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ottxor 13/06/01 21:36:29 |
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|
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Modified: ChangeLog |
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Added: gromacs-4.6.2.ebuild |
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Removed: gromacs-4.6.1.ebuild |
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Log: |
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version bump |
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|
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(Portage version: 2.2.0_alpha177/cvs/Linux x86_64, signed Manifest commit with key C2000586) |
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|
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Revision Changes Path |
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1.126 sci-chemistry/gromacs/ChangeLog |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.126&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.126&content-type=text/plain |
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diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?r1=1.125&r2=1.126 |
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|
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Index: ChangeLog |
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=================================================================== |
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RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v |
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retrieving revision 1.125 |
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retrieving revision 1.126 |
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diff -u -r1.125 -r1.126 |
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--- ChangeLog 28 May 2013 03:28:04 -0000 1.125 |
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+++ ChangeLog 1 Jun 2013 21:36:28 -0000 1.126 |
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@@ -1,6 +1,12 @@ |
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# ChangeLog for sci-chemistry/gromacs |
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# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 |
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-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.125 2013/05/28 03:28:04 ottxor Exp $ |
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+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.126 2013/06/01 21:36:28 ottxor Exp $ |
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+ |
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+*gromacs-4.6.2 (01 Jun 2013) |
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+ |
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+ 01 Jun 2013; Christoph Junghans <ottxor@g.o> +gromacs-4.6.2.ebuild, |
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+ -files/gromacs-4.6.1-openmm.patch, -gromacs-4.6.1.ebuild: |
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+ version bump |
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|
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28 May 2013; Christoph Junghans <ottxor@g.o> gromacs-4.6.1.ebuild: |
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fixed a typo, which prevented cuda build |
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|
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|
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|
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1.1 sci-chemistry/gromacs/gromacs-4.6.2.ebuild |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.2.ebuild?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.2.ebuild?rev=1.1&content-type=text/plain |
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|
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Index: gromacs-4.6.2.ebuild |
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=================================================================== |
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# Copyright 1999-2013 Gentoo Foundation |
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# Distributed under the terms of the GNU General Public License v2 |
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# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.2.ebuild,v 1.1 2013/06/01 21:36:28 ottxor Exp $ |
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|
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EAPI=5 |
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|
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TEST_PV="4.6.2" |
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MANUAL_PV="4.6.2" |
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|
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CMAKE_MAKEFILE_GENERATOR="ninja" |
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|
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inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs |
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|
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if [[ $PV = *9999* ]]; then |
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EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
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https://gerrit.gromacs.org/gromacs.git |
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git://github.com/gromacs/gromacs.git |
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http://repo.or.cz/r/gromacs.git" |
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EGIT_BRANCH="release-4-6" |
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inherit git-2 |
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LIVE_DEPEND="doc? ( |
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dev-texlive/texlive-latex |
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dev-texlive/texlive-latexextra |
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media-gfx/imagemagick |
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sys-apps/coreutils |
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)" |
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else |
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SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz |
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doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf ) |
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test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )" |
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LIVE_DEPEND="" |
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fi |
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|
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ACCE_IUSE="sse2 sse4_1 avx128fma avx256" |
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|
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DESCRIPTION="The ultimate molecular dynamics simulation package" |
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HOMEPAGE="http://www.gromacs.org/" |
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|
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# see COPYING for details |
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# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
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# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
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LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
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SLOT="0/${PV}" |
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KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos" |
