* [gentoo-commits] gentoo-x86 commit in sci-chemistry/gromacs: ChangeLog gromacs-4.5.4.ebuild
@ 2011-03-21 16:24 Alexey Shvetsov (alexxy)
0 siblings, 0 replies; 7+ messages in thread
From: Alexey Shvetsov (alexxy) @ 2011-03-21 16:24 UTC (permalink / raw
To: gentoo-commits
alexxy 11/03/21 16:24:53
Modified: ChangeLog
Added: gromacs-4.5.4.ebuild
Log:
[sci-chemistry/gromacs] Version bump
(Portage version: 2.2.0_alpha28/cvs/Linux x86_64)
Revision Changes Path
1.71 sci-chemistry/gromacs/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.71&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.71&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?r1=1.70&r2=1.71
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v
retrieving revision 1.70
retrieving revision 1.71
diff -u -r1.70 -r1.71
--- ChangeLog 17 Mar 2011 22:26:20 -0000 1.70
+++ ChangeLog 21 Mar 2011 16:24:52 -0000 1.71
@@ -1,6 +1,11 @@
# ChangeLog for sci-chemistry/gromacs
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.70 2011/03/17 22:26:20 alexxy Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.71 2011/03/21 16:24:52 alexxy Exp $
+
+*gromacs-4.5.4 (21 Mar 2011)
+
+ 21 Mar 2011; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.5.4.ebuild:
+ Version bump
17 Mar 2011; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.5.3-r4.ebuild:
Clean up ebuild a bit
1.1 sci-chemistry/gromacs/gromacs-4.5.4.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild?rev=1.1&content-type=text/plain
Index: gromacs-4.5.4.ebuild
===================================================================
# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild,v 1.1 2011/03/21 16:24:52 alexxy Exp $
EAPI="3"
LIBTOOLIZE="true"
TEST_PV="4.0.4"
MANUAL_PV="4.5.3"
inherit autotools-utils bash-completion flag-o-matic multilib toolchain-funcs
SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
doc? (
http://www.gromacs.org/@api/deki/files/133/=manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
if [ "${PV%9999}" != "${PV}" ]; then
EGIT_REPO_URI="git://git.gromacs.org/gromacs"
EGIT_BRANCH="release-4-5-patches"
inherit git
else
SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
fi
DESCRIPTION="The ultimate molecular dynamics simulation package"
HOMEPAGE="http://www.gromacs.org/"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
IUSE="X altivec blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
mpi +single-precision sse sse2 static-libs test +threads +xml zsh-completion"
DEPEND="
app-shells/tcsh
X? ( x11-libs/libX11
x11-libs/libSM
x11-libs/libICE )
dmalloc? ( dev-libs/dmalloc )
blas? ( virtual/blas )
fftw? ( sci-libs/fftw:3.0 )
gsl? ( sci-libs/gsl )
lapack? ( virtual/lapack )
mpi? ( virtual/mpi )
xml? ( dev-libs/libxml2:2 )"
RDEPEND="${DEPEND}"
RESTRICT="test"
#gromacs has gnu exec stacks for speedup
QA_EXECSTACK="usr/lib/libgmx.so.*
usr/lib/libgmx_d.so.*"
src_prepare() {
if use mpi && use threads; then
elog "mdrun uses only threads OR mpi, and gromacs favours the"
elog "use of mpi over threads, so a mpi-version of mdrun will"
elog "be compiled. If you want to run mdrun on shared memory"
elog "machines only, you can safely disable mpi"
fi
autotools-utils_src_prepare || die
eautoreconf || die
GMX_DIRS=""
use single-precision && GMX_DIRS+=" float"
use double-precision && GMX_DIRS+=" double"
#if neither single-precision nor double-precision is enabled
#build at least default (single)
[ -z "$GMX_DIRS" ] && GMX_DIRS+=" float"
for x in ${GMX_DIRS}; do
mkdir -p "${WORKDIR}/${P}_${x}" || die
use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}"
done
}
src_configure() {
#from gromacs configure
if ! use fftw; then
ewarn "WARNING: The built-in FFTPACK routines are slow."
