* [gentoo-commits] gentoo-x86 commit in sci-chemistry/gromacs: gromacs-4.6.ebuild ChangeLog
@ 2013-01-19 21:49 Christoph Junghans (ottxor)
0 siblings, 0 replies; 3+ messages in thread
From: Christoph Junghans (ottxor) @ 2013-01-19 21:49 UTC (permalink / raw
To: gentoo-commits
ottxor 13/01/19 21:49:38
Modified: ChangeLog
Added: gromacs-4.6.ebuild
Log:
version bump
(Portage version: 2.2.0_alpha155/cvs/Linux x86_64, signed Manifest commit with key C2000586)
Revision Changes Path
1.117 sci-chemistry/gromacs/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.117&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.117&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?r1=1.116&r2=1.117
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v
retrieving revision 1.116
retrieving revision 1.117
diff -u -r1.116 -r1.117
--- ChangeLog 29 Dec 2012 23:00:35 -0000 1.116
+++ ChangeLog 19 Jan 2013 21:49:38 -0000 1.117
@@ -1,6 +1,11 @@
# ChangeLog for sci-chemistry/gromacs
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.116 2012/12/29 23:00:35 ottxor Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.117 2013/01/19 21:49:38 ottxor Exp $
+
+*gromacs-4.6 (19 Jan 2013)
+
+ 19 Jan 2013; Christoph Junghans <ottxor@gentoo.org> +gromacs-4.6.ebuild:
+ version bump
29 Dec 2012; Christoph Junghans <ottxor@gentoo.org>
gromacs-4.6_beta3-r1.ebuild:
1.1 sci-chemistry/gromacs/gromacs-4.6.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.ebuild?rev=1.1&content-type=text/plain
Index: gromacs-4.6.ebuild
===================================================================
# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.ebuild,v 1.1 2013/01/19 21:49:38 ottxor Exp $
EAPI=5
TEST_PV="4.6"
MANUAL_PV="4.6"
CMAKE_MAKEFILE_GENERATOR="ninja"
inherit bash-completion-r1 cmake-utils eutils multilib toolchain-funcs
if [[ $PV = *9999* ]]; then
EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
https://gerrit.gromacs.org/gromacs.git
git://github.com/gromacs/gromacs.git
http://repo.or.cz/r/gromacs.git"
EGIT_BRANCH="release-4-6"
inherit git-2
PDEPEND="doc? ( ~app-doc/${PN}-manual-${PV} )"
else
SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf )
test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
fi
ACCE_IUSE="sse2 sse41 avx128fma avx256"
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"
KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
CDEPEND="
X? (
x11-libs/libX11
x11-libs/libSM
x11-libs/libICE
)
blas? ( virtual/blas )
cuda? ( dev-util/nvidia-cuda-toolkit )
fftw? ( sci-libs/fftw:3.0 )
gsl? ( sci-libs/gsl )
lapack? ( virtual/lapack )
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )"
DEPEND="${CDEPEND}
virtual/pkgconfig"
RDEPEND="${CDEPEND}"
REQUIRED_USE="
|| ( single-precision double-precision )
cuda? ( single-precision )
mkl? ( !blas !fftw !lapack )"
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_prepare() {
#notes/todos
# -on apple: there is framework support
#add user patches from /etc/portage/patches/sci-chemistry/gromacs
epatch_user
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 "${WORKDIR}/regressiontests-${TEST_PV}" "${WORKDIR}/${P}_${x}/tests" || die
done
fi
}
src_configure() {
local mycmakeargs_pre=( ) extra fft_opts=( )
#go from slowest to fastest acceleration
local acce="None"
use sse2 && acce="SSE2"
use sse41 && acce="SSE4.1"
use avx128fma && acce="AVX_128_FMA"
use avx256 && acce="AVX_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 gsl GMX_GSL)
$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
$(cmake-utils_use openmp GMX_OPENMP)
$(cmake-utils_use offensive GMX_COOL_QUOTES)
-DGMX_DEFAULT_SUFFIX=off
-DGMX_ACCELERATION="$acce"
-DGMXLIB="$(get_libdir)"
-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-DGMX_PREFIX_LIBMD=ON
-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
-DGMX_USE_GCC44_BUG_WORKAROUND=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
[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
local cuda=$(cmake-utils_use cuda GMX_GPU)
[[ ${x} = "double" ]] && use cuda && cuda="-DGMX_GPU=OFF"
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 ${cuda} -DGMX_OPENMM=OFF
-DGMX_BINARY_SUFFIX="_mpi${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
use mpi || continue
einfo "Compiling for ${x} precision with mpi"
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
cmake-utils_src_compile mdrun
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
use mpi || continue
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
DESTDIR="${D}" cmake-utils_src_make install-mdrun
done
rm -f "${ED}"/usr/bin/GMXRC*
newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
if use zsh-completion ; then
insinto /usr/share/zsh/site-functions
newins "${ED}"/usr/bin/completion.zsh _${PN}
fi
rm -f "${ED}"/usr/bin/completion.*
cd "${S}"
dodoc AUTHORS INSTALL* README*
if use doc; then
dohtml -r "${ED}usr/share/gromacs/html/"
if [[ $PV = *9999* ]]; then
insinto /usr/share/gromacs
doins "admin/programs.txt"
ls -1 "${ED}"/usr/bin | sed -e '/_d$/d' > "${T}"/programs.list
doins "${T}"/programs.list
else
dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf"
fi
fi
rm -rf "${ED}usr/share/gromacs/html/"
}
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"
if use offensive; then
einfo
einfo $(g_luck)
