From 270c2d9cc78bbdd3435cab762bec0e9245d3cf53 Mon Sep 17 00:00:00 2001 From: Alexey Shvetsov Date: Mon, 5 Jul 2010 10:41:17 +0000 Subject: [PATCH] [sci-chemistry/gromacs] Gromacs 3.x moved to sci overlay since its unmaintained and no longer supported Package-Manager: portage-2.2_rc67_p182/cvs/Linux x86_64 --- sci-chemistry/gromacs/ChangeLog | 7 +- sci-chemistry/gromacs/Manifest | 12 +- sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild | 217 ----------------- sci-chemistry/gromacs/gromacs-3.3.3.ebuild | 220 ------------------ 4 files changed, 10 insertions(+), 446 deletions(-) delete mode 100644 sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild delete mode 100644 sci-chemistry/gromacs/gromacs-3.3.3.ebuild diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog index a53093593f04..17310fffd5b7 100644 --- a/sci-chemistry/gromacs/ChangeLog +++ b/sci-chemistry/gromacs/ChangeLog @@ -1,12 +1,17 @@ # ChangeLog for sci-chemistry/gromacs # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.52 2010/07/04 16:48:12 alexxy Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.53 2010/07/05 10:41:17 alexxy Exp $ *gromacs-4.0.7-r4 (04 Jul 2010) 04 Jul 2010; Alexey Shvetsov +gromacs-4.0.7-r4.ebuild: Fix bug #326331. thanks to Christoph Junghans + 05 Jul 2010; Alexey Shvetsov -gromacs-3.3.1-r1.ebuild, + -gromacs-3.3.3.ebuild: + Gromacs 3.x moved to sci overlay since its unmaintained and no longer + supported + *gromacs-4.0.7-r3 (27 Jun 2010) 27 Jun 2010; Alexey Shvetsov -gromacs-4.0.7.ebuild, diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index e9bd2073a8ba..4f149f9b3c1d 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -9,24 +9,20 @@ AUX gromacs-4.0.9999-configure-gfortran.patch 760 RMD160 1700579b0c2dfb8cbb743d7 AUX gromacs-4.0.9999-docdir.patch 1352 RMD160 336ab23b4b65430caf3205650a8787e8e33d2137 SHA1 77e0cc966c4d755f603b2d0ab9a075c0ee6b7361 SHA256 8ead457b06f7f943455a95494be4648e539934699d29e955d2e05ac02f1ca4ef DIST ffamber_v4.0-doc.tar.gz 7915520 RMD160 aeadb18bd88bcd9e6fc45af22af15c51e32c66a3 SHA1 8d4969fa7eec660b41f769874be9698980b49ed0 SHA256 0b3395570dfe9bf808a297fcb120e1f525f38a91791fbafe6e444d542d7754aa DIST gmxtest-4.0.4.tgz 14845017 RMD160 c7c583415438bdef4c9996da9064254e9460cf16 SHA1 998179aa2bfbc4f80514f10ed774762f85c854c3 SHA256 6a7f787f4bb7cbecb688115ff0854a5ffd2ef33487d7bce4b031e63848b6f361 -DIST gromacs-3.3.1.tar.gz 7992897 RMD160 48e6f9098ac4f5b834f4beb050846c60aea18fff SHA1 8c67ee772cadf93067b3c8bcec65d7b3520df1dc SHA256 3df40151ff5364fab1c4d8692ec247d8245437e954882a803178cbe6b812d81f -DIST gromacs-3.3.3.tar.gz 8013789 RMD160 c7b495423eb07682e88bd7d5c61e0aa9156a17d1 SHA1 318802e39f3ca3e847261a3b96906266e32deba2 SHA256 b95becbe410b71fe9bc19b91dfeb98b940dbb2d66613c9e1de7f6d21fb7534fa DIST gromacs-4.0.4.tar.gz 8443779 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db0a32e29093..000000000000 --- a/sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild +++ /dev/null @@ -1,217 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild,v 1.14 2010/06/24 13:08:43 jlec Exp $ - -inherit eutils fortran multilib - -IUSE="3dnow X altivec double-precision mpi sse sse2" - -# mopac7 qm/mm is broken until we can get files from -# http://md.chem.rug.nl/~groenhof/qmmm.html -# or somewhere else... - -DESCRIPTION="The ultimate molecular dynamics simulation package" -SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz" -HOMEPAGE="http://www.gromacs.org/" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="alpha amd64 ppc64 sparc x86" - -DEPEND=">=sci-libs/fftw-3.0.1 - mpi? ( virtual/mpi ) - >=sys-devel/binutils-2.12 - app-shells/tcsh - X? ( x11-libs/libX11 - x11-libs/libXt - x11-libs/libXp - x11-libs/libXext - x11-proto/xproto - x11-libs/openmotif )" - -RDEPEND="${DEPEND} - !sci-mathematics/num-utils" - -src_unpack() { - - unpack ${A} - cd "${S}" -# Fix typos in a couple of files. - sed -e "s:_nb_kerne010_x86_64_sse2:_nb_kernel010_x86_64_sse2:" \ - -i src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/nb_kernel010_x86_64_sse2.intel_syntax.s \ - -i src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/nb_kernel010_x86_64_sse2.s \ - || die "Failed to fix sse2 typo." - - 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" - -# Rename disco manpage to fix bug #210083 - sed "s:disco.1:g_disco.1:" \ - -i "${S}"/man/man1/Makefile.am \ - || die "sed failed to rename disco" - - mv "${S}"/man/man1/disco.1 "${S}"/man/man1/g_disco.1 - - cd "${WORKDIR}" && mv ${P} ${P}-single ; - - use double-precision && cp -prP ${P}-single ${P}-double ; - - if use mpi ; then - cp -prP ${P}-single ${P}-single-mpi - use double-precision && cp -prP ${P}-double ${P}-double-mpi - fi -} - -src_compile() { - # static should work but something's broken. - # gcc spec file may be screwed up. - # Static linking should try -lgcc instead of -lgcc_s. - # For more info: - # http://lists.debian.org/debian-gcc/2002/debian-gcc-200201/msg00150.html - - # We will compile single precision by default, and suffix double-precision with _d. - # Sparc is the only arch I can test on that needs to use fortran. - local myconf ; - - case "${ARCH}" in - - x86) - myconf="$myconf $(use_enable sse ia32-sse)" - myconf="$myconf $(use_enable sse2 ia32-sse)" - myconf="$myconf $(use_enable 3dnow ia32-3dnow)" - - # If you don't enable at least one of the above, you must use g77, not gfortran. - if ! use sse && ! use sse2 && ! use 3dnow ; then - - if ! has_version "=sys-devel/gcc-3*" ; then - die "If you must run gromacs without sse (not recommended) gfortran will not work." - else myconf="$myconf --enable-fortran" && fortran_pkg_setup - - fi - fi - ;; - - amd64) - myconf="$myconf --enable-x86-64-sse" - ;; - - ppc) - if use altivec ; then - myconf="$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." - fi - myconf="$myconf --enable-fortran" && fortran_pkg_setup - fi - ;; - - ppc64) - if use altivec ; then - myconf="$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." - fi - 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 - ;; - - ia64) - myconf="$myconf --enable-ia64-asm" - ;; - - alpha) - myconf="$myconf --enable-axp-asm --disable-fortran" - ;; - - esac - - myconf="--enable-shared \ - --datadir=/usr/share \ - --bindir=/usr/bin \ - --libdir=/usr/$(get_libdir) \ - --with-fft=fftw3 \ - $(use_with X x) \ - ${myconf}" - - # $(use_with mopac7 qmmm-mopac) \ - - cd "${WORKDIR}"/${P}-single - econf ${myconf} --enable-float || die "configure single-precision failed" - - emake || die "emake single failed" - - if use mpi ; then - cd "${WORKDIR}"/${P}-single-mpi - econf ${myconf} --enable-float --enable-mpi --program-suffix=_mpi \ - || die "failed to configure single-mpi mdrun" - emake mdrun || die "failed to make single-precision mpi mdrun" ; - fi - - if use double-precision ; then - cd "${WORKDIR}"/${P}-double - - econf ${myconf} --enable-double --program-suffix=_d \ - || die "configure double-precision failed" - - emake || die "emake double failed" - - if use mpi ; then - cd "${WORKDIR}"/${P}-double-mpi - econf ${myconf} --enable-double --enable-mpi --program-suffix=_mpi_d \ - || die "failed to configure double-mpi mdrun" ; - - emake mdrun \ - || die "failed to make double-precision mpi mdrun" ; - fi - fi - -} - -src_install () { - cd "${WORKDIR}"/${P}-single ; - emake DESTDIR="${D}" install || die "installing single failed" - - if use mpi ; then - cd "${WORKDIR}"/${P}-single-mpi - emake DESTDIR="${D}" install-mdrun \ - || die "installing mdrun_mpi failed" - fi - - if use double-precision ; then - cd "${WORKDIR}"/${P}-double && emake DESTDIR="${D}" install \ - || die "installing double failed" - - if use mpi ; then - cd "${WORKDIR}"/${P}-double-mpi - emake DESTDIR="${D}" install-mdrun \ - || die "installing mdrun_mpi_d failed" - fi - - fi - - dodoc AUTHORS INSTALL README - - # Move html and leave examples and templates under /usr/share/gromacs. - mv "${D}"/usr/share/"${PN}"/html "${D}"/usr/share/doc/"${PF}"/ -} diff --git a/sci-chemistry/gromacs/gromacs-3.3.3.ebuild b/sci-chemistry/gromacs/gromacs-3.3.3.ebuild deleted file mode 100644 index fcd77b0ed8f2..000000000000 --- a/sci-chemistry/gromacs/gromacs-3.3.3.ebuild +++ /dev/null @@ -1,220 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-3.3.3.ebuild,v 1.3 2010/06/24 13:08:43 jlec Exp $ -EAPI="1" -LIBTOOLIZE="true" -inherit autotools eutils flag-o-matic 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" - -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" - -# 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 ) - blas? ( virtual/blas ) - gsl? ( sci-libs/gsl ) - lapack? ( virtual/lapack ) - mpi? ( virtual/mpi ) - xml? ( dev-libs/libxml2 )" - -RDEPEND="${DEPEND} - !sci-mathematics/num-utils" - -FORTRAN="g77 gfortran ifc" - -src_unpack() { - - unpack ${A} - cd "${S}" - # 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" - - # Rename disco manpage to fix bug #210083. - sed "s:disco.1:g_disco.1:" \ - -i "${S}"/man/man1/Makefile.am \ - || die "sed failed to rename disco" - - mv "${S}"/man/man1/disco.1 "${S}"/man/man1/g_disco.1 - - eautoreconf - - cd "${WORKDIR}" - mv "${P}" "${P}-single" - if ( use double-precision ) ; then - einfo "Moving sources for Multiprecision Build" - cp -prP "${P}-single" "${P}-double" - fi -} - -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 ; - - 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="${myconf} --enable-fortran" && fortran_pkg_setup - fi - ;; - esac - - # if we need external blas - if use blas; then - export LIBS="${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) \ - --with-fft=fftw3 \ - $(use_with gsl) \ - $(use_enable mpi) \ - $(use_with X x) \ - $(use_with xml) \ - $(use_enable static all-static) \ - ${myconf}" - - if ( use double-precision && use single-precision ); then - einfo "Building Single Precison Gromacs" - cd "${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 ${myconf_d} || die "Double Precision econf failed" - emake || die "Double Precision emake failed" - - elif use double-precision ; then - einfo "Building Double Precison Gromacs" - cd "${WORKDIR}"/"${P}"-double - myconf_d="${myconf} --enable-double --disable-float --program-suffix=''" - econf ${myconf_d} || die "Double Precision econf failed" - emake || die "Double Precision emake failed" - - elif use single-precision ; then - einfo "Building Single Precison Gromacs" - cd "${WORKDIR}"/"${P}"-single - myconf_s="${myconf} --enable-float --disable-double --program-suffix=''" - econf ${myconf_s} || die "configure failed" - emake || die "Single Precision emake failed" - fi -} - -src_install() { - if use single-precision ; then - einfo "Installing Single Precision" - cd "${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="${D}" install || die "Installing Double Precision failed" - fi - - dodoc AUTHORS INSTALL README - # Move html and leave examples and templates under /usr/share/gromacs. - mv "${D}"/usr/share/"${PN}"/html "${D}"/usr/share/doc/"${PF}"/ -} -- 2.26.2