From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1Q8tkY-0007gA-Pr for garchives@archives.gentoo.org; Sun, 10 Apr 2011 12:28:19 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 83E841C002; Sun, 10 Apr 2011 12:28:11 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id 346AA1C002 for ; Sun, 10 Apr 2011 12:28:11 +0000 (UTC) Received: from pelican.gentoo.org (unknown [66.219.59.40]) (using TLSv1 with cipher ADH-CAMELLIA256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 981A01B407B for ; Sun, 10 Apr 2011 12:28:10 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id 09F3480065 for ; Sun, 10 Apr 2011 12:28:10 +0000 (UTC) From: "Christoph Junghans" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Christoph Junghans" Message-ID: <368c9147cba1ee104621c52d0c25fa298ca93614.kleiner_otti@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/ X-VCS-Repository: proj/sci X-VCS-Files: sci-chemistry/gromacs/ChangeLog sci-chemistry/gromacs/gromacs-4.0.9999.ebuild sci-chemistry/gromacs/metadata.xml X-VCS-Directories: sci-chemistry/gromacs/ X-VCS-Committer: kleiner_otti X-VCS-Committer-Name: Christoph Junghans X-VCS-Revision: 368c9147cba1ee104621c52d0c25fa298ca93614 Date: Sun, 10 Apr 2011 12:28:10 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: X-Archives-Hash: e9bf4a6910b5eaa8581c443549ec1059 commit: 368c9147cba1ee104621c52d0c25fa298ca93614 Author: Christoph Junghans gentoo org> AuthorDate: Sun Apr 10 12:27:32 2011 +0000 Commit: Christoph Junghans gmx de> CommitDate: Sun Apr 10 12:27:32 2011 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3D368c9147 [sci-chemistry/gromacs] remove 4.0.* (EOM) (Portage version: 2.1.9.42/git/Linux i686, signed Manifest commit with ke= y C2000586) --- sci-chemistry/gromacs/ChangeLog | 3 + sci-chemistry/gromacs/gromacs-4.0.9999.ebuild | 297 -------------------= ------ sci-chemistry/gromacs/metadata.xml | 1 - 3 files changed, 3 insertions(+), 298 deletions(-) diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/Chan= geLog index 206d8b4..0aeec1b 100644 --- a/sci-chemistry/gromacs/ChangeLog +++ b/sci-chemistry/gromacs/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ =20 + 10 Apr 2011; Christoph Junghans -gromacs-4.0.9999.= ebuild: + remove 4.0.* (EOM) + 08 Mar 2011; Christoph Junghans gromacs-4.5.9999.e= build, gromacs-9999.ebuild: added fixes from 4.5.3-r4 diff --git a/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild b/sci-chemistr= y/gromacs/gromacs-4.0.9999.ebuild deleted file mode 100644 index 61f8cc2..0000000 --- a/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild +++ /dev/null @@ -1,297 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3D"3" - -LIBTOOLIZE=3D"true" -TEST_PV=3D"4.0.4" - -EGIT_REPO_URI=3D"git://git.gromacs.org/gromacs" -EGIT_BRANCH=3D"release-4-0-patches" - -inherit autotools bash-completion eutils git multilib toolchain-funcs - -DESCRIPTION=3D"The ultimate molecular dynamics simulation package" -HOMEPAGE=3D"http://www.gromacs.org/" -SRC_URI=3D"test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tg= z ) - doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf -> gromacs-manu= al-4.0.pdf ) - ffamber? ( http://ffamber.cnsm.csulb.edu/ffamber_v4.0-doc.tar.gz )" - -LICENSE=3D"GPL-2" -SLOT=3D"0" -KEYWORDS=3D"~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux" -IUSE=3D"X blas dmalloc doc -double-precision ffamber +fftw fkernels +gsl= lapack -mpi +single-precision static static-libs test +xml zsh-completion" - -DEPEND=3D" - X? ( - x11-libs/libX11 - x11-libs/libSM - x11-libs/libICE - ) - dmalloc? ( dev-libs/dmalloc ) - blas? ( virtual/blas ) - fftw? ( sci-libs/fftw:3.0 ) - gsl? ( sci-libs/gsl ) - lapack? ( virtual/lapack ) - mpi? ( virtual/mpi ) - xml? ( dev-libs/libxml2:2 )" -RDEPEND=3D"${DEPEND} - app-shells/tcsh" - -RESTRICT=3D"test" - -QA_EXECSTACK=3D"usr/lib/libgmx.so.* - usr/lib/libgmx_d.so.