| 1 |
jlec 15/03/06 09:42:31 |
| 2 |
|
| 3 |
Modified: metadata.xml ChangeLog |
| 4 |
Added: gromacs-5.0.4-r1.ebuild |
| 5 |
Log: |
| 6 |
Install missing header |
| 7 |
|
| 8 |
(Portage version: 2.2.18/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!) |
| 9 |
|
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Revision Changes Path |
| 11 |
1.22 sci-chemistry/gromacs/metadata.xml |
| 12 |
|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/metadata.xml?rev=1.22&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/metadata.xml?rev=1.22&content-type=text/plain |
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diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/metadata.xml?r1=1.21&r2=1.22 |
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|
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Index: metadata.xml |
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=================================================================== |
| 19 |
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/metadata.xml,v |
| 20 |
retrieving revision 1.21 |
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retrieving revision 1.22 |
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diff -u -r1.21 -r1.22 |
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--- metadata.xml 31 Jan 2015 20:23:56 -0000 1.21 |
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+++ metadata.xml 6 Mar 2015 09:42:31 -0000 1.22 |
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@@ -9,10 +9,10 @@ |
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<use> |
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<flag name="cuda">Enable cuda non-bonded kernels</flag> |
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<flag name="double-precision">More precise calculations at the expense of speed</flag> |
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- <flag name="single-precision">Single precision version of gromacs (default)</flag> |
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- <flag name="boost">Enable external boost library</flag> |
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- <flag name="tng">Enable new trajectory format - tng</flag> |
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- <flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag> |
| 33 |
+ <flag name="single-precision">Single precision version of gromacs (default)</flag> |
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+ <flag name="boost">Enable external boost library</flag> |
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+ <flag name="tng">Enable new trajectory format - tng</flag> |
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+ <flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag> |
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<!-- acceleration optimization flags --> |
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<flag name="offensive">Enable gromacs partly offensive quotes</flag> |
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<flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag> |
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|
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|
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|
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1.156 sci-chemistry/gromacs/ChangeLog |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.156&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.156&content-type=text/plain |
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diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?r1=1.155&r2=1.156 |
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|
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Index: ChangeLog |
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=================================================================== |
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RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v |
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retrieving revision 1.155 |
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retrieving revision 1.156 |
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diff -u -r1.155 -r1.156 |
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--- ChangeLog 26 Feb 2015 19:04:02 -0000 1.155 |
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+++ ChangeLog 6 Mar 2015 09:42:31 -0000 1.156 |
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@@ -1,6 +1,12 @@ |
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# ChangeLog for sci-chemistry/gromacs |
