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author | 2008-07-05 01:31:18 -0400 | |
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committer | 2008-07-05 01:31:18 -0400 | |
commit | 5d03f9e07f034bf4eee086573b54b8ea24b59e4e (patch) | |
tree | f9a74b4011f51e585acf45b1f2798367533e7e60 /overlay | |
parent | Added quick NFSroot HOWTO (diff) | |
download | clustering-livecd-5d03f9e07f034bf4eee086573b54b8ea24b59e4e.tar.gz clustering-livecd-5d03f9e07f034bf4eee086573b54b8ea24b59e4e.tar.bz2 clustering-livecd-5d03f9e07f034bf4eee086573b54b8ea24b59e4e.zip |
stateless.sh reWORK (nfs nodes now boot)
Imported sci-chemistry/gromacs from Bug 193532
Diffstat (limited to 'overlay')
-rw-r--r-- | overlay/sci-chemistry/gromacs/Manifest | 2 | ||||
-rw-r--r-- | overlay/sci-chemistry/gromacs/gromacs-3.3.3.ebuild | 213 | ||||
-rw-r--r-- | overlay/sys-cluster/beowulf-head/Manifest | 4 |
3 files changed, 217 insertions, 2 deletions
diff --git a/overlay/sci-chemistry/gromacs/Manifest b/overlay/sci-chemistry/gromacs/Manifest new file mode 100644 index 0000000..abdf9c1 --- /dev/null +++ b/overlay/sci-chemistry/gromacs/Manifest @@ -0,0 +1,2 @@ +DIST gromacs-3.3.3.tar.gz 8013789 RMD160 c7b495423eb07682e88bd7d5c61e0aa9156a17d1 SHA1 318802e39f3ca3e847261a3b96906266e32deba2 SHA256 b95becbe410b71fe9bc19b91dfeb98b940dbb2d66613c9e1de7f6d21fb7534fa +EBUILD gromacs-3.3.3.ebuild 6083 RMD160 c4d9109897552655932a06c22fab2121e400433f SHA1 f933a478376aaca8b6dcf1d38616b8fed924d598 SHA256 52a227049f109e255e6b5819ac48fd90c8c7f2731c5bfd167f18c42f8d6c5691 diff --git a/overlay/sci-chemistry/gromacs/gromacs-3.3.3.ebuild b/overlay/sci-chemistry/gromacs/gromacs-3.3.3.ebuild new file mode 100644 index 0000000..1197744 --- /dev/null +++ b/overlay/sci-chemistry/gromacs/gromacs-3.3.3.ebuild @@ -0,0 +1,213 @@ +# Copyright 1999-2008 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ +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 )" + +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 + + # if we don't set C[XX]FLAGS configure will set: -O3 -finline-functions + # -funroll-all-loops + # append-flags "-O3 -finline-functions -funroll-all-loops" + # use x86 && append-flags "-malign-double" + + # 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 "${ARCH}" in + + x86) + if ( use sse || use sse2 ) ; then + myconf="${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}"/"${P}"-single + myconf="${myconf} --enable-float" + econf ${myconf} || die "Single Precision econf failed" + emake || die "Single Precision emake failed" + + einfo "Building Double Precision Gromacs" + cd "${WORKDIR}"/"${P}"-double + myconf="${myconf} --enable-double --program-suffix=_d" + econf ${myconf} || die "Double Precision econf failed" + emake || die "Double Precision emake failed" + else + use single-precision && cd "${WORKDIR}"/"${P}"-single + use double-precision && cd "${WORKDIR}"/"${P}"-double + cd "${WORKDIR}"/"${P}" + myconf="${myconf} $(use_enable double-precision double) \ + $(use_enable single-precision float) --program-suffix='' " + econf ${myconf} || die "configure failed" + emake || die "emake failed" + fi +} + +src_install() { + if ( use single-precision ); then + einfo "Installing Single Precision" + cd "${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}"/ +} diff --git a/overlay/sys-cluster/beowulf-head/Manifest b/overlay/sys-cluster/beowulf-head/Manifest index 449637a..dc2f003 100644 --- a/overlay/sys-cluster/beowulf-head/Manifest +++ b/overlay/sys-cluster/beowulf-head/Manifest @@ -1,3 +1,3 @@ -AUX cluster.conf 1592 RMD160 58464c00571c6c84e7ed1d63686f0d02f88b1597 SHA1 1d35aaba87de3a40de6a5922777f0760453cbf75 SHA256 8065a6610621e233d966b5c45f154fcba1ca1c699f42c86af7ae9f5b16053d65 -EBUILD beowulf-head-0.1.ebuild 4120 RMD160 3d3fcbe754d847355b51b8a2d069ab360f5ef6a9 SHA1 ffcf9be5d4c3cb7333ec55be0323a0aa2789fcfb SHA256 cc174265ba8eb540bac2b476f3ce27466af325c8752bf12d6ae1113a7c6e01d5 +AUX cluster.conf 2401 RMD160 e5f37c56b03791f6a884bfad6b37ec17f27045cf SHA1 685c32c8deab47c326e7e05f41caa127e11de863 SHA256 e0142db68ecb9182161b9818d1a8cf944cf316ae694c095123c6d4f8a6f0ce10 +EBUILD beowulf-head-0.1.ebuild 4558 RMD160 c7f9a2e729524d7fb600ef1ae709cb8e56be5f86 SHA1 da07cdbaa572424a387f897fc0b0bf48d37dfc09 SHA256 9c45ca4868bd4ec12622020a49b1eedac03ffd289fb7ad71c06b0831a80a53ca MISC ChangeLog 101 RMD160 d735719ccc09237e68e4e984eb5451000b06c382 SHA1 79098d1e8ae451f0430d363da6b717966ade6e78 SHA256 8dd010e2772026c4a6b86839842931b99c85c44a5e9f380864cc275b55587ac2 |