[gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/

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From: "Christoph Junghans" <kleiner_otti@gmx.de>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
Date: Sat, 19 Feb 2011 14:50:02 +0000 (UTC)	[thread overview]
Message-ID: <a1ede7522ea24fe66830f0ab16e10452275fbe1c.kleiner_otti@gentoo> (raw)

commit:     a1ede7522ea24fe66830f0ab16e10452275fbe1c
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 19 15:00:14 2011 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sat Feb 19 15:00:14 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a1ede752

[sci-chemistry/gromacs] 4.5.3-r3 InCVS

(Portage version: 2.1.9.25/git/Linux i686, signed Manifest commit with key C2000586)

---
 sci-chemistry/gromacs/ChangeLog               |    3 +
 sci-chemistry/gromacs/gromacs-4.5.3-r3.ebuild |  259 -------------------------
 2 files changed, 3 insertions(+), 259 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index ddbf77b..4642b67 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  19 Feb 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.5.3-r3.ebuild:
+  InCVS
+
 *gromacs-4.5.3-r3 (17 Feb 2011)
 
   17 Feb 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.5.3-r2.ebuild,

diff --git a/sci-chemistry/gromacs/gromacs-4.5.3-r3.ebuild b/sci-chemistry/gromacs/gromacs-4.5.3-r3.ebuild
deleted file mode 100644
index b45ac1b..0000000
--- a/sci-chemistry/gromacs/gromacs-4.5.3-r3.ebuild
+++ /dev/null
@@ -1,259 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="3"
-
-LIBTOOLIZE="true"
-TEST_PV="4.0.4"
-MANUAL_PV="4.5.3"
-
-inherit autotools-utils bash-completion flag-o-matic multilib toolchain-funcs
-
-SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
-		doc? (
-		http://www.gromacs.org/@api/deki/files/133/=manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
-
-if [ "${PV%9999}" != "${PV}" ]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs"
-	EGIT_BRANCH="release-4-5-patches"
-	inherit git
-else
-	PATCHES=( ${WORKDIR}/${P}_upstream20110217.patch.bz2 )
-	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
-	mirror://gentoo/${P}_upstream20110217.patch.bz2"
-fi
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X altivec blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
-mpi +single-precision sse sse2 static-libs test +threads +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="${DEPEND}"
-
-RESTRICT="test"
-
-#gromacs has gnu exec stacks for speedup
-QA_EXECSTACK="usr/lib/libgmx.so.*
-	usr/lib/libgmx_d.so.*"
-
-src_prepare() {
-	if use mpi && use threads; then
-		elog "mdrun uses only threads OR mpi, and gromacs favours the"
-		elog "use of mpi over threads, so a mpi-version of mdrun will"
-		elog "be compiled. If you want to run mdrun on shared memory"
-		elog "machines only, you can safely disable mpi"
-	fi
-
-	autotools-utils_src_prepare || die
-
-	sed -e '/AC_INIT/s/4\.5\.3-dev/4.5.3-2011-02-17/' -i configure.ac \
-		|| die "Failed to change version in configure.ac"
-
-	eautoreconf || die
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-	#if neither single-precision nor double-precision is enabled
-	#build at least default (single)
-	[ -z "$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() {
-	#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 5.0 anyway
-	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
-	if use fkernels; then
-		use threads && eerror "You cannot compile fortran kernel with threads"
-		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
-
-	# if we need external blas or lapack
-	use blas && export LIBS+=" -lblas"
-	use lapack && export LIBS+=" -llapack"
-	local sseflag="x86-64-sse"
-	use x86 && sseflag="ia32-sse"
-
-	#a bug in gromacs autotools
-	use sse && append-flags -msse
-	use sse2 && append-flags -msse2
-
-	for x in ${GMX_DIRS}; do
-		local suffix="" sse="sse"
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[ "${x}" = "double" ] && suffix="_d"
-		[ "${x}" = "double" ] && sse="sse2"
-		myeconfargs=(
-			--bindir="${EPREFIX}"/usr/bin
-			--docdir="${EPREFIX}"/usr/share/doc/"${PF}"
-			--enable-"${x}"
-			$(use_with dmalloc)
-			$(use_with fftw fft fftw3)
-			$(use_with gsl)
-			$(use_with X x)
-			$(use_with xml)
-			$(use_enable threads)
-			$(use_enable altivec ppc-altivec)
-			$(use_enable ia64 ia64-asm)
-			$(use_with lapack external-lapack)
-			$(use_with blas external-blas)
-			$(use_enable fkernels fortran)
-			--disable-bluegene
-			--disable-la-files
-			--disable-power6
-			--disable-ia32-sse
-			--disable-x86-64-sse
-			$(use_enable $sse $sseflag)
-		)
-		#disable ia32-sse and x86-64-sse and enable what we really need in last line
-
-		einfo "Configuring for ${x} precision"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			autotools-utils_src_configure --disable-mpi	--program-suffix="${suffix}" \
-			CC="$(tc-getCC)" F77="$(tc-getFC)"
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			autotools-utils_src_configure --enable-mpi --program-suffix="_mpi${suffix}" \
-			CC="$(tc-getCC)" F77="$(tc-getFC)"
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			autotools-utils_src_compile
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			autotools-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 ${GMX_DIRS}; do
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			autotools-utils_src_install
-		use mpi || continue
-		#autotools-utils_src_install does not support args
-		#using autotools-utils_src_compile instead
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			autotools-utils_src_compile install-mdrun DESTDIR="${D}"
-
-		#stolen from autotools-utils_src_install see comment above
-		local args
-		has static-libs ${IUSE//+} && ! use	static-libs || args='none'
-		remove_libtool_files ${args}
-	done
-
-	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${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*
-
-	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.*
-
-	# 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
-	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 $(g_luck)
-	elog "For more Gromacs cool quotes (gcq) add luck to your .bashrc"
-	elog
-	elog "Gromacs can use sci-chemistry/vmd to read additional file formats"
-	elog
-}

next             reply	other threads:[~2011-02-19 14:50 UTC|newest]

