diff options
| -rw-r--r-- | sci-chemistry/gromacs/Manifest | 8 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-4.5.1.ebuild | 259 |
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 -} |