From fab849d1daed0ba7f2ac497d07985c3dbb692543 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sun, 16 Jun 2019 21:23:20 +0100 Subject: gentoo resync : 16.06.2019 --- sci-chemistry/gromacs/Manifest | 9 +- sci-chemistry/gromacs/gromacs-2016.5.ebuild | 275 ---------------------- sci-chemistry/gromacs/gromacs-2016.9999.ebuild | 275 ---------------------- sci-chemistry/gromacs/gromacs-2019.2.ebuild | 2 +- sci-chemistry/gromacs/gromacs-2019.3.ebuild | 307 +++++++++++++++++++++++++ 5 files changed, 312 insertions(+), 556 deletions(-) delete mode 100644 sci-chemistry/gromacs/gromacs-2016.5.ebuild delete mode 100644 sci-chemistry/gromacs/gromacs-2016.9999.ebuild create mode 100644 sci-chemistry/gromacs/gromacs-2019.3.ebuild (limited to 'sci-chemistry/gromacs') diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 7b4a1c176053..ba4761ab8503 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -1,17 +1,16 @@ -DIST gromacs-2016.5.tar.gz 27369491 BLAKE2B 4a8bf1ae3e298ac2e26ec476130720dc3ef00db5d999e3a45fdbfd7fbfe7e94fbc86be6ff0f2f23552769c8bc851ce49c73f6fc1ab13f372523279b93e7794d7 SHA512 9cb8ff88871aa5df0967c60ba303c03296c6fa3c215cd01b26259df7753f0014f04222078ab4b84a66a1f709997837134d5c0f74da19b78322e410010c9d9e10 DIST gromacs-2018.3.tar.gz 29915626 BLAKE2B 6e6eeafecdd923a25b4a2a78a8e89f793639b57ffbd63f19d133d8474302f9a381041f138a509dadb42b36e25fe508729e860efb6b0c75cdbf01d924b0a8fd83 SHA512 3c4d6eb3942d7b54d01c94c6f6f5ae706e0f5d4f9901ea11a56fde4df97b1a9112007f2cb13feea0f19f30c89f57ae80ff53a8f5203b8cdff103aa903cd0dc8f DIST gromacs-2018.7.tar.gz 29912662 BLAKE2B 0714b28ec2443f3201275fc2fa6db1202a059161362134d4de03a900a3a67fe9d31ba8c058d5ee971198fecd69379fcd389f03d25c61f50b8460c43ba5c564d5 SHA512 fbc3b847b70b1396f412b8f4a1b977268651f8d53a222dcf6349fe563ff6319e096484209a24351e382bc9162a949b3900591f5b469c32dd9effeb894f03c172 DIST gromacs-2019.2.tar.gz 33437869 BLAKE2B bebe4942688dace148856d4491b687b8e0fd2c86d7fbd9eecdb46824d316a0fc3854464ecafa79d8db92327ee8467be204b050c11f1e71132184efd812c3bf09 SHA512 da7ff24e8485774e22d1c2464fbe64675c3305ef0e21a3d17e363201031952e5d4a9b81f572d5284fb6f2596ed99daf62fe78d653387d9d714274f46bc750183 -DIST regressiontests-2016.5.tar.gz 67641413 BLAKE2B 4fcd30c198f3acbbabf1104c040d9a686de49536a97dbeb14732bfa0ed3cf37aa61b1b0f45393668985b993d1f1862a8985e416af819cf9793f5964f3e4f43cc SHA512 31764fd99cc4185d61de5d4443ee482c27b13533451a24aa0e4899997ce275a63685424eafacae38b1a3ffd4ce0d5ebe02a90348953b04c104f91376f0edfdff +DIST gromacs-2019.3.tar.gz 33441419 BLAKE2B 79319dd23982c65c7c4d8e5f633cef0c7fd99a38a4e0cc9030a3ffb0fdfc07a4fbfbcfa942896f23a143b747e044fae645498a3e6992497d1f1a7d966f80b2b0 SHA512 de9f54d095b45ea7efd1043f83a40f6c778a6e3e2067a01f48d1ce843d68d226061933ca28a3edb635b795a8ddd5ef9deb8ed1114aa3235bc8039db8ff7d0218 DIST regressiontests-2018.3.tar.gz 67857855 BLAKE2B acd7a05ae79d1b4eb47d0c68a3fec9ee19f028a5019f39c37a033f48cf6da2a468375180ad6ceca9ac4f685a8bead38550663a47d6427b51f84c32a5c810e5f0 SHA512 57980d49efe6dcc3b3d14b5913a30c68fc1de5b679ef986fec1a149c76f67139b0299c3ee2825451461294fab5f345c7ad4f42e90f8991b81aafe9c369f3ff0b DIST regressiontests-2018.7.tar.gz 67856738 BLAKE2B 955ae8b5e74f90fec704cf41fbd00bd8c09d754f950551fe0adfcd407db6fdb4491a3815149ea37d36c747316c79d462e823b9f6b26f2376bf90d87aad95731b SHA512 c2ff390750bd99faebcd8d5dd8ad6dbf2b00113ed888bddddf985dbf95d7f347093adb67f3c396547b3e2990de330fddb7efe83ded91a72cf97c82a1dac7e826 DIST regressiontests-2019.2.tar.gz 67643003 BLAKE2B 