ewarn "Are you sure you don\'t want to use FFTW?"
ewarn "It is free and much faster..."
fi
if [[ $(gcc-version) == "4.1" ]]; then
eerror "gcc 4.1 is not supported by gromacs"
eerror "please run test suite"
die
fi
#note for gentoo-PREFIX on apple: use --enable-apple-64bit
#fortran will gone in gromacs 5.0 anyway
#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
if use fkernels; then
use threads && eerror "You cannot compile fortran kernel with threads"
ewarn "Fortran kernels are usually not faster than C kernels and assembly"
ewarn "I hope, you know what are you doing..."
fi
if use double-precision ; then
#from gromacs manual
elog
elog "For most simulations single precision is accurate enough. In some"
elog "cases double precision is required to get reasonable results:"
elog
elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
elog " and the calculation and diagonalization of the Hessian "
elog "-calculation of the constraint force between two large groups of atoms"
elog "-energy conservation: this can only be done without temperature coupling and"
elog " without cutoffs"
elog
fi
if use mpi ; then
elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
elog "we configure/compile gromacs twice (with and without mpi) and only"
elog "install mdrun with mpi support. In addtion you will get libgmx and"
elog "libmd with and without mpi support."
fi
# if we need external blas or lapack
use blas && export LIBS+=" $(pkg-config blas --libs)"
use lapack && export LIBS+=" $(pkg-config lapack --libs)"
local sseflag="x86-64-sse"
use x86 && sseflag="ia32-sse"
#a bug in gromacs autotools
use sse && append-flags -msse
use sse2 && append-flags -msse2
for x in ${GMX_DIRS}; do
local suffix="" sse="sse"
#if we build single and double - double is suffixed
use double-precision && use single-precision && \
[ "${x}" = "double" ] && suffix="_d"
#double uses sse2, single sse
[ "${x}" = "double" ] && sse="sse2"
myeconfargs=(
--bindir="${EPREFIX}"/usr/bin
--docdir="${EPREFIX}"/usr/share/doc/"${PF}"
--enable-"${x}"
$(use_with dmalloc)
$(use_with fftw fft fftw3)
$(use_with gsl)
$(use_with X x)
$(use_with xml)
$(use_enable threads)
$(use_enable altivec ppc-altivec)
$(use_enable ia64 ia64-asm)
$(use_with lapack external-lapack)
$(use_with blas external-blas)
$(use_enable fkernels fortran)
--disable-bluegene
--disable-la-files
--disable-power6
--disable-ia32-sse
--disable-x86-64-sse
$(use_enable $sse $sseflag)
)
#disable ia32-sse and x86-64-sse and enable what we really need in last line
einfo "Configuring for ${x} precision"
AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\
autotools-utils_src_configure --disable-mpi --program-suffix="${suffix}" \
CC="$(tc-getCC)" F77="$(tc-getFC)"
use mpi || continue
einfo "Configuring for ${x} precision with mpi"
AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
autotools-utils_src_configure --enable-mpi --program-suffix="_mpi${suffix}" \
CC="$(tc-getCC)" F77="$(tc-getFC)"
done
}
src_compile() {
for x in ${GMX_DIRS}; do
einfo "Compiling for ${x} precision"
AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\
autotools-utils_src_compile
use mpi || continue
einfo "Compiling for ${x} precision with mpi"
AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
autotools-utils_src_compile mdrun
done
}
src_test() {
for x in ${GMX_DIRS}; do
local oldpath="${PATH}"
export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
cd "${WORKDIR}/${P}_${x}"
emake -j1 tests || die "${x} Precision test failed"
export PATH="${oldpath}"
done
}
src_install() {
for x in ${GMX_DIRS}; do
AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}" \
autotools-utils_src_install
use mpi || continue
#autotools-utils_src_install does not support args
#using autotools-utils_src_compile instead
AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
autotools-utils_src_compile install-mdrun DESTDIR="${D}"
#stolen from autotools-utils_src_install see comment above
local args
has static-libs ${IUSE//+} && ! use static-libs || args='none'
remove_libtool_files ${args}
done
sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs"
doenvd "${T}/80gromacs"
rm -f "${ED}"/usr/bin/GMXRC*
dobashcompletion "${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.*
# Fix typos in a couple of files.
sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
|| die "Failed to fixup demo script."
