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commit: 4e81ca7f2ecb846aa9df25b6d179e1826fe5bde3 |
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Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> |
3 |
AuthorDate: Sat Jan 5 21:20:54 2019 +0000 |
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Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> |
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CommitDate: Fri Jan 11 11:57:34 2019 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4e81ca7f |
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|
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sci-chemistry/gromacs: Drop 5.1.3 and 5.1.9999 |
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|
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Never updated to latest available point release in Gentoo, 5.1.3 is from 2016. |
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|
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Package-Manager: Portage-2.3.54, Repoman-2.3.12 |
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Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org> |
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|
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sci-chemistry/gromacs/Manifest | 2 - |
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sci-chemistry/gromacs/gromacs-5.1.3.ebuild | 267 -------------------------- |
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sci-chemistry/gromacs/gromacs-5.1.9999.ebuild | 267 -------------------------- |
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sci-chemistry/gromacs/metadata.xml | 1 - |
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4 files changed, 537 deletions(-) |
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|
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diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest |
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index 412eb6bbdb7..4d0e90e75ae 100644 |
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--- a/sci-chemistry/gromacs/Manifest |
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+++ b/sci-chemistry/gromacs/Manifest |
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@@ -3,10 +3,8 @@ DIST gromacs-2016.5.tar.gz 27369491 BLAKE2B 4a8bf1ae3e298ac2e26ec476130720dc3ef0 |
26 |
DIST gromacs-2018.3.tar.gz 29915626 BLAKE2B 6e6eeafecdd923a25b4a2a78a8e89f793639b57ffbd63f19d133d8474302f9a381041f138a509dadb42b36e25fe508729e860efb6b0c75cdbf01d924b0a8fd83 SHA512 3c4d6eb3942d7b54d01c94c6f6f5ae706e0f5d4f9901ea11a56fde4df97b1a9112007f2cb13feea0f19f30c89f57ae80ff53a8f5203b8cdff103aa903cd0dc8f |
27 |
DIST gromacs-2018.4.tar.gz 29918276 BLAKE2B daf3f91e47bab61befee4ecd91e4885835fc5ded408462c239c824567e64b5710fb252456c6be2bf0e4ce1a2119747fca9d8fb0532286bb93d6ccdd289fe57ab SHA512 8ef0b90b2c266bb706c8fdba12e763de9c21aad197c1c71f48c06378644a734a3694172804db6c916a4974a9832b128512f2445d0b72783811e64edd22d27955 |
28 |
DIST gromacs-2019.tar.gz 33428725 BLAKE2B 307838a5ee1a85554d6f2ef8cd9c9dd2f3d9cacd32c534545c23483b5f3a1c7d027bfbdf224b90661cd8cd3fb85c0c99c66cbd619698245a0cb45ebd512dec5d SHA512 54b11530e8ff671461e3ae9418d991fe242957943c944798cddf6efe740eee670a562cd5201dbba68b045f4bafd3afa2dc8de27e0643c7def4e05eaf0ccb5769 |
29 |
-DIST gromacs-5.1.3.tar.gz 27095702 BLAKE2B b7fd8fa10e8c4f4368ac551338c59374dc35f85c9fdae5d64eec62929b8f04ea724a084959b3618cd8a151bf3e0a0c84c8f75de953722effca82a4928941ce73 SHA512 9ab26e1b2268f8d567b89b2d99d0b75b937b28edceaec56d17ca3243c76faa31255ffc0c45d762c7c693fe500b00e36ad43b80572d1d7f92dc87f9d2d98c0ba6 |
30 |
DIST regressiontests-2016.2.tar.gz 67095329 BLAKE2B fec8a663845ad67374c8a230d1590fa9e5079460198f41cee3b788aaa1c72e8ec9dcda48bc68a594f15003d11bf6617d46cc1a09c16b7a333587b43904a16ba6 SHA512 e0aceb56d1f38a7e6ab9fdaac5063fd20c5b3a162ffb6eddd0e6dc7dff9b724bfe31363493a9437e9f9d5421a534b375960fcb31e903a4901a0fa94ed8511294 |
31 |
DIST regressiontests-2016.5.tar.gz 67641413 BLAKE2B 4fcd30c198f3acbbabf1104c040d9a686de49536a97dbeb14732bfa0ed3cf37aa61b1b0f45393668985b993d1f1862a8985e416af819cf9793f5964f3e4f43cc SHA512 31764fd99cc4185d61de5d4443ee482c27b13533451a24aa0e4899997ce275a63685424eafacae38b1a3ffd4ce0d5ebe02a90348953b04c104f91376f0edfdff |
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DIST regressiontests-2018.3.tar.gz 67857855 BLAKE2B acd7a05ae79d1b4eb47d0c68a3fec9ee19f028a5019f39c37a033f48cf6da2a468375180ad6ceca9ac4f685a8bead38550663a47d6427b51f84c32a5c810e5f0 SHA512 57980d49efe6dcc3b3d14b5913a30c68fc1de5b679ef986fec1a149c76f67139b0299c3ee2825451461294fab5f345c7ad4f42e90f8991b81aafe9c369f3ff0b |
