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authorChristoph Junghans <ottxor@gentoo.org>2011-04-04 18:56:42 +0000
committerChristoph Junghans <ottxor@gentoo.org>2011-04-04 18:56:42 +0000
commit4ebb21ee14f1530155acb51419824d0d9e80a499 (patch)
tree21aaa45082c75feb9eaa2ef25b6e0021c4d4d84d /sci-chemistry/gromacs
parentFollowing the change in gnome-panel, drop in-process support for bonobo apple... (diff)
downloadgentoo-2-4ebb21ee14f1530155acb51419824d0d9e80a499.tar.gz
gentoo-2-4ebb21ee14f1530155acb51419824d0d9e80a499.tar.bz2
gentoo-2-4ebb21ee14f1530155acb51419824d0d9e80a499.zip
Removed old
(Portage version: 2.1.9.42/cvs/Linux i686)
Diffstat (limited to 'sci-chemistry/gromacs')
-rw-r--r--sci-chemistry/gromacs/ChangeLog6
-rw-r--r--sci-chemistry/gromacs/gromacs-4.0.7-r5.ebuild300
-rw-r--r--sci-chemistry/gromacs/gromacs-4.5.3-r3.ebuild260
-rw-r--r--sci-chemistry/gromacs/gromacs-4.5.3.ebuild258
4 files changed, 5 insertions, 819 deletions
diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 6629662e4621..938e46814f6b 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -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 1.78 2011/04/04 18:46:56 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.79 2011/04/04 18:56:42 ottxor Exp $
+
+ 04 Apr 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.0.7-r5.ebuild,
+ -gromacs-4.5.3.ebuild, -gromacs-4.5.3-r3.ebuild:
+ Removed old
04 Apr 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.4.ebuild:
Removed sse use flag (fixed bug #361933)
diff --git a/sci-chemistry/gromacs/gromacs-4.0.7-r5.ebuild b/sci-chemistry/gromacs/gromacs-4.0.7-r5.ebuild
deleted file mode 100644
index 0744795ddb66..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.0.7-r5.ebuild
+++ /dev/null
@@ -1,300 +0,0 @@
-# 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-4.0.7-r5.ebuild,v 1.3 2011/03/02 17:55:01 jlec Exp $
-
-EAPI="3"
-
-LIBTOOLIZE="true"
-TEST_PV="4.0.4"
-
-inherit autotools bash-completion eutils multilib toolchain-funcs
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
- mirror://gentoo/${P}_upstream2010-09-15.patch.bz2
- mirror://gentoo/${P}_missing_distfiles.patch.bz2
- test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
- doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf -> gromacs-manual-4.0.pdf )
- ffamber? ( http://ffamber.cnsm.csulb.edu/ffamber_v4.0-doc.tar.gz )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X blas dmalloc doc -double-precision ffamber +fftw fkernels +gsl lapack
-mpi +single-precision static static-libs test +xml zsh-completion"
-
-DEPEND="app-shells/tcsh
- X? ( x11-libs/libX11
- x11-libs/libSM
- x11-libs/libICE )
- dmalloc? ( dev-libs/dmalloc )
- blas? ( virtual/blas )
- fftw? ( sci-libs/fftw:3.0 )
- gsl? ( sci-libs/gsl )
- lapack? ( virtual/lapack )
- mpi? ( virtual/mpi )
- xml? ( dev-libs/libxml2:2 )"
-
-RDEPEND="${DEPEND}"
-
-RESTRICT="test"
-
-QA_EXECSTACK="usr/lib/libgmx.so.*
- usr/lib/libgmx_d.so.*"
-
-use static && QA_EXECSTACK="$QA_EXECSTACK usr/bin/*"
-
-src_prepare() {
-
- ( use single-precision || use double-precision ) || \
- die "Nothing to compile, enable single-precision and/or double-precision"
-
- if use static; then
- use X && die "You cannot compile a static version with X support, disable X or static"
- use xml && die "You cannot compile a static version with xml support
- (see bug #306479), disable xml or static"
- fi
-
- epatch "${WORKDIR}/${P}_upstream2010-09-15.patch"
- epatch "${WORKDIR}/${P}_missing_distfiles.patch"
- sed -e '/AC_INIT/s/4\.0\.7/&-2010-09-15/' -i configure.ac \
- || die "Failed to change version in configure.ac"
-
- # Fix typos in a couple of files.
- sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
- || die "Failed to fixup demo script."
-
- epatch_user
- eautoreconf
- GMX_DIRS=""
- use single-precision && GMX_DIRS+=" single"
- use double-precision && GMX_DIRS+=" double"
- for x in ${GMX_DIRS}; do
- mkdir "${S}-${x}" || die
- use test && cp -r "${WORKDIR}"/gmxtest "${S}-${x}"
- use mpi || continue
- mkdir "${S}-${x}_mpi" || die
- done
-}
-
-src_configure() {
- local myconf
- local myconfsingle
- local myconfdouble
- local suffixdouble
-
- #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 [[ $(gcc-version) == "4.1" ]]; then
- eerror "gcc 4.1 is not supported by gromacs"
- eerror "please run test suite"
- die
- fi
-
- #note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
- #fortran will gone in gromacs 4.1 anyway
- #note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
- if use fkernels; then
- ewarn "Fortran kernels are usually not faster than C kernels and assembly"
- ewarn "I hope, you know what are you doing..."
- myconf="${myconf} --enable-fortran"
- 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} $(use_with lapack external-lapack)"
- fi
-
- # by default its better to have dynamicaly linked binaries
- if use static; then
- #gmx build static libs by default
- myconf="${myconf} --disable-shared $(use_enable static all-static)"
- else
- myconf="${myconf} --disable-all-static --enable-shared $(use_enable static-libs static)"
- fi
-
- myconf="--datadir="${EPREFIX}"/usr/share \
- --bindir="${EPREFIX}"/usr/bin \
- --libdir="${EPREFIX}"/usr/$(get_libdir) \
- --docdir="${EPREFIX}"/usr/share/doc/"${PF}" \
- $(use_with dmalloc) \
- $(use_with fftw fft fftw3) \
- $(use_with gsl) \
- $(use_with X x) \
- $(use_with xml) \
- ${myconf}"
-
- #if we build single and double - double is suffixed
- if ( use double-precision && use single-precision ); then
- suffixdouble="_d"
- else
- suffixdouble=""
- fi
-
- if use double-precision ; then
- #from gromacs manual
- elog
- elog "For most simulations single precision is accurate enough. In some"
- elog "cases double precision is required to get reasonable results:"
- elog
- elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
- elog " and the calculation and diagonalization of the Hessian "
- elog "-calculation of the constraint force between two large groups of atoms"
- elog "-energy conservation: this can only be done without temperature coupling and"
- elog " without cutoffs"
- elog
- fi
-
- if use mpi ; then
- elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
- elog "we configure/compile gromacs twice (with and without mpi) and only"
- elog "install mdrun with mpi support. In addtion you will get libgmx and"
- elog "libmd with and without mpi support."
