1 |
commit: 2782ae81285c65d9724740b3d5d8a6f1b1e53a1c |
2 |
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
3 |
AuthorDate: Mon Oct 22 16:27:11 2018 +0000 |
4 |
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
5 |
CommitDate: Mon Oct 22 16:27:11 2018 +0000 |
6 |
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2782ae81 |
7 |
|
8 |
sci-chemistry/gromacs: Fix deps. Drop unneded |
9 |
|
10 |
Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org> |
11 |
Package-Manager: Portage-2.3.49, Repoman-2.3.11 |
12 |
|
13 |
sci-chemistry/gromacs/Manifest | 4 - |
14 |
sci-chemistry/gromacs/gromacs-2016.2.ebuild | 4 +- |
15 |
sci-chemistry/gromacs/gromacs-2016.5.ebuild | 4 +- |
16 |
sci-chemistry/gromacs/gromacs-2016.9999.ebuild | 4 +- |
17 |
sci-chemistry/gromacs/gromacs-2018.1.ebuild | 272 ------------------------- |
18 |
sci-chemistry/gromacs/gromacs-2018.2.ebuild | 271 ------------------------ |
19 |
sci-chemistry/gromacs/gromacs-2018.3.ebuild | 4 +- |
20 |
sci-chemistry/gromacs/gromacs-2018.9999.ebuild | 4 +- |
21 |
sci-chemistry/gromacs/gromacs-9999.ebuild | 4 +- |
22 |
9 files changed, 12 insertions(+), 559 deletions(-) |
23 |
|
24 |
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest |
25 |
index face173e388..71ac5f61019 100644 |
26 |
--- a/sci-chemistry/gromacs/Manifest |
27 |
+++ b/sci-chemistry/gromacs/Manifest |
28 |
@@ -1,14 +1,10 @@ |
29 |
DIST gromacs-2016.2.tar.gz 27339623 BLAKE2B c3548f4abdc4c1b09a79a3da99d7ca8060daca7307e4c5b81bd97d54adfb9621fbccf1ea7fd96c3676d6b44c20f9f4cd2168ce131799792512fad3b8b1ac0522 SHA512 f5e74bb8c126823c90d205ac0f0835e61fdd13a4550bc15aa9c972ee9b187f6451cdc90877c17276d2f889d61abb5eaa5ea1b54f7cbf3da67074146c749c1aa6 |
30 |
DIST gromacs-2016.5.tar.gz 27369491 BLAKE2B 4a8bf1ae3e298ac2e26ec476130720dc3ef00db5d999e3a45fdbfd7fbfe7e94fbc86be6ff0f2f23552769c8bc851ce49c73f6fc1ab13f372523279b93e7794d7 SHA512 9cb8ff88871aa5df0967c60ba303c03296c6fa3c215cd01b26259df7753f0014f04222078ab4b84a66a1f709997837134d5c0f74da19b78322e410010c9d9e10 |
31 |
-DIST gromacs-2018.1.tar.gz 29895119 BLAKE2B 45cc674bd78dc7dc56388a899ae50da9f10eb4dc80dad461f7e298894ee845eae744010013e682f3be4b03c1f04624111266e84cd9721415b23f87d544846827 SHA512 d29f152e9f115c7de07881c6af4cc05481e0a5520bd33142a09507e8c4df9f8b6c9d6d96efcb7adaaf4e0127b76ab247421d43918bd7e7779d6e71f5984db715 |
32 |
-DIST gromacs-2018.2.tar.gz 29899294 BLAKE2B a4d7111fdfb2c6919ef7a94aded634c5e14c4ca6ee6411c6c84289a9c88c39d731e89d3b01f14b2370d7de7782964e8db378aa6baabdd85cf46b689504f0738a SHA512 d444b503e24a9875b0ab7622772946ef73ab2c897da6ff45ac908f147ea398ba2404b064a8784996fd34b25e188e36f12a492e0070427e0929f422d934205d28 |
33 |
DIST gromacs-2018.3.tar.gz 29915626 BLAKE2B 6e6eeafecdd923a25b4a2a78a8e89f793639b57ffbd63f19d133d8474302f9a381041f138a509dadb42b36e25fe508729e860efb6b0c75cdbf01d924b0a8fd83 SHA512 3c4d6eb3942d7b54d01c94c6f6f5ae706e0f5d4f9901ea11a56fde4df97b1a9112007f2cb13feea0f19f30c89f57ae80ff53a8f5203b8cdff103aa903cd0dc8f |
34 |
DIST gromacs-5.0.4.tar.gz 26342095 BLAKE2B 27a2483e23533ad627114c0005fa0d49a311b359c31aed6378bdd768c9dda03c3b19f11d961f0bd3b82a1711737d4b7dce13cad5fc56d058dd0110fe21421ee3 SHA512 bc62b623bf71dcaa948aaf7563a3d3afa973da0702062848a20323db202e862dcee413197dacd1472866ccb40fce7709e283177b1c6c49514064f23e6c46b5ee |
35 |
DIST gromacs-5.1.3.tar.gz 27095702 BLAKE2B b7fd8fa10e8c4f4368ac551338c59374dc35f85c9fdae5d64eec62929b8f04ea724a084959b3618cd8a151bf3e0a0c84c8f75de953722effca82a4928941ce73 SHA512 9ab26e1b2268f8d567b89b2d99d0b75b937b28edceaec56d17ca3243c76faa31255ffc0c45d762c7c693fe500b00e36ad43b80572d1d7f92dc87f9d2d98c0ba6 |
36 |
DIST regressiontests-2016.2.tar.gz 67095329 BLAKE2B fec8a663845ad67374c8a230d1590fa9e5079460198f41cee3b788aaa1c72e8ec9dcda48bc68a594f15003d11bf6617d46cc1a09c16b7a333587b43904a16ba6 SHA512 e0aceb56d1f38a7e6ab9fdaac5063fd20c5b3a162ffb6eddd0e6dc7dff9b724bfe31363493a9437e9f9d5421a534b375960fcb31e903a4901a0fa94ed8511294 |