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DIST regressiontests-2018.4.tar.gz 67860326 BLAKE2B 0160f701a8fa14ba4f175f4fca9894104bc5cc6aa5f02ac57200fd5a8f74a29b595df609e704cb70fcd9a03529bcf758fb4547e35557a45c0546d819c2681983 SHA512 baaac0c918684216ada5254a7c3a1f5b3ea00b1a63d6085d569095139b2a0c9de4ed330d4694f7eaedab729ed5dcea547390781b3d2f7c2ffdf02e0541a90efe |
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DIST regressiontests-2019.tar.gz 67597618 BLAKE2B fb950d8518cf1e28db5ebb99bdda8d269c5e43dd49a117bdaae9f00857abc7c096766fb90ff1d2d95a12a875ba2e243b707bfc81a45d07fc8b340a154cf2ad0f SHA512 081e56d052c0a0d021a8a1566f802911e261e1f2b5b2141350fe2372bcad0844042f26121167ed31a31490bd4e042068690c4905fcbc80b539686a074621fc5e |
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-DIST regressiontests-5.1.3.tar.gz 66994083 BLAKE2B 7009f65ad0138664ac84e57f8bc7cce5d18a59f99943e56b6642583120bfce279e005ac0bacd2db8904ea477a48e2b938c64de46a65fa5d08fce6009d53583c3 SHA512 486e86eb3b75bae822abe82dac4e1098aa13723bd04214021f835a2f0b847303f015a9ececc33aa5ae63d31a2eeae07e512f22464b6c0e26d1286b0781578022 |
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|
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diff --git a/sci-chemistry/gromacs/gromacs-5.1.3.ebuild b/sci-chemistry/gromacs/gromacs-5.1.3.ebuild |
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deleted file mode 100644 |
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index 0b84b86b413..00000000000 |
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--- a/sci-chemistry/gromacs/gromacs-5.1.3.ebuild |
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+++ /dev/null |
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@@ -1,267 +0,0 @@ |
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-# Copyright 1999-2018 Gentoo Authors |
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-# Distributed under the terms of the GNU General Public License v2 |
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- |
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-EAPI=6 |
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- |
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-CMAKE_MAKEFILE_GENERATOR="ninja" |
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- |
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-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs |
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- |
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-if [[ $PV = *9999* ]]; then |
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- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
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- https://gerrit.gromacs.org/gromacs.git |
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- https://github.com/gromacs/gromacs.git |
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- http://repo.or.cz/r/gromacs.git" |
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- [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}" |
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- inherit git-r3 |
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-else |
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- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
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- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" |
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- KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
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-fi |
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- |
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-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
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- |
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-DESCRIPTION="The ultimate molecular dynamics simulation package" |
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-HOMEPAGE="http://www.gromacs.org/" |
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- |
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-# see COPYING for details |
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-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
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-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
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-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
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-SLOT="0/${PV}" |
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-IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
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- |
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-CDEPEND=" |
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- X? ( |
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- x11-libs/libX11 |
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- x11-libs/libSM |
