1 |
commit: 232da478246f898cf749e5df52f18f2214810236 |
2 |
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
3 |
AuthorDate: Tue Jan 22 11:00:03 2019 +0000 |
4 |
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
5 |
CommitDate: Tue Jan 22 11:00:28 2019 +0000 |
6 |
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=232da478 |
7 |
|
8 |
sci-chemistry/gromacs: Version bump |
9 |
|
10 |
Package-Manager: Portage-2.3.57, Repoman-2.3.12 |
11 |
Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org> |
12 |
|
13 |
sci-chemistry/gromacs/Manifest | 2 + |
14 |
sci-chemistry/gromacs/gromacs-2018.5.ebuild | 270 ++++++++++++++++++++++++++++ |
15 |
2 files changed, 272 insertions(+) |
16 |
|
17 |
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest |
18 |
index b00c9962824..ffe2062f32b 100644 |
19 |
--- a/sci-chemistry/gromacs/Manifest |
20 |
+++ b/sci-chemistry/gromacs/Manifest |
21 |
@@ -1,8 +1,10 @@ |
22 |
DIST gromacs-2016.5.tar.gz 27369491 BLAKE2B 4a8bf1ae3e298ac2e26ec476130720dc3ef00db5d999e3a45fdbfd7fbfe7e94fbc86be6ff0f2f23552769c8bc851ce49c73f6fc1ab13f372523279b93e7794d7 SHA512 9cb8ff88871aa5df0967c60ba303c03296c6fa3c215cd01b26259df7753f0014f04222078ab4b84a66a1f709997837134d5c0f74da19b78322e410010c9d9e10 |
23 |
DIST gromacs-2018.3.tar.gz 29915626 BLAKE2B 6e6eeafecdd923a25b4a2a78a8e89f793639b57ffbd63f19d133d8474302f9a381041f138a509dadb42b36e25fe508729e860efb6b0c75cdbf01d924b0a8fd83 SHA512 3c4d6eb3942d7b54d01c94c6f6f5ae706e0f5d4f9901ea11a56fde4df97b1a9112007f2cb13feea0f19f30c89f57ae80ff53a8f5203b8cdff103aa903cd0dc8f |
24 |
DIST gromacs-2018.4.tar.gz 29918276 BLAKE2B daf3f91e47bab61befee4ecd91e4885835fc5ded408462c239c824567e64b5710fb252456c6be2bf0e4ce1a2119747fca9d8fb0532286bb93d6ccdd289fe57ab SHA512 8ef0b90b2c266bb706c8fdba12e763de9c21aad197c1c71f48c06378644a734a3694172804db6c916a4974a9832b128512f2445d0b72783811e64edd22d27955 |
25 |
+DIST gromacs-2018.5.tar.gz 29911866 BLAKE2B 6f060d99ed6180ebc2c1b11d26548a8179312aaf9b356edcb8c6959a4aba5c081604a54e3d78d63dc0d8719a50a0bf5864b6b0186c280b38f59806d4e097857c SHA512 cb6c7624e6fa93c618ea0b412a3cac5f03ca07d2641231888b53501dc7de21e2b1a2d8630a9dbb065256c22a945e3d7b1c823a1b9f0fa01090e4e411eb34f4fb |
26 |
DIST gromacs-2019.tar.gz 33428725 BLAKE2B 307838a5ee1a85554d6f2ef8cd9c9dd2f3d9cacd32c534545c23483b5f3a1c7d027bfbdf224b90661cd8cd3fb85c0c99c66cbd619698245a0cb45ebd512dec5d SHA512 54b11530e8ff671461e3ae9418d991fe242957943c944798cddf6efe740eee670a562cd5201dbba68b045f4bafd3afa2dc8de27e0643c7def4e05eaf0ccb5769 |
27 |
DIST regressiontests-2016.5.tar.gz 67641413 BLAKE2B 4fcd30c198f3acbbabf1104c040d9a686de49536a97dbeb14732bfa0ed3cf37aa61b1b0f45393668985b993d1f1862a8985e416af819cf9793f5964f3e4f43cc SHA512 31764fd99cc4185d61de5d4443ee482c27b13533451a24aa0e4899997ce275a63685424eafacae38b1a3ffd4ce0d5ebe02a90348953b04c104f91376f0edfdff |
28 |
DIST regressiontests-2018.3.tar.gz 67857855 BLAKE2B acd7a05ae79d1b4eb47d0c68a3fec9ee19f028a5019f39c37a033f48cf6da2a468375180ad6ceca9ac4f685a8bead38550663a47d6427b51f84c32a5c810e5f0 SHA512 57980d49efe6dcc3b3d14b5913a30c68fc1de5b679ef986fec1a149c76f67139b0299c3ee2825451461294fab5f345c7ad4f42e90f8991b81aafe9c369f3ff0b |
29 |
DIST regressiontests-2018.4.tar.gz 67860326 BLAKE2B 0160f701a8fa14ba4f175f4fca9894104bc5cc6aa5f02ac57200fd5a8f74a29b595df609e704cb70fcd9a03529bcf758fb4547e35557a45c0546d819c2681983 SHA512 baaac0c918684216ada5254a7c3a1f5b3ea00b1a63d6085d569095139b2a0c9de4ed330d4694f7eaedab729ed5dcea547390781b3d2f7c2ffdf02e0541a90efe |
