sci-chemistry/gromacs: add 2021.6

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

2 files changed, 358 insertions, 0 deletions

diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 6b31f7f7e8cb..f999c8f5def4 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -4,6 +4,7 @@ DIST gromacs-2020.4.tar.gz 29149899 BLAKE2B a07c8efd96137d58c1edf4ac9b5aafeb16d9
 DIST gromacs-2020.7.tar.gz 29175554 BLAKE2B 98f1aa415946f8eb113febc81105f0c1b0919b96fc3c55a0ab83bf3950ff509b81eade92e645adb0bc2b407df239e20cf3f19828b6e08616437c8693c1fddcc8 SHA512 1d375c44cec38445e56cea252623b5b6c565680268999d4b6c14d6dc38759a27227655b2d29efaab9f9115d3677b446cb555e11cddafa0dc10c4827caaa2477b
 DIST gromacs-2021.3.tar.gz 37987972 BLAKE2B d71995c7d5a34978246e33dc637ac3d273e547afcf72d1a107026650f03286ecdf27e4b9a70113b3c3a01af59ad49ac5c813aa6e5d2e8eb29fd05582a7a28d34 SHA512 da420917d06de2e192dfbb4e1b9f46989ed05b5c7e641c657104ed8f2bd8b22509bffd1ecfd7c965c80544eafa6af12d6d0aba7e1e7d9d14a4a88fb3fbf394a5
 DIST gromacs-2021.5.tar.gz 38023772 BLAKE2B 45e1f080b86626423e471f06b48b615db1913048f9f6998da8ce45408339b32f829d33dd2af57297a7d307fcffd556c333a58c309ee0f2adb021ca3755619b05 SHA512 56c1b312fc8e52ec6f86e445d2fa2d07107c461b35d4dc8cdf95580f05fd8e6c5fd671d0e72b2b9e74e3232bc8c41db496fe4bcaf2b9a3ae3c2cfa93489a31c5
+DIST gromacs-2021.6.tar.gz 38012702 BLAKE2B 023ae37dc53643758afa050fd179cd66f3c6d6266f6afceee5eb35c890a3ae284956f2bc2409156d6e1fa03a7f23f7b04c27e1820547fd5f147b344d94da7d40 SHA512 65d7874e5cd838ce4f29d033c66304738ccc30f1987f9f8541725058b2fc4551302a399f6ce773e81ac9485963187c48feaf92c71789f4c345c82bd335f806a7
 DIST gromacs-2022.2.tar.gz 40350604 BLAKE2B 789c8abc13b5c64af6b9d66efcf70449330b7e6a4bc127ba299e36eea925e9485809c11480ffd857805d9b453df363ce9bb05bc54b439801334767651defc0ef SHA512 9f33518d2035afb37fc40377e575d497ff32bef2adb702669b35b1b51b1694b1113c5634fa6febd41955b6dfbfd055e7d523e1919bda1bf169a6d0c25700cef7
 DIST gromacs-2022.3.tar.gz 40359623 BLAKE2B 23beacf7208df89aea6c3effe483361451a9ff20428fe79ec163a5eee4dc0db0bb00a2bee84bc9377ad272f216fd372eab1b77e8542ce231ac785b41b582fa15 SHA512 1a6a1674ed17dfd93dcd51537cd13c9df5bb9bd91c3a26601032f83b788a93689bac8070eb8e495a786d41cc9d474885538cbaffa4229da70dfa640ee42b7c60
 DIST manual-2018.8.pdf 10025023 BLAKE2B afb0a6e6a72d78df743fcb57e7c1716848589e571dd35167b957a9b407ca27978ccfb6cb9e0df9c9439b888f352501a00ba32281ed1e0b4193bd606f1d77152e SHA512 b1972f7ce965bfc9377542993c5943ea4868a8ed23a969d4203264746d6bea3a7a65c6379196ece37fd6d68ec7ec80f827bde87d1049284af7082759a124f1d5
@@ -12,6 +13,7 @@ DIST manual-2020.4.pdf 11851608 BLAKE2B 7b7bdf08e8946fcc448543b08391b94a67fee60a
 DIST manual-2020.7.pdf 11850780 BLAKE2B 38594e87993badfbbcf47d6010a7f67d3c3426dab85e1462916b4d62be27b5764953f912cf2b71ee24877e0bfa27b3f74431da2da81b4977d58cb66b2cc795a3 SHA512 4f184f2c90e0bac01a48069cc546cd5b04fa5f543f90dd2d68c6d17be278152fd09456b6a6c5c8236f8fb85a174d6ec7a1c7b44d437b4e6fea5d0ada73cec0f6