- fi
-
- myconfdouble="${myconf} --enable-double --program-suffix='${suffixdouble}'"
- myconfsingle="${myconf} --enable-float --program-suffix=''"
- for x in ${GMX_DIRS}; do
- einfo "Configuring for ${x} precision"
- cd "${S}-${x}"
- local p=myconf${x}
- ECONF_SOURCE="${S}" econf ${!p} --disable-mpi CC="$(tc-getCC)" F77="$(tc-getFC)"
- use mpi || continue
- cd "${S}-${x}_mpi"
- ECONF_SOURCE="${S}" econf ${!p} --enable-mpi CC="$(tc-getCC)" F77="$(tc-getFC)"
- done
-}
-
-src_compile() {
- for x in ${GMX_DIRS}; do
- cd "${S}-${x}"
- einfo "Compiling for ${x} precision"
- emake || die "emake for ${x} precision failed"
- use mpi || continue
- cd "${S}-${x}_mpi"
- emake mdrun || die "emake mdrun for ${x} precision failed"
- done
-}
-
-src_test() {
- for x in ${GMX_DIRS}; do
- local oldpath="${PATH}"
- export PATH="${S}-${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
- cd "${S}-${x}"
- emake -j1 tests || die "${x} Precision test failed"
- export PATH="${oldpath}"
- done
-}
-
-src_install() {
- for x in ${GMX_DIRS}; do
- cd "${S}-${x}"
- emake DESTDIR="${D}" install || die "emake install for ${x} failed"
- use mpi || continue
- cd "${S}-${x}_mpi"
- emake DESTDIR="${D}" install-mdrun || die "emake install-mdrun for ${x} failed"
- done
- #we have pkg-config files
- rm "${ED}"/usr/$(get_libdir)/*.la
-
- sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
- doenvd "${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.*
-
- cd "${S}"
- dodoc AUTHORS INSTALL README
- if use doc; then
- newdoc "${DISTDIR}/gromacs-manual-4.0.pdf" "manual-4.0.pdf"
- dohtml -r "${ED}usr/share/gromacs/html/"
- fi
- rm -rf "${ED}usr/share/gromacs/html/"
-
- if use ffamber; then
- use doc && dodoc "${WORKDIR}/ffamber_v4.0/README/pdfs/*.pdf"
- # prepare vdwradii.dat
- cat >>"${ED}"/usr/share/gromacs/top/vdwradii.dat <<-EOF
- SOL MW 0
- SOL LP 0
- EOF
- # regenerate aminoacids.dat
- cat "${WORKDIR}"/ffamber_v4.0/aminoacids*.dat \
- "${ED}"/usr/share/gromacs/top/aminoacids.dat \
- | awk '{print $1}' | sort -u | tail -n+4 | wc -l \
- >> "${ED}"/usr/share/gromacs/top/aminoacids.dat.new
- cat "${WORKDIR}"/ffamber_v4.0/aminoacids*.dat \
- "${ED}"/usr/share/gromacs/top/aminoacids.dat \
- | awk '{print $1}' | sort -u | tail -n+4 \
- >> "${ED}"/usr/share/gromacs/top/aminoacids.dat.new
- mv -f "${ED}"/usr/share/gromacs/top/aminoacids.dat.new \
- "${ED}"/usr/share/gromacs/top/aminoacids.dat
- # copy ff files
- for x in ffamber94 ffamber96 ffamber99 ffamber99p ffamber99sb \
- ffamberGS ffamberGSs ffamber03 ; do
- einfo "Adding ${x} to gromacs"
- cp "${WORKDIR}"/ffamber_v4.0/${x}/* "${ED}"/usr/share/gromacs/top
- done
- # copy suplementary files
- cp "${WORKDIR}"/ffamber_v4.0/*.gro "${ED}"/usr/share/gromacs/top
- cp "${WORKDIR}"/ffamber_v4.0/*.itp "${ED}"/usr/share/gromacs/top
- # actualy add records to FF.dat
- cat >>"${ED}"/usr/share/gromacs/top/FF.dat.new <<-EOF
- ffamber94 AMBER94 Cornell protein/nucleic forcefield
- ffamber96 AMBER96 Kollman protein/nucleic forcefield
- ffamberGS AMBER-GS Garcia & Sanbonmatsu forcefield
- ffamberGSs AMBER-GSs Nymeyer & Garcia forcefield
- ffamber99 AMBER99 Wang protein/nucleic acid forcefield
- ffamber99p AMBER99p protein/nucleic forcefield
- ffamber99sb AMBER99sb Hornak protein/nucleic forcefield
- ffamber03 AMBER03 Duan protein/nucleic forcefield
- EOF
- cat "${ED}"/usr/share/gromacs/top/FF.dat \
- "${ED}"/usr/share/gromacs/top/FF.dat.new \
- | tail -n+2 > "${ED}"/usr/share/gromacs/top/FF.dat.new2
- cat "${ED}"/usr/share/gromacs/top/FF.dat.new2 | wc -l > \
- "${ED}"/usr/share/gromacs/top/FF.dat
- cat "${ED}"/usr/share/gromacs/top/FF.dat.new2 >> \
- "${ED}"/usr/share/gromacs/top/FF.dat
- rm -f "${ED}"/usr/share/gromacs/top/FF.dat.new*
- 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
-}