einfo "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
fi
einfo
elog "Gromacs can use sci-chemistry/vmd to read additional file formats"
}
^ permalink raw reply [flat|nested] 3+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-chemistry/gromacs: gromacs-4.6.ebuild ChangeLog
@ 2013-01-25 17:20 Christoph Junghans (ottxor)
0 siblings, 0 replies; 3+ messages in thread
From: Christoph Junghans (ottxor) @ 2013-01-25 17:20 UTC (permalink / raw
To: gentoo-commits
ottxor 13/01/25 17:20:09
Modified: gromacs-4.6.ebuild ChangeLog
Log:
added ~arm tested by me
(Portage version: 2.2.0_alpha161/cvs/Linux x86_64, signed Manifest commit with key C2000586)
Revision Changes Path
1.2 sci-chemistry/gromacs/gromacs-4.6.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.ebuild?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.ebuild?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.ebuild?r1=1.1&r2=1.2
Index: gromacs-4.6.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.ebuild,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- gromacs-4.6.ebuild 19 Jan 2013 21:49:38 -0000 1.1
+++ gromacs-4.6.ebuild 25 Jan 2013 17:20:09 -0000 1.2
@@ -1,6 +1,6 @@
# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.ebuild,v 1.1 2013/01/19 21:49:38 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.ebuild,v 1.2 2013/01/25 17:20:09 ottxor Exp $
EAPI=5
@@ -35,7 +35,7 @@
# 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"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
CDEPEND="
1.118 sci-chemistry/gromacs/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.118&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.118&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?r1=1.117&r2=1.118
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v
retrieving revision 1.117
retrieving revision 1.118
diff -u -r1.117 -r1.118
--- ChangeLog 19 Jan 2013 21:49:38 -0000 1.117
+++ ChangeLog 25 Jan 2013 17:20:09 -0000 1.118
@@ -1,6 +1,9 @@
# ChangeLog for sci-chemistry/gromacs
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.117 2013/01/19 21:49:38 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.118 2013/01/25 17:20:09 ottxor Exp $
+
+ 25 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.ebuild:
+ added ~arm tested by me
*gromacs-4.6 (19 Jan 2013)
^ permalink raw reply [flat|nested] 3+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-chemistry/gromacs: gromacs-4.6.ebuild ChangeLog
@ 2013-02-09 18:02 Pacho Ramos (pacho)
0 siblings, 0 replies; 3+ messages in thread
From: Pacho Ramos (pacho) @ 2013-02-09 18:02 UTC (permalink / raw
To: gentoo-commits
pacho 13/02/09 18:02:45
Modified: gromacs-4.6.ebuild ChangeLog
Log:
Use readme.gentoo.eclass for elog message (#456068)
(Portage version: 2.1.11.50/cvs/Linux x86_64, signed Manifest commit with key A188FBD4)
Revision Changes Path
1.3 sci-chemistry/gromacs/gromacs-4.6.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.ebuild?rev=1.3&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.ebuild?rev=1.3&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.ebuild?r1=1.2&r2=1.3
Index: gromacs-4.6.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.ebuild,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- gromacs-4.6.ebuild 25 Jan 2013 17:20:09 -0000 1.2
+++ gromacs-4.6.ebuild 9 Feb 2013 18:02:45 -0000 1.3
@@ -1,6 +1,6 @@
# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.ebuild,v 1.2 2013/01/25 17:20:09 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.ebuild,v 1.3 2013/02/09 18:02:45 pacho Exp $
EAPI=5
@@ -9,7 +9,7 @@
CMAKE_MAKEFILE_GENERATOR="ninja"
-inherit bash-completion-r1 cmake-utils eutils multilib toolchain-funcs
+inherit bash-completion-r1 cmake-utils eutils multilib readme.gentoo toolchain-funcs
if [[ $PV = *9999* ]]; then
EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
@@ -83,6 +83,8 @@
cp -al "${WORKDIR}/regressiontests-${TEST_PV}" "${WORKDIR}/${P}_${x}/tests" || die
done
fi
+
+ DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
}
src_configure() {
@@ -209,6 +211,8 @@
fi
fi
rm -rf "${ED}usr/share/gromacs/html/"
+
+ readme.gentoo_create_doc
}
pkg_postinst() {
@@ -222,5 +226,5 @@
einfo "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
fi
einfo
- elog "Gromacs can use sci-chemistry/vmd to read additional file formats"
+ readme.gentoo_print_elog
}
1.119 sci-chemistry/gromacs/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.119&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.119&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?r1=1.118&r2=1.119
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v
retrieving revision 1.118
retrieving revision 1.119
diff -u -r1.118 -r1.119
--- ChangeLog 25 Jan 2013 17:20:09 -0000 1.118
+++ ChangeLog 9 Feb 2013 18:02:45 -0000 1.119
@@ -1,6 +1,9 @@
# ChangeLog for sci-chemistry/gromacs
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.118 2013/01/25 17:20:09 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.119 2013/02/09 18:02:45 pacho Exp $
+
+ 09 Feb 2013; Pacho Ramos <pacho@gentoo.org> gromacs-4.6.ebuild:
+ Use readme.gentoo.eclass for elog message (#456068)
25 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.ebuild:
added ~arm tested by me
^ permalink raw reply [flat|nested] 3+ messages in thread
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