[gentoo-commits] gentoo-x86 commit in sci-chemistry/gromacs: metadata.xml ChangeLog gromacs-4.0.7-r3.ebuild gromacs-4.0.7-r1.ebuild gromacs-4.0.7.ebuild

[Alexey Shvetsov (alexxy)]

alexxy      10/06/27 19:06:33

  Modified:             metadata.xml ChangeLog
  Added:                gromacs-4.0.7-r3.ebuild
  Removed:              gromacs-4.0.7-r1.ebuild gromacs-4.0.7.ebuild
  Log:
  [sci-chemistry/gromacs] Update ebuild to eapi3+prefix support. add amberports and latest upstream patches
  (Portage version: 2.2_rc67_p177/cvs/Linux x86_64)

Revision  Changes    Path
1.10                 sci-chemistry/gromacs/metadata.xml

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/metadata.xml?rev=1.10&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/metadata.xml?rev=1.10&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/metadata.xml?r1=1.9&r2=1.10

Index: metadata.xml
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/metadata.xml,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- metadata.xml	21 Jun 2010 15:33:27 -0000	1.9
+++ metadata.xml	27 Jun 2010 19:06:33 -0000	1.10
@@ -3,10 +3,12 @@
 <pkgmetadata>
 <herd>sci-chemistry</herd>
 <use>
-	<flag name='dmalloc'>Enable debugging with the dmalloc library</flag>
-	<flag name='double-precision'>More precise calculations at the expense of speed</flag>
-	<flag name='fkernels'>Enable building of Fortran Kernels for platforms that
-	dont have assembly loops</flag>
-	<flag name='single-precision'>Single precision version of gromacs</flag>
+  <flag name='dmalloc'>Enable use of Debug Malloc</flag>
+  <flag name='double-precision'>More precise calculations at the expense of speed</flag>
+  <flag name='ffamber'>Enable ffamber ports for gromacs</flag>
+  <flag name='fkernels'>Enable building of Fortran Kernels for platforms
+	  that dont have assembly loops</flag>
+  <flag name='single-precision'>Single precision version of gromacs</flag>
+  <flag name='zsh-completion'>Enable zsh completion support</flag>
 </use>
 </pkgmetadata>



1.51                 sci-chemistry/gromacs/ChangeLog

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.51&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.51&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?r1=1.50&r2=1.51

Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v
retrieving revision 1.50
retrieving revision 1.51
diff -u -r1.50 -r1.51
--- ChangeLog	24 Jun 2010 13:08:43 -0000	1.50
+++ ChangeLog	27 Jun 2010 19:06:33 -0000	1.51
@@ -1,6 +1,15 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.50 2010/06/24 13:08:43 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.51 2010/06/27 19:06:33 alexxy Exp $
+
+*gromacs-4.0.7-r3 (27 Jun 2010)
+
+  27 Jun 2010; Alexey Shvetsov <alexxy@g.o> -gromacs-4.0.7.ebuild,
+  -gromacs-4.0.7-r1.ebuild, +gromacs-4.0.7-r3.ebuild,
+  -files/gromacs-4.0.7-docdir.patch,
+  +files/gromacs-4.0.7_upstream2010-06-08.patch:
+  Added patches from upstream stable branch. Added ffamber ports. Also fixed
+  bugs #301854 and #284431. Big thank to Christoph Junghans
 
   24 Jun 2010; Justin Lecher <jlec@g.o> gromacs-3.3.1-r1.ebuild,
   gromacs-3.3.3.ebuild:



1.1                  sci-chemistry/gromacs/gromacs-4.0.7-r3.ebuild

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.7-r3.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.7-r3.ebuild?rev=1.1&content-type=text/plain

Index: gromacs-4.0.7-r3.ebuild
===================================================================
# Copyright 1999-2010 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-r3.ebuild,v 1.1 2010/06/27 19:06:33 alexxy Exp $

EAPI="3"

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 )
		ffamber? ( http://ffamber.cnsm.csulb.edu/ffamber_v4.0-doc.tar.gz )"

LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
IUSE="X blas dmalloc doc -double-precision ffamber +fftw fkernels +gsl lapack
mpi +single-precision static static-libs 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}_upstream2010-06-08.patch.gz"
	sed -e '/AC_INIT/s/4\.0\.7/&-2010-06-08/' -i configure.ac \
		|| die "Failed to change version in configure.ac"
	epatch "${FILESDIR}/${PN}-4.0.9999-docdir.patch"
	epatch "${FILESDIR}/${PN}-4.0.9999-ccache.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=\"${ED}usr/$( 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=\"${ED}usr/$( 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}-4.0.9999-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
		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 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

	# by default its better to have dynamicaly linked binaries
	if use static; then
		#gmx build static libs by default
		myconf="${myconf} $(use_enable static all-static)"
	else
		myconf="${myconf} --enable-shared $(use_enable static-libs static)"
	fi

	myconf="--datadir="${EPREFIX}"/usr/share \
			--bindir="${EPREFIX}"/usr/bin \
			--libdir="${EPREFIX}"/usr/$(get_libdir) \
			--docdir="${EPREFIX}"/usr/share/doc/"${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="_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}-${x}"
		emake DESTDIR="${ED}" install || die "emake install for ${x} failed"
		use mpi || continue
		cd "${S}-${x}_mpi"
		emake DESTDIR="${ED}" install-mdrun || die "emake install-mdrun for ${x} failed"
	done

	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
	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 _${PN}
	fi
	rm -r "${ED}"/usr/bin/completion.*

	cd "${S}"
	dodoc AUTHORS INSTALL README
	use doc && dodoc "${DISTDIR}/manual-4.0.pdf"

	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
}