37 |
DIST regressiontests-2016.5.tar.gz 67641413 BLAKE2B 4fcd30c198f3acbbabf1104c040d9a686de49536a97dbeb14732bfa0ed3cf37aa61b1b0f45393668985b993d1f1862a8985e416af819cf9793f5964f3e4f43cc SHA512 31764fd99cc4185d61de5d4443ee482c27b13533451a24aa0e4899997ce275a63685424eafacae38b1a3ffd4ce0d5ebe02a90348953b04c104f91376f0edfdff |
38 |
-DIST regressiontests-2018.1.tar.gz 67859956 BLAKE2B f561eb9373b4e0e5faae2aa91e3cb3911c096c1fce96755fc7a8a7b3a25b53bda88ef90d04d3a6fce414bf9dba44d0933827f080949306d5c98f60e5a1797412 SHA512 81c9a62fca859923c1e27214b32b0cff1dd48224dd4ad9301554036b842ccc400a2729752ba71b284e0c5b6c1769ce7de5fe2c9ba4fc7cf0917fd4ced9883112 |
39 |
-DIST regressiontests-2018.2.tar.gz 67855795 BLAKE2B 32504a7d9315f404b4a57fd45dd59540166b0e73d51ad5938b6a18cafc491cda5c00fe204dedba9c51a3f859759fb1d8c894c0607d71d49701269cf909617584 SHA512 6cc4bd4716f8b7aba69b840facd160f1abb32def2349cc441b89e12bf8df21dc4a4ca23acc4e47bf7ec3ae55b8e3f9a28beab044833b9d8ddfcf5e21d2878a5a |
40 |
DIST regressiontests-2018.3.tar.gz 67857855 BLAKE2B acd7a05ae79d1b4eb47d0c68a3fec9ee19f028a5019f39c37a033f48cf6da2a468375180ad6ceca9ac4f685a8bead38550663a47d6427b51f84c32a5c810e5f0 SHA512 57980d49efe6dcc3b3d14b5913a30c68fc1de5b679ef986fec1a149c76f67139b0299c3ee2825451461294fab5f345c7ad4f42e90f8991b81aafe9c369f3ff0b |
41 |
DIST regressiontests-5.0.4.tar.gz 65193251 BLAKE2B c5e5f23adcc2639fe652bc252533307c7fda44453d506603242968bd8588c7394028b2c3c7a9252f807a050d40e8f78735e904dfe517d3db8ae962051f4826c1 SHA512 747725fa28c1c9525596bdeeb8809e45268e19036c11dac67d043aa1c51748688ca37eb6014eb7e819eb927a8b9ca2631d0ace4cdff8ed491b08c316c530ab65 |
42 |
DIST regressiontests-5.1.3.tar.gz 66994083 BLAKE2B 7009f65ad0138664ac84e57f8bc7cce5d18a59f99943e56b6642583120bfce279e005ac0bacd2db8904ea477a48e2b938c64de46a65fa5d08fce6009d53583c3 SHA512 486e86eb3b75bae822abe82dac4e1098aa13723bd04214021f835a2f0b847303f015a9ececc33aa5ae63d31a2eeae07e512f22464b6c0e26d1286b0781578022 |
43 |
|
44 |
diff --git a/sci-chemistry/gromacs/gromacs-2016.2.ebuild b/sci-chemistry/gromacs/gromacs-2016.2.ebuild |
45 |
index 3b371d27308..15acf0b2cf7 100644 |
46 |
--- a/sci-chemistry/gromacs/gromacs-2016.2.ebuild |
47 |
+++ b/sci-chemistry/gromacs/gromacs-2016.2.ebuild |
48 |
@@ -1,4 +1,4 @@ |
49 |
-# Copyright 1999-2017 Gentoo Foundation |
50 |
+# Copyright 1999-2018 Gentoo Authors |
51 |
# Distributed under the terms of the GNU General Public License v2 |
52 |
|
53 |
EAPI=6 |
54 |
@@ -41,7 +41,7 @@ CDEPEND=" |
55 |
blas? ( virtual/blas ) |
56 |
cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
57 |
fftw? ( sci-libs/fftw:3.0 ) |
58 |
- hwloc? ( sys-apps/hwloc ) |
59 |
+ hwloc? ( <sys-apps/hwloc-2 ) |
60 |
lapack? ( virtual/lapack ) |
61 |
mkl? ( sci-libs/mkl ) |
62 |
mpi? ( virtual/mpi ) |
63 |
|
64 |
diff --git a/sci-chemistry/gromacs/gromacs-2016.5.ebuild b/sci-chemistry/gromacs/gromacs-2016.5.ebuild |
65 |
index e86fdf946c7..69ec80d2cbe 100644 |
66 |
--- a/sci-chemistry/gromacs/gromacs-2016.5.ebuild |
67 |
+++ b/sci-chemistry/gromacs/gromacs-2016.5.ebuild |
68 |
@@ -1,4 +1,4 @@ |
69 |
-# Copyright 1999-2018 Gentoo Foundation |
70 |
+# Copyright 1999-2018 Gentoo Authors |
71 |
# Distributed under the terms of the GNU General Public License v2 |
72 |
|
73 |
EAPI=6 |
74 |
@@ -42,7 +42,7 @@ CDEPEND=" |
75 |
blas? ( virtual/blas ) |
76 |
cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
77 |
fftw? ( sci-libs/fftw:3.0 ) |
78 |
- hwloc? ( sys-apps/hwloc ) |
79 |
+ hwloc? ( <sys-apps/hwloc-2 ) |
80 |
lapack? ( virtual/lapack ) |
81 |
mkl? ( sci-libs/mkl ) |
82 |
mpi? ( virtual/mpi ) |
83 |
|
84 |
diff --git a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild b/sci-chemistry/gromacs/gromacs-2016.9999.ebuild |