diff --git a/sci-chemistry/gromacs/gromacs-4.5.3-r3.ebuild b/sci-chemistry/gromacs/gromacs-4.5.3-r3.ebuild
deleted file mode 100644
index cdf58f62e996..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.5.3-r3.ebuild
+++ /dev/null
@@ -1,260 +0,0 @@
-# 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-4.5.3-r3.ebuild,v 1.2 2011/03/02 17:55:01 jlec 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
- PATCHES=( ${WORKDIR}/${P}_upstream20110217.patch )
- SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
- mirror://gentoo/${P}_upstream20110217.patch.bz2"
-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="${DEPEND}"
-
-RESTRICT="test"
-
-#gromacs has gnu exec stacks for speedup
-QA_EXECSTACK="usr/lib/libgmx.so.*
- usr/lib/libgmx_d.so.*"
-
-src_prepare() {
- if use mpi && use threads; then
- elog "mdrun uses only threads OR mpi, and gromacs favours the"
- elog "use of mpi over threads, so a mpi-version of mdrun will"
- elog "be compiled. If you want to run mdrun on shared memory"
- elog "machines only, you can safely disable mpi"
- fi
-
- autotools-utils_src_prepare || die
-
- sed -e '/AC_INIT/s/4\.5\.3-dev/4.5.3-2011-02-17/' -i configure.ac \
- || die "Failed to change version in configure.ac"
-
- eautoreconf || die
-
- GMX_DIRS=""
- use single-precision && GMX_DIRS+=" float"
- use double-precision && GMX_DIRS+=" double"
- #if neither single-precision nor double-precision is enabled
- #build at least default (single)
- [ -z "$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+=" -lblas"
- use lapack && export LIBS+=" -llapack"
- 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}"\
- 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
-}
diff --git a/sci-chemistry/gromacs/gromacs-4.5.3.ebuild b/sci-chemistry/gromacs/gromacs-4.5.3.ebuild
deleted file mode 100644
index bf3313ee566d..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.5.3.ebuild
+++ /dev/null
@@ -1,258 +0,0 @@
-# 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-4.5.3.ebuild,v 1.3 2011/03/02 17:55:01 jlec Exp $
-
-EAPI="3"
-
-LIBTOOLIZE="true"
-TEST_PV="4.0.4"
-MANUAL_PV="4.5.3"
-
-inherit autotools bash-completion eutils multilib toolchain-funcs
-
-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-${TEST_PV}.tgz )
- doc? ( http://www.gromacs.org/@api/deki/files/133/=manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
-mpi +single-precision static static-libs test +threads +xml zsh-completion"
-
-DEPEND="app-shells/tcsh
- X? ( x11-libs/libX11
- x11-libs/libSM
- x11-libs/libICE )
- dmalloc? ( dev-libs/dmalloc )
- blas? ( virtual/blas )
- fftw? ( sci-libs/fftw:3.0 )
- gsl? ( sci-libs/gsl )
- lapack? ( virtual/lapack )
- mpi? ( virtual/mpi )
- xml? ( dev-libs/libxml2:2 )"
-
-RDEPEND="${DEPEND}"
-
-RESTRICT="test"
-
-QA_EXECSTACK="usr/lib/libgmx.so.*
- usr/lib/libgmx_d.so.*"
-
-use static && QA_EXECSTACK="$QA_EXECSTACK usr/bin/*"
-
-src_prepare() {
-
- ( use single-precision || use double-precision ) || \
- die "Nothing to compile, enable single-precision and/or double-precision"
-
- 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
-
- if use static; then
- use X && die "You cannot compile a static version with X support, disable X or static"
- use xml && die "You cannot compile a static version with xml support
- (see bug #306479), disable xml or static"
- fi
- epatch_user
- eautoreconf
- GMX_DIRS=""
- use single-precision && GMX_DIRS+=" single"
- use double-precision && GMX_DIRS+=" double"
- for x in ${GMX_DIRS}; do
- mkdir "${S}-${x}" || die
- use test && cp -r "${WORKDIR}"/gmxtest "${S}-${x}"
- use mpi || continue
- mkdir "${S}-${x}_mpi" || die
- done
-}
-
-src_configure() {
- local myconf
- local myconfsingle
- local myconfdouble
- local suffixdouble
-
- #leave all assembly options enabled mdrun is smart enough to deside itself
- #there so no gentoo on bluegene!
