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From: "Alexey Shvetsov" <alexxy@gentoo.org>
To: gentoo-commits@lists.gentoo.org
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Reply-To: gentoo-dev@lists.gentoo.org, "Alexey Shvetsov" <alexxy@gentoo.org>
Message-ID: <1386043178.ec5a4f359119a8d3bd186f4f3a24481a0089f98c.alexxy@gentoo>
Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
X-VCS-Repository: proj/sci
X-VCS-Files: sci-chemistry/gromacs/ChangeLog sci-chemistry/gromacs/gromacs-9999.ebuild
X-VCS-Directories: sci-chemistry/gromacs/
X-VCS-Committer: alexxy
X-VCS-Committer-Name: Alexey Shvetsov
X-VCS-Revision: ec5a4f359119a8d3bd186f4f3a24481a0089f98c
X-VCS-Branch: master
Date: Tue, 3 Dec 2013 04:00:04 +0000 (UTC)
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commit: ec5a4f359119a8d3bd186f4f3a24481a0089f98c
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Tue Dec 3 03:59:38 2013 +0000
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Tue Dec 3 03:59:38 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ec5a4f35
Slightly update live ebuild for master branch
Package-Manager: portage-2.2.7
---
sci-chemistry/gromacs/ChangeLog | 3 +
sci-chemistry/gromacs/gromacs-9999.ebuild | 280 ++++++++++++++++++------------
2 files changed, 172 insertions(+), 111 deletions(-)
diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 9a16c48..fc03b04 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+ Slightly update live ebuild for master branch
+
01 Jun 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
sync with gx86
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 36a6d2d..706734c 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -2,28 +2,47 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI="5"
+EAPI=5
-TEST_PV="4.0.4"
+TEST_PV="5.0-beta1"
+MANUAL_PV="5.0-beta1"
-EGIT_REPO_URI="git://git.gromacs.org/gromacs http://repo.or.cz/r/gromacs.git"
-EGIT_BRANCH="master"
+CMAKE_MAKEFILE_GENERATOR="ninja"
-ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
+inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
-#to find external blas/lapack
-CMAKE_MIN_VERSION="2.8.5-r2"
+if [[ $PV = *9999* ]]; then
+ EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
+ https://gerrit.gromacs.org/gromacs.git
+ git://github.com/gromacs/gromacs.git
+ http://repo.or.cz/r/gromacs.git"
+ EGIT_BRANCH="master"
+ inherit git-2
+ LIVE_DEPEND="doc? (
+ dev-texlive/texlive-latex
+ dev-texlive/texlive-latexextra
+ media-gfx/imagemagick
+ sys-apps/coreutils
+ )"
+else
+ SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
+ doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf )
+ test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
+ LIVE_DEPEND=""
+fi
-inherit bash-completion-r1 cmake-utils eutils git-2 multilib toolchain-funcs
+ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
DESCRIPTION="The ultimate molecular dynamics simulation package"
HOMEPAGE="http://www.gromacs.org/"
-LICENSE="GPL-2"
+# see COPYING for details
+# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
+# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
+LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
SLOT="0/${PV}"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X blas doc -double-precision +fftw gsl lapack mpi +single-precision test
-+threads xml zsh-completion ${ACCE_IUSE}"
+KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
CDEPEND="
X? (
@@ -32,99 +51,121 @@ CDEPEND="
x11-libs/libICE
)
blas? ( virtual/blas )
+ cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
fftw? ( sci-libs/fftw:3.0 )
gsl? ( sci-libs/gsl )
lapack? ( virtual/lapack )
+ mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
- xml? ( dev-libs/libxml2:2 )"
+ "
DEPEND="${CDEPEND}
- virtual/pkgconfig"
+ virtual/pkgconfig
+ ${LIVE_DEPEND}"
RDEPEND="${CDEPEND}"
-RESTRICT="test"
-
-src_prepare() {
- #add user patches from /etc/portage/patches/sci-chemistry/gromacs
- epatch_user
-
- 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
+REQUIRED_USE="
+ || ( single-precision double-precision )
+ cuda? ( single-precision )
+ mkl? ( !blas !fftw !lapack )"
- GMX_DIRS=""
- use single-precision && GMX_DIRS+=" float"
- use double-precision && GMX_DIRS+=" double"
- #if neither single-precision nor double-precision is enabled
- #build at least default (single)
- [ -z "$GMX_DIRS" ] && GMX_DIRS+=" float"
+DOCS=( AUTHORS README )
+HTML_DOCS=( "${ED}"/usr/share/gromacs/html/ )
- for x in ${GMX_DIRS}; do
- mkdir -p "${WORKDIR}/${P}_${x}" || die
- use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}"
- done
+pkg_pretend() {
+ [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
+ use openmp && ! tc-has-openmp && \
+ die "Please switch to an openmp compatible compiler"
}
-src_configure() {
- local mycmakeargs_pre=( )
- #from gromacs configure
- if use fftw; then
- mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3")
+src_unpack() {
+ if [[ ${PV} != *9999 ]]; then
+ default
else
- mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack")
- ewarn "WARNING: The built-in FFTPACK routines are slow."