 DIST manual-2021.3.pdf 12255076 BLAKE2B 6ca516b6832507c9d4100679d1f9bc9e3ab17d226849b050764b0d0626247dc57ce49985f9a7fc0061f3df278923a83faa367ca8ab91c37e5624dc584a51a822 SHA512 5d53798f30ea00fcb4e1b35f7eaa4bebfc05dafa4f2d0c197dcf2b57a624ad3a98b74fd90722e40d0ac13a6fff4ca231f9d6340f52ba94659c827c53c2f1cb16
 DIST manual-2021.5.pdf 12253641 BLAKE2B 8850715a2bb21345e1c9735aca1a5dd2ad916e5a18881e7c9f3dda6f055ca12d9d379b74218138999ce50769efd8b9dd6447afbf70bbbefa2564dfb9fb276b91 SHA512 7635108c935e4953d722df6a16ee43edf97eef7e49f047218728f68f61f8f185192ff1d8b13a573b643b040955af211355a7b560c8a894c858d7f71249d41296
+DIST manual-2021.6.pdf 12256595 BLAKE2B 5d808e38571b38c1f6e0d115f6e604238206cc001f59d05ed855e80c324c0e6fd7767adb723b3d0edd1267ae5973a3b83b76bd04d2dc99769e6440600d8e2146 SHA512 64fe56422d7417f6f61b10346c99e24c3f423f0cedc3794e0809250282bc87ef692b47ae6c3f95ad7994aa3860ed82035cbacc76eb78a2f54a29052a05260af2
 DIST manual-2022.2.pdf 13075063 BLAKE2B 1c9e525d45f1b9955f1aa2c4afa8c958b8ea62c51c28fafdebe302e3e5f6e04c97d1852e4ab2ba18149778d62959d9e7e42be9e4cd98f8187029cc590b1dfd9a SHA512 9b4d9b13547e0210b633394e0c9cba183a827409b08d3b2995a4b64df7b7e7aef0441af240bf4cfcb2e24594ade27c25fee454b9fcf4bb5df0ded464c4f6368d
 DIST manual-2022.3.pdf 13080874 BLAKE2B 3e70da8f70281c78084f5f9af86cdcda187c7b3085f08d95487992a65e31b7dae0b3e66d914dc0bccaf1bfe4c672d2018f38d0bde679759545aca55d1df1f554 SHA512 f634eac722d4a6f77820ef46024d9209de97fb6afb52333f200c2717049d8d09e31f0ef7bac8f154d79ae43fa31541ed6c3d839dd088433222ebdace298b5fae
 DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb
@@ -20,5 +22,6 @@ DIST regressiontests-2020.4.tar.gz 48542144 BLAKE2B 1dcde67525d40ababa74d9e8ba2d
 DIST regressiontests-2020.7.tar.gz 48541487 BLAKE2B 255608b52158c6c01e7c7c4dcf075128ecf22b2f26d32e8c203de8a4bc69c60ec95f49cf8ccd64abc3073c5e8dca9d6b01daed9dfb8f67bce2dd068ed01acd05 SHA512 2458582f94f3c9f4e1454824ce3940b4f5b6cb2151d06846c42e7a9448296fd2a6df4f53be9624e0d3317d2b59f89bb5348eb8b2970d7b46ac22ca989ef3458a
 DIST regressiontests-2021.3.tar.gz 48515038 BLAKE2B ee79d8adddc9c68f7d59d9e568b12bf4d1fe0e44c2810fee846ad6f689bbcacf60f5c266433946329e64e3127bc2d37a3f81f69c070c636b411b38067650c2cf SHA512 e14baa22ef2902a23125bbd9143ae7a9a4810498b321794ff1989f8d044d47db5db41d5225798fda08016c05e5f7f315178b5a6e35cdf01e3b6604670a8ce7a2
 DIST regressiontests-2021.5.tar.gz 48537298 BLAKE2B 860ac34aa8706ecdafab4472162775ce12726d93839079ebf9b7df8c2c6a1b47baa8a635c24cf4cb4551a32237c3de7da3197ec136b5bbf48663edc3943720ad SHA512 3605d04b2602339fb7d33e2776da2ada337ca58a3802472d47f490d4e8dd04249a950bf34608a498eedebf69f344c0311bac8f7fcb58ce0ebbb6d608ee39aa2e
+DIST regressiontests-2021.6.tar.gz 48537070 BLAKE2B 982fad6b23da5c1e6d32009f9f08772419c08f15549aea85ec0cd144c7faf5b48ed9b49a2cae662c28008514911cc18e0b39b994854d95f4f206e728b76f3fe5 SHA512 9c0ca29df822bc13005fd35bdb85cc075ea667112ae1670af0d8306cdd2bd348a9f9904bd10da6db458d9c11f4d44860e1fc62e9686d2c6e396e265d18768ba4
