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Gentoo's Bugzilla – Attachment 188807 Details for
Bug 260995
Please stabilize sci-chemistry/gromacs-4.0.5
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[patch]
gromacs from 4.0.3 to 4.0.4 patch
gromacs-4.0.3.ebuild.patch (text/plain), 9.00 KB, created by
Christoph Junghans (RETIRED)
on 2009-04-18 16:52:31 UTC
(
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Description:
gromacs from 4.0.3 to 4.0.4 patch
Filename:
MIME Type:
Creator:
Christoph Junghans (RETIRED)
Created:
2009-04-18 16:52:31 UTC
Size:
9.00 KB
patch
obsolete
>--- gromacs-4.0.3.ebuild 2009-04-18 18:43:48.000000000 +0200 >+++ gromacs-4.0.4.ebuild 2009-04-18 17:01:30.000000000 +0200 >@@ -1,35 +1,29 @@ > # 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-4.0.3.ebuild,v 1.2 2009/03/08 19:50:46 maekke Exp $ >+# $Header: $ > > EAPI="1" > > LIBTOOLIZE="true" > >-inherit autotools eutils flag-o-matic fortran multilib >+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" >+SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz >+ test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${PV}.tgz ) >+ doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )" > > LICENSE="GPL-2" > SLOT="0" >-KEYWORDS="~alpha amd64 ~ppc64 ~sparc x86" >-IUSE="3dnow X altivec blas double-precision gsl lapack mpi +single-precision sse sse2 static xml" >+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86" >+IUSE="X blas dmalloc doc -double-precision fftw fkernels gsl lapack mpi +single-precision static test +xml zsh-completion" > >-# mopac7 qm/mm is broken until we can get files from >-# http://md.chem.rug.nl/~groenhof/qmmm.html >-# or somewhere else... >- >-DEPEND=">=sci-libs/fftw-3.0.1 >- app-shells/tcsh >- X? ( x11-libs/libX11 >- x11-libs/libXt >- x11-libs/libXp >- x11-libs/libXext >- x11-proto/xproto >- x11-libs/openmotif ) >+DEPEND="app-shells/tcsh >+ X? ( x11-libs/libX11 ) >+ dmalloc? ( dev-libs/dmalloc ) > blas? ( virtual/blas ) >+ fftw? ( >=sci-libs/fftw-3.0.1 ) > gsl? ( sci-libs/gsl ) > lapack? ( virtual/lapack ) > mpi? ( virtual/mpi ) >@@ -37,10 +31,7 @@ > > RDEPEND="${DEPEND}" > >-FORTRAN="g77 gfortran ifc" >- > src_unpack() { >- > unpack ${A} > cd "${S}" > # Fix typos in a couple of files. >@@ -64,6 +55,8 @@ > -i src/tools/Makefile.am \ > || die "sed tools/Makefile.am failed" > >+ use fkernels && epatch "${FILESDIR}/${P}-configure-gfortran.patch" >+ > eautoreconf > > cd "${WORKDIR}" >@@ -75,74 +68,37 @@ > } > > src_compile() { >- >- # static should work but something's broken. >- # gcc spec file may be screwed up. >- # Static linking should try -lgcc instead of -lgcc_s. >- # For more info: >- # http://lists.debian.org/debian-gcc/2002/debian-gcc-200201/msg00150.html >- >- # We will compile single precision by default, and suffix double-precision with _d. >- # Sparc is the only arch I can test on that needs to use fortran. > local myconf ; > local myconf_s ; > local myconf_d ; >+ local suffix_d ; > >- case "${ARCH}" in >- >- x86) >- if ( use sse || use sse2 ) ; then >- myconf="${myconf} --enable-ia32-sse" >- fi >- myconf="$myconf $(use_enable 3dnow ia32-3dnow)" >- >- if ( ! use sse && ! use sse2 && ! use 3dnow ) ; then >- if ! has_version "=sys-devel/gcc-3*" ; then >- die "If you must run gromacs without sse (not recommended) gfortran will not work." >- else >- myconf="${myconf} --enable-fortran" && fortran_pkg_setup >- fi >- else >- myconf="${myconf} --disable-fortran" >- fi >- ;; >- >- amd64) >- myconf="$myconf --enable-x86-64-sse --disable-fortran" >- ;; >- >- ppc*) >- if use altivec ; then >- myconf="${myconf} --enable-ppc-altivec --disable-fortran" >- else >- if ! has_version "=sys-devel/gcc-3*" ; then >- die "If you must run gromacs without sse (not recommended) gfortran will not work." >- else >- myconf="${myconf} --enable-fortran" && fortran_pkg_setup >- fi >- fi >- ;; >- >- ia64) >- myconf="$myconf --enable-ia64-asm --disable-fortran" >- ;; >- >- alpha) >- if ! has_version "=sys-devel/gcc-3*" ; then >- die "If you must run gromacs without sse (not recommended) gfortran will not work." >- else >- myconf="$myconf --enable-fortran" && fortran_pkg_setup >- fi >- ;; >- >- sparc) >- if ! has_version "=sys-devel/gcc-3*" ; then >- die "If you must run gromacs without sse (not recommended) gfortran will not work." >- else >- myconf="${myconf} --enable-fortran" && fortran_pkg_setup >- fi >- ;; >- esac >+ #leave all assembly options enabled mdrun is smart enough to deside itself >+ #there so no gentoo on bluegene! >+ myconf="${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="${myconf} --disable-fortran" >+ fi > > # if we need external blas > if use blas; then >@@ -159,7 +115,8 @@ > myconf="--datadir=/usr/share \ > --bindir=/usr/bin \ > --libdir=/usr/$(get_libdir) \ >- --with-fft=fftw3 \ >+ $(use_with dmalloc) \ >+ $(use_with fftw fft fftw3) \ > $(use_with gsl) \ > $(use_enable mpi) \ > $(use_with X x) \ >@@ -167,35 +124,58 @@ > $(use_enable static all-static) \ > ${myconf}" > >+ #if we build both double is suffixed > if ( use double-precision && use single-precision ); then >- einfo "Building Single Precison Gromacs" >- cd "${WORKDIR}"/"${P}"-single >- myconf_s="${myconf} --enable-float --disable-double --program-suffix=''" >- econf ${myconf_s} || die "Single Precision econf failed" >- emake || die "Single Precision emake failed" >- >- einfo "Building Double Precision Gromacs" >- cd "${WORKDIR}"/"${P}"-double >- myconf_d="${myconf} --enable-double --disable-float --program-suffix=_d" >- econf ${myconf_d} || die "Double Precision econf failed" >- emake || die "Double Precision emake failed" >+ suffix_d="_d" >+ else >+ suffix_d="" >+ fi > >- elif use double-precision ; then >+ if use double-precision ; then >+ #from gromacs manual >+ elog >+ elog For most simulations single precision is accurate enough. In some >+ elog cases double precision is required to get reasonable results: >+ elog >+ elog -normal mode analysis, for the conjugate gradient or l-bfgs minimization >+ elog and the calculation and diagonalization of the Hessian >+ elog -calculation of the constraint force between two large groups of atoms >+ elog -energy conservation: this can only be done without temperature coupling and >+ elog without cutoffs >+ elog > einfo "Building Double Precison Gromacs" > cd "${WORKDIR}"/"${P}"-double >- myconf_d="${myconf} --enable-double --disable-float --program-suffix=''" >+ myconf_d="${myconf} --enable-double --program-suffix='${suffix_d}'" > econf ${myconf_d} || die "Double Precision econf failed" > emake || die "Double Precision emake failed" >+ fi > >- elif use single-precision ; then >+ if use single-precision ; then > einfo "Building Single Precison Gromacs" > cd "${WORKDIR}"/"${P}"-single >- myconf_s="${myconf} --enable-float --disable-double --program-suffix=''" >+ myconf_s="${myconf} --enable-float --program-suffix=''" > econf ${myconf_s} || die "configure failed" > emake || die "Single Precision emake failed" > fi > } > >+src_test() { >+ if use single-precision ; then >+ export PATH="${WORKDIR}/${P}-single/src/kernel:${WORKDIR}/${P}-single/src/tools:$PATH" >+ cd "${WORKDIR}/gmxtest" >+ #test is broken, only do simple tests >+ ./gmxtest.pl simple || die "Single Precision test failed" >+ fi >+ >+ if use double-precision ; then >+ export PATH="${WORKDIR}/${P}-double/src/kernel:${WORKDIR}/${P}-double/src/tools:$PATH" >+ cd "${WORKDIR}/gmxtest" >+ use single-precision && ./gmxtest.pl clean >+ #test is broken, only do simple tests >+ ./gmxtest.pl -double simple || die "Double Precision test failed" >+ fi >+} >+ > src_install() { > if use single-precision ; then > einfo "Installing Single Precision" >@@ -208,8 +188,36 @@ > cd "${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 ${D}/usr/bin/completion.* > > dodoc AUTHORS INSTALL README >- # Move html and leave examples and templates under /usr/share/gromacs. >- mv "${D}"/usr/share/"${PN}"/html "${D}"/usr/share/doc/"${PF}"/ >+ if use doc; then >+ # Move html and leave examples and templates under /usr/share/gromacs. >+ mv "${D}"/usr/share/"${PN}"/html "${D}"/usr/share/doc/"${PF}"/ >+ dodoc "${DISTDIR}"/manual-4.0.pdf >+ fi >+} >+ >+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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Attachments on
bug 260995
:
187861
|
187866
|
188799
| 188807 |
190685
|
190780
|
217095