# 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@gentoo.org> -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@gentoo.org> gromacs-3.3.1-r1.ebuild,
gromacs-3.3.3.ebuild:
AUX gromacs-4.0.4-configure-gfortran.patch 731 RMD160 1ccea4fafd6837461114fc36bc31db4f9390fc08 SHA1 0ec79e9ab691cbae5f116adaa3245ef0b123a598 SHA256 5b902eac127bc84e188224fbfe0182ab3fa3b03c200325ada9cd628bb913b479
AUX gromacs-4.0.4-sparc-cyclecounter.patch 492 RMD160 0edd643a6dc11820e9785561f03047795044311f SHA1 66c0339c308b3d661def0e184311be510e804c3b SHA256 01565b45b73b32d8d6f83bf1fdf750de4215b24935d992c81191a52d01eb6bed
-AUX gromacs-4.0.7-docdir.patch 2907 RMD160 271f4ccc401cfa03ca3b2b911d0c15ec1fc55d3a SHA1 f6361e2b07cae020a6548c50dacb24611d701d43 SHA256 258a76992ed840ad242a1bf1799a2d83dbf860af85e74b154446acf252a2714a
+AUX gromacs-4.0.7_upstream2010-06-08.patch.gz 11876 RMD160 d65c9cf0386319953113ac1a5dc548768a745345 SHA1 823a72c4126d789ae38921bd46743414d4f391c1 SHA256 91d3eee79a0ec20df506e59bab789fe15428b4323548af5f97ccbae506036879
AUX gromacs-4.0.9999-ccache.patch 678 RMD160 043d0e207e04a275fe00a3bd2b28f8dc0dfd4b7f SHA1 08bc5ac8bc0b28f68e1ede994d49616dd920af5d SHA256 ca477d54351c418f1d39dda29373a1426c9403ec0d2f21c28fc7568227d47632
AUX gromacs-4.0.9999-configure-gfortran.patch 760 RMD160 1700579b0c2dfb8cbb743d795aa9f0f9f467c06b SHA1 e6924d3598b20195fcb6809e64f333def5b0f919 SHA256 1a59dfde8a3db8db729bd19691a5945e02be2725fa66ec0b125ab3b931518761
AUX gromacs-4.0.9999-docdir.patch 1352 RMD160 336ab23b4b65430caf3205650a8787e8e33d2137 SHA1 77e0cc966c4d755f603b2d0ab9a075c0ee6b7361 SHA256 8ead457b06f7f943455a95494be4648e539934699d29e955d2e05ac02f1ca4ef
+DIST ffamber_v4.0-doc.tar.gz 7915520 RMD160 aeadb18bd88bcd9e6fc45af22af15c51e32c66a3 SHA1 8d4969fa7eec660b41f769874be9698980b49ed0 SHA256 0b3395570dfe9bf808a297fcb120e1f525f38a91791fbafe6e444d542d7754aa
DIST gmxtest-4.0.4.tgz 14845017 RMD160 c7c583415438bdef4c9996da9064254e9460cf16 SHA1 998179aa2bfbc4f80514f10ed774762f85c854c3 SHA256 6a7f787f4bb7cbecb688115ff0854a5ffd2ef33487d7bce4b031e63848b6f361
DIST gromacs-3.3.1.tar.gz 7992897 RMD160 48e6f9098ac4f5b834f4beb050846c60aea18fff SHA1 8c67ee772cadf93067b3c8bcec65d7b3520df1dc SHA256 3df40151ff5364fab1c4d8692ec247d8245437e954882a803178cbe6b812d81f
DIST gromacs-3.3.3.tar.gz 8013789 RMD160 c7b495423eb07682e88bd7d5c61e0aa9156a17d1 SHA1 318802e39f3ca3e847261a3b96906266e32deba2 SHA256 b95becbe410b71fe9bc19b91dfeb98b940dbb2d66613c9e1de7f6d21fb7534fa
EBUILD gromacs-3.3.3.ebuild 6363 RMD160 02cc3ab83e9897408f971355a453b731006edce3 SHA1 eb3790b6d7bcf32ec81bd1e64987b93536c0e573 SHA256 42f87016396ca4fb7b71cdcba9e0d110e3311e2d4acabca2bbdb3c073b4c428f
EBUILD gromacs-4.0.4.ebuild 6918 RMD160 d31ffadfe240147555b227c36456d81c35f5f5dc SHA1 52b59952c4fb4861ed6bbe2f48ba4c3443b07cd4 SHA256 078f3942a1b5bf671326be97dacb22f37783c082c154bf193e28e18c4e314d3e