cd "${S}"
dodoc AUTHORS INSTALL* README*
if use doc; then
newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
dohtml -r "${ED}usr/share/gromacs/html/"
fi
rm -rf "${ED}usr/share/gromacs/html/"
}
pkg_postinst() {
env-update && source /etc/profile
elog
elog "Please read and cite:"
elog "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
elog "http://dx.doi.org/10.1021/ct700301q"
elog
bash-completion_pkg_postinst
elog
elog $(g_luck)
elog "For more Gromacs cool quotes (gcq) add luck to your .bashrc"
elog
elog "Gromacs can use sci-chemistry/vmd to read additional file formats"
elog
}
^ permalink raw reply [flat|nested] 7+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-chemistry/gromacs: ChangeLog gromacs-4.5.4.ebuild
@ 2011-03-22 18:10 Christoph Junghans (ottxor)
0 siblings, 0 replies; 7+ messages in thread
From: Christoph Junghans (ottxor) @ 2011-03-22 18:10 UTC (permalink / raw
To: gentoo-commits
ottxor 11/03/22 18:10:26
Modified: ChangeLog gromacs-4.5.4.ebuild
Log:
New manual, added back pkg-config to DEPEND
(Portage version: 2.1.9.42/cvs/Linux i686)
Revision Changes Path
1.72 sci-chemistry/gromacs/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.72&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.72&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?r1=1.71&r2=1.72
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v
retrieving revision 1.71
retrieving revision 1.72
diff -u -r1.71 -r1.72
--- ChangeLog 21 Mar 2011 16:24:52 -0000 1.71
+++ ChangeLog 22 Mar 2011 18:10:25 -0000 1.72
@@ -1,6 +1,9 @@
# ChangeLog for sci-chemistry/gromacs
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.71 2011/03/21 16:24:52 alexxy Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.72 2011/03/22 18:10:25 ottxor Exp $
+
+ 22 Mar 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.4.ebuild:
+ New manual, added back pkg-config to DEPEND
*gromacs-4.5.4 (21 Mar 2011)
1.2 sci-chemistry/gromacs/gromacs-4.5.4.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild?r1=1.1&r2=1.2
Index: gromacs-4.5.4.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- gromacs-4.5.4.ebuild 21 Mar 2011 16:24:52 -0000 1.1
+++ gromacs-4.5.4.ebuild 22 Mar 2011 18:10:25 -0000 1.2
@@ -1,18 +1,17 @@
# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild,v 1.1 2011/03/21 16:24:52 alexxy Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild,v 1.2 2011/03/22 18:10:25 ottxor Exp $
EAPI="3"
LIBTOOLIZE="true"
TEST_PV="4.0.4"
-MANUAL_PV="4.5.3"
+MANUAL_PV="4.5.4"
inherit autotools-utils bash-completion flag-o-matic multilib toolchain-funcs
SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
- doc? (
- http://www.gromacs.org/@api/deki/files/133/=manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
+ doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
if [ "${PV%9999}" != "${PV}" ]; then
EGIT_REPO_URI="git://git.gromacs.org/gromacs"
@@ -31,8 +30,7 @@
IUSE="X altivec blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
mpi +single-precision sse sse2 static-libs test +threads +xml zsh-completion"
-DEPEND="
- app-shells/tcsh
+CDEPEND="
X? ( x11-libs/libX11
x11-libs/libSM
x11-libs/libICE )
@@ -43,8 +41,10 @@
