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Diffstat (limited to 'sci-chemistry/gromacs/gromacs-4.0.9999.ebuild')
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-4.0.9999.ebuild | 234 |
1 files changed, 234 insertions, 0 deletions
diff --git a/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild new file mode 100644 index 000000000..63fd0da23 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild @@ -0,0 +1,234 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI="2" + +LIBTOOLIZE="true" +TEST_PV="4.0.4" + +inherit autotools bash-completion eutils fortran git multilib + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" +SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz ) + doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86" +IUSE="X blas dmalloc doc -double-precision +fftw fkernels gsl lapack mpi +single-precision static test +xml zsh-completion" + +DEPEND="app-shells/tcsh + X? ( x11-libs/libX11 ) + dmalloc? ( dev-libs/dmalloc ) + blas? ( virtual/blas ) + fftw? ( sci-libs/fftw:3.0 ) + gsl? ( sci-libs/gsl ) + lapack? ( virtual/lapack ) + mpi? ( virtual/mpi ) + xml? ( dev-libs/libxml2 )" + +RDEPEND="${DEPEND}" + +RESTRICT="test" + +EGIT_REPO_URI="git://git.gromacs.org/gromacs" +EGIT_BRANCH="release-4-0-patches" + +src_prepare() { + # 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 + + cd "${WORKDIR}" + + use test && mv gmxtest "${P}" + mv "${P}" "${P}-single" + if ( use double-precision ) ; then + einfo "Moving sources for Multiprecision Build" + cp -prP "${P}-single" "${P}-double" + fi +} + +src_configure() { + local myconf ; + local myconf_s ; + local myconf_d ; + local suffix_d ; + + #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 [[ $(gcc-version) == "4.1" ]]; then + ewarn "gcc 4.1 is not supported by gromacs" + ewarn "please run test suite" + fi + + #fortran will gone in gromacs 4.1 anyway + #note for gentoo-PREFIX on aix, fortran (xlf) is still much faster + if use fkernels; then + ewarn "Fortran kernels are usually not faster than C kernels and assembly" + ewarn "I hope, you know what are you doing..." + FORTRAN="g77 gfortran ifc" + myconf="${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_enable mpi) \ + $(use_with X x) \ + $(use_with xml) \ + $(use_enable static all-static) \ + ${myconf}" + + #if we build both double is suffixed + if ( use double-precision && use single-precision ); then + suffix_d="_d" + else + suffix_d="" + fi + + if use double-precision ; then + #from gromacs manual + elog + elog "For most simulations single precision is accurate enough. In some" + elog "cases double precision is required to get reasonable results:" + elog + elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization" + elog " and the calculation and diagonalization of the Hessian " + elog "-calculation of the constraint force between two large groups of atoms" + elog "-energy conservation: this can only be done without temperature coupling and" + elog " without cutoffs" + elog + einfo "Configuring Double Precison Gromacs" + cd "${WORKDIR}"/"${P}"-double + myconf_d="${myconf} --enable-double --program-suffix='${suffix_d}'" + econf ${myconf_d} || die "Double Precision econf failed" + fi + + if use single-precision ; then + einfo "Configuring Single Precison Gromacs" + cd "${WORKDIR}"/"${P}"-single + myconf_s="${myconf} --enable-float --program-suffix=''" + econf ${myconf_s} || die "configure failed" + fi +} + +src_compile() { + if use double-precision ; then + einfo "Building Double Precison Gromacs" + cd "${WORKDIR}"/"${P}"-double + emake || die "Double Precision emake failed" + fi + + if use single-precision ; then + einfo "Building Single Precison Gromacs" + cd "${WORKDIR}"/"${P}"-single + emake || die "Single Precision emake failed" + fi +} + +src_test() { + if use single-precision ; then + export PATH="${WORKDIR}/${P}-single/src/kernel:${WORKDIR}/${P}-single/src/tools:$PATH" + cd "${WORKDIR}"/"${P}"-single + emake -j1 tests || die "Single Precision test failed" + fi + + if use double-precision ; then + export PATH="${WORKDIR}/${P}-double/src/kernel:${WORKDIR}/${P}-double/src/tools:$PATH" + cd "${WORKDIR}"/"${P}"-double + emake -j1 tests || die "Double Precision test failed" + fi +} + +src_install() { + if use single-precision ; then + einfo "Installing Single Precision" + cd "${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="${D}" install || die "Installing Double Precision failed" + fi + + sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${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.* + + 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 +} |