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- x11-libs/libICE |
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- ) |
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- blas? ( virtual/blas ) |
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- boost? ( >=dev-libs/boost-1.55 ) |
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- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
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- fftw? ( sci-libs/fftw:3.0 ) |
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- lapack? ( virtual/lapack ) |
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- mkl? ( sci-libs/mkl ) |
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- mpi? ( virtual/mpi ) |
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- " |
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-DEPEND="${CDEPEND} |
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- virtual/pkgconfig |
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- doc? ( |
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- app-doc/doxygen |
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- dev-texlive/texlive-latex |
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- dev-texlive/texlive-latexextra |
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- media-gfx/imagemagick |
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- )" |
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-RDEPEND="${CDEPEND}" |
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- |
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-REQUIRED_USE=" |
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- || ( single-precision double-precision ) |
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- cuda? ( single-precision ) |
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- mkl? ( !blas !fftw !lapack )" |
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- |
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-DOCS=( AUTHORS README ) |
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- |
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-if [[ ${PV} != *9999 ]]; then |
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- S="${WORKDIR}/${PN}-${PV/_/-}" |
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-fi |
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- |
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-pkg_pretend() { |
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- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
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- use openmp && ! tc-has-openmp && \ |
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- die "Please switch to an openmp compatible compiler" |
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-} |
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- |
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-src_unpack() { |
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- if [[ ${PV} != *9999 ]]; then |
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- default |
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- else |
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- git-r3_src_unpack |
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- if use test; then |
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- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
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- EGIT_BRANCH="${EGIT_BRANCH}" \ |
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- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
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- git-r3_src_unpack |
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- fi |
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- fi |
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-} |
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- |
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-src_prepare() { |
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- #notes/todos |
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- # -on apple: there is framework support |
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- |
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- cmake-utils_src_prepare |
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- |
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- use cuda && cuda_src_prepare |
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- |
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- GMX_DIRS="" |
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- use single-precision && GMX_DIRS+=" float" |
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- use double-precision && GMX_DIRS+=" double" |
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- |
