diff options
author | Christoph Junghans <ottxor@gentoo.org> | 2011-04-04 18:56:42 +0000 |
---|---|---|
committer | Christoph Junghans <ottxor@gentoo.org> | 2011-04-04 18:56:42 +0000 |
commit | 4ebb21ee14f1530155acb51419824d0d9e80a499 (patch) | |
tree | 21aaa45082c75feb9eaa2ef25b6e0021c4d4d84d /sci-chemistry/gromacs | |
parent | Following the change in gnome-panel, drop in-process support for bonobo apple... (diff) | |
download | gentoo-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/ChangeLog | 6 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-4.0.7-r5.ebuild | 300 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-4.5.3-r3.ebuild | 260 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-4.5.3.ebuild | 258 |
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 -} |