commit: fcd7e8dd5e5268f59d4543d37ba2318e38ab0f8a
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Thu Feb 25 12:35:57 2016 +0000
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Thu Feb 25 12:35:57 2016 +0000
URL: https://gitweb.gentoo.org/dev/alexxy.git/commit/?id=fcd7e8dd
sci-chemistry/gromacs: Sync with overlay version. But still eapi5
Package-Manager: portage-2.2.26
sci-chemistry/gromacs/gromacs-9999.ebuild | 57 +++++++++++++++++--------------
sci-chemistry/gromacs/metadata.xml | 21 +++++-------
2 files changed, 40 insertions(+), 38 deletions(-)
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild
b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 9529978..a099448 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -1,16 +1,14 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: $
+# $Id$
EAPI=5
-TEST_PV="5.0-rc1"
-
CMAKE_MAKEFILE_GENERATOR="ninja"
PYTHON_COMPAT=( python{3_2,3_3,3_4,3_5} )
-inherit bash-completion-r1 cmake-utils cuda eutils multilib python-single-r1
readme.gentoo toolchain-funcs
+inherit bash-completion-r1 cmake-utils cuda eutils multilib python-single-r1
readme.gentoo-r1 toolchain-funcs
if [[ $PV = *9999* ]]; then
if use python; then
@@ -21,12 +19,14 @@ if [[ $PV = *9999* ]]; then
https://gerrit.gromacs.org/gromacs.git
git://github.com/gromacs/gromacs.git
http://repo.or.cz/r/gromacs.git";
- EGIT_BRANCH="master"
+ [[ $PV = 9999 ]] && EGIT_BRANCH="master" ||
EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}"
+ inherit git-r3
+ KEYWORDS=""
fi
- inherit git-r3
else
SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
- test? (
http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
+ test? (
http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
+ KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux
~x64-macos ~x86-macos"
fi
ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4
cpu_flags_x86_avx cpu_flags_x86_avx2"
@@ -39,8 +39,7 @@ HOMEPAGE="http://www.gromacs.org/";
# 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=""
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl
mpi +offensive openmp python +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive
openmp python +single-precision test +threads +tng ${ACCE_IUSE}"
CDEPEND="
X? (
@@ -56,8 +55,8 @@ CDEPEND="
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
python? (
- dev-python/numpy
- dev-python/sip
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/sip[${PYTHON_USEDEP}]
)
"
DEPEND="${CDEPEND}
@@ -100,8 +99,8 @@ src_unpack() {
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="${WORKDIR}/regressiontests"\
+ EGIT_BRANCH="${EGIT_BRANCH}" \
+ EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
git-r3_src_unpack
fi
fi
@@ -169,10 +168,9 @@ src_configure() {
$(cmake-utils_use openmp GMX_OPENMP)
$(cmake-utils_use offensive GMX_COOL_QUOTES)
$(cmake-utils_use boost GMX_EXTERNAL_BOOST)
+ $(cmake-utils_use python GMX_PYTHON_BINDINGS)
$(cmake-utils_use tng GMX_USE_TNG)
$(cmake-utils_use doc GMX_BUILD_MANUAL)
- $(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES)
- $(cmake-utils_use python GMX_PYTHON_BINDINGS)
-DGMX_DEFAULT_SUFFIX=off
-DGMX_SIMD="$acce"
-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
@@ -206,6 +204,8 @@ src_configure() {
-DGMX_LIBS_SUFFIX="${suffix}"
)
BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+ [[ ${CHOST} != *-darwin* ]] || \
+ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/'
"${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
use mpi || continue
einfo "Configuring for ${x} precision with mpi"
mycmakeargs=(
@@ -220,6 +220,8 @@ src_configure() {
-DGMX_LIBS_SUFFIX="_mpi${suffix}"
)
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc"
cmake-utils_src_configure
+ [[ ${CHOST} != *-darwin* ]] || \
+ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/'
"${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
done
}
@@ -228,9 +230,7 @@ src_compile() {
einfo "Compiling for ${x} precision"
BUILD_DIR="${WORKDIR}/${P}_${x}"\
cmake-utils_src_compile
- # generate bash completion
- BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_compile completion
+ # not 100% necessary for rel ebuilds as available from website
if use doc; then
BUILD_DIR="${WORKDIR}/${P}_${x}"\
cmake-utils_src_compile manual
@@ -256,17 +256,24 @@ src_install() {
if use doc; then
newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf
"${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 "${ED}"usr/lib*/libtng*.a
+ if use tng; then
+ insinto /usr/include/tng
+ doins src/external/tng_io/include/tng/*h
+ fi
+ # drop unneeded stuff
+ rm "${ED}"usr/bin/GMXRC* || die
+ for x in "${ED}"usr/bin/gmx-completion-*.bash ; do
+ local n=${x##*/gmx-completion-}
+ n="${n%.bash}"
+ cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
+ newbashcomp "${T}"/"${n}" "${n}"
+ done
+ rm "${ED}"usr/bin/gmx-completion*.bash || die
readme.gentoo_create_doc
}
diff --git a/sci-chemistry/gromacs/metadata.xml
b/sci-chemistry/gromacs/metadata.xml
index 87e0f0a..753027d 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -1,27 +1,22 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
<pkgmetadata>
- <herd>sci-chemistry</herd>
- <maintainer>
+ <maintainer type="person">
<email>[email protected]</email>
<name>Christoph Junghans</name>
</maintainer>
+ <maintainer type="project">
+ <email>[email protected]</email>
+ <name>Gentoo Chemistry Project</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>
+ <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>
<!-- 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>
