* [gentoo-commits] gentoo-x86 commit in sci-chemistry/gromacs: ChangeLog gromacs-4.0.5.ebuild gromacs-4.0.3.ebuild
@ 2009-05-14 16:17 Alexey Shvetsov (alexxy)
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From: Alexey Shvetsov (alexxy) @ 2009-05-14 16:17 UTC (permalink / raw
To: gentoo-commits
alexxy 09/05/14 16:17:39
Modified: ChangeLog
Added: gromacs-4.0.5.ebuild
Removed: gromacs-4.0.3.ebuild
Log:
Drop old version; Fix keywords for 4.0.5. Sorry =)
(Portage version: 2.2_rc33/cvs/Linux x86_64)
Revision Changes Path
1.40 sci-chemistry/gromacs/ChangeLog
file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.40&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.40&content-type=text/plain
diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gromacs/ChangeLog?r1=1.39&r2=1.40
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v
retrieving revision 1.39
retrieving revision 1.40
diff -u -r1.39 -r1.40
--- ChangeLog 14 May 2009 08:25:06 -0000 1.39
+++ ChangeLog 14 May 2009 16:17:39 -0000 1.40
@@ -1,6 +1,15 @@
# ChangeLog for sci-chemistry/gromacs
# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.39 2009/05/14 08:25:06 fauli Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.40 2009/05/14 16:17:39 alexxy Exp $
+
+ 14 May 2009; Alexey Shvetsov <alexxy@gentoo.org> -gromacs-4.0.3.ebuild,
+ +gromacs-4.0.5.ebuild:
+ Drop old version; Fix keywords for 4.0.5. Sorry =)
+
+*gromacs-4.0.5 (14 May 2009)
+
+ 14 May 2009; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.0.5.ebuild:
+ Bump new version with bugfixes. Bug #269754
14 May 2009; Christian Faulhammer <fauli@gentoo.org> gromacs-4.0.4.ebuild:
stable x86, bug 260995
1.1 sci-chemistry/gromacs/gromacs-4.0.5.ebuild
file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.5.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.5.ebuild?rev=1.1&content-type=text/plain
Index: gromacs-4.0.5.ebuild
===================================================================
# Copyright 1999-2009 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.5.ebuild,v 1.1 2009/05/14 16:17:39 alexxy Exp $
EAPI="2"
LIBTOOLIZE="true"
TEST_PV="4.0.4"
inherit autotools bash-completion eutils fortran multilib
DESCRIPTION="The ultimate molecular dynamics simulation package"
HOMEPAGE="http://www.gromacs.org/"
SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86"
IUSE="X blas dmalloc doc -double-precision +fftw fkernels gsl lapack mpi +single-precision static test +xml zsh-completion"
DEPEND="app-shells/tcsh
X? ( x11-libs/libX11 )
dmalloc? ( dev-libs/dmalloc )
blas? ( virtual/blas )
fftw? ( sci-libs/fftw:3.0 )
gsl? ( sci-libs/gsl )
lapack? ( virtual/lapack )
mpi? ( virtual/mpi )
xml? ( dev-libs/libxml2 )"
RDEPEND="${DEPEND}"
RESTRICT="test"
src_prepare() {
epatch "${FILESDIR}/${PN}-4.0.4-sparc-cyclecounter.patch"
# Fix typos in a couple of files.
sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
|| die "Failed to fixup demo script."
# Fix a sandbox violation that occurs when re-emerging with mpi.
sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
-i src/tools/Makefile.am \
|| die "sed tools/Makefile.am failed"
sed -e "s:\$\$libdir:\$temp_libdir:" \
-i src/tools/Makefile.am \
|| die "sed tools/Makefile.am failed"
sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
-i src/tools/Makefile.am \
|| die "sed tools/Makefile.am failed"
sed -e "s:\$\$libdir:\$\$temp_libdir:" \
-i src/tools/Makefile.am \
|| die "sed tools/Makefile.am failed"
use fkernels && epatch "${FILESDIR}/${PN}-4.0.4-configure-gfortran.patch"
eautoreconf
cd "${WORKDIR}"
use test && mv gmxtest "${P}"
mv "${P}" "${P}-single"
if ( use double-precision ) ; then
einfo "Moving sources for Multiprecision Build"
cp -prP "${P}-single" "${P}-double"
fi
}
src_configure() {
local myconf ;
local myconf_s ;
local myconf_d ;
local suffix_d ;
#leave all assembly options enabled mdrun is smart enough to deside itself
#there so no gentoo on bluegene!
myconf="${myconf} --disable-bluegene"
#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 [[ $(gcc-version) == "4.1" ]]; then
ewarn "gcc 4.1 is not supported by gromacs"
ewarn "please run test suite"
fi
#fortran will gone in gromacs 4.1 anyway
#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
if use fkernels; then
ewarn "Fortran kernels are usually not faster than C kernels and assembly"
ewarn "I hope, you know what are you doing..."
