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author | Alexey Shvetsov <alexxy@gentoo.org> | 2009-12-07 20:51:47 +0000 |
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committer | Alexey Shvetsov <alexxy@gentoo.org> | 2009-12-07 20:51:47 +0000 |
commit | e1c991544996aebecd96f637e1497d1380d81950 (patch) | |
tree | 471a7b1a3453c9094277eac92cc7e4f3ee6c3f03 /sci-chemistry | |
parent | old (diff) | |
download | gentoo-2-e1c991544996aebecd96f637e1497d1380d81950.tar.gz gentoo-2-e1c991544996aebecd96f637e1497d1380d81950.tar.bz2 gentoo-2-e1c991544996aebecd96f637e1497d1380d81950.zip |
[sci-chemistry/gromacs] Version Bump
(Portage version: 2.2_rc55/cvs/Linux x86_64)
Diffstat (limited to 'sci-chemistry')
-rw-r--r-- | sci-chemistry/gromacs/ChangeLog | 7 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-4.0.7.ebuild | 235 |
2 files changed, 241 insertions, 1 deletions
diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog index 29c7b2b6b4cf..1037295874ef 100644 --- a/sci-chemistry/gromacs/ChangeLog +++ b/sci-chemistry/gromacs/ChangeLog @@ -1,6 +1,11 @@ # ChangeLog for sci-chemistry/gromacs # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.45 2009/10/31 19:20:05 armin76 Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.46 2009/12/07 20:51:47 alexxy Exp $ + +*gromacs-4.0.7 (07 Dec 2009) + + 07 Dec 2009; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.0.7.ebuild: + Version bump 31 Oct 2009; Raúl Porcel <armin76@gentoo.org> gromacs-4.0.5.ebuild: sparc stable wrt #260995 diff --git a/sci-chemistry/gromacs/gromacs-4.0.7.ebuild b/sci-chemistry/gromacs/gromacs-4.0.7.ebuild new file mode 100644 index 000000000000..f1f63cee3a47 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-4.0.7.ebuild @@ -0,0 +1,235 @@ +# 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-4.0.7.ebuild,v 1.1 2009/12/07 20:51:47 alexxy Exp $ + +EAPI="2" + +LIBTOOLIZE="true" +TEST_PV="4.0.4" + +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 + test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz ) + doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86" +IUSE="X blas dmalloc doc -double-precision +fftw fkernels +gsl lapack mpi +single-precision static test +xml zsh-completion" + +DEPEND="app-shells/tcsh + X? ( x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE ) + dmalloc? ( dev-libs/dmalloc ) + blas? ( virtual/blas ) + fftw? ( sci-libs/fftw:3.0 ) + gsl? ( sci-libs/gsl ) + lapack? ( virtual/lapack ) + mpi? ( virtual/mpi ) + xml? ( dev-libs/libxml2 )" + +RDEPEND="${DEPEND}" + +RESTRICT="test" + +src_prepare() { + + epatch "${FILESDIR}/${P}-docdir.patch" + # 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" + + use fkernels && epatch "${FILESDIR}/${PN}-4.0.4-configure-gfortran.patch" + + 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 [[ $(gcc-version) == "4.1" ]]; then + ewarn "gcc 4.1 is not supported by gromacs" + ewarn "please run test suite" + fi + + #note for gentoo-PREFIX on apple: use --enable-apple-64bit + + #fortran will gone in gromacs 4.1 anyway + #note for gentoo-PREFIX on aix, fortran (xlf) is still much faster + if use fkernels; then + ewarn "Fortran kernels are usually not faster than C kernels and assembly" + ewarn "I hope, you know what are you doing..." + FORTRAN="g77 gfortran ifc" + myconf="${myconf} --enable-fortran" && fortran_pkg_setup + else + myconf="${myconf} --disable-fortran" + fi + + # if we need external blas + if use blas; then + export LIBS="${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) \ + --docdir=/usr/share/doc/"${PF}" \ + $(use_with dmalloc) \ + $(use_with fftw fft fftw3) \ + $(use_with gsl) \ + $(use_with X x) \ + $(use_with xml) \ + $(use_enable static all-static) \ + ${myconf}" + + #if we build single and double - double is suffixed + if ( use double-precision && use single-precision ); then + suffixdouble="_d" + else + suffixdouble="" + fi + + if use double-precision ; then + #from gromacs manual + elog + elog "For most simulations single precision is accurate enough. In some" + elog "cases double precision is required to get reasonable results:" + elog + elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization" + elog " and the calculation and diagonalization of the Hessian " + elog "-calculation of the constraint force between two large groups of atoms" + elog "-energy conservation: this can only be done without temperature coupling and" + elog " without cutoffs" + elog + fi + + if use mpi ; then + elog "You have enabled mpi, only mdrun will make use of mpi, that is why" + elog "we configure/compile gromacs twice (with and without mpi) and only" + elog "install mdrun with mpi support. In addtion you will get libgmx and" + elog "libmd with and without mpi support." + fi + + myconfdouble="${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 ${!p} --disable-mpi + use mpi || continue + cd "${S}-${x}_mpi" + ECONF_SOURCE="${S}" econf ${!p} --enable-mpi + 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 ${x} failed" + done + + sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${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.* + + cd "${S}" + dodoc AUTHORS INSTALL README + use doc && dodoc "${DISTDIR}"/manual-4.0.pdf +} + +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 +} |