lapack? ( virtual/lapack )
mpi? ( virtual/mpi )
xml? ( dev-libs/libxml2:2 )"
-
-RDEPEND="${DEPEND}"
+DEPEND="${CDEPEND}
+ dev-util/pkgconfig"
+RDEPEND="${CDEPEND}
+ app-shells/tcsh"
RESTRICT="test"
@@ -128,7 +128,7 @@
local sseflag="x86-64-sse"
use x86 && sseflag="ia32-sse"
- #a bug in gromacs autotools
+ #missing flag in autotools (bug #339837)
use sse && append-flags -msse
use sse2 && append-flags -msse2
^ permalink raw reply [flat|nested] 7+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-chemistry/gromacs: ChangeLog gromacs-4.5.4.ebuild
@ 2011-03-25 10:52 Kacper Kowalik (xarthisius)
0 siblings, 0 replies; 7+ messages in thread
From: Kacper Kowalik (xarthisius) @ 2011-03-25 10:52 UTC (permalink / raw
To: gentoo-commits
xarthisius 11/03/25 10:52:14
Modified: ChangeLog gromacs-4.5.4.ebuild
Log:
ppc64 stable wrt #357017
(Portage version: 2.2.0_alpha27/cvs/Linux x86_64)
Revision Changes Path
1.73 sci-chemistry/gromacs/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.73&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.73&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?r1=1.72&r2=1.73
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v
retrieving revision 1.72
retrieving revision 1.73
diff -u -r1.72 -r1.73
--- ChangeLog 22 Mar 2011 18:10:25 -0000 1.72
+++ ChangeLog 25 Mar 2011 10:52:14 -0000 1.73
@@ -1,6 +1,9 @@
# ChangeLog for sci-chemistry/gromacs
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.72 2011/03/22 18:10:25 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.73 2011/03/25 10:52:14 xarthisius Exp $
+
+ 25 Mar 2011; Kacper Kowalik <xarthisius@gentoo.org> gromacs-4.5.4.ebuild:
+ ppc64 stable wrt #357017
22 Mar 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.4.ebuild:
New manual, added back pkg-config to DEPEND
1.3 sci-chemistry/gromacs/gromacs-4.5.4.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild?rev=1.3&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild?rev=1.3&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild?r1=1.2&r2=1.3
Index: gromacs-4.5.4.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- gromacs-4.5.4.ebuild 22 Mar 2011 18:10:25 -0000 1.2
+++ gromacs-4.5.4.ebuild 25 Mar 2011 10:52:14 -0000 1.3
@@ -1,6 +1,6 @@
# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild,v 1.2 2011/03/22 18:10:25 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild,v 1.3 2011/03/25 10:52:14 xarthisius Exp $
EAPI="3"
@@ -26,7 +26,7 @@
LICENSE="GPL-2"
SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~alpha ~amd64 ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
IUSE="X altivec blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
mpi +single-precision sse sse2 static-libs test +threads +xml zsh-completion"
^ permalink raw reply [flat|nested] 7+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-chemistry/gromacs: ChangeLog gromacs-4.5.4.ebuild
@ 2011-04-02 15:43 Kacper Kowalik (xarthisius)
0 siblings, 0 replies; 7+ messages in thread
From: Kacper Kowalik (xarthisius) @ 2011-04-02 15:43 UTC (permalink / raw
To: gentoo-commits
xarthisius 11/04/02 15:43:13
Modified: ChangeLog gromacs-4.5.4.ebuild
Log:
Revert to ~ppc64