85 |
index 7e426ddfdf5..69ec80d2cbe 100644 |
86 |
--- a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild |
87 |
+++ b/sci-chemistry/gromacs/gromacs-2016.9999.ebuild |
88 |
@@ -1,4 +1,4 @@ |
89 |
-# Copyright 1999-2017 Gentoo Foundation |
90 |
+# Copyright 1999-2018 Gentoo Authors |
91 |
# Distributed under the terms of the GNU General Public License v2 |
92 |
|
93 |
EAPI=6 |
94 |
@@ -42,7 +42,7 @@ CDEPEND=" |
95 |
blas? ( virtual/blas ) |
96 |
cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
97 |
fftw? ( sci-libs/fftw:3.0 ) |
98 |
- hwloc? ( sys-apps/hwloc ) |
99 |
+ hwloc? ( <sys-apps/hwloc-2 ) |
100 |
lapack? ( virtual/lapack ) |
101 |
mkl? ( sci-libs/mkl ) |
102 |
mpi? ( virtual/mpi ) |
103 |
|
104 |
diff --git a/sci-chemistry/gromacs/gromacs-2018.1.ebuild b/sci-chemistry/gromacs/gromacs-2018.1.ebuild |
105 |
deleted file mode 100644 |
106 |
index 11f2b2483a3..00000000000 |
107 |
--- a/sci-chemistry/gromacs/gromacs-2018.1.ebuild |
108 |
+++ /dev/null |
109 |
@@ -1,272 +0,0 @@ |
110 |
-# Copyright 1999-2018 Gentoo Foundation |
111 |
-# Distributed under the terms of the GNU General Public License v2 |
112 |
- |
113 |
-EAPI=6 |
114 |
- |
115 |
-CMAKE_MAKEFILE_GENERATOR="ninja" |
116 |
- |
117 |
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils |
118 |
- |
119 |
-if [[ $PV = *9999* ]]; then |
120 |
- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
121 |
- https://gerrit.gromacs.org/gromacs.git |
122 |
- https://github.com/gromacs/gromacs.git |
123 |
- http://repo.or.cz/r/gromacs.git" |
124 |
- [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" |
125 |
- inherit git-r3 |
126 |
- KEYWORDS="" |
127 |
-else |
128 |
- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
129 |
- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" |
130 |
- KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
131 |
-fi |
132 |
- |
133 |
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
134 |
- |
135 |
-DESCRIPTION="The ultimate molecular dynamics simulation package" |
136 |
-HOMEPAGE="http://www.gromacs.org/" |
137 |
- |
138 |
-# see COPYING for details |
139 |
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
140 |
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
141 |
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
142 |
-SLOT="0/${PV}" |
143 |
-IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
144 |
- |
145 |
-CDEPEND=" |
146 |
- X? ( |
147 |
- x11-libs/libX11 |
148 |
- x11-libs/libSM |
149 |
- x11-libs/libICE |
150 |
- ) |
151 |
- blas? ( virtual/blas ) |
152 |
- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
153 |
- opencl? ( virtual/opencl ) |
154 |
- fftw? ( sci-libs/fftw:3.0 ) |
155 |
- hwloc? ( sys-apps/hwloc ) |
156 |
- lapack? ( virtual/lapack ) |
157 |
- mkl? ( sci-libs/mkl ) |
158 |
- mpi? ( virtual/mpi ) |
159 |
- " |
160 |
-DEPEND="${CDEPEND} |
161 |
- virtual/pkgconfig |
162 |
- doc? ( |
163 |
- app-doc/doxygen |
164 |
- dev-texlive/texlive-latex |
165 |
- dev-texlive/texlive-latexextra |
166 |
- media-gfx/imagemagick |
167 |
- )" |
168 |
-RDEPEND="${CDEPEND}" |
169 |
- |
170 |
-REQUIRED_USE=" |
171 |
- || ( single-precision double-precision ) |
172 |
- cuda? ( single-precision ) |
173 |
- cuda? ( !opencl ) |
174 |
- mkl? ( !blas !fftw !lapack )" |
175 |
- |
176 |
-DOCS=( AUTHORS README ) |
177 |
- |
178 |
-if [[ ${PV} != *9999 ]]; then |
179 |
- S="${WORKDIR}/${PN}-${PV/_/-}" |
180 |
-fi |
181 |
- |
182 |
-pkg_pretend() { |
183 |
- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
184 |
- use openmp && ! tc-has-openmp && \ |
185 |
- die "Please switch to an openmp compatible compiler" |
186 |
-} |
187 |
- |
188 |
-src_unpack() { |
189 |
- if [[ ${PV} != *9999 ]]; then |
190 |
- default |
191 |
- else |
192 |
- git-r3_src_unpack |
193 |
- if use test; then |
194 |
- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
195 |
- EGIT_BRANCH="${EGIT_BRANCH}" \ |
196 |
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
197 |
- git-r3_src_unpack |
198 |
- fi |
199 |
- fi |
200 |
-} |
201 |
- |
202 |
-src_prepare() { |
203 |
- #notes/todos |
204 |
- # -on apple: there is framework support |
205 |
- |
206 |
- xdg_environment_reset #591952 |
207 |
- |
208 |
- cmake-utils_src_prepare |
209 |
- |
210 |
- use cuda && cuda_src_prepare |
211 |
- |
212 |
- GMX_DIRS="" |
213 |
- use single-precision && GMX_DIRS+=" float" |
214 |
- use double-precision && GMX_DIRS+=" double" |
215 |
- |
216 |
- if use test; then |
217 |
- for x in ${GMX_DIRS}; do |
218 |
- mkdir -p "${WORKDIR}/${P}_${x}" || die |
219 |
- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
220 |
- done |
221 |
- fi |
222 |
- |
223 |
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
224 |
-} |
225 |
- |
226 |
-src_configure() { |
227 |
- local mycmakeargs_pre=( ) extra fft_opts=( ) |
228 |
- |
229 |
- #go from slowest to fastest acceleration |
230 |
- local acce="None" |
231 |
- use cpu_flags_x86_sse2 && acce="SSE2" |
232 |
- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
233 |
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
234 |
- use cpu_flags_x86_avx && acce="AVX_256" |
235 |
- use cpu_flags_x86_avx2 && acce="AVX2_256" |
236 |
- |
237 |
- #to create man pages, build tree binaries are executed (bug #398437) |
238 |
- [[ ${CHOST} = *-darwin* ]] && \ |
239 |
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
240 |
- |
241 |
- if use fftw; then |
242 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
243 |
- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
244 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
245 |
- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
246 |
- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
247 |
- ) |
248 |
- elif use mkl; then |
249 |
- local bits=$(get_libdir) |
250 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
251 |
- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
252 |
- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
253 |
- ) |
254 |
- else |
255 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
256 |
- fi |
257 |
- |
258 |
- mycmakeargs_pre+=( |
259 |
- "${fft_opts[@]}" |
260 |
- -DGMX_X11=$(usex X) |
261 |
- -DGMX_EXTERNAL_BLAS=$(usex blas) |
262 |
- -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
263 |
- -DGMX_OPENMP=$(usex openmp) |
264 |
- -DGMX_COOL_QUOTES=$(usex offensive) |
265 |
- -DGMX_USE_TNG=$(usex tng) |
266 |
- -DGMX_BUILD_MANUAL=$(usex doc) |
267 |
- -DGMX_HWLOC=$(usex hwloc) |
268 |
- -DGMX_DEFAULT_SUFFIX=off |
269 |
- -DGMX_SIMD="$acce" |
270 |
- -DGMX_LIB_INSTALL_DIR="$(get_libdir)" |
271 |
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
272 |
- -DBUILD_TESTING=$(usex test) |
273 |
- -DGMX_BUILD_UNITTESTS=$(usex test) |
274 |
- ${extra} |
275 |
- ) |
276 |
- |
277 |
- for x in ${GMX_DIRS}; do |
278 |
- einfo "Configuring for ${x} precision" |
279 |
- local suffix="" |
280 |
- #if we build single and double - double is suffixed |
281 |
- use double-precision && use single-precision && \ |
282 |
- [[ ${x} = "double" ]] && suffix="_d" |
283 |
- local p |
284 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
285 |
- local cuda=( "-DGMX_GPU=OFF" ) |
286 |
- [[ ${x} = "float" ]] && use cuda && \ |
287 |
- cuda=( "-DGMX_GPU=ON" ) |
288 |
- local opencl=( "-DGMX_USE_OPENCL=OFF" ) |
289 |
- use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) |
290 |
- mycmakeargs=( |
291 |
- ${mycmakeargs_pre[@]} ${p} |
292 |
- -DGMX_MPI=OFF |
293 |
- -DGMX_THREAD_MPI=$(usex threads) |
294 |
- "${opencl[@]}" |
295 |
- "${cuda[@]}" |
296 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
297 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
