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alexxy 14/10/02 15:34:59 |
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|
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Modified: ChangeLog |
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Added: gromacs-5.0.2.ebuild |
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Log: |
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Version bump =D |
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|
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(Portage version: 2.2.14_rc1/cvs/Linux x86_64, signed Manifest commit with key F82F92E6) |
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|
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Revision Changes Path |
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1.146 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=1.146&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.146&content-type=text/plain |
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diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?r1=1.145&r2=1.146 |
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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 1.145 |
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retrieving revision 1.146 |
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diff -u -r1.145 -r1.146 |
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--- ChangeLog 6 Sep 2014 18:44:08 -0000 1.145 |
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+++ ChangeLog 2 Oct 2014 15:34:59 -0000 1.146 |
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@@ -1,6 +1,11 @@ |
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# ChangeLog for sci-chemistry/gromacs |
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# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 |
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-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.145 2014/09/06 18:44:08 ottxor Exp $ |
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+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.146 2014/10/02 15:34:59 alexxy Exp $ |
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+ |
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+*gromacs-5.0.2 (02 Oct 2014) |
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+ |
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+ 02 Oct 2014; Alexey Shvetsov <alexxy@g.o> +gromacs-5.0.2.ebuild: |
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+ Version bump =D |
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|
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*gromacs-5.0.1 (06 Sep 2014) |
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|
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|
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|
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1.1 sci-chemistry/gromacs/gromacs-5.0.2.ebuild |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.2.ebuild?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.2.ebuild?rev=1.1&content-type=text/plain |
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|
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Index: gromacs-5.0.2.ebuild |
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=================================================================== |
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# Copyright 1999-2014 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-5.0.2.ebuild,v 1.1 2014/10/02 15:34:59 alexxy Exp $ |
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|
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EAPI=5 |
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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 [[ $PV = *9999* ]]; then |
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EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
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https://gerrit.gromacs.org/gromacs.git |
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git://github.com/gromacs/gromacs.git |
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http://repo.or.cz/r/gromacs.git" |
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EGIT_BRANCH="release-5-0" |
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inherit git-r3 |
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KEYWORDS="" |
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else |
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SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
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test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" |
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KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
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fi |
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|
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ACCE_IUSE="sse2 sse4_1 avx_128_fma avx_256 avx2_256" |
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|
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DESCRIPTION="The ultimate molecular dynamics simulation package" |
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HOMEPAGE="http://www.gromacs.org/" |
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|
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# see COPYING for details |
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# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
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# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
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LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
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SLOT="0/${PV}" |
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IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
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|
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CDEPEND=" |
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X? ( |
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x11-libs/libX11 |
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x11-libs/libSM |
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x11-libs/libICE |
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) |
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blas? ( virtual/blas ) |
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boost? ( >=dev-libs/boost-1.55 ) |
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cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
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fftw? ( sci-libs/fftw:3.0 ) |
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lapack? ( virtual/lapack ) |
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mkl? ( sci-libs/mkl ) |
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mpi? ( virtual/mpi ) |
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" |
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DEPEND="${CDEPEND} |
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virtual/pkgconfig |
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doc? ( |
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app-doc/doxygen |
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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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)" |
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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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mkl? ( !blas !fftw !lapack )" |
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|
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DOCS=( AUTHORS README ) |
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|
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if [[ ${PV} != *9999 ]]; then |
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S="${WORKDIR}/${PN}-${PV/_/-}" |
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fi |
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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 [[ ${PV} != *9999 ]]; then |
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default |
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else |
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git-r3_src_unpack |
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if use test; then |
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EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
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EGIT_BRANCH="master" EGIT_COMMIT="master" \ |
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EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
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git-r3_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 avx_128_fma && acce="AVX_128_FMA" |
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use avx_256 && acce="AVX_256" |
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use avx2_256 && acee="AVX2_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 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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$(cmake-utils_use boost GMX_EXTERNAL_BOOST) |
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$(cmake-utils_use tng GMX_USE_TNG) |
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$(cmake-utils_use doc GMX_BUILD_MANUAL) |
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$(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES) |
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-DGMX_DEFAULT_SUFFIX=off |
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-DGMX_SIMD="$acce" |
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-DGMX_LIB_INSTALL_DIR="$(get_libdir)" |
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-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
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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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-DBUILD_TESTING=OFF |
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-DGMX_BUILD_UNITTESTS=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" |
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local suffix="" |
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#if we build single and double - double is suffixed |
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use double-precision && use single-precision && \ |
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[[ ${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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[[ ${x} = "float" ]] && use cuda && \ |
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cuda=( -DGMX_GPU=ON ) |
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mycmakeargs=( |
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${mycmakeargs_pre[@]} ${p} |
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-DGMX_MPI=OFF |
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$(cmake-utils_use threads GMX_THREAD_MPI) |
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"${cuda[@]}" |
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-DGMX_OPENMM=OFF |
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"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
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-DGMX_BINARY_SUFFIX="${suffix}" |
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-DGMX_LIBS_SUFFIX="${suffix}" |
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) |
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BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
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[[ ${CHOST} != *-darwin* ]] || \ |
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sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
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use mpi || continue |
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einfo "Configuring for ${x} precision with mpi" |
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mycmakeargs=( |
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${mycmakeargs_pre[@]} ${p} |
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-DGMX_THREAD_MPI=OFF |
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-DGMX_MPI=ON ${cuda} |
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-DGMX_OPENMM=OFF |
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-DGMX_BUILD_MDRUN_ONLY=ON |
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-DBUILD_SHARED_LIBS=OFF |
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-DGMX_BUILD_MANUAL=OFF |
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-DGMX_BINARY_SUFFIX="_mpi${suffix}" |
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-DGMX_LIBS_SUFFIX="_mpi${suffix}" |
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) |
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BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
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[[ ${CHOST} != *-darwin* ]] || \ |
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sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
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done |
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} |
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|
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src_compile() { |
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for x in ${GMX_DIRS}; do |
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einfo "Compiling for ${x} precision" |
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BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
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cmake-utils_src_compile |
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# generate bash completion |
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BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
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cmake-utils_src_compile completion |
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if use doc; then |
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BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
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cmake-utils_src_compile manual |
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fi |
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use mpi || continue |
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einfo "Compiling for ${x} precision with mpi" |
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BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
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cmake-utils_src_compile |
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done |
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} |
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|
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src_test() { |
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for x in ${GMX_DIRS}; do |
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BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
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cmake-utils_src_make check |
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done |
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} |
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|
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src_install() { |
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for x in ${GMX_DIRS}; do |
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BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
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cmake-utils_src_install |
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if use doc; then |
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newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
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fi |
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newbashcomp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash gromacs |
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use mpi || continue |
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BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
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cmake-utils_src_install |
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done |
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# drop unneeded stuff |
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rm "${ED}"usr/bin/GMXRC* || die |
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|
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readme.gentoo_create_doc |
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} |
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|
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pkg_postinst() { |
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einfo |
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einfo "Please read and cite:" |
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einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
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einfo "http://dx.doi.org/10.1021/ct700301q" |
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einfo |
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readme.gentoo_print_elog |
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} |
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