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commit: 6c21e41bbd14c03b35ff24c4dc253ccedf6173a6 |
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Author: Christoph Junghans <ottxor <AT> gentoo <DOT> org> |
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AuthorDate: Wed Sep 3 22:53:28 2014 +0000 |
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Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org> |
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CommitDate: Wed Sep 3 22:53:40 2014 +0000 |
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URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6c21e41b |
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|
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drop old |
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|
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Package-Manager: portage-2.2.8-r1 |
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|
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--- |
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sci-chemistry/gromacs/ChangeLog | 4 + |
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sci-chemistry/gromacs/gromacs-5.0_rc1.ebuild | 268 --------------------------- |
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2 files changed, 4 insertions(+), 268 deletions(-) |
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|
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diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog |
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index b89772c..2b74e15 100644 |
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--- a/sci-chemistry/gromacs/ChangeLog |
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+++ b/sci-chemistry/gromacs/ChangeLog |
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@@ -2,6 +2,10 @@ |
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# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 |
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# $Header: $ |
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|
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+ 03 Sep 2014; Christoph Junghans <ottxor@g.o> -Manifest, |
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+ -gromacs-5.0_rc1.ebuild: |
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+ drop old |
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+ |
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03 Sep 2014; Christoph Junghans <ottxor@g.o> gromacs-5.0.9999.ebuild: |
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live update |
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|
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|
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diff --git a/sci-chemistry/gromacs/gromacs-5.0_rc1.ebuild b/sci-chemistry/gromacs/gromacs-5.0_rc1.ebuild |
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deleted file mode 100644 |
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index 34e34f4..0000000 |
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--- a/sci-chemistry/gromacs/gromacs-5.0_rc1.ebuild |
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+++ /dev/null |
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@@ -1,268 +0,0 @@ |
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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: $ |
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- |
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-EAPI=5 |
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- |
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-TEST_PV="5.0-rc1" |
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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 [[ $PV = *9999* ]]; then |
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- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
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- https://gerrit.gromacs.org/gromacs.git |
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- git://github.com/gromacs/gromacs.git |
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- http://repo.or.cz/r/gromacs.git" |
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- EGIT_BRANCH="release-5-0" |
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- inherit git-r3 |
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-else |
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- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
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- test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )" |
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-fi |
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- |
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-ACCE_IUSE="sse2 sse4_1 avx_128_fma avx_256 avx2_256" |
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- |
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-DESCRIPTION="The ultimate molecular dynamics simulation package" |
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-HOMEPAGE="http://www.gromacs.org/" |
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- |
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-# see COPYING for details |
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-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
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-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
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-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
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-SLOT="0/${PV}" |
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-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
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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 [[ ${PV} != *9999 ]]; then |
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- default |
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- else |
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- git-r3_src_unpack |
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- if use test; then |
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- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
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- EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \ |
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- EGIT_SOURCEDIR="${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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- 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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- 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}_${x}"/manual/gromacs.pdf "${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}_${x}_mpi" \ |
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- cmake-utils_src_install |
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- done |
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- # drop unneeded stuff |
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- rm -f "${ED}"usr/bin/gmx-completion* |
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- rm -f "${ED}"usr/bin/g_options* |
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- rm -f "${ED}"usr/bin/GMXRC* |
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- rm -f "${ED}"usr/lib*/libtng*.a |
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- |
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- #workaround for libtng |
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- if [[ $(get_libdir) != lib ]]; then |
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- mv "${ED}"usr/lib/libtng* "${ED}usr/$(get_libdir)" || die |
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- rmdir "${ED}"usr/lib || die |
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- fi |
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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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-} |