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# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
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-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.155 2015/02/26 19:04:02 maekke Exp $ |
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+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.156 2015/03/06 09:42:31 jlec Exp $ |
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+ |
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+*gromacs-5.0.4-r1 (06 Mar 2015) |
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+ |
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+ 06 Mar 2015; Justin Lecher <jlec@g.o> +gromacs-5.0.4-r1.ebuild, |
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+ metadata.xml: |
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+ Install missing header |
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|
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26 Feb 2015; Markus Meier <maekke@g.o> gromacs-5.0.4.ebuild: |
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arm stable, bug #538370 |
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|
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|
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|
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1.1 sci-chemistry/gromacs/gromacs-5.0.4-r1.ebuild |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.4-r1.ebuild?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.4-r1.ebuild?rev=1.1&content-type=text/plain |
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|
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Index: gromacs-5.0.4-r1.ebuild |
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=================================================================== |
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# Copyright 1999-2015 Gentoo Foundation |
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# Distributed under the terms of the GNU General Public License v2 |
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# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.4-r1.ebuild,v 1.1 2015/03/06 09:42:31 jlec Exp $ |
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|
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EAPI=5 |
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|
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CMAKE_MAKEFILE_GENERATOR="ninja" |
| 88 |
|
| 89 |
inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs |
| 90 |
|
| 91 |
if [[ $PV = *9999* ]]; then |
| 92 |
EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
| 93 |
https://gerrit.gromacs.org/gromacs.git |
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git://github.com/gromacs/gromacs.git |
| 95 |
http://repo.or.cz/r/gromacs.git" |
| 96 |
EGIT_BRANCH="release-5-0" |
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inherit git-r3 |
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KEYWORDS="" |
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else |
| 100 |
SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
| 101 |
test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" |
| 102 |
KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
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fi |
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|
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ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
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|
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DESCRIPTION="The ultimate molecular dynamics simulation package" |
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HOMEPAGE="http://www.gromacs.org/" |
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|
| 110 |
# see COPYING for details |
| 111 |
# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
| 112 |
# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
| 113 |
LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
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SLOT="0/${PV}" |
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IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
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|
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CDEPEND=" |
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X? ( |
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x11-libs/libX11 |
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x11-libs/libSM |
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x11-libs/libICE |
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) |
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blas? ( virtual/blas ) |
