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commit: cc3e44706a85a7cc2fd370391f29e6fa54ea8b68 |
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Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> |
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AuthorDate: Sat Jan 5 21:23:05 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=cc3e4470 |
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|
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sci-chemistry/gromacs: Drop 2016.2 |
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|
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2016.5 is stable. |
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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-2016.2.ebuild | 275 ---------------------------- |
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2 files changed, 277 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 4d0e90e75ae..b00c9962824 100644 |
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--- a/sci-chemistry/gromacs/Manifest |
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+++ b/sci-chemistry/gromacs/Manifest |
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@@ -1,9 +1,7 @@ |
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-DIST gromacs-2016.2.tar.gz 27339623 BLAKE2B c3548f4abdc4c1b09a79a3da99d7ca8060daca7307e4c5b81bd97d54adfb9621fbccf1ea7fd96c3676d6b44c20f9f4cd2168ce131799792512fad3b8b1ac0522 SHA512 f5e74bb8c126823c90d205ac0f0835e61fdd13a4550bc15aa9c972ee9b187f6451cdc90877c17276d2f889d61abb5eaa5ea1b54f7cbf3da67074146c749c1aa6 |
| 25 |
DIST gromacs-2016.5.tar.gz 27369491 BLAKE2B 4a8bf1ae3e298ac2e26ec476130720dc3ef00db5d999e3a45fdbfd7fbfe7e94fbc86be6ff0f2f23552769c8bc851ce49c73f6fc1ab13f372523279b93e7794d7 SHA512 9cb8ff88871aa5df0967c60ba303c03296c6fa3c215cd01b26259df7753f0014f04222078ab4b84a66a1f709997837134d5c0f74da19b78322e410010c9d9e10 |
| 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 regressiontests-2016.2.tar.gz 67095329 BLAKE2B fec8a663845ad67374c8a230d1590fa9e5079460198f41cee3b788aaa1c72e8ec9dcda48bc68a594f15003d11bf6617d46cc1a09c16b7a333587b43904a16ba6 SHA512 e0aceb56d1f38a7e6ab9fdaac5063fd20c5b3a162ffb6eddd0e6dc7dff9b724bfe31363493a9437e9f9d5421a534b375960fcb31e903a4901a0fa94ed8511294 |
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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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|
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diff --git a/sci-chemistry/gromacs/gromacs-2016.2.ebuild b/sci-chemistry/gromacs/gromacs-2016.2.ebuild |
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deleted file mode 100644 |
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index 15acf0b2cf7..00000000000 |
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--- a/sci-chemistry/gromacs/gromacs-2016.2.ebuild |
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+++ /dev/null |
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@@ -1,275 +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 xdg-utils |
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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:0:4}" |
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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 cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
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- |
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-CDEPEND=" |
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- X? ( |
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- x11-libs/libX11 |
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- x11-libs/libSM |
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- x11-libs/libICE |
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- ) |
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- blas? ( virtual/blas ) |
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- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
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- fftw? ( sci-libs/fftw:3.0 ) |
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- hwloc? ( <sys-apps/hwloc-2 ) |
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- lapack? ( virtual/lapack ) |
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- mkl? ( sci-libs/mkl ) |
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- mpi? ( virtual/mpi ) |
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- " |
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-DEPEND="${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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- dev-libs/tinyxml2 |
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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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- xdg_environment_reset #591952 |
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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 && has_version "<sci-libs/mkl-11.3"; 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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- 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/*/linux/mkl/include)" |
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- -DMKL_LIBRARIES="$(echo /opt/intel/*/linux/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
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- ) |
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- else |
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- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