4178de5d62f194a81f97e442c10f123dc59c5e63f2078f7f07135709f3f6e530e0d237bf40264b285c084519d5ace75dfcbcddc16dc740c4f17233dc33542e45 SHA512 c1f25bc770d3f0a873c887d5563c1cd88179e81211b70ce6f5015696e6fa0b6931a8da7a449f2b223f3105b9e2e7eca67248e96fbfc2a7fd5fb360ba616f22ff -EBUILD gromacs-2016.5.ebuild 7973 BLAKE2B 72b0552595f3187c91bfff89cbe49ac5dbfa1396d82f32428e1519e98aff243f5a68e1c7679386abc8eb0bbb62f40f594def4fa2bf8460134631f5c9e734c456 SHA512 a269b5bc8a484bd27b75f0301267d432d1d0ffa3389f190779acf474410401f8b81fd5ae4fec286472c99e75076da592f06566a777773518b25f2b2b29f9967c -EBUILD gromacs-2016.9999.ebuild 7976 BLAKE2B 24237f4e253faef5df7600baafa01ac9db0e7eacee6c4a5cef6e9e17961e159c701ef8573b3cea4703511f759d7659c5bbd925c8739c1bcf172f9fdf296c7cb2 SHA512 80307361e6b22dcf182bf77c587c31089eb1e85cbda69276bcc90fd85f10a143f69b2568b4ace41104d602793de3fd7219271ca28228ae0b621e23e7c7b58227 +DIST regressiontests-2019.3.tar.gz 67640462 BLAKE2B ed6c176a144e0407be66585be5d6090c31c047498bc5f48f59685108de91f2f9ddb2d22b291a15e6ffa1db848aae19b94a79c8c3d34b1067680f759a179953dd SHA512 822e905fb488ce308eb9324d93f78106da5252c773c7941d49c6162e73bdff109aeca1f0d57216c6dd6536a4c41d80013fa1cee2f5206b0c4160a3e5b4a31315 EBUILD gromacs-2018.3.ebuild 7824 BLAKE2B cc5ec314f5338c269d00bb8ec7af34f38134c59dd7009fc593cfa559cc68e69753f17bd8b77f5156f08999a83980d1e1c5684fd9ed489386af309f1babf850aa SHA512 d47c8c6e1e4c1dc5cd2429e5c77f04af822b5995cdd1f93a1331442dfe95d0192bda5565d3837575100f2fe841f1006cd38698ced727525c716d1925c0e65579 EBUILD gromacs-2018.7.ebuild 7825 BLAKE2B 8ec9d3451720801d0249a6964b3df6dfd774e66a6ec790a0ebaba967d9d9fa23785ed5c229e8821de40f663d6adfaaab1c056ac36b78ebb1ce8213b0bffee7f7 SHA512 5e39cf72d8344c4690161a1ce4a6961ff2fa492167d4dc768de623c3ead7bb40d42a808f5a20386c39530bc33e9d74feca69181929a387c2fb1d41e69dfe7f91 EBUILD gromacs-2018.9999.ebuild 7827 BLAKE2B 97a2437061a55854dd2799c8bdbec6a342586fc480785ea52de8d6b612c747ace1fba0a1fc3dbec9904cafcb3abdabd363ba0d6285cfc44f60964047c52f5b74 SHA512 975f2bcfdd93df006ec2a8f439a2a90e4c9079c58209ec2828b5647d96c29f7eef7fd0c79da844cc8d4e449b573a75884b19c951649c0028133d3fa87b03934c -EBUILD gromacs-2019.2.ebuild 9113 BLAKE2B 9e111d428ab09ddabe000b17e645a1d35de5efb88cfc3989a2119be9e3533eb8c4c3d8df9e396e0dc8140081e6cdfa8e70323e32e0a56c8b88e39b5d27482fc0 SHA512 b8f234c0dfe092a26d86e6ac856fd9c3221dbda55686d2ea341ba42883fa0b29ed188dfee37bb7859ba069a90a83ddaa2ab117f8694c696ceb58350d25fe393f +EBUILD gromacs-2019.2.ebuild 9112 BLAKE2B 54e93c462fec627d154f385ec910c682a3b57fcded8bec082d1dddc73d774e876422d9b24cd50f9984f1a412db7e85e1e862fd94ac295d6e0318d24e07d53a6c SHA512 4c4906a7a982cfe9fffd4375c469b8f637b3e73ea4dde7ce37d517e916b59418a2f80a007ae516be7611b4a6f6379ac444df6946f70968671bccdf0060d85e97 +EBUILD gromacs-2019.3.ebuild 9114 BLAKE2B 9286e7663d622e30ca491577c880827006f3bb2a68d2e3fd9c26fdc97541c12ebef06ab9d3b73ea89e0bbb079e79188c10b387366948920ee631c37da0be4ac5 SHA512 70fd567f7cdb9d8f2c7609b56c4522b5c3cc8094856ace84c001daeae390de788ff3c103987a44f09a11bf9cc6802a071511140bbd881423cefb8e70d1f8189c EBUILD gromacs-2019.9999.ebuild 9114 BLAKE2B 9286e7663d622e30ca491577c880827006f3bb2a68d2e3fd9c26fdc97541c12ebef06ab9d3b73ea89e0bbb079e79188c10b387366948920ee631c37da0be4ac5 SHA512 70fd567f7cdb9d8f2c7609b56c4522b5c3cc8094856ace84c001daeae390de788ff3c103987a44f09a11bf9cc6802a071511140bbd881423cefb8e70d1f8189c EBUILD gromacs-9999.ebuild 8094 BLAKE2B 932061da2ed5e2e20d1ca0c1ef9000fd946bbe3720cea6d585863e4bf2d7821b7e7b934d4d33d20a4c6040865c58c61c11f5bc8ce98812ad4f946a95b1c1fb83 SHA512 