(Portage version: 2.2.0_alpha29/cvs/Linux x86_64)
Revision Changes Path
1.74 sci-chemistry/gromacs/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.74&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.74&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?r1=1.73&r2=1.74
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v
retrieving revision 1.73
retrieving revision 1.74
diff -u -r1.73 -r1.74
--- ChangeLog 25 Mar 2011 10:52:14 -0000 1.73
+++ ChangeLog 2 Apr 2011 15:43:13 -0000 1.74
@@ -1,6 +1,9 @@
# ChangeLog for sci-chemistry/gromacs
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.73 2011/03/25 10:52:14 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.74 2011/04/02 15:43:13 xarthisius Exp $
+
+ 02 Apr 2011; Kacper Kowalik <xarthisius@gentoo.org> gromacs-4.5.4.ebuild:
+ Revert to ~ppc64
25 Mar 2011; Kacper Kowalik <xarthisius@gentoo.org> gromacs-4.5.4.ebuild:
ppc64 stable wrt #357017
1.4 sci-chemistry/gromacs/gromacs-4.5.4.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild?rev=1.4&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild?rev=1.4&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild?r1=1.3&r2=1.4
Index: gromacs-4.5.4.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- gromacs-4.5.4.ebuild 25 Mar 2011 10:52:14 -0000 1.3
+++ gromacs-4.5.4.ebuild 2 Apr 2011 15:43:13 -0000 1.4
@@ -1,6 +1,6 @@
# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild,v 1.3 2011/03/25 10:52:14 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild,v 1.4 2011/04/02 15:43:13 xarthisius Exp $
EAPI="3"
@@ -26,7 +26,7 @@
LICENSE="GPL-2"
SLOT="0"
-KEYWORDS="~alpha ~amd64 ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
IUSE="X altivec blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
mpi +single-precision sse sse2 static-libs test +threads +xml zsh-completion"
^ permalink raw reply [flat|nested] 7+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-chemistry/gromacs: ChangeLog gromacs-4.5.4.ebuild
@ 2011-04-02 15:45 Samuli Suominen (ssuominen)
0 siblings, 0 replies; 7+ messages in thread
From: Samuli Suominen (ssuominen) @ 2011-04-02 15:45 UTC (permalink / raw
To: gentoo-commits
ssuominen 11/04/02 15:45:21
Modified: ChangeLog gromacs-4.5.4.ebuild
Log:
Remove illegal QA_EXECSTACK for source based package.
(Portage version: 2.2.0_alpha29/cvs/Linux x86_64)
Revision Changes Path
1.75 sci-chemistry/gromacs/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.75&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.75&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?r1=1.74&r2=1.75
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v
retrieving revision 1.74
retrieving revision 1.75
diff -u -r1.74 -r1.75
--- ChangeLog 2 Apr 2011 15:43:13 -0000 1.74
+++ ChangeLog 2 Apr 2011 15:45:21 -0000 1.75
@@ -1,6 +1,9 @@
# ChangeLog for sci-chemistry/gromacs
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.74 2011/04/02 15:43:13 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.75 2011/04/02 15:45:21 ssuominen Exp $
+
+ 02 Apr 2011; Samuli Suominen <ssuominen@gentoo.org> gromacs-4.5.4.ebuild:
+ Remove illegal QA_EXECSTACK for source based package.
