* [gentoo-commits] gentoo-x86 commit in sci-chemistry/gromacs: metadata.xml gromacs-5.0.ebuild ChangeLog
@ 2014-06-30 3:24 Alexey Shvetsov (alexxy)
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From: Alexey Shvetsov (alexxy) @ 2014-06-30 3:24 UTC (permalink / raw
To: gentoo-commits
alexxy 14/06/30 03:24:05
Modified: metadata.xml ChangeLog
Added: gromacs-5.0.ebuild
Log:
[sci-chemistry/gromacs] GROMACS 5.0 finaly relesed
(Portage version: 2.2.10/cvs/Linux x86_64, signed Manifest commit with key F82F92E6)
Revision Changes Path
1.20 sci-chemistry/gromacs/metadata.xml
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/metadata.xml?rev=1.20&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/metadata.xml?rev=1.20&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/metadata.xml?r1=1.19&r2=1.20
Index: metadata.xml
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/metadata.xml,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -r1.19 -r1.20
--- metadata.xml 31 Dec 2013 23:35:05 -0000 1.19
+++ metadata.xml 30 Jun 2014 03:24:04 -0000 1.20
@@ -1,21 +1,27 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci-chemistry</herd>
- <maintainer>
- <email>ottxor@gentoo.org</email>
- <name>Christoph Junghans</name>
- </maintainer>
- <use>
- <flag name="cuda">Enable cuda non-bonded kernels</flag>
- <flag name="double-precision">More precise calculations at the expense of speed</flag>
- <flag name="single-precision">Single precision version of gromacs (default)</flag>
- <!-- acceleration optimization flags -->
- <flag name="sse4_1">Enable sse4.1 acceleration</flag>
- <flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
- <flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
- <flag name="offensive">Enable gromacs partly offensive quotes</flag>
- <flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag>
- <flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag>
- </use>
+ <herd>sci-chemistry</herd>
+ <maintainer>
+ <email>ottxor@gentoo.org</email>
+ <name>Christoph Junghans</name>
+ </maintainer>
+ <use>
+ <flag name="cuda">Enable cuda non-bonded kernels</flag>
+ <flag name="double-precision">More precise calculations at the expense of speed</flag>
+ <flag name="single-precision">Single precision version of gromacs (default)</flag>
+ <flag name="boost">Enable external boost library</flag>
+ <flag name="tng">Enable new trajectory format - tng</flag>
+ <flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag>
+ <!-- acceleration optimization flags -->
+ <flag name="sse4_1">Enable sse4.1 acceleration</flag>
+ <flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
+ <flag name="avx_128_fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
+ <flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
+ <flag name="avx_256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
+ <flag name="avx2_256">Enable 256bit avx2 (e.g. Intel Haswell)</flag>
+ <flag name="offensive">Enable gromacs partly offensive quotes</flag>
+ <flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag>
+ <flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag>
+ </use>
</pkgmetadata>
1.140 sci-chemistry/gromacs/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.140&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.140&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?r1=1.139&r2=1.140
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v
retrieving revision 1.139
retrieving revision 1.140
diff -u -r1.139 -r1.140
--- ChangeLog 26 Mar 2014 21:42:49 -0000 1.139
+++ ChangeLog 30 Jun 2014 03:24:04 -0000 1.140
@@ -1,6 +1,12 @@
# ChangeLog for sci-chemistry/gromacs
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.139 2014/03/26 21:42:49 maekke Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.140 2014/06/30 03:24:04 alexxy Exp $
+
+*gromacs-5.0 (30 Jun 2014)
+
+ 30 Jun 2014; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-5.0.ebuild,
+ metadata.xml:
+ [sci-chemistry/gromacs] GROMACS 5.0 finaly relesed
26 Mar 2014; Markus Meier <maekke@gentoo.org> gromacs-4.6.5.ebuild:
arm stable, bug #496632
1.1 sci-chemistry/gromacs/gromacs-5.0.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.ebuild?rev=1.1&content-type=text/plain
Index: gromacs-5.0.ebuild
===================================================================
# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.ebuild,v 1.1 2014/06/30 03:24:04 alexxy Exp $
EAPI=5
TEST_PV="5.0"
CMAKE_MAKEFILE_GENERATOR="ninja"
inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
if [[ $PV = *9999* ]]; then
EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
https://gerrit.gromacs.org/gromacs.git
git://github.com/gromacs/gromacs.git
http://repo.or.cz/r/gromacs.git"
EGIT_BRANCH="release-5-0"
inherit git-r3
else
SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
fi
ACCE_IUSE="sse2 sse4_1 avx_128_fma avx_256 avx2_256"
DESCRIPTION="The ultimate molecular dynamics simulation package"
HOMEPAGE="http://www.gromacs.org/"
# see COPYING for details
# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
SLOT="0/${PV}"
KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
CDEPEND="
X? (
x11-libs/libX11
x11-libs/libSM
x11-libs/libICE
)
blas? ( virtual/blas )
boost? ( >=dev-libs/boost-1.55 )
cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