EBUILD gromacs-4.0.5.ebuild 6762 RMD160 c9945b966f14d1aa3fab96928a8c1269f2d0b4fb SHA1 535119ceb458903fd294f21959df4338eafd475d SHA256 dc76914d616ac4f750e9073601f1fc9cd30ab6f7b15a01152b95ef625a755c3b
-EBUILD gromacs-4.0.7-r1.ebuild 6994 RMD160 907cc8109b7d5896efc679069bc43682a449a720 SHA1 fcd74a2fca7720b6c24f48f3c072a687f53e9e44 SHA256 b5f64f313bf8e60d2a5a8191b0c82d3163fee3acb8b28be83a2500daa9d04204
-EBUILD gromacs-4.0.7.ebuild 6928 RMD160 815938e16b9ac35362f12a429f37d6f1d8e67f04 SHA1 d039d72b88bee2d9cc9afdf428bf230493df8c20 SHA256 f139ed8f9bc5c148c23af2fb9dd6f9b872093c4f4bda5e0ddfc84c6e53a57f59
-MISC ChangeLog 9921 RMD160 ca192c4727fa3e0a22900151e58fce4bb0acebb7 SHA1 1e6503b247cb03e1209aa076d176abf3e0fcde29 SHA256 f6d768d223428e983c93c8bc8c959542b8f3f5f3ce45c77d5420720be18465f7
-MISC metadata.xml 522 RMD160 458230ff3b81403772be684ebced439683293270 SHA1 10646959a2319c7c4bc6323f91781a5a90ec6910 SHA256 9c56043a88f3e9846ce9fec497bbb79f12261baf37a3f1690716ad07649ea36c
+EBUILD gromacs-4.0.7-r3.ebuild 9489 RMD160 7f125dc953d744dab91e8b8c34b5d1406fea91b1 SHA1 b14ce5def015cda74fbf7dadd9642a9599f7caeb SHA256 38f44e6c07fdf539a4253d63ec2ccdd604f679016545f6b7ade5d7e7a80ee068
+MISC ChangeLog 10308 RMD160 c3a45df5addfd418cb67a8ad1e4af733a1addcf0 SHA1 f001fb5d7d315a62bfeb5d5fbbbf01e57c162f9b SHA256 d7d5ea4106c29cadfb0980034e3e03e5dc2578de98dad95dd90b3b8b9184e767
+MISC metadata.xml 643 RMD160 e9ffc42d792f15f3d4438a0de225277ec4814041 SHA1 c83fd4a32d896b7a2586667bc684d46f9daf8693 SHA256 177885ec674e8630a9c9451a0e0a35fc83615b39b387a67002e27f1b0d6b19b2
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-3hMAnjlOqDRzQS1iySD0PNXQr6g7F1zV
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+++ /dev/null
-diff -Naur gromacs-4.0.5.orig/share/html/Makefile.am gromacs-4.0.5/share/html/Makefile.am
---- gromacs-4.0.5.orig/share/html/Makefile.am 2006-03-06 10:52:20.000000000 +0100
-+++ gromacs-4.0.5/share/html/Makefile.am 2009-11-29 22:27:24.000000000 +0100
-@@ -4,7 +4,7 @@
- #
- SUBDIRS = . images online
-
--htmldir = ${pkgdatadir}/html
-+htmldir = @htmldir@/html
-
- html_DATA = online.html gmxfaq.html
-
-diff -Naur gromacs-4.0.5.orig/share/html/Makefile.in gromacs-4.0.5/share/html/Makefile.in
---- gromacs-4.0.5.orig/share/html/Makefile.in 2009-05-09 11:12:24.000000000 +0200
-+++ gromacs-4.0.5/share/html/Makefile.in 2009-11-29 22:28:16.000000000 +0100
-@@ -172,7 +172,7 @@
- host_cpu = @host_cpu@
- host_os = @host_os@
- host_vendor = @host_vendor@
--htmldir = ${pkgdatadir}/html
-+htmldir = @htmldir@/html
- includedir = @includedir@
- infodir = @infodir@
- install_sh = @install_sh@
-diff -Naur gromacs-4.0.5.orig/share/html/images/Makefile.am gromacs-4.0.5/share/html/images/Makefile.am
---- gromacs-4.0.5.orig/share/html/images/Makefile.am 2006-03-06 10:52:20.000000000 +0100
-+++ gromacs-4.0.5/share/html/images/Makefile.am 2009-11-29 23:00:57.000000000 +0100