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- 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) |
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- -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) |
| 200 |
- -DGMX_USE_TNG=$(usex tng) |
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- -DGMX_BUILD_MANUAL=$(usex doc) |
| 202 |
- -DGMX_HWLOC=$(usex hwloc) |
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- -DGMX_DEFAULT_SUFFIX=off |
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- -DGMX_SIMD="$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/" |
| 207 |
- -DBUILD_TESTING=OFF |
| 208 |
- -DGMX_BUILD_UNITTESTS=OFF |
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- -DGMX_EXTERNAL_TINYXML2=ON |
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- ${extra} |
| 211 |
- ) |
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- |
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- for x in ${GMX_DIRS}; do |
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- einfo "Configuring for ${x} precision" |
| 215 |
- local suffix="" |
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- #if we build single and double - double is suffixed |
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- use double-precision && use single-precision && \ |
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- [[ ${x} = "double" ]] && suffix="_d" |
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- local p |
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- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
| 221 |
- local cuda=( "-DGMX_GPU=OFF" ) |
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- [[ ${x} = "float" ]] && use cuda && \ |
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- cuda=( -DGMX_GPU=ON ) |
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- mycmakeargs=( |
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- ${mycmakeargs_pre[@]} ${p} |
| 226 |
- -DGMX_MPI=OFF |
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- -DGMX_THREAD_MPI=$(usex threads) |
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- "${cuda[@]}" |
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- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
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- -DGMX_BINARY_SUFFIX="${suffix}" |
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- -DGMX_LIBS_SUFFIX="${suffix}" |
| 232 |
- ) |
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- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
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- [[ ${CHOST} != *-darwin* ]] || \ |
| 235 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
| 236 |
- use mpi || continue |
| 237 |
- einfo "Configuring for ${x} precision with mpi" |
| 238 |
- mycmakeargs=( |
| 239 |
- ${mycmakeargs_pre[@]} ${p} |
| 240 |
- -DGMX_THREAD_MPI=OFF |
| 241 |
- -DGMX_MPI=ON ${cuda} |
| 242 |
- -DGMX_OPENMM=OFF |
| 243 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
| 244 |
- -DBUILD_SHARED_LIBS=OFF |
| 245 |
- -DGMX_BUILD_MANUAL=OFF |
| 246 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
| 247 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
| 248 |
- ) |
| 249 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
| 250 |
- [[ ${CHOST} != *-darwin* ]] || \ |
| 251 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
| 252 |
- done |
| 253 |
-} |
| 254 |
- |
| 255 |
-src_compile() { |
| 256 |
- for x in ${GMX_DIRS}; do |
| 257 |
- einfo "Compiling for ${x} precision" |
| 258 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| 259 |
- cmake-utils_src_compile |
| 260 |
- # not 100% necessary for rel ebuilds as available from website |
| 261 |
- if use doc; then |
| 262 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| 263 |
- cmake-utils_src_compile manual |
| 264 |
- fi |
| 265 |
- use mpi || continue |
| 266 |
- einfo "Compiling for ${x} precision with mpi" |
| 267 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
| 268 |
- cmake-utils_src_compile |
| 269 |
- done |
| 270 |
-} |
| 271 |
- |
| 272 |
-src_test() { |
| 273 |
- for x in ${GMX_DIRS}; do |
| 274 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| 275 |
- cmake-utils_src_make check |
| 276 |
- done |
| 277 |
-} |
| 278 |
- |
| 279 |
-src_install() { |
| 280 |
- for x in ${GMX_DIRS}; do |
| 281 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
| 282 |
- cmake-utils_src_install |
| 283 |
- if use doc; then |
| 284 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
| 285 |
- fi |
| 286 |
- use mpi || continue |
| 287 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
| 288 |
- cmake-utils_src_install |
| 289 |
- done |
| 290 |
- |
| 291 |
- if use tng; then |
| 292 |
- insinto /usr/include/tng |
| 293 |
- doins src/external/tng_io/include/tng/*h |
| 294 |
- fi |
| 295 |
- # drop unneeded stuff |
| 296 |
- rm "${ED}"usr/bin/GMXRC* || die |
| 297 |
- for x in "${ED}"usr/bin/gmx-completion-*.bash ; do |
| 298 |
- local n=${x##*/gmx-completion-} |
| 299 |
- n="${n%.bash}" |
| 300 |
- cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
| 301 |
- newbashcomp "${T}"/"${n}" "${n}" |
| 302 |
- done |
| 303 |
- rm "${ED}"usr/bin/gmx-completion*.bash || die |
| 304 |
- readme.gentoo_create_doc |
| 305 |
-} |
| 306 |
- |
| 307 |
-pkg_postinst() { |
| 308 |
- einfo |
| 309 |
- einfo "Please read and cite:" |
| 310 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
| 311 |
- einfo "https://dx.doi.org/10.1021/ct700301q" |
| 312 |
- einfo |
| 313 |
- readme.gentoo_print_elog |
| 314 |
-} |
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