FORTRAN="g77 gfortran ifc"
myconf="${myconf} --enable-fortran" && fortran_pkg_setup
else
myconf="${myconf} --disable-fortran"
fi
# if we need external blas
if use blas; then
export LIBS="${LIBS} -lblas"
myconf="${myconf} $(use_with blas external-blas)"
fi
# if we need external lapack
if use lapack; then
export LIBS="${LIBS} -llapack"
myconf="${myconf} $(use_with lapack external-lapack)"
fi
myconf="--datadir=/usr/share \
--bindir=/usr/bin \
--libdir=/usr/$(get_libdir) \
--docdir=/usr/share/doc/"${PF}" \
$(use_with dmalloc) \
$(use_with fftw fft fftw3) \
$(use_with gsl) \
$(use_enable mpi) \
$(use_with X x) \
$(use_with xml) \
$(use_enable static all-static) \
${myconf}"
#if we build both double is suffixed
if ( use double-precision && use single-precision ); then
suffix_d="_d"
else
suffix_d=""
fi
if use double-precision ; then
#from gromacs manual
elog
elog "For most simulations single precision is accurate enough. In some"
elog "cases double precision is required to get reasonable results:"
elog
elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
elog " and the calculation and diagonalization of the Hessian "
elog "-calculation of the constraint force between two large groups of atoms"
elog "-energy conservation: this can only be done without temperature coupling and"
elog " without cutoffs"
elog
einfo "Configuring Double Precison Gromacs"
cd "${WORKDIR}"/"${P}"-double
myconf_d="${myconf} --enable-double --program-suffix='${suffix_d}'"
econf ${myconf_d} || die "Double Precision econf failed"
fi
if use single-precision ; then
einfo "Configuring Single Precison Gromacs"
cd "${WORKDIR}"/"${P}"-single
myconf_s="${myconf} --enable-float --program-suffix=''"
econf ${myconf_s} || die "configure failed"
fi
}
src_compile() {
if use double-precision ; then
einfo "Building Double Precison Gromacs"
cd "${WORKDIR}"/"${P}"-double
emake || die "Double Precision emake failed"
fi
if use single-precision ; then
einfo "Building Single Precison Gromacs"
cd "${WORKDIR}"/"${P}"-single
emake || die "Single Precision emake failed"
fi
}
src_test() {
if use single-precision ; then
export PATH="${WORKDIR}/${P}-single/src/kernel:${WORKDIR}/${P}-single/src/tools:$PATH"
cd "${WORKDIR}"/"${P}"-single
emake -j1 tests || die "Single Precision test failed"
fi
if use double-precision ; then
export PATH="${WORKDIR}/${P}-double/src/kernel:${WORKDIR}/${P}-double/src/tools:$PATH"
cd "${WORKDIR}"/"${P}"-double
emake -j1 tests || die "Double Precision test failed"
fi
}
src_install() {
if use single-precision ; then
einfo "Installing Single Precision"
cd "${WORKDIR}"/"${P}"-single
emake DESTDIR="${D}" install || die "Installing Single Precision failed"
fi
if use double-precision ; then
einfo "Installing Double Precision"
cd "${WORKDIR}"/"${P}"-double
emake DESTDIR="${D}" install || die "Installing Double Precision failed"
fi
sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${D}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
doenvd "${T}/80gromacs"
rm -f "${D}"/usr/bin/GMXRC*
dobashcompletion "${D}"/usr/bin/completion.bash ${PN}
if use zsh-completion ; then
insinto /usr/share/zsh/site-functions
newins "${D}"/usr/bin/completion.zsh _${PN}
fi
rm -r "${D}"/usr/bin/completion.*
dodoc AUTHORS INSTALL README
use doc && dodoc "${DISTDIR}"/manual-4.0.pdf
}
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 $(luck)
elog "For more Gromacs cool quotes \(gcq\) add luck to your .bashrc"
elog
}
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2009-05-14 16:17 [gentoo-commits] gentoo-x86 commit in sci-chemistry/gromacs: ChangeLog gromacs-4.0.5.ebuild gromacs-4.0.3.ebuild Alexey Shvetsov (alexxy)
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