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- if use test; then |
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- for x in ${GMX_DIRS}; do |
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- mkdir -p "${WORKDIR}/${P}_${x}" || die |
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- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
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- done |
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- fi |
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- |
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- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
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-} |
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- |
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-src_configure() { |
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- local mycmakeargs_pre=( ) extra fft_opts=( ) |
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- |
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- #go from slowest to fastest acceleration |
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- local acce="None" |
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- use cpu_flags_x86_sse2 && acce="SSE2" |
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- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
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- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
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- use cpu_flags_x86_avx && acce="AVX_256" |
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- use cpu_flags_x86_avx2 && acce="AVX2_256" |
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- |
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- #to create man pages, build tree binaries are executed (bug #398437) |
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- [[ ${CHOST} = *-darwin* ]] && \ |
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- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
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- |
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- if use fftw; then |
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- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
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- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
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- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
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- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
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- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
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- ) |
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- elif use mkl; then |
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- local bits=$(get_libdir) |
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- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
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- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
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- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
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- ) |
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- else |
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- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
184 |
- fi |
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- |
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- mycmakeargs_pre+=( |
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- "${fft_opts[@]}" |
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- -DGMX_X11=$(usex X) |
189 |
- -DGMX_EXTERNAL_BLAS=$(usex blas) |
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- -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
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- -DGMX_OPENMP=$(usex openmp) |
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- -DGMX_COOL_QUOTES=$(usex offensive) |
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- -DGMX_EXTERNAL_BOOST=$(usex boost) |
194 |
- -DGMX_USE_TNG=$(usex tng) |
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- -DGMX_BUILD_MANUAL=$(usex doc) |
196 |
- -DGMX_DEFAULT_SUFFIX=off |
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- -DGMX_SIMD="$acce" |
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- -DGMX_LIB_INSTALL_DIR="$(get_libdir)" |
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- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
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- -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF |
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- -DGMX_USE_GCC44_BUG_WORKAROUND=OFF |
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- -DBUILD_TESTING=$(usex test) |
203 |
- -DGMX_BUILD_UNITTESTS=$(usex test) |
204 |
- ${extra} |
205 |
- ) |
206 |
- |
207 |
- for x in ${GMX_DIRS}; do |
208 |
- einfo "Configuring for ${x} precision" |
209 |
- local suffix="" |
210 |
- #if we build single and double - double is suffixed |
211 |
- use double-precision && use single-precision && \ |
212 |
- [[ ${x} = "double" ]] && suffix="_d" |
213 |
- local p |
214 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
215 |
- local cuda=( "-DGMX_GPU=OFF" ) |
216 |
- [[ ${x} = "float" ]] && use cuda && \ |
217 |
- cuda=( -DGMX_GPU=ON ) |
218 |
- mycmakeargs=( |
219 |
- ${mycmakeargs_pre[@]} ${p} |
220 |
- -DGMX_MPI=OFF |
221 |
- -DGMX_THREAD_MPI=$(usex threads) |
222 |
- "${cuda[@]}" |
223 |
- -DGMX_OPENMM=OFF |
224 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
225 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
226 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
227 |
- ) |
228 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
229 |
- [[ ${CHOST} != *-darwin* ]] || \ |
230 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
231 |
- use mpi || continue |
232 |
- einfo "Configuring for ${x} precision with mpi" |
233 |
- mycmakeargs=( |
234 |
- ${mycmakeargs_pre[@]} ${p} |
235 |
- -DGMX_THREAD_MPI=OFF |
236 |
- -DGMX_MPI=ON ${cuda} |
237 |
- -DGMX_OPENMM=OFF |
238 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
239 |
- -DBUILD_SHARED_LIBS=OFF |
240 |
- -DGMX_BUILD_MANUAL=OFF |
241 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
242 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
243 |
- ) |
244 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
245 |
- [[ ${CHOST} != *-darwin* ]] || \ |
246 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
247 |
- done |
248 |
-} |
249 |
- |
250 |
-src_compile() { |
251 |
- for x in ${GMX_DIRS}; do |
252 |
- einfo "Compiling for ${x} precision" |
253 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
254 |
- cmake-utils_src_compile |
255 |
- # not 100% necessary for rel ebuilds as available from website |
256 |
- if use doc; then |
257 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
258 |
- cmake-utils_src_compile manual |
259 |
- fi |
260 |
- use mpi || continue |
261 |
- einfo "Compiling for ${x} precision with mpi" |
262 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
263 |
- cmake-utils_src_compile |
264 |
- done |
265 |
-} |
266 |
- |
267 |
-src_test() { |
268 |
- for x in ${GMX_DIRS}; do |
269 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
270 |
- cmake-utils_src_make check |
271 |
- done |
272 |
-} |
273 |
- |
274 |
-src_install() { |
275 |
- for x in ${GMX_DIRS}; do |
276 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
277 |
- cmake-utils_src_install |
278 |
- if use doc; then |
279 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
280 |
- fi |
281 |
- use mpi || continue |
282 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
283 |
- cmake-utils_src_install |
284 |
- done |
285 |
- |
286 |
- if use tng; then |
287 |
- insinto /usr/include/tng |
288 |
- doins src/external/tng_io/include/tng/*h |
289 |
- fi |
290 |
- # drop unneeded stuff |
291 |
- rm "${ED}"usr/bin/GMXRC* || die |
292 |
- for x in "${ED}"usr/bin/gmx-completion-*.bash ; do |
293 |
- local n=${x##*/gmx-completion-} |
294 |
- n="${n%.bash}" |
295 |
- cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
296 |
- newbashcomp "${T}"/"${n}" "${n}" |
297 |
- done |
298 |
- rm "${ED}"usr/bin/gmx-completion*.bash || die |
299 |
- readme.gentoo_create_doc |
300 |
-} |
301 |
- |
302 |
-pkg_postinst() { |
303 |
- einfo |
304 |
- einfo "Please read and cite:" |
305 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
306 |
- einfo "https://dx.doi.org/10.1021/ct700301q" |
307 |
- einfo |
308 |
- readme.gentoo_print_elog |
309 |
-} |
310 |
|
311 |
diff --git a/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild |
312 |
deleted file mode 100644 |
313 |
index 0b84b86b413..00000000000 |
314 |
--- a/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild |
315 |
+++ /dev/null |
316 |
@@ -1,267 +0,0 @@ |
317 |
-# Copyright 1999-2018 Gentoo Authors |
318 |
-# Distributed under the terms of the GNU General Public License v2 |
319 |
- |
320 |
-EAPI=6 |
321 |
- |
322 |
-CMAKE_MAKEFILE_GENERATOR="ninja" |
323 |
- |
324 |
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs |
325 |
- |
326 |
-if [[ $PV = *9999* ]]; then |
327 |
- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
328 |
- https://gerrit.gromacs.org/gromacs.git |
329 |
- https://github.com/gromacs/gromacs.git |
330 |
- http://repo.or.cz/r/gromacs.git" |
331 |
- [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}" |
