stateless.sh reWORK (nfs nodes now boot)

Imported sci-chemistry/gromacs from Bug 193532

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