30 |
+DIST regressiontests-2018.5.tar.gz 67856231 BLAKE2B 3f9548a97088d552584e2115dbc25b7d54680b10bbfb732e96e064a3fc9eda1c21426875044cc664a1e2be37224209fe027310597aed45f4a033684d7552b5a0 SHA512 65134496efe04a978a4e9ce62873edcf98dc405d0fb93c82fafd0a0675465ccb662be4cb7e142c1a7a38e833e10a9ccdac5ea7ecd1bb61d3dfbdb92d78ac37b6 |
31 |
DIST regressiontests-2019.tar.gz 67597618 BLAKE2B fb950d8518cf1e28db5ebb99bdda8d269c5e43dd49a117bdaae9f00857abc7c096766fb90ff1d2d95a12a875ba2e243b707bfc81a45d07fc8b340a154cf2ad0f SHA512 081e56d052c0a0d021a8a1566f802911e261e1f2b5b2141350fe2372bcad0844042f26121167ed31a31490bd4e042068690c4905fcbc80b539686a074621fc5e |
32 |
|
33 |
diff --git a/sci-chemistry/gromacs/gromacs-2018.5.ebuild b/sci-chemistry/gromacs/gromacs-2018.5.ebuild |
34 |
new file mode 100644 |
35 |
index 00000000000..fcd96820cdb |
36 |
--- /dev/null |
37 |
+++ b/sci-chemistry/gromacs/gromacs-2018.5.ebuild |
38 |
@@ -0,0 +1,270 @@ |
39 |
+# Copyright 1999-2019 Gentoo Authors |
40 |
+# Distributed under the terms of the GNU General Public License v2 |
41 |
+ |
42 |
+EAPI=6 |
43 |
+ |
44 |
+CMAKE_MAKEFILE_GENERATOR="ninja" |
45 |
+ |
46 |
+inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils |
47 |
+ |
48 |
+if [[ $PV = *9999* ]]; then |
49 |
+ EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
50 |
+ https://gerrit.gromacs.org/gromacs.git |
51 |
+ https://github.com/gromacs/gromacs.git |
52 |
+ http://repo.or.cz/r/gromacs.git" |
53 |
+ [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" |
54 |
+ inherit git-r3 |
55 |
+else |
56 |
+ SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
57 |
+ test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" |
58 |
+ KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
59 |
+fi |
60 |
+ |
61 |
+ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
62 |
+ |
63 |
+DESCRIPTION="The ultimate molecular dynamics simulation package" |
64 |
+HOMEPAGE="http://www.gromacs.org/" |
65 |
+ |
66 |
+# see COPYING for details |
67 |
+# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
68 |
+# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
69 |
+LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
70 |
+SLOT="0/${PV}" |
71 |
+IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
72 |
+ |
73 |
+CDEPEND=" |
74 |
+ X? ( |
75 |
+ x11-libs/libX11 |
76 |
+ x11-libs/libSM |
77 |
+ x11-libs/libICE |
78 |
+ ) |
79 |
+ blas? ( virtual/blas ) |
80 |
+ cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
81 |
+ opencl? ( virtual/opencl ) |
82 |
+ fftw? ( sci-libs/fftw:3.0 ) |
83 |
+ hwloc? ( <sys-apps/hwloc-2 ) |
84 |
+ lapack? ( virtual/lapack ) |
85 |
+ mkl? ( sci-libs/mkl ) |
86 |
+ mpi? ( virtual/mpi ) |
87 |
+ " |
88 |
+DEPEND="${CDEPEND} |
89 |
+ virtual/pkgconfig |
90 |
+ doc? ( |
91 |
+ app-doc/doxygen |
92 |
+ dev-texlive/texlive-latex |
93 |
+ dev-texlive/texlive-latexextra |
94 |
+ media-gfx/imagemagick |
95 |
+ )" |
96 |
+RDEPEND="${CDEPEND}" |
97 |
+ |
98 |
+REQUIRED_USE=" |
99 |
+ || ( single-precision double-precision ) |
100 |
+ cuda? ( single-precision ) |
101 |
+ cuda? ( !opencl ) |
102 |
+ mkl? ( !blas !fftw !lapack )" |
103 |
+ |
104 |
+DOCS=( AUTHORS README ) |
105 |
+ |
106 |
+if [[ ${PV} != *9999 ]]; then |
107 |
+ S="${WORKDIR}/${PN}-${PV/_/-}" |
108 |
+fi |
109 |
+ |
110 |
+pkg_pretend() { |
111 |
+ [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
112 |
+ use openmp && ! tc-has-openmp && \ |
113 |
+ die "Please switch to an openmp compatible compiler" |
