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authorChristoph Junghans <kleiner_otti@gmx.de>2010-09-27 19:55:33 +0200
committerChristoph Junghans <kleiner_otti@gmx.de>2010-09-27 19:56:34 +0200
commit8f37e9ebc4158de5dc6bf1c9142001ba7fa085e3 (patch)
tree159ca3fc77eb17b3aac448c3e10bbef3558c8daa
parent[dev-tex/revtex] Corrected texmf installation directory (diff)
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[sci-chemistry/gromacs] version 4.5.1 now in tree
(Portage version: 2.1.8.3/git/Linux i686) (Signed Manifest commit)
-rw-r--r--sci-chemistry/gromacs/Manifest8
-rw-r--r--sci-chemistry/gromacs/gromacs-4.5.1.ebuild259
2 files changed, 3 insertions, 264 deletions
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 9d7a2327a..76835c164 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -3,11 +3,9 @@ Hash: SHA1
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-4.5.1.tar.gz 10304547 RMD160 116ca5bc4644d1460086cfb2097961abd11db63b SHA1 cbe52c3ec613fe8b652cd24b86c4fdf31b58c71b SHA256 768a02ee995f950b442dc131c25c1b946f1907d2286fd3fa3eb7fa967ed8efb0
DIST manual-4.0.pdf 2135100 RMD160 b963642f8e1433f11328c3d0c4b1645c9de506da SHA1 8ae951ee15b2a7dc626331fce36511bc8766144c SHA256 646f810477eee2d710de6019c52056550413d0ba77baf9680195c835ddafe80a
DIST manual-4.5-beta2.pdf 2317594 RMD160 3936ca2ec810ae2e74c57f19a993fda8152bedcd SHA1 d995be380e6453056330c5f5bfed95fbf4cb554f SHA256 fdeb0cd0be5244cdfddc17a643199ddf043e0a9d37811998300df86541483c61
EBUILD gromacs-4.0.9999.ebuild 9253 RMD160 b1d0cc7e6e51a718fd01d72947b3e2e22059a0d2 SHA1 888c75e12238560e741bc9e2a4198cfee2ab3701 SHA256 3da8f43fd21df44375cf03b1fe46c594aa51c2f72307c4a9eec9747330d54a8d
-EBUILD gromacs-4.5.1.ebuild 7428 RMD160 a2205a735fa14d34a98bc88ee2dbf20153966c2e SHA1 8a927e5217eaf9c57c25bcefe8a315600c4d261e SHA256 9264000e86e930d26e38ab53d460754ff461965de1817c3b2c6c70d6414a9124
EBUILD gromacs-4.5.9999.ebuild 7467 RMD160 84ca2c188addeb9823b6c5da01138c14b85f4277 SHA1 6f713d3d098b6b49bb3769f3c5bb835d1c4b8bb9 SHA256 aedbbe05bf932418e237c1ac5f9a77c03559eafdf60f0cecc082ce6834f07878
EBUILD gromacs-9999.ebuild 7851 RMD160 a92cfefd23992e1e49e72b0d7e850ecc7715bcd4 SHA1 7d9bea15ca33e677e5c461dbb3627112522d7e5f SHA256 c0a561f207198a58a8f6d507ba943a10af40b4a6f01c5f230a86d05db528c582
MISC ChangeLog 5658 RMD160 b18635eae8b4777ab5a73f443200500508b1e72c SHA1 e0b8a4d90a4aee0a0956817f9df077766a5b8601 SHA256 94464b430f371acb24ca4efc7776d5a7dc745af98a6260cec74e1542a40e123c
@@ -15,7 +13,7 @@ MISC metadata.xml 643 RMD160 e9ffc42d792f15f3d4438a0de225277ec4814041 SHA1 c83fd
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v2.0.16 (GNU/Linux)
-iEYEARECAAYFAkyWkBQACgkQy0OE/ans1/m2TQCfdInsQI37n6KxkKd8gsfLZgZO
-9JYAnRqG+lQ+9W2ZLJpubDzFIseNCQIi
-=igOi
+iEYEARECAAYFAkyg2pUACgkQy0OE/ans1/mprACcDw6eNGqqySIJojOEMJdF30sU
+sjYAn22KqFi6PfCD1q+DlhwjPR30lVbv
+=NH/T
-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/gromacs/gromacs-4.5.1.ebuild b/sci-chemistry/gromacs/gromacs-4.5.1.ebuild
deleted file mode 100644
index f210a8dc0..000000000
--- a/sci-chemistry/gromacs/gromacs-4.5.1.ebuild
+++ /dev/null
@@ -1,259 +0,0 @@
-# Copyright 1999-2010 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-beta2"
-
-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-${TEST_PV}.tgz )
- doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
-mpi +single-precision static 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="${DEPEND}"
-
-RESTRICT="test"
-
-QA_EXECSTACK="usr/lib/libgmx.so.*
- usr/lib/libgmx_d.so.*"
-
-use static && QA_EXECSTACK="$QA_EXECSTACK usr/bin/*"
-
-pkg_setup() {
- if use fkernels; then
- FORTRAN="g77 gfortran ifc"
- fortran_pkg_setup
- else
- FORTRANC=""
- fi
-}
-
-src_prepare() {
-
- ( use single-precision || use double-precision ) || \
- die "Nothing to compile, enable single-precision and/or double-precision"
-
- 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
-
- 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_user
- 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 [[ $(gcc-version) == "4.1" ]]; then
- eerror "gcc 4.1 is not supported by gromacs"
- eerror "please run test suite"
- die
- fi
-
- #note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
- #fortran will gone in gromacs 4.1 anyway
- #note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
- if use fkernels; then
- ewarn "Fortran kernels are usually not faster than C kernels and assembly"
- ewarn "I hope, you know what are you doing..."
- myconf="${myconf} --enable-fortran"
- 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) \
- $(use_enable threads) \
- ${myconf}"
-
- #if we build single and double - double is suffixed
- if ( use double-precision && use single-precision ); then
- suffixdouble="_d"
- else
- suffixdouble=""
- fi
-
- if use double-precision ; then
- #from gromacs manual
- elog
- elog "For most simulations single precision is accurate enough. In some"
- elog "cases double precision is required to get reasonable results:"
- elog
- elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
- elog " and the calculation and diagonalization of the Hessian "
- elog "-calculation of the constraint force between two large groups of atoms"
- elog "-energy conservation: this can only be done without temperature coupling and"
- elog " without cutoffs"
- elog
- fi
-
- if use mpi ; then
- elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
- elog "we configure/compile gromacs twice (with and without mpi) and only"
- elog "install mdrun with mpi support. In addtion you will get libgmx and"
- elog "libmd with and without mpi support."
- fi
-
- myconfdouble="${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}-${x}"
- emake DESTDIR="${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 ${x} failed"
- done
-
- sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${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.*
-
- # 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
- dodoc "${DISTDIR}/manual-${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
-}