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boost? ( >=dev-libs/boost-1.55 ) |
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cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
| 126 |
fftw? ( sci-libs/fftw:3.0 ) |
| 127 |
lapack? ( virtual/lapack ) |
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mkl? ( sci-libs/mkl ) |
| 129 |
mpi? ( virtual/mpi ) |
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" |
| 131 |
DEPEND="${CDEPEND} |
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virtual/pkgconfig |
| 133 |
doc? ( |
| 134 |
app-doc/doxygen |
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dev-texlive/texlive-latex |
| 136 |
dev-texlive/texlive-latexextra |
| 137 |
media-gfx/imagemagick |
| 138 |
)" |
| 139 |
RDEPEND="${CDEPEND}" |
| 140 |
|
| 141 |
REQUIRED_USE=" |
| 142 |
|| ( single-precision double-precision ) |
| 143 |
cuda? ( single-precision ) |
| 144 |
mkl? ( !blas !fftw !lapack )" |
| 145 |
|
| 146 |
DOCS=( AUTHORS README ) |
| 147 |
|
| 148 |
if [[ ${PV} != *9999 ]]; then |
| 149 |
S="${WORKDIR}/${PN}-${PV/_/-}" |
| 150 |
fi |
| 151 |
|
| 152 |
pkg_pretend() { |
| 153 |
[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
| 154 |
use openmp && ! tc-has-openmp && \ |
| 155 |
die "Please switch to an openmp compatible compiler" |
| 156 |
} |
| 157 |
|
| 158 |
src_unpack() { |
| 159 |
if [[ ${PV} != *9999 ]]; then |
| 160 |
default |
| 161 |
else |
| 162 |
git-r3_src_unpack |
| 163 |
if use test; then |
| 164 |
EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
| 165 |
EGIT_BRANCH="master" EGIT_COMMIT="master" \ |
| 166 |
EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
| 167 |
git-r3_src_unpack |
| 168 |
fi |
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fi |
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} |
| 171 |
|
| 172 |
src_prepare() { |
| 173 |
#notes/todos |
| 174 |
# -on apple: there is framework support |
| 175 |
|
| 176 |
cmake-utils_src_prepare |
| 177 |
|
| 178 |
use cuda && cuda_src_prepare |
| 179 |
|
| 180 |
GMX_DIRS="" |
| 181 |
use single-precision && GMX_DIRS+=" float" |
| 182 |
use double-precision && GMX_DIRS+=" double" |
| 183 |
|
| 184 |
if use test; then |
| 185 |
for x in ${GMX_DIRS}; do |
| 186 |
mkdir -p "${WORKDIR}/${P}_${x}" || die |
| 187 |
cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
| 188 |
done |
| 189 |
fi |
| 190 |
|
| 191 |
DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
| 192 |
} |
| 193 |
|
| 194 |
src_configure() { |
| 195 |
local mycmakeargs_pre=( ) extra fft_opts=( ) |
| 196 |
|
| 197 |
#go from slowest to fastest acceleration |
| 198 |
local acce="None" |
| 199 |
use cpu_flags_x86_sse2 && acce="SSE2" |
| 200 |
use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
| 201 |
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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|
| 205 |
#to create man pages, build tree binaries are executed (bug #398437) |
| 206 |
[[ ${CHOST} = *-darwin* ]] && \ |
| 207 |
extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
| 208 |
|
| 209 |
if use fftw; then |
| 210 |
fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
| 211 |
elif use mkl && has_version "=sci-libs/mkl-10*"; then |
| 212 |
fft_opts=( -DGMX_FFT_LIBRARY=mkl |
| 213 |
-DMKL_INCLUDE_DIR="${MKLROOT}/include" |
| 214 |
-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
| 215 |
) |
| 216 |
elif use mkl; then |
| 217 |
local bits=$(get_libdir) |
| 218 |
fft_opts=( -DGMX_FFT_LIBRARY=mkl |
| 219 |
-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
| 220 |
-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
| 221 |
) |
| 222 |
else |
| 223 |
fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
| 224 |
fi |
| 225 |
|
| 226 |
mycmakeargs_pre+=( |
| 227 |
"${fft_opts[@]}" |
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$(cmake-utils_use X GMX_X11) |
| 229 |
$(cmake-utils_use blas GMX_EXTERNAL_BLAS) |
| 230 |
$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK) |
| 231 |
$(cmake-utils_use openmp GMX_OPENMP) |
| 232 |
$(cmake-utils_use offensive GMX_COOL_QUOTES) |
| 233 |
$(cmake-utils_use boost GMX_EXTERNAL_BOOST) |
| 234 |
$(cmake-utils_use tng GMX_USE_TNG) |
| 235 |
$(cmake-utils_use doc GMX_BUILD_MANUAL) |
| 236 |
$(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES) |
| 237 |
-DGMX_DEFAULT_SUFFIX=off |
| 238 |
-DGMX_SIMD="$acce" |
| 239 |
-DGMX_LIB_INSTALL_DIR="$(get_libdir)" |
| 240 |
-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
| 241 |
-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF |
| 242 |
-DGMX_USE_GCC44_BUG_WORKAROUND=OFF |
| 243 |
-DBUILD_TESTING=OFF |