02 Apr 2011; Kacper Kowalik <xarthisius@gentoo.org> gromacs-4.5.4.ebuild:
Revert to ~ppc64
1.5 sci-chemistry/gromacs/gromacs-4.5.4.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild?rev=1.5&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild?rev=1.5&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild?r1=1.4&r2=1.5
Index: gromacs-4.5.4.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- gromacs-4.5.4.ebuild 2 Apr 2011 15:43:13 -0000 1.4
+++ gromacs-4.5.4.ebuild 2 Apr 2011 15:45:21 -0000 1.5
@@ -1,6 +1,6 @@
# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild,v 1.4 2011/04/02 15:43:13 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild,v 1.5 2011/04/02 15:45:21 ssuominen Exp $
EAPI="3"
@@ -49,8 +49,12 @@
RESTRICT="test"
#gromacs has gnu exec stacks for speedup
-QA_EXECSTACK="usr/lib/libgmx.so.*
- usr/lib/libgmx_d.so.*"
+# - ebuild author
+#it's not legal to hide execstacks in source based packages by QA_ vars,
+#and if this were a binary-only package these libs would be in /opt instead
+# - ssuominen, for the QA team
+#QA_EXECSTACK="usr/lib/libgmx.so.*
+# usr/lib/libgmx_d.so.*"
src_prepare() {
if use mpi && use threads; then
^ permalink raw reply [flat|nested] 7+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-chemistry/gromacs: ChangeLog gromacs-4.5.4.ebuild
@ 2011-04-02 16:08 Kacper Kowalik (xarthisius)
0 siblings, 0 replies; 7+ messages in thread
From: Kacper Kowalik (xarthisius) @ 2011-04-02 16:08 UTC (permalink / raw
To: gentoo-commits
xarthisius 11/04/02 16:08:05
Modified: ChangeLog gromacs-4.5.4.ebuild
Log:
Bump to EAPI=4 for REQUIRED_USE on fkernels and threads wrt #361687. Mark ppc64 stable wrt #357017
(Portage version: 2.2.0_alpha29/cvs/Linux x86_64)
Revision Changes Path
1.76 sci-chemistry/gromacs/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.76&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.76&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?r1=1.75&r2=1.76
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v
retrieving revision 1.75
retrieving revision 1.76
diff -u -r1.75 -r1.76
--- ChangeLog 2 Apr 2011 15:45:21 -0000 1.75
+++ ChangeLog 2 Apr 2011 16:08:05 -0000 1.76
@@ -1,6 +1,10 @@
# ChangeLog for sci-chemistry/gromacs
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.75 2011/04/02 15:45:21 ssuominen Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.76 2011/04/02 16:08:05 xarthisius Exp $
+
+ 02 Apr 2011; Kacper Kowalik <xarthisius@gentoo.org> gromacs-4.5.4.ebuild:
+ Bump to EAPI=4 for REQUIRED_USE on fkernels and threads wrt #361687. Mark
+ ppc64 stable wrt #357017
02 Apr 2011; Samuli Suominen <ssuominen@gentoo.org> gromacs-4.5.4.ebuild:
Remove illegal QA_EXECSTACK for source based package.
1.6 sci-chemistry/gromacs/gromacs-4.5.4.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild?rev=1.6&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild?rev=1.6&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild?r1=1.5&r2=1.6
Index: gromacs-4.5.4.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- gromacs-4.5.4.ebuild 2 Apr 2011 15:45:21 -0000 1.5
+++ gromacs-4.5.4.ebuild 2 Apr 2011 16:08:05 -0000 1.6
@@ -1,8 +1,8 @@
# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild,v 1.5 2011/04/02 15:45:21 ssuominen Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild,v 1.6 2011/04/02 16:08:05 xarthisius Exp $
-EAPI="3"
+EAPI="4"
LIBTOOLIZE="true"
TEST_PV="4.0.4"
@@ -26,9 +26,10 @@
LICENSE="GPL-2"
SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~alpha ~amd64 ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
IUSE="X altivec blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
mpi +single-precision sse sse2 static-libs test +threads +xml zsh-completion"
+REQUIRED_USE="fkernels? ( !threads )"
CDEPEND="
X? ( x11-libs/libX11
@@ -53,8 +54,8 @@
#it's not legal to hide execstacks in source based packages by QA_ vars,
#and if this were a binary-only package these libs would be in /opt instead
# - ssuominen, for the QA team
-#QA_EXECSTACK="usr/lib/libgmx.so.*
-# usr/lib/libgmx_d.so.*"