Thread overview: 102+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2011-02-19 14:50 Christoph Junghans [this message]
  -- strict thread matches above, loose matches on Subject: below --
2016-07-11 19:40 [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/ Alexey Shvetsov
2016-07-11 18:41 Alexey Shvetsov
2016-07-11 18:41 Alexey Shvetsov
2016-03-14  2:17 Christoph Junghans
2016-02-11  9:11 Justin Lecher
2015-12-15  0:24 Christoph Junghans
2015-08-20 23:28 Christoph Junghans
2015-06-21 13:01 Christoph Junghans
2015-06-16 17:53 Alexey Shvetsov
2015-03-08  0:06 Christoph Junghans
2015-01-31 20:19 Christoph Junghans
2014-12-21 23:12 Christoph Junghans
2014-11-25 16:05 Christoph Junghans
2014-10-09  9:32 Alexey Shvetsov
2014-09-07 18:49 Christoph Junghans
2014-09-06 18:45 Christoph Junghans
2014-09-04 15:06 Christoph Junghans
2014-09-03 22:53 Christoph Junghans
2014-09-03 22:53 Christoph Junghans
2014-07-07 19:57 Christoph Junghans
2014-06-26  5:36 Christoph Junghans
2014-04-14 23:59 Christoph Junghans
2014-04-08  8:14 Alexey Shvetsov
2014-03-05  0:44 Christoph Junghans
2014-02-20 13:26 Alexey Shvetsov
2014-02-16 23:04 Christoph Junghans
2014-02-05 12:09 Alexey Shvetsov
2014-02-05 12:02 Alexey Shvetsov
2014-01-28  7:55 Justin Lecher
2014-01-06 19:27 Justin Lecher
2014-01-06 18:48 Justin Lecher
2013-12-07 16:22 Justin Lecher
2013-12-06  9:34 Alexey Shvetsov
2013-12-05  6:00 Alexey Shvetsov
2013-12-05  3:41 Alexey Shvetsov
2013-12-05  3:40 Alexey Shvetsov
2013-12-03  4:47 Alexey Shvetsov
2013-12-03  4:16 Alexey Shvetsov
2013-12-03  4:06 Alexey Shvetsov
2013-12-03  4:00 Alexey Shvetsov
2013-06-02 17:40 Christoph Junghans
2013-05-05 17:34 Christoph Junghans
2013-03-15  9:34 Alexey Shvetsov
2013-03-15  9:30 Alexey Shvetsov
2013-03-10  1:04 Christoph Junghans
2013-03-09  1:48 Christoph Junghans
2013-03-06  2:04 Christoph Junghans
2013-02-12  4:21 Christoph Junghans
2013-01-30  3:29 Christoph Junghans
2013-01-30  3:29 Christoph Junghans
2013-01-28  4:48 Christoph Junghans
2013-01-21 20:30 Christoph Junghans
2013-01-21 19:19 Christoph Junghans
2013-01-21 14:33 Alexey Shvetsov
2013-01-21 14:00 Alexey Shvetsov
2013-01-18  2:58 Christoph Junghans
2013-01-18  1:56 Christoph Junghans
2012-12-30 23:31 Christoph Junghans
2012-12-29 22:59 Christoph Junghans
2012-12-27 21:44 Christoph Junghans
2012-12-26 22:36 Christoph Junghans
2012-12-26 18:58 Christoph Junghans
2012-12-26  3:59 Christoph Junghans
2012-12-26  1:03 Christoph Junghans
2012-12-22 19:46 Christoph Junghans
2012-12-20  5:51 Christoph Junghans
2012-12-08 22:15 Christoph Junghans
2012-11-30 21:18 Christoph Junghans
2012-11-27  5:43 Christoph Junghans
2012-11-19  0:48 Christoph Junghans
2012-10-04 14:39 Christoph Junghans
2012-10-03 14:54 Christoph Junghans
2012-08-09  5:15 Christoph Junghans
2012-07-25  1:25 Christoph Junghans
2012-06-19 14:10 Alexey Shvetsov
2012-06-11  2:15 Christoph Junghans
2012-04-28  1:21 Christoph Junghans
2012-04-19 19:43 Alexey Shvetsov
2012-03-04  1:23 Christoph Junghans
2012-03-04  1:23 Christoph Junghans
2012-03-04  1:23 Christoph Junghans
2012-02-12  1:34 Christoph Junghans
2012-02-05 21:31 Christoph Junghans
2012-02-05  0:30 Christoph Junghans
2011-09-28  7:32 Christoph Junghans
2011-09-10 14:52 Christoph Junghans
2011-07-18 18:30 Christoph Junghans
2011-06-25 17:22 Justin Lecher
2011-06-25 12:58 Christoph Junghans
2011-06-21 20:26 Christoph Junghans
2011-06-21 11:54 Justin Lecher
2011-06-19 20:28 Christoph Junghans
2011-05-01 15:13 Christoph Junghans
2011-04-10 12:28 Christoph Junghans
2011-03-17 23:18 Alexey Shvetsov
2011-03-08 20:59 Christoph Junghans
2011-03-07 12:01 Justin Lecher
2011-03-01 15:31 Alexey Shvetsov
2011-02-17 22:29 Christoph Junghans
2011-02-14 21:00 Christoph Junghans
2011-02-13 17:27 Christoph Junghans

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