| 244 |
-DGMX_BUILD_UNITTESTS=OFF |
| 245 |
${extra} |
| 246 |
) |
| 247 |
|
| 248 |
for x in ${GMX_DIRS}; do |
| 249 |
einfo "Configuring for ${x} precision" |
| 250 |
local suffix="" |
| 251 |
#if we build single and double - double is suffixed |
| 252 |
use double-precision && use single-precision && \ |
| 253 |
[[ ${x} = "double" ]] && suffix="_d" |
| 254 |
local p |
| 255 |
[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
| 256 |
local cuda=( "-DGMX_GPU=OFF" ) |
| 257 |
[[ ${x} = "float" ]] && use cuda && \ |
| 258 |
cuda=( -DGMX_GPU=ON ) |
| 259 |
mycmakeargs=( |
| 260 |
${mycmakeargs_pre[@]} ${p} |
| 261 |
-DGMX_MPI=OFF |
| 262 |
$(cmake-utils_use threads GMX_THREAD_MPI) |
| 263 |
"${cuda[@]}" |
| 264 |
-DGMX_OPENMM=OFF |
| 265 |
"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
| 266 |
-DGMX_BINARY_SUFFIX="${suffix}" |
| 267 |
-DGMX_LIBS_SUFFIX="${suffix}" |
| 268 |
) |
| 269 |
BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
| 270 |
[[ ${CHOST} != *-darwin* ]] || \ |
| 271 |
sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
| 272 |
use mpi || continue |
| 273 |
einfo "Configuring for ${x} precision with mpi" |
| 274 |
mycmakeargs=( |
| 275 |
${mycmakeargs_pre[@]} ${p} |
| 276 |
-DGMX_THREAD_MPI=OFF |
| 277 |
-DGMX_MPI=ON ${cuda} |
| 278 |
-DGMX_OPENMM=OFF |
| 279 |
-DGMX_BUILD_MDRUN_ONLY=ON |
| 280 |
-DBUILD_SHARED_LIBS=OFF |
| 281 |
-DGMX_BUILD_MANUAL=OFF |
| 282 |
-DGMX_BINARY_SUFFIX="_mpi${suffix}" |
| 283 |
-DGMX_LIBS_SUFFIX="_mpi${suffix}" |
| 284 |
) |
| 285 |
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
| 286 |
[[ ${CHOST} != *-darwin* ]] || \ |
| 287 |
sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
| 288 |
done |
| 289 |
} |
| 290 |
|
| 291 |
src_compile() { |
| 292 |
for x in ${GMX_DIRS}; do |
| 293 |
einfo "Compiling for ${x} precision" |
| 294 |
BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| 295 |
cmake-utils_src_compile |
| 296 |
# generate bash completion, not 100% necessary for |
| 297 |
# rel ebuilds as bundled |
| 298 |
BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| 299 |
cmake-utils_src_compile completion |
| 300 |
# not 100% necessary for rel ebuilds as available from website |
| 301 |
if use doc; then |
| 302 |
BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| 303 |
cmake-utils_src_compile manual |
| 304 |
fi |
| 305 |
use mpi || continue |
| 306 |
einfo "Compiling for ${x} precision with mpi" |
| 307 |
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
| 308 |
cmake-utils_src_compile |
| 309 |
done |
| 310 |
} |
| 311 |
|
| 312 |
src_test() { |
| 313 |
for x in ${GMX_DIRS}; do |
| 314 |
BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| 315 |
cmake-utils_src_make check |
| 316 |
done |
| 317 |
} |
| 318 |
|
| 319 |
src_install() { |
| 320 |
for x in ${GMX_DIRS}; do |
| 321 |
BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
| 322 |
cmake-utils_src_install |
| 323 |
if use doc; then |
| 324 |
newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
| 325 |
fi |
| 326 |
#release ebuild does this automatically |
| 327 |
if [[ $PV = *9999* ]]; then |
| 328 |
cp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash "${ED}/usr/bin" || die |
| 329 |
echo "complete -o nospace -F _gmx_compl gmx" > "${ED}/usr/bin/gmx-completion-gmx.bash" || die |
| 330 |
fi |
| 331 |
use mpi || continue |
| 332 |
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
| 333 |
cmake-utils_src_install |
| 334 |
done |
| 335 |
|
| 336 |
if use tng; then |
| 337 |
insinto /usr/include/tng |
| 338 |
doins src/external/tng_io/include/tng/*h |
| 339 |
fi |
| 340 |
# drop unneeded stuff |
| 341 |
rm "${ED}"usr/bin/GMXRC* || die |
| 342 |
#concatenate all gmx-completion*, starting with gmx-completion.bash (fct defs) |
| 343 |
#little hacckery as some gmx-completion* newlines ,so cat won't work |
| 344 |
for x in "${ED}"usr/bin/gmx-completion{,?*}.bash ; do |
| 345 |
echo $(<${x}) |
| 346 |
done > "${T}"/gmx-bashcomp || die |
| 347 |
newbashcomp "${T}"/gmx-bashcomp gmx |
| 348 |
bashcomp_alias gmx mdrun |
| 349 |
rm "${ED}"usr/bin/gmx-completion{,?*}.bash || die |
| 350 |
if use double-precision && use single-precision; then |
| 351 |
bashcomp_alias gmx gmx_d |
| 352 |
bashcomp_alias gmx mdrun_d |
| 353 |
fi |
| 354 |
readme.gentoo_create_doc |
| 355 |
} |
| 356 |
|
| 357 |
pkg_postinst() { |
| 358 |
einfo |
| 359 |
einfo "Please read and cite:" |
| 360 |
einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
| 361 |
einfo "http://dx.doi.org/10.1021/ct700301q" |
| 362 |
einfo |
| 363 |
readme.gentoo_print_elog |
| 364 |
} |
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