332 |
- inherit git-r3 |
333 |
-else |
334 |
- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
335 |
- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" |
336 |
- KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
337 |
-fi |
338 |
- |
339 |
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
340 |
- |
341 |
-DESCRIPTION="The ultimate molecular dynamics simulation package" |
342 |
-HOMEPAGE="http://www.gromacs.org/" |
343 |
- |
344 |
-# see COPYING for details |
345 |
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
346 |
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
347 |
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
348 |
-SLOT="0/${PV}" |
349 |
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
350 |
- |
351 |
-CDEPEND=" |
352 |
- X? ( |
353 |
- x11-libs/libX11 |
354 |
- x11-libs/libSM |
355 |
- x11-libs/libICE |
356 |
- ) |
357 |
- blas? ( virtual/blas ) |
358 |
- boost? ( >=dev-libs/boost-1.55 ) |
359 |
- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
360 |
- fftw? ( sci-libs/fftw:3.0 ) |
361 |
- lapack? ( virtual/lapack ) |
362 |
- mkl? ( sci-libs/mkl ) |
363 |
- mpi? ( virtual/mpi ) |
364 |
- " |
365 |
-DEPEND="${CDEPEND} |
366 |
- virtual/pkgconfig |
367 |
- doc? ( |
368 |
- app-doc/doxygen |
369 |
- dev-texlive/texlive-latex |
370 |
- dev-texlive/texlive-latexextra |
371 |
- media-gfx/imagemagick |
372 |
- )" |
373 |
-RDEPEND="${CDEPEND}" |
374 |
- |
375 |
-REQUIRED_USE=" |
376 |
- || ( single-precision double-precision ) |
377 |
- cuda? ( single-precision ) |
378 |
- mkl? ( !blas !fftw !lapack )" |
379 |
- |
380 |
-DOCS=( AUTHORS README ) |
381 |
- |
382 |
-if [[ ${PV} != *9999 ]]; then |
383 |
- S="${WORKDIR}/${PN}-${PV/_/-}" |
384 |
-fi |
385 |
- |
386 |
-pkg_pretend() { |
387 |
- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
388 |
- use openmp && ! tc-has-openmp && \ |
389 |
- die "Please switch to an openmp compatible compiler" |
390 |
-} |
391 |
- |
392 |
-src_unpack() { |
393 |
- if [[ ${PV} != *9999 ]]; then |
394 |
- default |
395 |
- else |
396 |
- git-r3_src_unpack |
397 |
- if use test; then |
398 |
- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
399 |
- EGIT_BRANCH="${EGIT_BRANCH}" \ |
400 |
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
401 |
- git-r3_src_unpack |
402 |
- fi |
403 |
- fi |
404 |
-} |
405 |
- |
406 |
-src_prepare() { |
407 |
- #notes/todos |
408 |
- # -on apple: there is framework support |
409 |
- |
410 |
- cmake-utils_src_prepare |
411 |
- |
412 |
- use cuda && cuda_src_prepare |
413 |
- |
414 |
- GMX_DIRS="" |
415 |
- use single-precision && GMX_DIRS+=" float" |
416 |
- use double-precision && GMX_DIRS+=" double" |
417 |
- |
418 |
- if use test; then |
419 |
- for x in ${GMX_DIRS}; do |
420 |
- mkdir -p "${WORKDIR}/${P}_${x}" || die |
421 |
- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
422 |
- done |
423 |
- fi |
424 |
- |
425 |
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
426 |
-} |
427 |
- |
428 |
-src_configure() { |
429 |
- local mycmakeargs_pre=( ) extra fft_opts=( ) |
430 |
- |
431 |
- #go from slowest to fastest acceleration |
432 |
- local acce="None" |
433 |
- use cpu_flags_x86_sse2 && acce="SSE2" |
434 |
- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
435 |
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
436 |
- use cpu_flags_x86_avx && acce="AVX_256" |
437 |
- use cpu_flags_x86_avx2 && acce="AVX2_256" |
438 |
- |
439 |
- #to create man pages, build tree binaries are executed (bug #398437) |
440 |
- [[ ${CHOST} = *-darwin* ]] && \ |
441 |
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
442 |
- |
443 |
- if use fftw; then |
444 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
445 |
- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
446 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
447 |
- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
448 |
- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
449 |
- ) |
450 |
- elif use mkl; then |
451 |
- local bits=$(get_libdir) |
452 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
453 |
- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
454 |
- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
455 |
- ) |
456 |
- else |
457 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
458 |
- fi |
459 |
- |
460 |
- mycmakeargs_pre+=( |
461 |
- "${fft_opts[@]}" |
462 |
- -DGMX_X11=$(usex X) |
463 |
- -DGMX_EXTERNAL_BLAS=$(usex blas) |
464 |
- -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
465 |
- -DGMX_OPENMP=$(usex openmp) |
466 |
- -DGMX_COOL_QUOTES=$(usex offensive) |
467 |
- -DGMX_EXTERNAL_BOOST=$(usex boost) |
468 |
- -DGMX_USE_TNG=$(usex tng) |
469 |
- -DGMX_BUILD_MANUAL=$(usex doc) |
470 |
- -DGMX_DEFAULT_SUFFIX=off |
471 |
- -DGMX_SIMD="$acce" |
472 |
