gentoo-overlay/sci-chemistry/gromacs/gromacs-2020.7-r1.ebuild

# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2

EAPI=8

CMAKE_MAKEFILE_GENERATOR="ninja"

PYTHON_COMPAT=( python3_{10..12} )

DISTUTILS_OPTIONAL=1
DISTUTILS_USE_PEP517=no
DISTUTILS_SINGLE_IMPL=1

inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils

if [[ ${PV} = *9999* ]]; then
	EGIT_REPO_URI="
		https://gitlab.com/gromacs/gromacs.git
		https://github.com/gromacs/gromacs.git
		"
	[[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
	inherit git-r3
else
	SRC_URI="
		https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
		doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
		test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
	KEYWORDS="amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos"
fi

ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"

DESCRIPTION="The ultimate molecular dynamics simulation package"
HOMEPAGE="https://www.gromacs.org/"

# see COPYING for details
# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
SLOT="0/${PV}"
IUSE="X blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"

CDEPEND="
	X? (
		x11-libs/libX11
		x11-libs/libSM
		x11-libs/libICE
		)
	blas? ( virtual/blas )
	cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14:= )
	opencl? ( virtual/opencl )
	fftw? ( sci-libs/fftw:3.0= )
	hwloc? ( sys-apps/hwloc:= )
	lapack? ( virtual/lapack )
	lmfit? ( sci-libs/lmfit:= )
	mkl? ( sci-libs/mkl )
	mpi? ( virtual/mpi )
	${PYTHON_DEPS}
	"
BDEPEND="${CDEPEND}
	virtual/pkgconfig
	build-manual? (
		app-text/doxygen
		$(python_gen_cond_dep '
			dev-python/sphinx[${PYTHON_USEDEP}]
		')
		media-gfx/mscgen
		media-gfx/graphviz
		dev-texlive/texlive-latex
		dev-texlive/texlive-latexextra
		media-gfx/imagemagick
	)"
RDEPEND="${CDEPEND}"

REQUIRED_USE="
	|| ( single-precision double-precision )
	doc? ( !build-manual )
	cuda? ( single-precision )
	opencl? ( single-precision )
	cuda? ( !opencl )
	mkl? ( !blas !fftw !lapack )
	${PYTHON_REQUIRED_USE}"

DOCS=( AUTHORS README )

RESTRICT="!test? ( test )"

if [[ ${PV} != *9999 ]]; then
	S="${WORKDIR}/${PN}-${PV/_/-}"
fi

PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" )

pkg_pretend() {
	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
}

pkg_setup() {
	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
	python-single-r1_pkg_setup
}

src_unpack() {
	if [[ ${PV} != *9999 ]]; then
		default
	else
		git-r3_src_unpack
		if use test; then
			EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git" \
			EGIT_BRANCH="${EGIT_BRANCH}" \
			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
				git-r3_src_unpack
		fi
	fi
}

src_prepare() {
	#notes/todos
	# -on apple: there is framework support

	xdg_environment_reset #591952

	cmake_src_prepare

	use cuda && cuda_src_prepare

	GMX_DIRS=""
	use single-precision && GMX_DIRS+=" float"
	use double-precision && GMX_DIRS+=" double"

	if use test; then
		for x in ${GMX_DIRS}; do
			mkdir -p "${WORKDIR}/${P}_${x}" || die
			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
		done
	fi

	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
	if use build-manual; then
		# try to create policy for imagemagik
		mkdir -p "${HOME}"/.config/ImageMagick
		cat >> "${HOME}"/.config/ImageMagick/policy.xml <<- EOF
		<?xml version="1.0" encoding="UTF-8"?>
		<!DOCTYPE policymap [
		<!ELEMENT policymap (policy)+>
		!ATTLIST policymap xmlns CDATA #FIXED ''>
		<!ELEMENT policy EMPTY>
		<!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
			name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
			stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
		]>
		<policymap>
			<policy domain="coder" rights="read | write" pattern="PS" />
			<policy domain="coder" rights="read | write" pattern="PS2" />
			<policy domain="coder" rights="read | write" pattern="PS3" />
			<policy domain="coder" rights="read | write" pattern="EPS" />
			<policy domain="coder" rights="read | write" pattern="PDF" />
			<policy domain="coder" rights="read | write" pattern="XPS" />
		</policymap>
		EOF
	fi
}

src_configure() {
	local mycmakeargs_pre=( ) extra fft_opts=( )

	if use custom-cflags; then
		#go from slowest to fastest acceleration
		local acce="None"
		use cpu_flags_x86_sse2 && acce="SSE2"
		use cpu_flags_x86_sse4_1 && acce="SSE4.1"
		use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
		use cpu_flags_x86_avx && acce="AVX_256"
		use cpu_flags_x86_avx2 && acce="AVX2_256"
	else
		strip-flags
	fi