298 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
299 |
- ) |
300 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
301 |
- [[ ${CHOST} != *-darwin* ]] || \ |
302 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
303 |
- use mpi || continue |
304 |
- einfo "Configuring for ${x} precision with mpi" |
305 |
- mycmakeargs=( |
306 |
- ${mycmakeargs_pre[@]} ${p} |
307 |
- -DGMX_THREAD_MPI=OFF |
308 |
- -DGMX_MPI=ON ${cuda} |
309 |
- -DGMX_OPENMM=OFF |
310 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
311 |
- -DBUILD_SHARED_LIBS=OFF |
312 |
- -DGMX_BUILD_MANUAL=OFF |
313 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
314 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
315 |
- ) |
316 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
317 |
- [[ ${CHOST} != *-darwin* ]] || \ |
318 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
319 |
- done |
320 |
-} |
321 |
- |
322 |
-src_compile() { |
323 |
- for x in ${GMX_DIRS}; do |
324 |
- einfo "Compiling for ${x} precision" |
325 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
326 |
- cmake-utils_src_compile |
327 |
- # not 100% necessary for rel ebuilds as available from website |
328 |
- if use doc; then |
329 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
330 |
- cmake-utils_src_compile manual |
331 |
- fi |
332 |
- use mpi || continue |
333 |
- einfo "Compiling for ${x} precision with mpi" |
334 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
335 |
- cmake-utils_src_compile |
336 |
- done |
337 |
-} |
338 |
- |
339 |
-src_test() { |
340 |
- for x in ${GMX_DIRS}; do |
341 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
342 |
- cmake-utils_src_make check |
343 |
- done |
344 |
-} |
345 |
- |
346 |
-src_install() { |
347 |
- for x in ${GMX_DIRS}; do |
348 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
349 |
- cmake-utils_src_install |
350 |
- if use doc; then |
351 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
352 |
- fi |
353 |
- use mpi || continue |
354 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
355 |
- cmake-utils_src_install |
356 |
- done |
357 |
- |
358 |
- if use tng; then |
359 |
- insinto /usr/include/tng |
360 |
- doins src/external/tng_io/include/tng/*h |
361 |
- fi |
362 |
- # drop unneeded stuff |
363 |
- rm "${ED}"usr/bin/GMXRC* || die |
364 |
- for x in "${ED}"usr/bin/gmx-completion-*.bash ; do |
365 |
- local n=${x##*/gmx-completion-} |
366 |
- n="${n%.bash}" |
367 |
- cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
368 |
- newbashcomp "${T}"/"${n}" "${n}" |
369 |
- done |
370 |
- rm "${ED}"usr/bin/gmx-completion*.bash || die |
371 |
- readme.gentoo_create_doc |
372 |
-} |
373 |
- |
374 |
-pkg_postinst() { |
375 |
- einfo |
376 |
- einfo "Please read and cite:" |
377 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
378 |
- einfo "https://dx.doi.org/10.1021/ct700301q" |
379 |
- einfo |
380 |
- readme.gentoo_print_elog |
381 |
-} |
382 |
|
383 |
diff --git a/sci-chemistry/gromacs/gromacs-2018.2.ebuild b/sci-chemistry/gromacs/gromacs-2018.2.ebuild |
384 |
deleted file mode 100644 |
385 |
index d4ea677a994..00000000000 |
386 |
--- a/sci-chemistry/gromacs/gromacs-2018.2.ebuild |
387 |
+++ /dev/null |
388 |
@@ -1,271 +0,0 @@ |
389 |
-# Copyright 1999-2018 Gentoo Foundation |
390 |
-# Distributed under the terms of the GNU General Public License v2 |
391 |
- |
392 |
-EAPI=6 |
393 |
- |
394 |
-CMAKE_MAKEFILE_GENERATOR="ninja" |
395 |
- |
396 |
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils |
397 |
- |
398 |
-if [[ $PV = *9999* ]]; then |
399 |
- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
400 |
- https://gerrit.gromacs.org/gromacs.git |
401 |
- https://github.com/gromacs/gromacs.git |
402 |
- http://repo.or.cz/r/gromacs.git" |
403 |