e3987a36622751c20e6a5b3fa88d43c94e24a30cd513eb2e9f9375457413c9ad131ec3f3012ec94e7574d50233c00d9edd357a44413ac0873edb88df82487ba0 MISC metadata.xml 1123 BLAKE2B 5e945fdf580821b62aaf40c5b4b3252b366284f2df16f02e7c3cf913e5ad498a6a8548bc2e4275d8b80373f88d9879ab59d401e619595014262dcebfe8660f9f SHA512 bac0c94aee957487d8af8a1e06323cb286c8773cef2070d91aff9fdad63eb1bd55f2678dd58dca21b33d8d3e7110d2526e280abd538e3653aee638f6de72090d diff --git a/sci-chemistry/gromacs/gromacs-2016.5.ebuild b/sci-chemistry/gromacs/gromacs-2016.5.ebuild deleted file mode 100644 index bef5457975aa..000000000000 --- a/sci-chemistry/gromacs/gromacs-2016.5.ebuild +++ /dev/null @@ -1,275 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils - -if [[ $PV = *9999* ]]; then - EGIT_REPO_URI="git://git.gromacs.org/gromacs.git - https://gerrit.gromacs.org/gromacs.git - https://github.com/gromacs/gromacs.git - https://repo.or.cz/r/gromacs.git" - [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" - inherit git-r3 -else - SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz - test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-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="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 +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" - -CDEPEND=" - X? ( - x11-libs/libX11 - x11-libs/libSM - x11-libs/libICE - ) - blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) - fftw? ( sci-libs/fftw:3.0 ) - hwloc? ( "${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:" - einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " - einfo "https://dx.doi.org/10.1021/ct700301q" - einfo - readme.gentoo_print_elog -} diff --git a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild b/sci-chemistry/gromacs/gromacs-2016.9999.ebuild deleted file mode 100644 index 937bdf673d2a..000000000000 --- a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild +++ /dev/null @@ -1,275 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils - -if [[ $PV = *9999* ]]; then - EGIT_REPO_URI="git://git.gromacs.org/gromacs.git - https://gerrit.gromacs.org/gromacs.git - https://github.com/gromacs/gromacs.git - https://repo.or.cz/r/gromacs.git" - [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" - inherit git-r3 -else - SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz - test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-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="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 +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" - -CDEPEND=" - X? ( - x11-libs/libX11 - x11-libs/libSM - x11-libs/libICE - ) - blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) - fftw? ( sci-libs/fftw:3.0 ) - hwloc? ( "${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:" - einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " - einfo "https://dx.doi.org/10.1021/ct700301q" - einfo - readme.gentoo_print_elog -} diff --git a/sci-chemistry/gromacs/gromacs-2019.2.ebuild b/sci-chemistry/gromacs/gromacs-2019.2.ebuild index 066004be22c5..df6c7eaf37ff 100644 --- a/sci-chemistry/gromacs/gromacs-2019.2.ebuild +++ b/sci-chemistry/gromacs/gromacs-2019.2.ebuild @@ -19,7 +19,7 @@ if [[ $PV = *9999* ]]; then else SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="~amd64 ~arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" + KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-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" diff --git a/sci-chemistry/gromacs/gromacs-2019.3.ebuild b/sci-chemistry/gromacs/gromacs-2019.3.ebuild new