- ewarn "Are you sure you don\'t want to use FFTW?"
- ewarn "It is free and much faster..."
+ git-2_src_unpack
+ if use doc; then
+ EGIT_REPO_URI="git://git.gromacs.org/manual.git" \
+ EGIT_BRANCH="release-4-6" EGIT_NOUNPACK="yes" EGIT_COMMIT="release-4-6" \
+ EGIT_SOURCEDIR="${WORKDIR}/manual"\
+ git-2_src_unpack
+ fi
+ if use test; then
+ EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
+ EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
+ EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\
+ git-2_src_unpack
+ fi
fi
+}
- if [[ $(gcc-version) == "4.1" ]]; then
- eerror "gcc 4.1 is not supported by gromacs"
- eerror "please run test suite"
- die
- fi
+src_prepare() {
+ #notes/todos
+ # -on apple: there is framework support
- #note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
- 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
+ cmake-utils_src_prepare
+
+ use cuda && cuda_src_prepare
- 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."
+ GMX_DIRS=""
+ use single-precision && GMX_DIRS+=" float"
+ use double-precision && GMX_DIRS+=" double"
+
+ if use test; then
+ for x in ${GMX_DIRS}; do
+ mkdir -p "${WORKDIR}/${P}_${x}" || die
+ cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
+ done
fi
- #go from slowest to fasterest acceleration
+ DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
+}
+
+src_configure() {
+ local mycmakeargs_pre=( ) extra fft_opts=( )
+
+ #go from slowest to fastest acceleration
local acce="None"
use sse2 && acce="SSE2"
use sse4_1 && acce="SSE4.1"
use avx128fma && acce="AVX_128_FMA"
use avx256 && acce="AVX_256"
+ #to create man pages, build tree binaries are executed (bug #398437)
+ [[ ${CHOST} = *-darwin* ]] && \
+ extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
+
+ if use fftw; then
+ fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
+ elif use mkl && has_version "=sci-libs/mkl-10*"; then
+ fft_opts=( -DGMX_FFT_LIBRARY=mkl
+ -DMKL_INCLUDE_DIR="${MKLROOT}/include"
+ -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
+ )
+ elif use mkl; then
+ local bits=$(get_libdir)
+ fft_opts=( -DGMX_FFT_LIBRARY=mkl
+ -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
+ -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
+ )
+ else
+ fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
+ fi
+
mycmakeargs_pre+=(
+ "${fft_opts[@]}"
$(cmake-utils_use X GMX_X11)
$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
$(cmake-utils_use gsl GMX_GSL)
$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
- $(cmake-utils_use threads GMX_THREADS)
- $(cmake-utils_use xml GMX_XML)
+ $(cmake-utils_use openmp GMX_OPENMP)
+ $(cmake-utils_use offensive GMX_COOL_QUOTES)
-DGMX_DEFAULT_SUFFIX=off
-DGMX_ACCELERATION="$acce"
-DGMXLIB="$(get_libdir)"
+ -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+ -DGMX_PREFIX_LIBMD=ON
+ -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
+ -DGMX_USE_GCC44_BUG_WORKAROUND=OFF
+ ${extra}
)
for x in ${GMX_DIRS}; do
@@ -132,17 +173,32 @@ src_configure() {
local suffix=""
#if we build single and double - double is suffixed
use double-precision && use single-precision && \
- [ "${x}" = "double" ] && suffix="_d"
+ [[ ${x} = "double" ]] && suffix="_d"
local p
- [ "${x}" = "double" ] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
+ [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
+ local cuda=( "-DGMX_GPU=OFF" )
+ [[ ${x} = "float" ]] && use cuda && \
+ cuda=( -DGMX_GPU=ON )
mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
+ $(cmake-utils_use threads GMX_THREAD_MPI) "${cuda[@]}" -DGMX_OPENMM=OFF
+ "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+ if [[ ${x} = float ]] && use openmm; then
+ einfo "Configuring for openmm build"
+ mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