- [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" |
404 |
- inherit git-r3 |
405 |
- KEYWORDS="" |
406 |
-else |
407 |
- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
408 |
- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" |
409 |
- KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
410 |
-fi |
411 |
- |
412 |
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
413 |
- |
414 |
-DESCRIPTION="The ultimate molecular dynamics simulation package" |
415 |
-HOMEPAGE="http://www.gromacs.org/" |
416 |
- |
417 |
-# see COPYING for details |
418 |
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
419 |
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
420 |
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
421 |
-SLOT="0/${PV}" |
422 |
-IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
423 |
- |
424 |
-CDEPEND=" |
425 |
- X? ( |
426 |
- x11-libs/libX11 |
427 |
- x11-libs/libSM |
428 |
- x11-libs/libICE |
429 |
- ) |
430 |
- blas? ( virtual/blas ) |
431 |
- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
432 |
- opencl? ( virtual/opencl ) |
433 |
- fftw? ( sci-libs/fftw:3.0 ) |
434 |
- hwloc? ( sys-apps/hwloc ) |
435 |
- lapack? ( virtual/lapack ) |
436 |
- mkl? ( sci-libs/mkl ) |
437 |
- mpi? ( virtual/mpi ) |
438 |
- " |
439 |
-DEPEND="${CDEPEND} |
440 |
- virtual/pkgconfig |
441 |
- doc? ( |
442 |
- app-doc/doxygen |
443 |
- dev-texlive/texlive-latex |
444 |
- dev-texlive/texlive-latexextra |
445 |
- media-gfx/imagemagick |
446 |
- )" |
447 |
-RDEPEND="${CDEPEND}" |
448 |
- |
449 |
-REQUIRED_USE=" |
450 |
- || ( single-precision double-precision ) |
451 |
- cuda? ( single-precision ) |
452 |
- cuda? ( !opencl ) |
453 |
- mkl? ( !blas !fftw !lapack )" |
454 |
- |
455 |
-DOCS=( AUTHORS README ) |
456 |
- |
457 |
-if [[ ${PV} != *9999 ]]; then |
458 |
- S="${WORKDIR}/${PN}-${PV/_/-}" |
459 |
-fi |
460 |
- |
461 |
-pkg_pretend() { |
462 |
- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
463 |
- use openmp && ! tc-has-openmp && \ |
464 |
- die "Please switch to an openmp compatible compiler" |
465 |
-} |
466 |
- |
467 |
-src_unpack() { |
468 |
- if [[ ${PV} != *9999 ]]; then |
469 |
- default |
470 |
- else |
471 |
- git-r3_src_unpack |
472 |
- if use test; then |
473 |
- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
474 |
- EGIT_BRANCH="${EGIT_BRANCH}" \ |
475 |
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
476 |
- git-r3_src_unpack |
477 |
- fi |
478 |
- fi |
479 |
-} |
480 |
- |
481 |
-src_prepare() { |
482 |
- #notes/todos |
483 |
- # -on apple: there is framework support |
484 |
- |
485 |
- xdg_environment_reset #591952 |
486 |
- |
487 |
- cmake-utils_src_prepare |
488 |
- |
489 |
- use cuda && cuda_src_prepare |
490 |
- |
491 |
- GMX_DIRS="" |
492 |
- use single-precision && GMX_DIRS+=" float" |
493 |
- use double-precision && GMX_DIRS+=" double" |
494 |
- |
495 |
- if use test; then |
496 |
- for x in ${GMX_DIRS}; do |
497 |
- mkdir -p "${WORKDIR}/${P}_${x}" || die |
498 |
- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
499 |
- done |
500 |
- fi |
501 |
- |
502 |
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
503 |
-} |
504 |
- |
505 |
-src_configure() { |
506 |
- local mycmakeargs_pre=( ) extra fft_opts=( ) |
507 |
- |
508 |
- #go from slowest to fastest acceleration |
509 |
- local acce="None" |
510 |
- use cpu_flags_x86_sse2 && acce="SSE2" |
511 |
- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
512 |
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
513 |
- use cpu_flags_x86_avx && acce="AVX_256" |
514 |
- use cpu_flags_x86_avx2 && acce="AVX2_256" |
515 |
- |
516 |
- #to create man pages, build tree binaries are executed (bug #398437) |
517 |
- [[ ${CHOST} = *-darwin* ]] && \ |
518 |
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
519 |
- |
520 |
- if use fftw; then |