 DIST regressiontests-2022.2.tar.gz 48614810 BLAKE2B d39a9b29a023fa2462918206457bb222bf56f0c530b311a1e5572e8af6c561a9ba5cf7a445425a36f89804d120a5d05cb778998818ba11357ec67bfb05297de3 SHA512 6cd4b59515648aa5f9deec130454b4d667cce20a95d389b46883865d39a164ec23da303a52afb4459dda3c6b6a7804d0763c05424ea512e6c0725ce1ca684dc2
 DIST regressiontests-2022.3.tar.gz 48615675 BLAKE2B 731d9a210dcd481df937182a9a8239087549abd118d1386175ef68979e139ae33089cfc304e0389670ad15a196008c282ddf62968a7e8bfccac22c0a96add276 SHA512 98888ad908705ac29ae958591368e994b091a1619782b49601e41f576c821eb3c96a713449151b8db59d46bc6dd3bcb363f5d0cda354ce6b39a9bb93ba31f913
diff --git a/sci-chemistry/gromacs/gromacs-2021.6.ebuild b/sci-chemistry/gromacs/gromacs-2021.6.ebuild
new file mode 100644
index 000000000000..2f7f4f77115a
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-2021.6.ebuild
@@ -0,0 +1,355 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+PYTHON_COMPAT=( python3_{8..11} )
+
+DISTUTILS_USE_SETUPTOOLS=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
+		git://git.gromacs.org/gromacs.git"
+	[[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
+	inherit git-r3
+else
+	SRC_URI="
+		http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
+		doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
+		test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${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 cpu_flags_x86_avx512f cpu_flags_arm_neon"
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://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[profiler] )
+	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-doc/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 )
+	cuda? ( !opencl )
+	mkl? ( !blas !fftw !lapack )
+	${PYTHON_REQUIRED_USE}"
+
+DOCS=( AUTHORS README )
+
+RESTRICT="!test? ( test )"
+
+PATCHES=( "${FILESDIR}/${PN}-2021-musl-stdint.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 [[ ${PV} != *9999 ]]; then
+		default
+	else
+		git-r3_src_unpack
+		if use test; then
+			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
+			EGIT_BRANCH="${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=( )
+	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)
+	[[ ${CHOST} = *-darwin* ]] && \
+		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
+
+	if use fftw; then
+		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
+	elif use mkl && has_version "=sci-libs/mkl-10*"; then
+		fft_opts=( -DGMX_FFT_LIBRARY=mkl
+			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
+			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
+		)
+	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 gpu=( "-DGMX_GPU=OFF" )
+		[[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
+		use opencl && gpu=( "-DGMX_GPU=OPENCL" )
+		mycmakeargs=(
+			${mycmakeargs_pre[@]} ${p}
+			-DGMX_MPI=OFF
+			-DGMX_THREAD_MPI=$(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
+		use mpi || continue
+		einfo "Configuring for ${x} precision with mpi"
+		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/Gromacs_papers"
+	einfo
+	readme.gentoo_print_elog
+}