file mode 100644 index 000000000000..dc5c8185316e --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2019.3.ebuild @@ -0,0 +1,307 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +PYTHON_COMPAT=( python2_7 ) + +inherit bash-completion-r1 cmake-utils cuda eutils multilib python-single-r1 readme.gentoo-r1 toolchain-funcs xdg-utils + +if [[ $PV = *9999* ]]; then + EGIT_REPO_URI="git://git.gromacs.org/gromacs.git + https://gerrit.gromacs.org/gromacs.git + https://github.com/gromacs/gromacs.git + https://repo.or.cz/r/gromacs.git" + [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + inherit git-r3 +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz + test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" + KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-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="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 +doc -double-precision +fftw +gmxapi +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) + opencl? ( virtual/opencl ) + fftw? ( sci-libs/fftw:3.0 ) + hwloc? ( sys-apps/hwloc ) + lapack? ( virtual/lapack ) + lmfit? ( sci-libs/lmfit ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + " +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + dev-python/sphinx[${PYTHON_USEDEP}] + media-gfx/mscgen + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + )" +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + cuda? ( !opencl ) + mkl? ( !blas !fftw !lapack )" + +DOCS=( AUTHORS README ) + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +pkg_pretend() { + [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" + use openmp && ! tc-has-openmp && \ + die "Please switch to an openmp compatible compiler" +} + +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-utils_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" + + # try to create policy for imagemagik + mkdir -p ${HOME}/.config/ImageMagick + cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF + + + !ATTLIST policymap xmlns CDATA #FIXED ''> + + + ]> + + + + + + + + + EOF +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + #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" + + #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=$(usex doc) + -DGMX_HWLOC=$(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" ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + -DGMX_THREAD_MPI=$(usex threads) + -DGMXAPI=$(usex gmxapi) + "${opencl[@]}" + "${cuda[@]}" + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_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 ${cuda} + -DGMX_OPENMM=OFF + -DGMXAPI=OFF + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" + -DGMX_LIBS_SUFFIX="_mpi${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_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-utils_src_compile + # not 100% necessary for rel ebuilds as available from website + if use doc; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile manual + fi + use mpi || continue + einfo "Compiling for ${x} precision with mpi" + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake-utils_src_compile + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_make check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install + if use doc; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake-utils_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:" + einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " + einfo "https://dx.doi.org/10.1021/ct700301q" + einfo + readme.gentoo_print_elog +} -- cgit v1.2.3