fftw? ( sci-libs/fftw:3.0 )
lapack? ( virtual/lapack )
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
"
DEPEND="${CDEPEND}
virtual/pkgconfig
doc? (
app-doc/doxygen
dev-texlive/texlive-latex
dev-texlive/texlive-latexextra
media-gfx/imagemagick
)"
RDEPEND="${CDEPEND}"
REQUIRED_USE="
|| ( single-precision double-precision )
cuda? ( single-precision )
mkl? ( !blas !fftw !lapack )"
DOCS=( AUTHORS README )
if [[ ${PV} != *9999 ]]; then
S="${WORKDIR}/${PN}-${PV/_/-}"
fi
pkg_pretend() {
[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
use openmp && ! tc-has-openmp && \
die "Please switch to an openmp compatible compiler"
}
src_unpack() {
if [[ ${PV} != *9999 ]]; then
default
else
git-r3_src_unpack
if use test; then
EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\
git-r3_src_unpack
fi
fi
}
src_prepare() {
#notes/todos
# -on apple: there is framework support
cmake-utils_src_prepare
use cuda && cuda_src_prepare
GMX_DIRS=""
use single-precision && GMX_DIRS+=" float"
use double-precision && GMX_DIRS+=" double"
if use test; then
for x in ${GMX_DIRS}; do
mkdir -p "${WORKDIR}/${P}_${x}" || die
cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
done
fi
DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
}
src_configure() {
local mycmakeargs_pre=( ) extra fft_opts=( )
#go from slowest to fastest acceleration
local acce="None"
use sse2 && acce="SSE2"
use sse4_1 && acce="SSE4.1"
use avx_128_fma && acce="AVX_128_FMA"
use avx_256 && acce="AVX_256"
use avx2_256 && acee="AVX2_256"
#to create man pages, build tree binaries are executed (bug #398437)
[[ ${CHOST} = *-darwin* ]] && \
extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
if use fftw; then
fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
elif use mkl && has_version "=sci-libs/mkl-10*"; then
fft_opts=( -DGMX_FFT_LIBRARY=mkl
-DMKL_INCLUDE_DIR="${MKLROOT}/include"
-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
)
elif use mkl; then
local bits=$(get_libdir)
fft_opts=( -DGMX_FFT_LIBRARY=mkl
-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
)
else
fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
fi
mycmakeargs_pre+=(
"${fft_opts[@]}"
$(cmake-utils_use X GMX_X11)
$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
$(cmake-utils_use openmp GMX_OPENMP)
$(cmake-utils_use offensive GMX_COOL_QUOTES)
$(cmake-utils_use boost GMX_EXTERNAL_BOOST)
$(cmake-utils_use tng GMX_USE_TNG)
$(cmake-utils_use doc GMX_BUILD_MANUAL)
$(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES)
-DGMX_DEFAULT_SUFFIX=off
-DGMX_SIMD="$acce"
-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
-DBUILD_TESTING=OFF
-DGMX_BUILD_UNITTESTS=OFF
${extra}
)
for x in ${GMX_DIRS}; do
einfo "Configuring for ${x} precision"
local suffix=""
#if we build single and double - double is suffixed
use double-precision && use single-precision && \
[[ ${x} = "double" ]] && suffix="_d"
local p
[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
local cuda=( "-DGMX_GPU=OFF" )
[[ ${x} = "float" ]] && use cuda && \
cuda=( -DGMX_GPU=ON )
mycmakeargs=(
${mycmakeargs_pre[@]} ${p}
-DGMX_MPI=OFF
$(cmake-utils_use threads GMX_THREAD_MPI)
"${cuda[@]}"
-DGMX_OPENMM=OFF
"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-DGMX_BINARY_SUFFIX="${suffix}"
-DGMX_LIBS_SUFFIX="${suffix}"
)
BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
use mpi || continue
einfo "Configuring for ${x} precision with mpi"
mycmakeargs=(
${mycmakeargs_pre[@]} ${p}
-DGMX_THREAD_MPI=OFF
-DGMX_MPI=ON ${cuda}
-DGMX_OPENMM=OFF
-DGMX_BUILD_MDRUN_ONLY=ON
-DBUILD_SHARED_LIBS=OFF
-DGMX_BUILD_MANUAL=OFF
-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-DGMX_LIBS_SUFFIX="_mpi${suffix}"
)
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
done
}
src_compile() {
for x in ${GMX_DIRS}; do
einfo "Compiling for ${x} precision"
BUILD_DIR="${WORKDIR}/${P}_${x}"\
cmake-utils_src_compile
# generate bash completion
BUILD_DIR="${WORKDIR}/${P}_${x}"\
cmake-utils_src_compile completion
if use doc; then
BUILD_DIR="${WORKDIR}/${P}_${x}"\
cmake-utils_src_compile manual
fi
use mpi || continue
einfo "Compiling for ${x} precision with mpi"
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
cmake-utils_src_compile
done
}
src_test() {
for x in ${GMX_DIRS}; do
BUILD_DIR="${WORKDIR}/${P}_${x}"\
cmake-utils_src_make check
done
}
src_install() {
for x in ${GMX_DIRS}; do
BUILD_DIR="${WORKDIR}/${P}_${x}" \
cmake-utils_src_install
if use doc; then
newdoc "${WORKDIR}/${P}_${x}"/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
fi
newbashcomp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash gromacs
use mpi || continue
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
cmake-utils_src_install
done
# drop unneeded stuff
rm -f "${ED}"usr/bin/gmx-completion*
rm -f "${ED}"usr/bin/g_options*
rm -f "${ED}"usr/bin/GMXRC*
rm -f "${ED}"usr/$(get_libdir)/libtng*.a
readme.gentoo_create_doc
}
pkg_postinst() {
einfo
einfo "Please read and cite:"
einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
einfo "http://dx.doi.org/10.1021/ct700301q"
einfo
readme.gentoo_print_elog
}
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2014-06-30 3:24 [gentoo-commits] gentoo-x86 commit in sci-chemistry/gromacs: metadata.xml gromacs-5.0.ebuild ChangeLog Alexey Shvetsov (alexxy)
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