	#to create man pages, build tree binaries are executed (bug #398437)
	[[ ${CHOST} = *-darwin* ]] && \
		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"

	if use fftw; then
		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
	elif use mkl; then
		local bits=$(get_libdir)
		fft_opts=( -DGMX_FFT_LIBRARY=mkl
			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
		)
	else
		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
	fi

	if use lmfit; then
		local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL )
	else
		local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL )
	fi

	mycmakeargs_pre+=(
		"${fft_opts[@]}"
		"${lmfit_opts[@]}"
		-DGMX_X11=$(usex X)
		-DGMX_EXTERNAL_BLAS=$(usex blas)
		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
		-DGMX_OPENMP=$(usex openmp)
		-DGMX_COOL_QUOTES=$(usex offensive)
		-DGMX_USE_TNG=$(usex tng)
		-DGMX_BUILD_MANUAL=$(usex build-manual)
		-DGMX_HWLOC=$(usex hwloc)
		-DGMX_DEFAULT_SUFFIX=off
		-DGMX_SIMD="$acce"
		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
		-DBUILD_TESTING=$(usex test)
		-DGMX_BUILD_UNITTESTS=$(usex test)
		-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
		${extra}
	)

	for x in ${GMX_DIRS}; do
		einfo "Configuring for ${x} precision"
		local suffix=""
		#if we build single and double - double is suffixed
		use double-precision && use single-precision && \
			[[ ${x} = "double" ]] && suffix="_d"
		local p
		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
		local cuda=( "-DGMX_GPU=OFF" )
		[[ ${x} = "float" ]] && use cuda && \
			cuda=( "-DGMX_GPU=ON" )
		local opencl=( "-DGMX_USE_OPENCL=OFF" )
		use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" )
		local mycmakeargs=(
			${mycmakeargs_pre[@]} ${p}
			-DGMX_MPI=OFF
			-DGMX_THREAD_MPI=$(usex threads)
			-DGMXAPI=$(usex gmxapi)
			-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
			"${opencl[@]}"
			"${cuda[@]}"
			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
			-DGMX_BINARY_SUFFIX="${suffix}"
			-DGMX_LIBS_SUFFIX="${suffix}"
			-DGMX_PYTHON_PACKAGE=$(usex python)
			)
		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
		[[ ${CHOST} != *-darwin* ]] || \
		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
		use mpi || continue
		einfo "Configuring for ${x} precision with mpi"
		local mycmakeargs=(
			${mycmakeargs_pre[@]} ${p}
			-DGMX_THREAD_MPI=OFF
			-DGMX_MPI=ON
			-DGMX_OPENMM=OFF
			-DGMXAPI=OFF
			"${opencl[@]}"
			"${cuda[@]}"
			-DGMX_BUILD_MDRUN_ONLY=ON
			-DBUILD_SHARED_LIBS=OFF
			-DGMX_BUILD_MANUAL=OFF
			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
			)
		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure
		[[ ${CHOST} != *-darwin* ]] || \
		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
	done
}

src_compile() {
	for x in ${GMX_DIRS}; do
		einfo "Compiling for ${x} precision"
		BUILD_DIR="${WORKDIR}/${P}_${x}"\
			cmake_src_compile
		if use python; then
			BUILD_DIR="${WORKDIR}/${P}_${x}"\
				cmake_src_compile	python_packaging/all
			BUILD_DIR="${WORKDIR}/${P}" \
				distutils-r1_src_compile
		fi
		# not 100% necessary for rel ebuilds as available from website
		if use build-manual; then
			BUILD_DIR="${WORKDIR}/${P}_${x}"\
				cmake_src_compile manual
		fi
		use mpi || continue
		einfo "Compiling for ${x} precision with mpi"
		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
			cmake_src_compile
	done
}

src_test() {
	for x in ${GMX_DIRS}; do
		BUILD_DIR="${WORKDIR}/${P}_${x}"\
			cmake_src_compile check
	done
}

src_install() {
	for x in ${GMX_DIRS}; do
		BUILD_DIR="${WORKDIR}/${P}_${x}" \
			cmake_src_install
		if use python; then
			BUILD_DIR="${WORKDIR}/${P}_${x}" \
				cmake_src_install	python_packaging/install
		fi
		if use build-manual; then
			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
		fi

		if use doc; then
			if [[ ${PV} != *9999* ]]; then
				newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf"
			fi
		fi

		use mpi || continue
		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
			cmake_src_install
	done

	if use tng; then
		insinto /usr/include/tng
		doins src/external/tng_io/include/tng/*h
	fi
	# drop unneeded stuff
	rm "${ED}"/usr/bin/GMXRC* || die
	for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do
		local n=${x##*/gmx-completion-}
		n="${n%.bash}"
		cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
		newbashcomp "${T}"/"${n}" "${n}"
	done
	rm "${ED}"/usr/bin/gmx-completion*.bash || die
	readme.gentoo_create_doc
}

pkg_postinst() {
	einfo
	einfo  "Please read and cite gromacs related papers from list:"
	einfo  "https://www.gromacs.org/articles.html"
	einfo
	readme.gentoo_print_elog
}