- -DGMX_LIB_INSTALL_DIR="$(get_libdir)" |
473 |
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
474 |
- -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF |
475 |
- -DGMX_USE_GCC44_BUG_WORKAROUND=OFF |
476 |
- -DBUILD_TESTING=$(usex test) |
477 |
- -DGMX_BUILD_UNITTESTS=$(usex test) |
478 |
- ${extra} |
479 |
- ) |
480 |
- |
481 |
- for x in ${GMX_DIRS}; do |
482 |
- einfo "Configuring for ${x} precision" |
483 |
- local suffix="" |
484 |
- #if we build single and double - double is suffixed |
485 |
- use double-precision && use single-precision && \ |
486 |
- [[ ${x} = "double" ]] && suffix="_d" |
487 |
- local p |
488 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
489 |
- local cuda=( "-DGMX_GPU=OFF" ) |
490 |
- [[ ${x} = "float" ]] && use cuda && \ |
491 |
- cuda=( -DGMX_GPU=ON ) |
492 |
- mycmakeargs=( |
493 |
- ${mycmakeargs_pre[@]} ${p} |
494 |
- -DGMX_MPI=OFF |
495 |
- -DGMX_THREAD_MPI=$(usex threads) |
496 |
- "${cuda[@]}" |
497 |
- -DGMX_OPENMM=OFF |
498 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
499 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
500 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
501 |
- ) |
502 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
503 |
- [[ ${CHOST} != *-darwin* ]] || \ |
504 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
505 |
- use mpi || continue |
506 |
- einfo "Configuring for ${x} precision with mpi" |
507 |
- mycmakeargs=( |
508 |
- ${mycmakeargs_pre[@]} ${p} |
509 |
- -DGMX_THREAD_MPI=OFF |
510 |
- -DGMX_MPI=ON ${cuda} |
511 |
- -DGMX_OPENMM=OFF |
512 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
513 |
- -DBUILD_SHARED_LIBS=OFF |
514 |
- -DGMX_BUILD_MANUAL=OFF |
515 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
516 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
517 |
- ) |
518 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
519 |
- [[ ${CHOST} != *-darwin* ]] || \ |
520 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
521 |
- done |
522 |
-} |
523 |
- |
524 |
-src_compile() { |
525 |
- for x in ${GMX_DIRS}; do |
526 |
- einfo "Compiling for ${x} precision" |
527 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
528 |
- cmake-utils_src_compile |
529 |
- # not 100% necessary for rel ebuilds as available from website |
530 |
- if use doc; then |
531 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
532 |
- cmake-utils_src_compile manual |
533 |
- fi |
534 |
- use mpi || continue |
535 |
- einfo "Compiling for ${x} precision with mpi" |
536 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
537 |
- cmake-utils_src_compile |
538 |
- done |
539 |
-} |
540 |
- |
541 |
-src_test() { |
542 |
- for x in ${GMX_DIRS}; do |
543 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
544 |
- cmake-utils_src_make check |
545 |
- done |
546 |
-} |
547 |
- |
548 |
-src_install() { |
549 |
- for x in ${GMX_DIRS}; do |
550 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
551 |
- cmake-utils_src_install |
552 |
- if use doc; then |
553 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
554 |
- fi |
555 |
- use mpi || continue |
556 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
557 |
- cmake-utils_src_install |
558 |
- done |
559 |
- |
560 |
- if use tng; then |
561 |
- insinto /usr/include/tng |
562 |
- doins src/external/tng_io/include/tng/*h |
563 |
- fi |
564 |
- # drop unneeded stuff |
565 |
- rm "${ED}"usr/bin/GMXRC* || die |
566 |
- for x in "${ED}"usr/bin/gmx-completion-*.bash ; do |
567 |
- local n=${x##*/gmx-completion-} |
568 |
- n="${n%.bash}" |
569 |
- cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
570 |
- newbashcomp "${T}"/"${n}" "${n}" |
571 |
- done |
572 |
- rm "${ED}"usr/bin/gmx-completion*.bash || die |
573 |
- readme.gentoo_create_doc |
574 |
-} |
575 |
- |
576 |
-pkg_postinst() { |
577 |
- einfo |
578 |
- einfo "Please read and cite:" |
579 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
580 |
- einfo "https://dx.doi.org/10.1021/ct700301q" |
581 |
- einfo |
582 |
- readme.gentoo_print_elog |
583 |
-} |
584 |
|
585 |
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml |
586 |
index dce564d8220..493fbfa5be6 100644 |
587 |
--- a/sci-chemistry/gromacs/metadata.xml |
588 |
+++ b/sci-chemistry/gromacs/metadata.xml |
589 |
@@ -14,7 +14,6 @@ |
590 |
<flag name="opencl">Enable opencl non-bonded kernels</flag> |
591 |
<flag name="double-precision">More precise calculations at the expense of speed</flag> |
592 |
<flag name="single-precision">Single precision version of gromacs (default)</flag> |
593 |
- <flag name="boost">Enable external boost library</flag> |
594 |
<flag name="hwloc">Enable HWLoc lib support</flag> |
595 |
<flag name="tng">Enable new trajectory format - tng</flag> |
596 |
<flag name="lmfit">Use external <pkg>sci-libs/lmfit</pkg></flag> |