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IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}" |
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|
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CDEPEND=" |
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X? ( |
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x11-libs/libX11 |
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x11-libs/libSM |
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x11-libs/libICE |
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) |
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blas? ( virtual/blas ) |
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cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
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fftw? ( sci-libs/fftw:3.0 ) |
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gsl? ( sci-libs/gsl ) |
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lapack? ( virtual/lapack ) |
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mkl? ( sci-libs/mkl ) |
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mpi? ( virtual/mpi ) |
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openmm? ( |
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>=dev-util/nvidia-cuda-toolkit-4.2.9-r1 |
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sci-libs/openmm[cuda,opencl] |
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)" |
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DEPEND="${CDEPEND} |
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virtual/pkgconfig |
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${LIVE_DEPEND}" |
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RDEPEND="${CDEPEND}" |
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|
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REQUIRED_USE=" |
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|| ( single-precision double-precision ) |
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cuda? ( single-precision ) |
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openmm? ( single-precision ) |
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mkl? ( !blas !fftw !lapack )" |
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|
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DOCS=( AUTHORS README ) |
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HTML_DOCS=( "${ED}"/usr/share/gromacs/html/ ) |
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|
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pkg_pretend() { |
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[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
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use openmp && ! tc-has-openmp && \ |
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die "Please switch to an openmp compatible compiler" |
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} |
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|
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src_unpack() { |
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if [[ ${PV} != *9999 ]]; then |
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default |
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else |
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git-2_src_unpack |
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if use doc; then |
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EGIT_REPO_URI="git://git.gromacs.org/manual.git" \ |
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EGIT_BRANCH="release-4-6" EGIT_NOUNPACK="yes" EGIT_COMMIT="release-4-6" \ |
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EGIT_SOURCEDIR="${WORKDIR}/manual"\ |
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git-2_src_unpack |
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fi |
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if use test; then |
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EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
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EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \ |
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EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\ |
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git-2_src_unpack |
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fi |
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fi |
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} |
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|
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src_prepare() { |
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#notes/todos |
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# -on apple: there is framework support |
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|
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cmake-utils_src_prepare |
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|
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use cuda && cuda_src_prepare |
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|
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GMX_DIRS="" |
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use single-precision && GMX_DIRS+=" float" |
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use double-precision && GMX_DIRS+=" double" |
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|
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if use test; then |
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for x in ${GMX_DIRS}; do |
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mkdir -p "${WORKDIR}/${P}_${x}" || die |
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cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
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done |
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fi |
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|
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DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
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} |
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|
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src_configure() { |
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local mycmakeargs_pre=( ) extra fft_opts=( ) |
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|
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#go from slowest to fastest acceleration |
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local acce="None" |
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use sse2 && acce="SSE2" |
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use sse4_1 && acce="SSE4.1" |
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use avx128fma && acce="AVX_128_FMA" |
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use avx256 && acce="AVX_256" |
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|
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#to create man pages, build tree binaries are executed (bug #398437) |
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[[ ${CHOST} = *-darwin* ]] && \ |
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extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
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|
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if use fftw; then |
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fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
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elif use mkl && has_version "=sci-libs/mkl-10*"; then |
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fft_opts=( -DGMX_FFT_LIBRARY=mkl |