114 |
+} |
115 |
+ |
116 |
+src_unpack() { |
117 |
+ if [[ ${PV} != *9999 ]]; then |
118 |
+ default |
119 |
+ else |
120 |
+ git-r3_src_unpack |
121 |
+ if use test; then |
122 |
+ EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
123 |
+ EGIT_BRANCH="${EGIT_BRANCH}" \ |
124 |
+ EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
125 |
+ git-r3_src_unpack |
126 |
+ fi |
127 |
+ fi |
128 |
+} |
129 |
+ |
130 |
+src_prepare() { |
131 |
+ #notes/todos |
132 |
+ # -on apple: there is framework support |
133 |
+ |
134 |
+ xdg_environment_reset #591952 |
135 |
+ |
136 |
+ cmake-utils_src_prepare |
137 |
+ |
138 |
+ use cuda && cuda_src_prepare |
139 |
+ |
140 |
+ GMX_DIRS="" |
141 |
+ use single-precision && GMX_DIRS+=" float" |
142 |
+ use double-precision && GMX_DIRS+=" double" |
143 |
+ |
144 |
+ if use test; then |
145 |
+ for x in ${GMX_DIRS}; do |
146 |
+ mkdir -p "${WORKDIR}/${P}_${x}" || die |
147 |
+ cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
148 |
+ done |
149 |
+ fi |
150 |
+ |
151 |
+ DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
152 |
+} |
153 |
+ |
154 |
+src_configure() { |
155 |
+ local mycmakeargs_pre=( ) extra fft_opts=( ) |
156 |
+ |
157 |
+ #go from slowest to fastest acceleration |
158 |
+ local acce="None" |
159 |
+ use cpu_flags_x86_sse2 && acce="SSE2" |
160 |
+ use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
161 |
+ use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
162 |
+ use cpu_flags_x86_avx && acce="AVX_256" |
163 |
+ use cpu_flags_x86_avx2 && acce="AVX2_256" |
164 |
+ |
165 |
+ #to create man pages, build tree binaries are executed (bug #398437) |
166 |
+ [[ ${CHOST} = *-darwin* ]] && \ |
167 |
+ extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
168 |
+ |
169 |
+ if use fftw; then |
170 |
+ fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
171 |
+ elif use mkl && has_version "=sci-libs/mkl-10*"; then |
172 |
+ fft_opts=( -DGMX_FFT_LIBRARY=mkl |
173 |
+ -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
174 |
+ -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
175 |
+ ) |
176 |
+ elif use mkl; then |
177 |
+ local bits=$(get_libdir) |
178 |
+ fft_opts=( -DGMX_FFT_LIBRARY=mkl |
179 |
+ -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
180 |
+ -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
181 |
+ ) |
182 |
+ else |
183 |
+ fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
184 |
+ fi |
185 |
+ |
186 |
+ mycmakeargs_pre+=( |
187 |
+ "${fft_opts[@]}" |
188 |
+ -DGMX_X11=$(usex X) |
189 |
+ -DGMX_EXTERNAL_BLAS=$(usex blas) |
190 |
+ -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
191 |
+ -DGMX_OPENMP=$(usex openmp) |
192 |
+ -DGMX_COOL_QUOTES=$(usex offensive) |
193 |
+ -DGMX_USE_TNG=$(usex tng) |
194 |
+ -DGMX_BUILD_MANUAL=$(usex doc) |
195 |
+ -DGMX_HWLOC=$(usex hwloc) |
196 |
+ -DGMX_DEFAULT_SUFFIX=off |
197 |
+ -DGMX_SIMD="$acce" |
198 |
+ -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
199 |
+ -DBUILD_TESTING=$(usex test) |
200 |
+ -DGMX_BUILD_UNITTESTS=$(usex test) |
201 |
+ ${extra} |
202 |
+ ) |
203 |
+ |
204 |
+ for x in ${GMX_DIRS}; do |
205 |
+ einfo "Configuring for ${x} precision" |
206 |
+ local suffix="" |
207 |
+ #if we build single and double - double is suffixed |
208 |
+ use double-precision && use single-precision && \ |
209 |
+ [[ ${x} = "double" ]] && suffix="_d" |
210 |
+ local p |
211 |
+ [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