+#QA_EXECSTACK="usr/$(get_libdir)/libgmx.so.*
+# usr/$(get_libdir)/libgmx_d.so.*"
src_prepare() {
if use mpi && use threads; then
^ permalink raw reply [flat|nested] 7+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-chemistry/gromacs: ChangeLog gromacs-4.5.4.ebuild
@ 2011-04-04 18:46 Christoph Junghans (ottxor)
0 siblings, 0 replies; 7+ messages in thread
From: Christoph Junghans (ottxor) @ 2011-04-04 18:46 UTC (permalink / raw
To: gentoo-commits
ottxor 11/04/04 18:46:56
Modified: ChangeLog gromacs-4.5.4.ebuild
Log:
Removed sse use flag (fixes bug #361933)
(Portage version: 2.1.9.42/cvs/Linux i686)
Revision Changes Path
1.78 sci-chemistry/gromacs/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.78&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.78&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?r1=1.77&r2=1.78
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v
retrieving revision 1.77
retrieving revision 1.78
diff -u -r1.77 -r1.78
--- ChangeLog 2 Apr 2011 16:11:59 -0000 1.77
+++ ChangeLog 4 Apr 2011 18:46:56 -0000 1.78
@@ -1,6 +1,9 @@
# ChangeLog for sci-chemistry/gromacs
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.77 2011/04/02 16:11:59 armin76 Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.78 2011/04/04 18:46:56 ottxor Exp $
+
+ 04 Apr 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.4.ebuild:
+ Removed sse use flag (fixed bug #361933)
02 Apr 2011; Raúl Porcel <armin76@gentoo.org> gromacs-4.5.3-r4.ebuild:
alpha/sparc stable wrt #357017
1.7 sci-chemistry/gromacs/gromacs-4.5.4.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild?rev=1.7&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild?rev=1.7&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild?r1=1.6&r2=1.7
Index: gromacs-4.5.4.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- gromacs-4.5.4.ebuild 2 Apr 2011 16:08:05 -0000 1.6
+++ gromacs-4.5.4.ebuild 4 Apr 2011 18:46:56 -0000 1.7
@@ -1,6 +1,6 @@
# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild,v 1.6 2011/04/02 16:08:05 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4.ebuild,v 1.7 2011/04/04 18:46:56 ottxor Exp $
EAPI="4"
@@ -28,7 +28,7 @@
SLOT="0"
KEYWORDS="~alpha ~amd64 ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
IUSE="X altivec blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
-mpi +single-precision sse sse2 static-libs test +threads +xml zsh-completion"
+mpi +single-precision sse2 static-libs test +threads +xml zsh-completion"
REQUIRED_USE="fkernels? ( !threads )"
CDEPEND="
@@ -101,7 +101,6 @@
#fortran will gone in gromacs 5.0 anyway
#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
if use fkernels; then
- use threads && eerror "You cannot compile fortran kernel with threads"
ewarn "Fortran kernels are usually not faster than C kernels and assembly"
ewarn "I hope, you know what are you doing..."
fi
@@ -134,16 +133,12 @@
use x86 && sseflag="ia32-sse"
#missing flag in autotools (bug #339837)
- use sse && append-flags -msse
use sse2 && append-flags -msse2
for x in ${GMX_DIRS}; do
- local suffix="" sse="sse"
#if we build single and double - double is suffixed
use double-precision && use single-precision && \
[ "${x}" = "double" ] && suffix="_d"
- #double uses sse2, single sse
- [ "${x}" = "double" ] && sse="sse2"
myeconfargs=(
--bindir="${EPREFIX}"/usr/bin
--docdir="${EPREFIX}"/usr/share/doc/"${PF}"
@@ -164,7 +159,7 @@
--disable-power6
--disable-ia32-sse
--disable-x86-64-sse
- $(use_enable $sse $sseflag)
+ $(use_enable sse2 $sseflag)
)
#disable ia32-sse and x86-64-sse and enable what we really need in last line
^ permalink raw reply [flat|nested] 7+ messages in thread
end of thread, other threads:[~2011-04-04 18:47 UTC | newest]
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2011-04-04 18:46 Christoph Junghans (ottxor)
2011-04-02 16:08 Kacper Kowalik (xarthisius)
2011-04-02 15:45 Samuli Suominen (ssuominen)
2011-03-25 10:52 Kacper Kowalik (xarthisius)
2011-03-22 18:10 Christoph Junghans (ottxor)
2011-03-21 16:24 Alexey Shvetsov (alexxy)
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