*" - -use static && QA_EXECSTACK=3D"$QA_EXECSTACK usr/bin/*" - -src_prepare() { - - ( use single-precision || use double-precision ) || \ - die "Nothing to compile, enable single-precision and/or double-precisi= on" - - if use static; then - use X && die "You cannot compile a static version with X support, disa= ble X or static" - use xml && die "You cannot compile a static version with xml support - (see bug #306479), disable xml or static" - fi - - # 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=3D"" - use single-precision && GMX_DIRS+=3D" single" - use double-precision && GMX_DIRS+=3D" 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 its= elf - #there so no gentoo on bluegene! - myconf=3D"${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 [[ $(gcc-version) =3D=3D "4.1" ]]; then - eerror "gcc 4.1 is not supported by gromacs" - eerror "please run test suite" - die - fi - - #note for gentoo-PREFIX on apple: use --enable-apple-64bit - - #fortran will gone in gromacs 4.1 anyway - #note for gentoo-PREFIX on aix, fortran (xlf) is still much faster - if use fkernels; then - ewarn "Fortran kernels are usually not faster than C kernels and assem= bly" - ewarn "I hope, you know what are you doing..." - myconf=3D"${myconf} --enable-fortran" - else - myconf=3D"${myconf} --disable-fortran" - fi - - # if we need external blas - if use blas; then - export LIBS=3D"${LIBS} $(pkg-config --libs blas)" - myconf=3D"${myconf} $(use_with blas external-blas)" - fi - - # if we need external lapack - if use lapack; then - export LIBS=3D"${LIBS} $(pkg-config --libs lapack)" - myconf=3D"${myconf} $(use_with lapack external-lapack)" - fi - - # by default its better to have dynamicaly linked binaries - if use static; then - #gmx build static libs by default - myconf=3D"${myconf} --disable-shared $(use_enable static all-static)" - else - myconf=3D"${myconf} --disable-all-static --enable-shared $(use_enable = static-libs static)" - fi - - myconf=3D"--datadir=3D"${EPREFIX}"/usr/share \ - --bindir=3D"${EPREFIX}"/usr/bin \ - --libdir=3D"${EPREFIX}"/usr/$(get_libdir) \ - --docdir=3D"${EPREFIX}"/usr/share/doc/"${PF}" \ - $(use_with dmalloc) \ - $(use_with fftw fft fftw3) \ - $(use_with gsl) \ - $(use_with X x) \ - $(use_with xml) \ - ${myconf}" - - #if we build single and double - double is suffixed - if ( use double-precision && use single-precision ); then - suffixdouble=3D"_d" - else - suffixdouble=3D"" - fi - - if use double-precision ; then - #from gromacs manual - elog - elog "For most simulations single precision is accurate enough. In som= e" - elog "cases double precision is required to get reasonable results:" - elog - elog "-normal mode analysis, for the conjugate gradient or l-bfgs mini= mization" - elog " and the calculation and diagonalization of the Hessian " - elog "-calculation of the constraint force between two large groups of= atoms" - elog "-energy conservation: this can only be done without temperature = coupling and" - elog " without cutoffs" - elog - fi - - if use mpi ; then - elog "You have enabled mpi, only mdrun will make use of mpi, that is w= hy" - elog "we configure/compile gromacs twice (with and without mpi) and on= ly" - elog "install mdrun with mpi support. In addtion you will get libgmx a= nd" - elog "libmd with and without mpi support." - fi - - myconfdouble=3D"${myconf} --enable-double --program-suffix=3D'${suffixd= ouble}'" - myconfsingle=3D"${myconf} --enable-float --program-suffix=3D''" - for x in ${GMX_DIRS}; do - einfo "Configuring for ${x} precision" - cd "${S}-${x}" - local p=3Dmyconf${x} - ECONF_SOURCE=3D"${S}" econf ${!p} --disable-mpi CC=3D"$(tc-getCC)" F77= =3D"$(tc-getFC)" - use mpi || continue - cd "${S}-${x}_mpi" - ECONF_SOURCE=3D"${S}" econf ${!p} --enable-mpi CC=3D"$(tc-getCC)" F77=3D= "$(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 ${GMX_DIRS}; do - local oldpath=3D"${PATH}" - export PATH=3D"${S}-${x}/src/kernel:${S}-{x}/src/tools:${PATH}" - cd "${S}-${x}" - emake -j1 tests || die "${x} Precision test failed" - export PATH=3D"${oldpath}" - done -} - -src_install() { - for x in ${GMX_DIRS}; do - cd "${S}-${x}" - emake DESTDIR=3D"${D}" install || die "emake install for ${x} failed" - use mpi || continue - cd "${S}-${x}_mpi" - emake DESTDIR=3D"${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 > "${T}/80= gromacs" - doenvd "${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/metadata.xml b/sci-chemistry/gromacs/m= etadata.xml index 7c3c78c..4aa2d99 100644 --- a/sci-chemistry/gromacs/metadata.xml +++ b/sci-chemistry/gromacs/metadata.xml @@ -9,7 +9,6 @@ Enable use of Debug Malloc More precise calculations at the expen= se of speed - Enable ffamber ports for gromacs Enable building of Fortran Kernels for platfor= ms that dont have assembly loops Single precision version of gromacs (d= efault)