212 |
+ local cuda=( "-DGMX_GPU=OFF" ) |
213 |
+ [[ ${x} = "float" ]] && use cuda && \ |
214 |
+ cuda=( "-DGMX_GPU=ON" ) |
215 |
+ local opencl=( "-DGMX_USE_OPENCL=OFF" ) |
216 |
+ use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) |
217 |
+ mycmakeargs=( |
218 |
+ ${mycmakeargs_pre[@]} ${p} |
219 |
+ -DGMX_MPI=OFF |
220 |
+ -DGMX_THREAD_MPI=$(usex threads) |
221 |
+ "${opencl[@]}" |
222 |
+ "${cuda[@]}" |
223 |
+ "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
224 |
+ -DGMX_BINARY_SUFFIX="${suffix}" |
225 |
+ -DGMX_LIBS_SUFFIX="${suffix}" |
226 |
+ ) |
227 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
228 |
+ [[ ${CHOST} != *-darwin* ]] || \ |
229 |
+ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
230 |
+ use mpi || continue |
231 |
+ einfo "Configuring for ${x} precision with mpi" |
232 |
+ mycmakeargs=( |
233 |
+ ${mycmakeargs_pre[@]} ${p} |
234 |
+ -DGMX_THREAD_MPI=OFF |
235 |
+ -DGMX_MPI=ON ${cuda} |
236 |
+ -DGMX_OPENMM=OFF |
237 |
+ -DGMX_BUILD_MDRUN_ONLY=ON |
238 |
+ -DBUILD_SHARED_LIBS=OFF |
239 |
+ -DGMX_BUILD_MANUAL=OFF |
240 |
+ -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
241 |
+ -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
242 |
+ ) |
243 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
244 |
+ [[ ${CHOST} != *-darwin* ]] || \ |
245 |
+ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
246 |
+ done |
247 |
+} |
248 |
+ |
249 |
+src_compile() { |
250 |
+ for x in ${GMX_DIRS}; do |
251 |
+ einfo "Compiling for ${x} precision" |
252 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
253 |
+ cmake-utils_src_compile |
254 |
+ # not 100% necessary for rel ebuilds as available from website |
255 |
+ if use doc; then |
256 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
257 |
+ cmake-utils_src_compile manual |
258 |
+ fi |
259 |
+ use mpi || continue |
260 |
+ einfo "Compiling for ${x} precision with mpi" |
261 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
262 |
+ cmake-utils_src_compile |
263 |
+ done |
264 |
+} |
265 |
+ |
266 |
+src_test() { |
267 |
+ for x in ${GMX_DIRS}; do |
268 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
269 |
+ cmake-utils_src_make check |
270 |
+ done |
271 |
+} |
272 |
+ |
273 |
+src_install() { |
274 |
+ for x in ${GMX_DIRS}; do |
275 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
276 |
+ cmake-utils_src_install |
277 |
+ if use doc; then |
278 |
+ newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
279 |
+ fi |
280 |
+ use mpi || continue |
281 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
282 |
+ cmake-utils_src_install |
283 |
+ done |
284 |
+ |
285 |
+ if use tng; then |
286 |
+ insinto /usr/include/tng |
287 |
+ doins src/external/tng_io/include/tng/*h |
288 |
+ fi |
289 |
+ # drop unneeded stuff |
290 |
+ rm "${ED}"usr/bin/GMXRC* || die |
291 |
+ for x in "${ED}"usr/bin/gmx-completion-*.bash ; do |
292 |
+ local n=${x##*/gmx-completion-} |
293 |
+ n="${n%.bash}" |
294 |
+ cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
295 |
+ newbashcomp "${T}"/"${n}" "${n}" |
296 |
+ done |
297 |
+ rm "${ED}"usr/bin/gmx-completion*.bash || die |
298 |
+ readme.gentoo_create_doc |
299 |
+} |
300 |
+ |
301 |
+pkg_postinst() { |
302 |
+ einfo |
303 |
+ einfo "Please read and cite:" |
304 |
+ einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
305 |
+ einfo "https://dx.doi.org/10.1021/ct700301q" |
306 |
+ einfo |
307 |
+ readme.gentoo_print_elog |
308 |
+} |