- myconf="${myconf} --disable-bluegene"
-
- #we have pkg-config files
- myconf="${myconf} --disable-la-files"
-
- #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 [[ $(gcc-version) == "4.1" ]]; then
- eerror "gcc 4.1 is not supported by gromacs"
- eerror "please run test suite"
- die
- fi
-
- #note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
- #fortran will gone in gromacs 4.1 anyway
- #note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
- if use fkernels; then
- use threads && die "You cannot compile fortran kernel with threads"
- ewarn "Fortran kernels are usually not faster than C kernels and assembly"
- ewarn "I hope, you know what are you doing..."
- myconf="${myconf} --enable-fortran"
- 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} $(use_with lapack external-lapack)"
- fi
-
- # by default its better to have dynamicaly linked binaries
- if use static; then
- #gmx build static libs by default
- myconf="${myconf} --disable-shared $(use_enable static all-static)"
- else
- myconf="${myconf} --disable-all-static --enable-shared $(use_enable static-libs static)"
- fi
-
- myconf="--datadir="${EPREFIX}"/usr/share \
- --bindir="${EPREFIX}"/usr/bin \
- --libdir="${EPREFIX}"/usr/$(get_libdir) \
- --docdir="${EPREFIX}"/usr/share/doc/"${PF}" \
- $(use_with dmalloc) \
- $(use_with fftw fft fftw3) \
- $(use_with gsl) \
- $(use_with X x) \
- $(use_with xml) \
- $(use_enable threads) \
- ${myconf}"
-
- #if we build single and double - double is suffixed
- if ( use double-precision && use single-precision ); then
- suffixdouble="_d"
- else
- suffixdouble=""
- fi
-
- if use double-precision ; then
- #from gromacs manual
- elog
- elog "For most simulations single precision is accurate enough. In some"
- elog "cases double precision is required to get reasonable results:"
- elog
- elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
- elog " and the calculation and diagonalization of the Hessian "
- elog "-calculation of the constraint force between two large groups of atoms"
- elog "-energy conservation: this can only be done without temperature coupling and"
- elog " without cutoffs"
- elog
- fi
-
- if use mpi ; then
- elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
- elog "we configure/compile gromacs twice (with and without mpi) and only"
- elog "install mdrun with mpi support. In addtion you will get libgmx and"
- elog "libmd with and without mpi support."
- fi
-
- myconfdouble="${myconf} --enable-double --program-suffix='${suffixdouble}'"
- myconfsingle="${myconf} --enable-float --program-suffix=''"
- for x in ${GMX_DIRS}; do
- einfo "Configuring for ${x} precision"
- cd "${S}-${x}"
- local p=myconf${x}
- ECONF_SOURCE="${S}" econf ${!p} --disable-mpi CC="$(tc-getCC)" F77="$(tc-getFC)"
- use mpi || continue
- cd "${S}-${x}_mpi"
- ECONF_SOURCE="${S}" econf ${!p} --enable-mpi CC="$(tc-getCC)" F77="$(tc-getFC)"
- done
-}
-
-src_compile() {
- for x in ${GMX_DIRS}; do
- cd "${S}-${x}"
- einfo "Compiling for ${x} precision"
- emake || die "emake for ${x} precision failed"
- use mpi || continue
- cd "${S}-${x}_mpi"
- emake mdrun || die "emake mdrun for ${x} precision failed"
- done
-}
-
-src_test() {
- for x in ${GMX_DIRS}; do
- local oldpath="${PATH}"
- export PATH="${S}-${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
- cd "${S}-${x}"
- emake -j1 tests || die "${x} Precision test failed"
- export PATH="${oldpath}"
- done
-}
-
-src_install() {
- for x in ${GMX_DIRS}; do
- cd "${S}-${x}"
- emake DESTDIR="${D}" install || die "emake install for ${x} failed"
- use mpi || continue
- cd "${S}-${x}_mpi"
- emake DESTDIR="${D}" install-mdrun || die "emake install-mdrun for ${x} failed"
- done
-
- sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${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
-}