-@@ -2,7 +2,7 @@
- #
- # Don't edit - this file is generated automatically from Makefile.am
- #
--imagedir = ${pkgdatadir}/html/images
-+imagedir = @htmldir@/html/images
-
- image_DATA = \
- features.gif \
-diff -Naur gromacs-4.0.5.orig/share/html/images/Makefile.in gromacs-4.0.5/share/html/images/Makefile.in
---- gromacs-4.0.5.orig/share/html/images/Makefile.in 2009-05-09 11:12:24.000000000 +0200
-+++ gromacs-4.0.5/share/html/images/Makefile.in 2009-11-29 23:01:20.000000000 +0100
-@@ -186,7 +186,7 @@
- #
- # Don't edit - this file is generated automatically from Makefile.am
- #
--imagedir = ${pkgdatadir}/html/images
-+imagedir = @htmldir@/html/images
- image_DATA = \
- features.gif \
- flow_leftrightup.gif flow_vrule.gif \
-diff -Naur gromacs-4.0.5.orig/share/html/online/Makefile.am gromacs-4.0.5/share/html/online/Makefile.am
---- gromacs-4.0.5.orig/share/html/online/Makefile.am 2008-08-11 11:46:17.000000000 +0200
-+++ gromacs-4.0.5/share/html/online/Makefile.am 2009-11-29 23:01:47.000000000 +0100
-@@ -2,7 +2,7 @@
- #
- # Don't edit - this file is generated automatically from Makefile.am
- #
--onlinedir = ${pkgdatadir}/html/online
-+onlinedir = @htmldir@/html/online
-
- online_DATA = \
- cpt.html \
-diff -Naur gromacs-4.0.5.orig/share/html/online/Makefile.in gromacs-4.0.5/share/html/online/Makefile.in
---- gromacs-4.0.5.orig/share/html/online/Makefile.in 2009-05-09 11:12:24.000000000 +0200
-+++ gromacs-4.0.5/share/html/online/Makefile.in 2009-11-29 23:02:15.000000000 +0100
-@@ -186,7 +186,7 @@
- #
- # Don't edit - this file is generated automatically from Makefile.am
- #
--onlinedir = ${pkgdatadir}/html/online
-+onlinedir = @htmldir@/html/online
- online_DATA = \
- cpt.html \
- dat.html g_disre.html g_sorient.html ndx.html \
# 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-r1.ebuild,v 1.1 2010/01/24 19:39:09 alexxy Exp $
+# $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="2"
+EAPI="3"
LIBTOOLIZE="true"
TEST_PV="4.0.4"
HOMEPAGE="http://www.gromacs.org/"
SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
- doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )"
+ doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )
+ ffamber? ( http://ffamber.cnsm.csulb.edu/ffamber_v4.0-doc.tar.gz )"
LICENSE="GPL-2"
SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86"
-IUSE="X blas dmalloc doc -double-precision +fftw fkernels +gsl lapack mpi +single-precision static test +xml zsh-completion"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
+IUSE="X blas dmalloc doc -double-precision ffamber +fftw fkernels +gsl lapack
+mpi +single-precision static static-libs test +xml zsh-completion"
DEPEND="app-shells/tcsh
X? ( x11-libs/libX11
src_prepare() {
+ epatch "${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}/${PN}-4.0.9999-ccache.patch"
# Fix typos in a couple of files.
|| die "Failed to fixup demo script."