521 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
522 |
- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
523 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
524 |
- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
525 |
- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
526 |
- ) |
527 |
- elif use mkl; then |
528 |
- local bits=$(get_libdir) |
529 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
530 |
- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
531 |
- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
532 |
- ) |
533 |
- else |
534 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
535 |
- fi |
536 |
- |
537 |
- mycmakeargs_pre+=( |
538 |
- "${fft_opts[@]}" |
539 |
- -DGMX_X11=$(usex X) |
540 |
- -DGMX_EXTERNAL_BLAS=$(usex blas) |
541 |
- -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
542 |
- -DGMX_OPENMP=$(usex openmp) |
543 |
- -DGMX_COOL_QUOTES=$(usex offensive) |
544 |
- -DGMX_USE_TNG=$(usex tng) |
545 |
- -DGMX_BUILD_MANUAL=$(usex doc) |
546 |
- -DGMX_HWLOC=$(usex hwloc) |
547 |
- -DGMX_DEFAULT_SUFFIX=off |
548 |
- -DGMX_SIMD="$acce" |
549 |
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
550 |
- -DBUILD_TESTING=$(usex test) |
551 |
- -DGMX_BUILD_UNITTESTS=$(usex test) |
552 |
- ${extra} |
553 |
- ) |
554 |
- |
555 |
- for x in ${GMX_DIRS}; do |
556 |
- einfo "Configuring for ${x} precision" |
557 |
- local suffix="" |
558 |
- #if we build single and double - double is suffixed |
559 |
- use double-precision && use single-precision && \ |
560 |
- [[ ${x} = "double" ]] && suffix="_d" |
561 |
- local p |
562 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
563 |
- local cuda=( "-DGMX_GPU=OFF" ) |
564 |
- [[ ${x} = "float" ]] && use cuda && \ |
565 |
- cuda=( "-DGMX_GPU=ON" ) |
566 |
- local opencl=( "-DGMX_USE_OPENCL=OFF" ) |
567 |
- use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) |
568 |
- mycmakeargs=( |
569 |
- ${mycmakeargs_pre[@]} ${p} |
570 |
- -DGMX_MPI=OFF |
571 |
- -DGMX_THREAD_MPI=$(usex threads) |
572 |
- "${opencl[@]}" |
573 |
- "${cuda[@]}" |
574 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
575 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
576 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
577 |
- ) |
578 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
579 |
- [[ ${CHOST} != *-darwin* ]] || \ |
580 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
581 |
- use mpi || continue |
582 |
- einfo "Configuring for ${x} precision with mpi" |
583 |
- mycmakeargs=( |
584 |
- ${mycmakeargs_pre[@]} ${p} |
585 |
- -DGMX_THREAD_MPI=OFF |
586 |
- -DGMX_MPI=ON ${cuda} |
587 |
- -DGMX_OPENMM=OFF |
588 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
589 |
- -DBUILD_SHARED_LIBS=OFF |
590 |
- -DGMX_BUILD_MANUAL=OFF |
591 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
592 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
593 |
- ) |
594 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
595 |
- [[ ${CHOST} != *-darwin* ]] || \ |
596 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
597 |
- done |
598 |
-} |
599 |
- |
600 |
-src_compile() { |
601 |
- for x in ${GMX_DIRS}; do |
602 |
- einfo "Compiling for ${x} precision" |
603 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
604 |
- cmake-utils_src_compile |
605 |
- # not 100% necessary for rel ebuilds as available from website |
606 |
- if use doc; then |
607 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
608 |
- cmake-utils_src_compile manual |
609 |
- fi |
610 |
- use mpi || continue |
611 |
- einfo "Compiling for ${x} precision with mpi" |
612 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
613 |
- cmake-utils_src_compile |
614 |
- done |
615 |
-} |
616 |
- |
617 |
-src_test() { |
618 |
- for x in ${GMX_DIRS}; do |
