From: Alexey Shvetsov Date: Sun, 27 Jun 2010 19:06:33 +0000 (+0000) Subject: [sci-chemistry/gromacs] Update ebuild to eapi3+prefix support. add amberports and... X-Git-Url: http://git.tremily.us/gitweb.cgi?a=commitdiff_plain;h=0f60a68d9234808526afacd41be0c3ae3e822302;p=gentoo.git [sci-chemistry/gromacs] Update ebuild to eapi3+prefix support. add amberports and latest upstream patches Package-Manager: portage-2.2_rc67_p177/cvs/Linux x86_64 --- diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog index b383a4bcf902..f24ceea63123 100644 --- a/sci-chemistry/gromacs/ChangeLog +++ b/sci-chemistry/gromacs/ChangeLog @@ -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 -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 gromacs-3.3.1-r1.ebuild, gromacs-3.3.3.ebuild: diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 5b4cc69f1ed3..55b42079266f 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -3,10 +3,11 @@ Hash: SHA1 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 @@ -18,14 +19,13 @@ EBUILD gromacs-3.3.1-r1.ebuild 5894 RMD160 1df038d8f1a05cbd4add20be5da6c9a98b45d EBUILD gromacs-3.3.3.ebuild 6363 RMD160 02cc3ab83e9897408f971355a453b731006edce3 SHA1 eb3790b6d7bcf32ec81bd1e64987b93536c0e573 SHA256 42f87016396ca4fb7b71cdcba9e0d110e3311e2d4acabca2bbdb3c073b4c428f EBUILD gromacs-4.0.4.ebuild 6918 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+KEcAn37L+8sifFj2eKET4Cl/2R9GT2T4 +=CM19 -----END PGP SIGNATURE----- diff --git a/sci-chemistry/gromacs/files/gromacs-4.0.7-docdir.patch b/sci-chemistry/gromacs/files/gromacs-4.0.7-docdir.patch deleted file mode 100644 index b556947b9c2c..000000000000 --- a/sci-chemistry/gromacs/files/gromacs-4.0.7-docdir.patch +++ /dev/null @@ -1,72 +0,0 @@ -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 \ diff --git a/sci-chemistry/gromacs/files/gromacs-4.0.7_upstream2010-06-08.patch.gz b/sci-chemistry/gromacs/files/gromacs-4.0.7_upstream2010-06-08.patch.gz new file mode 100644 index 000000000000..41dcc8702ccd Binary files /dev/null and b/sci-chemistry/gromacs/files/gromacs-4.0.7_upstream2010-06-08.patch.gz differ diff --git a/sci-chemistry/gromacs/gromacs-4.0.7-r1.ebuild b/sci-chemistry/gromacs/gromacs-4.0.7-r3.ebuild similarity index 62% rename from sci-chemistry/gromacs/gromacs-4.0.7-r1.ebuild rename to sci-chemistry/gromacs/gromacs-4.0.7-r3.ebuild index abc141e621b4..bb224ca48383 100644 --- a/sci-chemistry/gromacs/gromacs-4.0.7-r1.ebuild +++ b/sci-chemistry/gromacs/gromacs-4.0.7-r3.ebuild @@ -1,8 +1,8 @@ # 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" @@ -13,12 +13,14 @@ 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-${TEST_PV}.tgz ) - doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )" + doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf ) + ffamber? ( http://ffamber.cnsm.csulb.edu/ffamber_v4.0-doc.tar.gz )" LICENSE="GPL-2" SLOT="0" -KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86" -IUSE="X blas dmalloc doc -double-precision +fftw fkernels +gsl lapack mpi +single-precision static test +xml zsh-completion" +KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux" +IUSE="X blas dmalloc doc -double-precision ffamber +fftw fkernels +gsl lapack +mpi +single-precision static static-libs test +xml zsh-completion" DEPEND="app-shells/tcsh X? ( x11-libs/libX11 @@ -38,6 +40,9 @@ RESTRICT="test" src_prepare() { + epatch "${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}/${PN}-4.0.9999-ccache.patch" # Fix typos in a couple of files. @@ -45,7 +50,7 @@ src_prepare() { || die "Failed to fixup demo script." # Fix a sandbox violation that occurs when re-emerging with mpi. - sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \ + sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${ED}usr/$( get_libdir )\" ; \\\\" \ -i src/tools/Makefile.am \ || die "sed tools/Makefile.am failed" @@ -53,7 +58,7 @@ src_prepare() { -i src/tools/Makefile.am \ || die "sed tools/Makefile.am failed" - sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \ + sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${ED}usr/$( get_libdir )\" ; \\\\" \ -i src/tools/Makefile.am \ || die "sed tools/Makefile.am failed" @@ -125,15 +130,16 @@ src_configure() { # by default its better to have dynamicaly linked binaries if use static; then + #gmx build static libs by default myconf="${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) \ @@ -206,26 +212,74 @@ src_test() { 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() { diff --git a/sci-chemistry/gromacs/gromacs-4.0.7.ebuild b/sci-chemistry/gromacs/gromacs-4.0.7.ebuild deleted file mode 100644 index 5b6f1bd4093d..000000000000 --- a/sci-chemistry/gromacs/gromacs-4.0.7.ebuild +++ /dev/null @@ -1,242 +0,0 @@ -# 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 -} diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml index bf268860cf37..c0e0dfc97a93 100644 --- a/sci-chemistry/gromacs/metadata.xml +++ b/sci-chemistry/gromacs/metadata.xml @@ -3,10 +3,12 @@ sci-chemistry - Enable debugging with the dmalloc library - More precise calculations at the expense of speed - Enable building of Fortran Kernels for platforms that - dont have assembly loops - Single precision version of gromacs + Enable use of Debug Malloc + More precise calculations at the expense of speed + Enable ffamber ports for gromacs + Enable building of Fortran Kernels for platforms + that dont have assembly loops + Single precision version of gromacs + Enable zsh completion support