# Fix a sandbox violation that occurs when re-emerging with mpi.
- sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
+ sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${ED}usr/$( get_libdir )\" ; \\\\" \
-i src/tools/Makefile.am \
|| die "sed tools/Makefile.am failed"
-i src/tools/Makefile.am \
|| die "sed tools/Makefile.am failed"
- sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
+ sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${ED}usr/$( get_libdir )\" ; \\\\" \
-i src/tools/Makefile.am \
|| die "sed tools/Makefile.am failed"
# by default its better to have dynamicaly linked binaries
if use static; then
+ #gmx build static libs by default
myconf="${myconf} $(use_enable static all-static)"
else
- myconf="${myconf} --enable-shared"
+ myconf="${myconf} --enable-shared $(use_enable static-libs static)"
fi
- myconf="--datadir=/usr/share \
- --bindir=/usr/bin \
- --libdir=/usr/$(get_libdir) \
- --docdir=/usr/share/doc/"${PF}" \
+ myconf="--datadir="${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) \
src_install() {
for x in ${GMX_DIRS}; do
cd "${S}-${x}"
- emake DESTDIR="${D}" install || die "emake install for ${x} failed"
+ emake DESTDIR="${ED}" install || die "emake install for ${x} failed"
use mpi || continue
cd "${S}-${x}_mpi"
- emake DESTDIR="${D}" install-mdrun || die "emake install-mdrun for ${x} failed"
+ emake DESTDIR="${ED}" install-mdrun || die "emake install-mdrun for ${x} failed"
done
- sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${D}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
+ sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
doenvd "${T}/80gromacs"
- rm -f "${D}"/usr/bin/GMXRC*
+ rm -f "${ED}"/usr/bin/GMXRC*
- dobashcompletion "${D}"/usr/bin/completion.bash ${PN}
+ dobashcompletion "${ED}"/usr/bin/completion.bash ${PN}
if use zsh-completion ; then
insinto /usr/share/zsh/site-functions
- newins "${D}"/usr/bin/completion.zsh _${PN}
+ newins "${ED}"/usr/bin/completion.zsh _${PN}
fi
- rm -r "${D}"/usr/bin/completion.*
+ rm -r "${ED}"/usr/bin/completion.*
cd "${S}"
dodoc AUTHORS INSTALL README
- use doc && dodoc "${DISTDIR}"/manual-4.0.pdf
+ use doc && dodoc "${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() {
+++ /dev/null
-# Copyright 1999-2009 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.ebuild,v 1.2 2009/12/08 15:08:23 alexxy Exp $
-
-EAPI="2"
-
-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-${TEST_PV}.tgz )
- doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86"
-IUSE="X blas dmalloc doc -double-precision +fftw fkernels +gsl lapack mpi +single-precision static test +xml zsh-completion"
-
-DEPEND="app-shells/tcsh
- X? ( x11-libs/libX11
- x11-libs/libSM
- x11-libs/libICE )
- dmalloc? ( dev-libs/dmalloc )
- blas? ( virtual/blas )
- fftw? ( sci-libs/fftw:3.0 )
- gsl? ( sci-libs/gsl )
- lapack? ( virtual/lapack )
- mpi? ( virtual/mpi )
- xml? ( dev-libs/libxml2 )"
-
-RDEPEND="${DEPEND}"
-
-RESTRICT="test"
-
-src_prepare() {
-
- epatch "${FILESDIR}/${P}-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=\"${D}usr/$( 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"
-
- use fkernels && epatch "${FILESDIR}/${PN}-4.0.4-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} $(use_with lapack external-lapack)"
- fi
-
- # by default its better to have dynamicaly linked binaries
- if use static; then
- myconf="${myconf} $(use_enable static all-static)"
- else
- myconf="${myconf} --enable-shared"
- fi
-
- myconf="--datadir=/usr/share \
- --bindir=/usr/bin \
- --libdir=/usr/$(get_libdir) \
- --docdir=/usr/share/doc/"${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}-${x}"
- emake DESTDIR="${D}" install || die "emake install for ${x} failed"
- use mpi || continue
- cd "${S}-${x}_mpi"
- emake DESTDIR="${D}" install-mdrun || die "emake install-mdrun for ${x} failed"
- done
-
- sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${D}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
- doenvd "${T}/80gromacs"
- rm -f "${D}"/usr/bin/GMXRC*
-
- dobashcompletion "${D}"/usr/bin/completion.bash ${PN}
- if use zsh-completion ; then
- insinto /usr/share/zsh/site-functions
- newins "${D}"/usr/bin/completion.zsh _${PN}
- fi
- rm -r "${D}"/usr/bin/completion.*
-
- cd "${S}"
- dodoc AUTHORS INSTALL README
- use doc && dodoc "${DISTDIR}"/manual-4.0.pdf
-}
-
-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
-}
<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>
projects / gentoo.git / commitdiff