sci-chemistry/gromacs: add 2024.5

Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>

2 files changed, 344 insertions, 0 deletions

diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 2b30108401c1..e220e77ac947 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,12 +1,15 @@
 DIST gromacs-2023.5.tar.gz 42079310 BLAKE2B e50dbe76396230f4a886280bdebcf7b131506679240e77d2a2263c3b5dbfe7ef754c4265fc04e9acad7932c7691de7f694cc23140a25d0d5be649a4120f45b0c SHA512 f3a34cf0d379d6d4964d7494af6c6617c0c092293ea38a3a248af2dd2a90cae04696d52e68126176065efc480977942b00efa441028e526e1555c7e84551fc0c
 DIST gromacs-2024.3.tar.gz 42373103 BLAKE2B f45af72ecdf119b423d98b84818eaca1aa2e3f43eaf1aff7435de2a5891079a880f19a654627ee2f43e3a38c9dcfa0638bc6eb6da201b3c9ce89b2dc32fc683b SHA512 13f23e581c2b63f6262e8359e7bed6a1a5f3164047ea38d2b6a44bcd2b20b61332705167435fe2ad30fe6f24f8ab49b982388550cdecb49167e4156e36286d3d
 DIST gromacs-2024.4.tar.gz 42356162 BLAKE2B 3a1019128a2cfd47fb3ab23962a6fcd5bac3b5519d4bfa1239956740226468986ba93e645eb3bc20117968c024823e948fd819a603315399d573275c91c6e51b SHA512 32a08e9417d4d36a29bdfde4e0448bc136bd3db79b5d5c84fa99d9f022ffca6a94b7bd1c7e7a335430fb6bdcf0181e3cbabeb46d13978c0f87b5d88787ea8d63
+DIST gromacs-2024.5.tar.gz 42353127 BLAKE2B c1fa6bd90390c9e13f11995ea9992902e136e15f6191ed47c9eac95384f97221533509ddd2bc4908f1d36fb790aab8a068fd1c00dd6f82e440f4719092b8ea37 SHA512 cb4f6bf4a6a53fb7ee4d8ed832d514d77d21eea3e1b86eec1bf51a4b6197a30aa8d68ca61919d7921c701af365077a9c84c12ef33d5584a1bc796b25709aa7af
 DIST gromacs-2025-rc.tar.gz 44424653 BLAKE2B 24f3d9ab02320604bb4e99a2bfe409061de92069684cec987355490eeeefd0cee2d665d7d1d4277904bf5025f6c59f0b3de36e6bf61b33f780c2ed2c758f6995 SHA512 0c40ea9b34b3f577ebe3843a65d5d384961224dd179434b98725a4f58190e9d0177b63407d276266a838e39b8d846f461672099787e683d7c8f4ad189cbc5571
 DIST manual-2023.5.pdf 13579081 BLAKE2B 42f687ebcdb79bfc77aabac4fd382940c23ba27da380b8eff342c2e9255a58fc11a0458220d1f71f3c13ab1cf6fdabad00ac1bad741781d0b787899165bea2cc SHA512 0661f166f7a8dc24b4244c0139f366832ddfc1298129df2a6e29800b5d1567318781ab547bc7e9ee54de7a62abba4996f8e3010c91d6917c248117e5711d7dbb
 DIST manual-2024.3.pdf 13676383 BLAKE2B fa5b310ee8977c525781492c70a18d40f8842f5fa43831ad0283c033f39968ba98e74ea618a4a9c25d88c3ed694071327220617b17f316ba2f29777c3edc95ca SHA512 8dd09913b89213a6673a5f5e3462fb963d1f30d68e0d58b846b7e2cf2f73baacb14fabab6591b680849607f4ca617cf288899729939b2c32021b4ee5ba06835f
 DIST manual-2024.4.pdf 13690684 BLAKE2B 7fac46df0da9d4cf7584599c7a71c4e1d11f75fc20a7a19ecc8069fdc2e9e35f0292e389f9c40d69dc96bdfea8d4ee370a54279b5531c0fb37c4cbd76caf7800 SHA512 5c4662527554171774adde5a3de220d775723154914838fd7fc3e40c981e1fccac0fd0def1acc500635cd39269d3bcc2edab5ec7aa85a7ea78350969d72ee13c
+DIST manual-2024.5.pdf 13693341 BLAKE2B b2e94b845f04201734c0a3ef834d013c2e65be53614329166d3b7e4ffcdfb71f3d25a4e8d9f852c4a7570b776532b7d0f00f9f62b76b1cd7fa8567ce22d44540 SHA512 b33a6689f965cfd867daee26b88693ab0696bb49db86e4f411030f36ce924e29f9cedbf3df51e3b02a223b91aa54394144795edb632336b8aa9eb164da8d4ded