619 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
620 |
- cmake-utils_src_make check |
621 |
- done |
622 |
-} |
623 |
- |
624 |
-src_install() { |
625 |
- for x in ${GMX_DIRS}; do |
626 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
627 |
- cmake-utils_src_install |
628 |
- if use doc; then |
629 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
630 |
- fi |
631 |
- use mpi || continue |
632 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
633 |
- cmake-utils_src_install |
634 |
- done |
635 |
- |
636 |
- if use tng; then |
637 |
- insinto /usr/include/tng |
638 |
- doins src/external/tng_io/include/tng/*h |
639 |
- fi |
640 |
- # drop unneeded stuff |
641 |
- rm "${ED}"usr/bin/GMXRC* || die |
642 |
- for x in "${ED}"usr/bin/gmx-completion-*.bash ; do |
643 |
- local n=${x##*/gmx-completion-} |
644 |
- n="${n%.bash}" |
645 |
- cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
646 |
- newbashcomp "${T}"/"${n}" "${n}" |
647 |
- done |
648 |
- rm "${ED}"usr/bin/gmx-completion*.bash || die |
649 |
- readme.gentoo_create_doc |
650 |
-} |
651 |
- |
652 |
-pkg_postinst() { |
653 |
- einfo |
654 |
- einfo "Please read and cite:" |
655 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
656 |
- einfo "https://dx.doi.org/10.1021/ct700301q" |
657 |
- einfo |
658 |
- readme.gentoo_print_elog |
659 |
-} |
660 |
|
661 |
diff --git a/sci-chemistry/gromacs/gromacs-2018.3.ebuild b/sci-chemistry/gromacs/gromacs-2018.3.ebuild |
662 |
index d4ea677a994..9190389751e 100644 |
663 |
--- a/sci-chemistry/gromacs/gromacs-2018.3.ebuild |
664 |
+++ b/sci-chemistry/gromacs/gromacs-2018.3.ebuild |
665 |
@@ -1,4 +1,4 @@ |
666 |
-# Copyright 1999-2018 Gentoo Foundation |
667 |
+# Copyright 1999-2018 Gentoo Authors |
668 |
# Distributed under the terms of the GNU General Public License v2 |
669 |
|
670 |
EAPI=6 |
671 |
@@ -43,7 +43,7 @@ CDEPEND=" |
672 |
cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
673 |
opencl? ( virtual/opencl ) |
674 |
fftw? ( sci-libs/fftw:3.0 ) |
675 |
- hwloc? ( sys-apps/hwloc ) |
676 |
+ hwloc? ( <sys-apps/hwloc-2 ) |
677 |
lapack? ( virtual/lapack ) |
678 |
mkl? ( sci-libs/mkl ) |
679 |
mpi? ( virtual/mpi ) |
680 |
|
681 |
diff --git a/sci-chemistry/gromacs/gromacs-2018.9999.ebuild b/sci-chemistry/gromacs/gromacs-2018.9999.ebuild |
682 |
index d4ea677a994..9190389751e 100644 |
683 |
--- a/sci-chemistry/gromacs/gromacs-2018.9999.ebuild |
684 |
+++ b/sci-chemistry/gromacs/gromacs-2018.9999.ebuild |
685 |
@@ -1,4 +1,4 @@ |
686 |
-# Copyright 1999-2018 Gentoo Foundation |
687 |
+# Copyright 1999-2018 Gentoo Authors |
688 |
# Distributed under the terms of the GNU General Public License v2 |
689 |
|
690 |
EAPI=6 |
691 |
@@ -43,7 +43,7 @@ CDEPEND=" |
692 |
cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
693 |
opencl? ( virtual/opencl ) |
694 |
fftw? ( sci-libs/fftw:3.0 ) |
695 |
- hwloc? ( sys-apps/hwloc ) |
696 |
+ hwloc? ( <sys-apps/hwloc-2 ) |
697 |
lapack? ( virtual/lapack ) |
698 |
mkl? ( sci-libs/mkl ) |
699 |
mpi? ( virtual/mpi ) |
700 |
|
701 |
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild |
702 |
index b38e62cc3e5..09180d2dc08 100644 |
703 |
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild |
704 |
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild |
705 |
@@ -1,4 +1,4 @@ |
706 |
-# Copyright 1999-2017 Gentoo Foundation |
707 |
+# Copyright 1999-2018 Gentoo Authors |
708 |
# Distributed under the terms of the GNU General Public License v2 |
709 |
|
710 |
EAPI=6 |
711 |
@@ -42,7 +42,7 @@ CDEPEND=" |
712 |
blas? ( virtual/blas ) |
713 |
cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
714 |
fftw? ( sci-libs/fftw:3.0 ) |
715 |
- hwloc? ( sys-apps/hwloc ) |
716 |
+ hwloc? ( <sys-apps/hwloc-2 ) |
717 |
lapack? ( virtual/lapack ) |
718 |
mkl? ( sci-libs/mkl ) |
719 |
mpi? ( virtual/mpi ) |