[sci-chemistry/gromacs] Version bump

Package-Manager: portage-2.2.0_alpha59/cvs/Linux x86_64

3 files changed, 269 insertions, 11 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 922905ec9125..25bb8a05b0be 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.94 2011/09/10 14:47:53 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.95 2011/09/27 16:58:52 alexxy Exp $
+
+*gromacs-4.5.5 (27 Sep 2011)
+
+  27 Sep 2011; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.5.5.ebuild:
+  Version bump
 
   10 Sep 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.4-r1.ebuild,
   gromacs-4.5.4-r2.ebuild:
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index d932e98a0b8e..b8f82cecfd86 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,23 +1,31 @@
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 EBUILD gromacs-4.5.4-r1.ebuild 8120 RMD160 111791f7aff880a5622e622e41cd7a10efeb3a89 SHA1 84e6a5e0a57a8eabace6a35b7ce271f355721d37 SHA256 a26cacd6a0b51ea14ddfe10758afda7719f194c5562b05fa0f4ca18a445277c6
 EBUILD gromacs-4.5.4-r2.ebuild 7743 RMD160 611705b9c01b331991d60736cd8d53592bc94024 SHA1 f3f2d63cfe0178d2aee329429e65dcfa7c1c8683 SHA256 cd77028e836682a9f01319db5d4a57fc3b167295b1f45b4ce29f8f9355f403c8
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diff --git a/sci-chemistry/gromacs/gromacs-4.5.5.ebuild b/sci-chemistry/gromacs/gromacs-4.5.5.ebuild
new file mode 100644
index 000000000000..e828c36109af
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-4.5.5.ebuild
@@ -0,0 +1,245 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.5.ebuild,v 1.1 2011/09/27 16:58:52 alexxy Exp $
+
+EAPI="4"
+
+TEST_PV="4.0.4"
+MANUAL_PV="4.5.4"
+
+#to find external blas/lapack
+CMAKE_MIN_VERSION="2.8.5-r2"
+
+inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
+
+if [ "${PV%9999}" != "${PV}" ]; then
+	EGIT_REPO_URI="git://git.gromacs.org/gromacs"
+	EGIT_BRANCH="release-4-5-patches"
+	inherit git-2
+else
+	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
+fi
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+SRC_URI="${SRC_URI}
+		http://dev.gentoo.org/~alexxy/gromacs/0001-Make-stack-non-executable-for-GAS-assembly.patch.gz
+		http://dev.gentoo.org/~alexxy/gromacs/0002-Make-stack-non-executable-for-ATT-assembly.patch.gz
+		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )
+		test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
+IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
+mpi +single-precision sse2 test +threads xml zsh-completion"
+REQUIRED_USE="fkernels? ( !threads )"
+
+CDEPEND="
+	X? (
+		x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE
+		)
+	blas? ( virtual/blas )
+	fftw? ( sci-libs/fftw:3.0 )
+	fkernels? ( virtual/fortran )
+	gsl? ( sci-libs/gsl )
+	lapack? ( virtual/lapack )
+	mpi? ( virtual/mpi )
+	xml? ( dev-libs/libxml2:2 )"
+DEPEND="${CDEPEND}
+	dev-util/pkgconfig"
+RDEPEND="${CDEPEND}
+	app-shells/tcsh"
+
+RESTRICT="test"
+
+pkg_setup() {
+	use fkernels && fortran-2_pkg_setup
+}
+
+src_prepare() {
+	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
+	epatch_user
+
+	if use mpi && use threads; then
+		elog "mdrun uses only threads OR mpi, and gromacs favours the"
+		elog "use of mpi over threads, so a mpi-version of mdrun will"
+		elog "be compiled. If you want to run mdrun on shared memory"
+		elog "machines only, you can safely disable mpi"
+	fi
+
+	# Add patches for non-exec stack
+	epatch "${WORKDIR}/0001-Make-stack-non-executable-for-GAS-assembly.patch"
+	epatch "${WORKDIR}/0002-Make-stack-non-executable-for-ATT-assembly.patch"
+
+	GMX_DIRS=""
+	use single-precision && GMX_DIRS+=" float"
+	use double-precision && GMX_DIRS+=" double"
+	#if neither single-precision nor double-precision is enabled
+	#build at least default (single)
+	[ -z "$GMX_DIRS" ] && GMX_DIRS+=" float"
+
+	for x in ${GMX_DIRS}; do
+		mkdir -p "${WORKDIR}/${P}_${x}" || die
+		use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}"
+	done
+}
+
+src_configure() {
+	local mycmakeargs_pre=( )
+	#from gromacs configure
+	if use fftw; then
+		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3")
+	else
+		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack")
+		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
+
+	#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..."
+	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
+
+	#go from slowest to fasterest acceleration
+	local acce="none"
+	use fkernels && acce="fortran"
+	use altivec && acce="altivec"
+	use ia64 && acce="ia64"
+	use sse2 && acce="sse"
+
+	mycmakeargs_pre+=(
+		$(cmake-utils_use X GMX_X11)
+		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
+		$(cmake-utils_use gsl GMX_GSL)
+		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
+		$(cmake-utils_use threads GMX_THREADS)
+		$(cmake-utils_use xml GMX_XML)
+		-DGMX_DEFAULT_SUFFIX=off
+		-DGMX_ACCELERATION="$acce"
+		-DLIB="$(get_libdir)"
+	)
+
+	for x in ${GMX_DIRS}; do
+		einfo "Configuring for ${x} precision"
+		local suffix=""
+		#if we build single and double - double is suffixed
+		use double-precision && use single-precision && \
+			[ "${x}" = "double" ] && suffix="_d"
+		local p
+		[ "${x}" = "double" ] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
+		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
+			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		use mpi || continue
+		einfo "Configuring for ${x} precision with mpi"
+		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON
+			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure
+	done
+}
+
+src_compile() {
+	for x in ${GMX_DIRS}; do
+		einfo "Compiling for ${x} precision"
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_compile
+		use mpi || continue
+		einfo "Compiling for ${x} precision with mpi"
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+			cmake-utils_src_compile mdrun
+	done
+}
+
+src_test() {
+	for x in ${GMX_DIRS}; do
+		local oldpath="${PATH}"
+		export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
+		cd "${WORKDIR}/${P}_${x}"
+		emake -j1 tests || die "${x} Precision test failed"
+		export PATH="${oldpath}"
+	done
+}
+
+src_install() {
+	for x in ${GMX_DIRS}; do
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" \
+			cmake-utils_src_install
+		use mpi || continue
+		#cmake-utils_src_install does not support args
+		#using cmake-utils_src_compile instead
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+			cmake-utils_src_make install-mdrun DESTDIR="${D}"
+	done
+
+	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
+	echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs"
+
+	doenvd "${T}/80gromacs"
+	rm -f "${ED}"/usr/bin/GMXRC*
+
+	newbashcomp "${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.*
+
+	# Fix typos in a couple of files.
+	sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
+		|| die "Failed to fixup demo script."
+
+	cd "${S}"
+	dodoc AUTHORS INSTALL* README*
+	if use doc; then
+		newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
+		dohtml -r "${ED}usr/share/gromacs/html/"
+	fi
+	rm -rf "${ED}usr/share/gromacs/html/"
+}
+
+pkg_postinst() {
+	env-update && source /etc/profile
+	einfo
+	einfo  "Please read and cite:"
+	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
+	einfo  "http://dx.doi.org/10.1021/ct700301q"
+	einfo
+	einfo  $(g_luck)
+	einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
+	einfo
+	elog  "Gromacs can use sci-chemistry/vmd to read additional file formats"
+}