 DIST manual-2025-rc.pdf 13789080 BLAKE2B e60b7199c3b97989210480b5efe1a8c339c2875cb8257d9a9898dd82282a43c9efb0fd6bc0be065df315590d0fe61fbb0869b85e526020795b6e10c6b5eff659 SHA512 20774686f02f2b2eb2e24b11d22c9d17bfe6f41be43474948285ee75778c456429316da1a9bc3bb727555295eeea4963ea49bb968e25df020ba830d304c3e6bb
 DIST regressiontests-2023.5.tar.gz 48619605 BLAKE2B f2549a34750c6866f054614a00a3360a09b82306e6bd5e5b848e18cdd3a3fabaac6203c5ca734901019403225dd47e0d662838abe9a1db7d07662f1c745b8e4f SHA512 3ccaf9db7dfba641a5e98ebff3d735cae3f679926aba443ffedec20dd6c85e67f0e9711ebad5dfa8105122d5411f5de6ded1802a7da4ddf0599657832c8c597a
 DIST regressiontests-2024.3.tar.gz 32776961 BLAKE2B 6a74977a396f8e82f7aba7a384cc840275b86d470597a4bbb93e97f1c13cd8fcf6d86ab26bdd4a89464b863954c9ed7dbd49af095e821573845f7bda43c2b90b SHA512 1c4afbbca82c9b9ad371713ef5e7e093ca766f25f6fbda55c79ea1aecb2f0a06bdb042d3c8a86e3d9bf9e8b8091244827dbff544f66037ffa56b0bcb341a9d2c
 DIST regressiontests-2024.4.tar.gz 32777006 BLAKE2B 41623de750b89410fa0a52037ea28d99a688b602b286cff732a6e8100b2b72072f579fc4f72bfe7c246ca086b6c6c1c10adb89874db6e1c9276494572e408a9f SHA512 dfbe8ee1b7c5b534842203f2295ea08875df6af3fb94798138b92ab8bc816719e3357db2935d2de4fd798d104ad7cb44860cd65887da7bb2438db422f35e6848
+DIST regressiontests-2024.5.tar.gz 32776573 BLAKE2B 5e397b6c601132ac96b826325bd0304d5939b87f0edaa89ba84d672a9df27351f26dbc9fde39fdb7a177be2743db93198316663a39145231741d08f3268d67cf SHA512 8594e8365f676f18f227b4d6b87fa6a1a8ceab8301302469a626380a7d29035a2cd8667b4d923b26491d3db9298d6660a9c9bde9274dfeba278dfabdb54ef424
 DIST regressiontests-2025-rc.tar.gz 32653300 BLAKE2B 6078855a0a2958732338f402fcce7e0cf0d117916930491977f894aa856ae40d968810f94e2f26f658201a8e00d2df782c27b942adab5d84063e4d2ed9dbfd07 SHA512 b9cfceef1495f43aaebc33d612c5c584c60418b2dab15d0ac78c8d5a52258221db7adce708f78bda70c3f9c48b6527777aceee32fafa603a4eca2d99ab166059
diff --git a/sci-chemistry/gromacs/gromacs-2024.5.ebuild b/sci-chemistry/gromacs/gromacs-2024.5.ebuild
new file mode 100644
index 000000000000..385f80b9f758
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-2024.5.ebuild
@@ -0,0 +1,341 @@
+# Copyright 1999-2025 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 )"
+	# since 2022 arm support was dropped (but not arm64)
+	KEYWORDS="~amd64 -arm ~arm64 ~riscv -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 cpu_flags_x86_avx512f cpu_flags_arm_neon"
+
+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="blas clang clang-cuda cuda  +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
+
+CDEPEND="
+	blas? ( virtual/blas )
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
+	opencl? ( virtual/opencl )
+	openmp? (
+		sys-devel/gcc[openmp]
+		llvm-core/clang-runtime[openmp]
+	)
+	fftw? ( sci-libs/fftw:3.0= )
+	hwloc? ( sys-apps/hwloc:= )
+	lapack? ( virtual/lapack )
+	mkl? ( sci-libs/mkl )
+	mpi? ( virtual/mpi[cxx] )
