[sci-chemistry/gromacs] Fix bug #326331. thanks to Christoph Junghans

(Portage version: 2.2_rc67_p177/cvs/Linux x86_64)

2 files changed, 313 insertions, 1 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index f24ceea63123..a53093593f04 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,11 @@
 # 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 1.51 2010/06/27 19:06:33 alexxy Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.52 2010/07/04 16:48:12 alexxy Exp $
+
+*gromacs-4.0.7-r4 (04 Jul 2010)
+
+  04 Jul 2010; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.0.7-r4.ebuild:
+  Fix bug #326331. thanks to Christoph Junghans
 
 *gromacs-4.0.7-r3 (27 Jun 2010)
 
diff --git a/sci-chemistry/gromacs/gromacs-4.0.7-r4.ebuild b/sci-chemistry/gromacs/gromacs-4.0.7-r4.ebuild
new file mode 100644
index 000000000000..f7fd10fb7df2
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-4.0.7-r4.ebuild
@@ -0,0 +1,307 @@
+# 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-r4.ebuild,v 1.1 2010/07/04 16:48:12 alexxy Exp $
+
+EAPI="3"
+
+LIBTOOLIZE="true"
+TEST_PV="4.0.4"
+
+inherit autotools bash-completion eutils fortran multilib toolchain-funcs
+
+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"
+
+QA_EXECSTACK="usr/lib/libgmx.so.*
+	usr/lib/libgmx_d.so.*"
+
+use static && QA_EXECSTACK="$QA_EXECSTACK usr/bin/*"
+
+src_prepare() {
+
+	( use single-precision || use double-precision ) || \
+		die "Nothing to compile, enable single-precision and/or double-precision"
+
+	if use static; then
+		use X && die "You cannot compile a static version with X support, disable X or static"
+		use xml && die "You cannot compile a static version with xml support
+		(see bug #306479), disable xml or static"
+	fi
+
+	epatch "${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}/${PN}-4.0.9999-docdir.patch"
+	# Fix typos in a couple of files.
+	sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
+		|| die "Failed to fixup demo script."
+
+	# Fix a sandbox violation that occurs when re-emerging with mpi.
+	sed "/libdir=\"\$(libdir)\"/ a\	temp_libdir=\"${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"
+
+	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} --disable-shared $(use_enable static all-static)"
+	else
+		myconf="${myconf} --disable-all-static --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 ${!p} --disable-mpi CC="$(tc-getCC)" F77="${FORTRANC}"
+		use mpi || continue
+		cd "${S}-${x}_mpi"
+		ECONF_SOURCE="${S}" econf ${!p} --enable-mpi CC="$(tc-getCC)" F77="${FORTRANC}"
+	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 _${PN}
+	fi
+	rm -f "${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
+}