+ -DGMX_THREAD_MPI=OFF -DGMX_GPU=OFF -DGMX_OPENMM=ON
+ -DOpenMM_PLUGIN_DIR="${EPREFIX}/usr/$(get_libdir)/plugins"
+ -DGMX_BINARY_SUFFIX="_openmm" -DGMX_LIBS_SUFFIX="_openmm" )
+ BUILD_DIR="${WORKDIR}/${P}_openmm" \
+ OPENMM_ROOT_DIR="${EPREFIX}/usr" cmake-utils_src_configure
+ fi
use mpi || continue
einfo "Configuring for ${x} precision with mpi"
- mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON
+ mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF
+ -DGMX_MPI=ON ${cuda} -DGMX_OPENMM=OFF
-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
done
}
@@ -151,6 +207,11 @@ src_compile() {
einfo "Compiling for ${x} precision"
BUILD_DIR="${WORKDIR}/${P}_${x}"\
cmake-utils_src_compile
+ if [[ ${x} = float ]] && use openmm; then
+ einfo "Compiling for openmm build"
+ BUILD_DIR="${WORKDIR}/${P}_openmm"\
+ cmake-utils_src_compile mdrun
+ fi
use mpi || continue
einfo "Compiling for ${x} precision with mpi"
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
@@ -160,11 +221,8 @@ src_compile() {
src_test() {
for x in ${GMX_DIRS}; do
- local oldpath="${PATH}"
- export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
- cd "${WORKDIR}/${P}_${x}"
- emake -j1 tests || die "${x} Precision test failed"
- export PATH="${oldpath}"
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake-utils_src_make check
done
}
@@ -172,40 +230,38 @@ src_install() {
for x in ${GMX_DIRS}; do
BUILD_DIR="${WORKDIR}/${P}_${x}" \
cmake-utils_src_install
+ if [[ ${x} = float ]] && use openmm; then
+ BUILD_DIR="${WORKDIR}/${P}_openmm" \
+ DESTDIR="${D}" cmake-utils_src_make install-mdrun
+ fi
+ #manual can only be build after gromacs was installed once in image
+ if use doc && [[ $PV = *9999* && ! -d ${WORKDIR}/manual_build ]]; then
+ mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" )
+ BUILD_DIR="${WORKDIR}"/manual_build \
+ CMAKE_USE_DIR="${WORKDIR}/manual" cmake-utils_src_configure
+ [[ ${CHOST} = *-darwin* ]] && \
+ export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}${DYLD_LIBRARY_PATH:+:}${ED}/usr/$(get_libdir)"
+ BUILD_DIR="${WORKDIR}"/manual_build cmake-utils_src_make
+ [[ ${CHOST} = *-darwin* ]] && DYLD_LIBRARY_PATH="${ED}/usr/$(get_libdir)"
+ newdoc "${WORKDIR}"/manual_build/gromacs.pdf "${PN}-manual-${PV}.pdf"
+ fi
use mpi || continue
- #cmake-utils_src_install does not support args
- #using cmake-utils_src_compile instead
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
- cmake-utils_src_make install-mdrun DESTDIR="${D}"
+ DESTDIR="${D}" cmake-utils_src_make install-mdrun
done
- sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
- echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs"
-
- doenvd "${T}/80gromacs"
- rm -f "${ED}"/usr/bin/GMXRC*
-
+ use doc && [[ $PV != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf"
newbashcomp "${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
- dohtml -r "${ED}usr/share/gromacs/html/"
- insinto /usr/share/gromacs
- doins "admin/programs.txt"
- ls -1 "${ED}"/usr/bin | sed -e '/_d$/d' > "${T}"/programs.list
- doins "${T}"/programs.list
- fi
- rm -rf "${ED}usr/share/gromacs/html/"
+ rm -f "${ED}"usr/bin/completion.*
+ rm -rf "${ED}"usr/share/gromacs/html
+ rm -f "${ED}"usr/bin/g_options*
+ rm -f "${ED}"usr/bin/GMXRC*
+
+ readme.gentoo_create_doc
}
pkg_postinst() {
@@ -213,9 +269,11 @@ pkg_postinst() {
einfo "Please read and cite:"
einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
einfo "http://dx.doi.org/10.1021/ct700301q"
+ if use offensive; then
+ einfo
+ einfo $(g_luck)
+ einfo "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
+ fi
einfo
- einfo $(g_luck)
- einfo "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
- einfo
- elog "Gromacs can use sci-chemistry/vmd to read additional file formats"
+ readme.gentoo_print_elog
}