+	sci-libs/lmfit:=
+	>=dev-cpp/muParser-2.3:=
+	${PYTHON_DEPS}
+	"
+BDEPEND="${CDEPEND}
+	virtual/pkgconfig
+	clang? ( >=llvm-core/clang-6:* )
+	build-manual? (
+		app-text/doxygen
+		$(python_gen_cond_dep '
+			dev-python/sphinx[${PYTHON_USEDEP}]
+			dev-python/sphinx-copybutton[${PYTHON_USEDEP}]
+			dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]
+			dev-python/sphinx-argparse[${PYTHON_USEDEP}]
+			dev-python/sphinxcontrib-autoprogram[${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 )
+	clang-cuda? ( clang cuda )
+	mkl? ( !blas !fftw !lapack )
+	${PYTHON_REQUIRED_USE}"
+
+DOCS=( AUTHORS README )
+
+RESTRICT="!test? ( test )"
+
+PATCHES=( "${FILESDIR}/${PN}-gcc-15.patch" )
+
+if [[ ${PV} != *9999 ]]; then
+	S="${WORKDIR}/${PN}-${PV/_/-}"
+fi
+
+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="${WORKDIR}/regressiontests"\
+				git-r3_src_unpack
+		fi
+	fi
+}
+
+src_prepare() {
+	#notes/todos
+	# -on apple: there is framework support
+
+	xdg_environment_reset #591952
+
+	# we can use clang as default
+	if use clang && ! tc-is-clang ; then
+		export CC=${CHOST}-clang
+		export CXX=${CHOST}-clang++
+	else
+		tc-export CXX CC
+	fi
+	# clang-cuda need to filter mfpmath
+	if use clang-cuda ; then
+		filter-mfpmath sse
+		filter-mfpmath i386
+	fi
+
+	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=( )
+	local acce="AUTO"
+
+	if use custom-cflags; then
+		#go from slowest to fastest acceleration
+		acce="None"
+		if (use amd64 || use x86); then
+			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"
+			use cpu_flags_x86_avx512f && acce="AVX_512"
+		elif (use arm); then
+			use cpu_flags_arm_neon && acce="ARM_NEON"
+		elif (use arm64); then
+			use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD"
+		fi
+	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/*${bits/lib}/libmkl_rt.so)"
+		)
+	else
+		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
+	fi
+
+	mycmakeargs_pre+=(
+		"${fft_opts[@]}"
+		"${lmfit_opts[@]}"
+		-DGMX_USE_LMFIT=EXTERNAL
+		-DGMX_USE_MUPARSER=EXTERNAL
+		-DGMX_EXTERNAL_BLAS=$(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 gpu=( "-DGMX_GPU=OFF" )
+		[[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
+		[[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" )
+		use opencl && gpu=( "-DGMX_GPU=OPENCL" )
+		local mycmakeargs=(
+			${mycmakeargs_pre[@]} ${p}
+			-DGMX_MPI=$(usex mpi)
+			-DGMX_THREAD_MPI=$(usex threads)
+			-DGMXAPI=$(usex gmxapi)
+			-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
+			"${gpu[@]}"
+			"$(use test && echo -DREGRESSIONTEST_PATH="${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
+	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
+	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-${PV}.pdf"
+			fi
+		fi
+	done
+
+	if use tng; then
+		insinto /usr/include/tng
+		doins src/external/tng_io/include/tng/*h
+	fi
+	# drop unneeded stuff
+	rm "${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
+}