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-DMKL_INCLUDE_DIR="${MKLROOT}/include" |
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-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
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) |
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elif use mkl; then |
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local bits=$(get_libdir) |
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fft_opts=( -DGMX_FFT_LIBRARY=mkl |
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-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
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-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
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) |
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else |
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fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
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fi |
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|
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mycmakeargs_pre+=( |
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"${fft_opts[@]}" |
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$(cmake-utils_use X GMX_X11) |
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$(cmake-utils_use blas GMX_EXTERNAL_BLAS) |
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$(cmake-utils_use gsl GMX_GSL) |
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$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK) |
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$(cmake-utils_use openmp GMX_OPENMP) |
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$(cmake-utils_use offensive GMX_COOL_QUOTES) |
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-DGMX_DEFAULT_SUFFIX=off |
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-DGMX_ACCELERATION="$acce" |
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-DGMXLIB="$(get_libdir)" |
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-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
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-DGMX_PREFIX_LIBMD=ON |
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-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF |
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-DGMX_USE_GCC44_BUG_WORKAROUND=OFF |
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${extra} |
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) |
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|
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for x in ${GMX_DIRS}; do |
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einfo "Configuring for ${x} precision" |
| 226 |
local suffix="" |
| 227 |
#if we build single and double - double is suffixed |
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use double-precision && use single-precision && \ |
| 229 |
[[ ${x} = "double" ]] && suffix="_d" |
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local p |
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[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
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local cuda=( "-DGMX_GPU=OFF" ) |
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[[ ${x} = "float" ]] && use cuda && \ |
| 234 |
cuda=( -DGMX_GPU=ON ) |
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mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF |
| 236 |
$(cmake-utils_use threads GMX_THREAD_MPI) "${cuda[@]}" -DGMX_OPENMM=OFF |
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"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
| 238 |
-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" ) |
| 239 |
BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
| 240 |
if [[ ${x} = float ]] && use openmm; then |
| 241 |
einfo "Configuring for openmm build" |
| 242 |
mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF |
| 243 |
-DGMX_THREAD_MPI=OFF -DGMX_GPU=OFF -DGMX_OPENMM=ON |
| 244 |
-DOpenMM_PLUGIN_DIR="${EPREFIX}/usr/$(get_libdir)/plugins" |
| 245 |
-DGMX_BINARY_SUFFIX="_openmm" -DGMX_LIBS_SUFFIX="_openmm" ) |
| 246 |
BUILD_DIR="${WORKDIR}/${P}_openmm" \ |
| 247 |
OPENMM_ROOT_DIR="${EPREFIX}/usr" cmake-utils_src_configure |
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fi |
| 249 |
use mpi || continue |
| 250 |
einfo "Configuring for ${x} precision with mpi" |
| 251 |
mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF |
| 252 |
-DGMX_MPI=ON ${cuda} -DGMX_OPENMM=OFF |
| 253 |
-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" ) |
| 254 |
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
| 255 |
done |
| 256 |
} |
| 257 |
|
| 258 |
src_compile() { |
| 259 |
for x in ${GMX_DIRS}; do |
| 260 |
einfo "Compiling for ${x} precision" |
| 261 |
BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| 262 |
cmake-utils_src_compile |
| 263 |
if [[ ${x} = float ]] && use openmm; then |
| 264 |
einfo "Compiling for openmm build" |
| 265 |
BUILD_DIR="${WORKDIR}/${P}_openmm"\ |
| 266 |
cmake-utils_src_compile mdrun |
| 267 |
fi |
| 268 |
use mpi || continue |
| 269 |
einfo "Compiling for ${x} precision with mpi" |
| 270 |
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
| 271 |
cmake-utils_src_compile mdrun |
| 272 |
done |
| 273 |
} |
| 274 |
|
| 275 |
src_test() { |
| 276 |
for x in ${GMX_DIRS}; do |
| 277 |
BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| 278 |
cmake-utils_src_make check |
| 279 |
done |
| 280 |
} |
| 281 |
|
| 282 |
src_install() { |
| 283 |
for x in ${GMX_DIRS}; do |
| 284 |
BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
| 285 |
cmake-utils_src_install |
| 286 |
if [[ ${x} = float ]] && use openmm; then |
| 287 |
BUILD_DIR="${WORKDIR}/${P}_openmm" \ |
| 288 |
DESTDIR="${D}" cmake-utils_src_make install-mdrun |
| 289 |
fi |
| 290 |
#manual can only be build after gromacs was installed once in image |
| 291 |
if use doc && [[ $PV = *9999* && ! -d ${WORKDIR}/manual_build ]]; then |
| 292 |
mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" ) |
| 293 |
BUILD_DIR="${WORKDIR}"/manual_build \ |
| 294 |
CMAKE_USE_DIR="${WORKDIR}/manual" cmake-utils_src_configure |
| 295 |
[[ ${CHOST} = *-darwin* ]] && \ |
| 296 |
export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}${DYLD_LIBRARY_PATH:+:}${ED}/usr/$(get_libdir)" |
| 297 |
BUILD_DIR="${WORKDIR}"/manual_build cmake-utils_src_make |
| 298 |
[[ ${CHOST} = *-darwin* ]] && DYLD_LIBRARY_PATH="${ED}/usr/$(get_libdir)" |
| 299 |
newdoc "${WORKDIR}"/manual_build/gromacs.pdf "${PN}-manual-${PV}.pdf" |
| 300 |
fi |
| 301 |
use mpi || continue |
| 302 |
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
| 303 |
DESTDIR="${D}" cmake-utils_src_make install-mdrun |
| 304 |
done |
| 305 |
|
| 306 |
use doc && [[ $PV != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf" |
| 307 |
newbashcomp "${ED}"/usr/bin/completion.bash ${PN} |
| 308 |
if use zsh-completion ; then |
| 309 |
insinto /usr/share/zsh/site-functions |
| 310 |
newins "${ED}"/usr/bin/completion.zsh _${PN} |
| 311 |
fi |
| 312 |
rm -f "${ED}"usr/bin/completion.* |
| 313 |
rm -rf "${ED}"usr/share/gromacs/html |
| 314 |
rm -f "${ED}"usr/bin/g_options* |
| 315 |
rm -f "${ED}"usr/bin/GMXRC* |
| 316 |
|
| 317 |
readme.gentoo_create_doc |
| 318 |
} |
| 319 |
|
| 320 |
pkg_postinst() { |
| 321 |
einfo |
| 322 |
einfo "Please read and cite:" |
| 323 |
einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
| 324 |
einfo "http://dx.doi.org/10.1021/ct700301q" |
| 325 |
if use offensive; then |
| 326 |
einfo |
| 327 |
einfo $(g_luck) |
| 328 |
einfo "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc" |
| 329 |
fi |
| 330 |
einfo |
| 331 |
readme.gentoo_print_elog |
| 332 |
} |
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