITHUB_SHA
	pip install --prefix $PREFIX dist/easybuild-easyblocks*tar.gz

	- name: run test suite
	env:
	EB_VERBOSE: 1
	EASYBUILD_MODULE_SYNTAX: ${{matrix.module_syntax}}
	run: \|
	# initialize environment for modules tool
	if [ -f $HOME/moduleshome ]; then export MODULESHOME=$(cat $HOME/moduleshome); fi
	source $(cat $HOME/mod_init); type module

	# make sure 'eb' is available via $PATH, and that $PYTHONPATH is set (some tests expect that);
	# also pick up changes to $PATH set by sourcing $MOD_INIT
	export PREFIX=/tmp/$USER/$GITHUB_SHA
	export PATH=$PREFIX/bin:$(cat $HOME/path)
	export PYTHONPATH=$PREFIX/lib/python${{matrix.python}}/site-packages:$PYTHONPATH

	# tell EasyBuild which modules tool is available
	if [[ ${{matrix.modules_tool}} =~ ^modules-tcl- ]]; then
	export EASYBUILD_MODULES_TOOL=EnvironmentModulesTcl
	elif [[ ${{matrix.modules_tool}} =~ ^modules-3 ]]; then
	export EASYBUILD_MODULES_TOOL=EnvironmentModulesC
	elif [[ ${{matrix.modules_tool}} =~ ^modules-4 ]]; then
	export EASYBUILD_MODULES_TOOL=EnvironmentModules
	else
	export EASYBUILD_MODULES_TOOL=Lmod
	fi

	eb --version
	eb --show-config
	# gather some useful info on test system
	eb --show-system-info

	# actively break "import setuptools" and "import pkg_resources",
	# since EasyBuild should not have a runtime requirement on setuptools
	echo 'raise ImportError("setuptools should no longer be relied on")' > $PREFIX/setuptools.py
	echo 'raise ImportError("setuptools should no longer be relied on")' > $PREFIX/pkg_resources.py
	export PYTHONPATH=$PREFIX:$PYTHONPATH

	# run test suite
	python -O -m test.easyblocks.suite
	# check output of --list-easyblocks
	eb --list-easyblocks > eb_list_easyblocks.out
	grep 'ConfigureMake\>' eb_list_easyblocks.out
	grep EB_GCC eb_list_easyblocks.out

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enable hwloc and HeFFTe support in GROMACS easyblock #5259

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enable hwloc and HeFFTe support in GROMACS easyblock #5259

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