aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorAlexey Shvetsov <alexxy@gentoo.org>2016-07-11 22:40:06 +0300
committerAlexey Shvetsov <alexxy@gentoo.org>2016-07-11 22:40:06 +0300
commite505c9758afd89769db26e1c46adce0215a0daea (patch)
tree83623b6b708117b8441c8afe67e007338f0ece8e /sci-chemistry
parentsci-chemistry/gromacs: Add myself as maintainer (diff)
downloadsci-e505c9758afd89769db26e1c46adce0215a0daea.tar.gz
sci-e505c9758afd89769db26e1c46adce0215a0daea.tar.bz2
sci-e505c9758afd89769db26e1c46adce0215a0daea.zip
sci-chemistry/gromacs: Add 2016 RC1
Package-Manager: portage-2.3.0
Diffstat (limited to 'sci-chemistry')
-rw-r--r--sci-chemistry/gromacs/Manifest2
-rw-r--r--sci-chemistry/gromacs/gromacs-2016.9999.ebuild10
-rw-r--r--sci-chemistry/gromacs/gromacs-2016_rc1.ebuild266
-rw-r--r--sci-chemistry/gromacs/gromacs-9999.ebuild10
-rw-r--r--sci-chemistry/gromacs/metadata.xml3
5 files changed, 278 insertions, 13 deletions
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
new file mode 100644
index 000000000..1fed511a1
--- /dev/null
+++ b/sci-chemistry/gromacs/Manifest
@@ -0,0 +1,2 @@
+DIST gromacs-2016-rc1.tar.gz 27322876 SHA256 69a307009cd9015b09af3c39ed4b193e71c59deccc3b34e758b3b9b5a34f7a47 SHA512 9c74ab718c9c894525524c0612aac93246be8aff86491f4b4854783d5e112c346b8c6bd185ec951a76aa398fdb2132abf42bb27b644440ceb6f6baeeede9c3a0 WHIRLPOOL cdb4d417770720069c6e1de2930d36f3a952ce9b2d111d1dd9a2f3b87d28cc199a17745db2c580da6606eb9dd59dfd9c4ddb5297de08202067dee0160a3a985e
+DIST regressiontests-2016-rc1.tar.gz 66629314 SHA256 63fcf8fcb1371478b705dd8f44f2c284ac8c6f3e7eb8146f751f6e0e0f2db415 SHA512 8900efb605d69aa723bab398556a9b0d94da2b25d55948a3903f2d5a47c0f89306fffe3b0c7e780508b301463243bc73191a9dee6494ab288ca89831e71f741a WHIRLPOOL a205113884c65de4e9a75f0af59a1be910cf82a7fca8ba561c13815793f98ee0af342a0318044c49c757c8b25cfebb8b42299e885345e7f1af695f2e2b591297
diff --git a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild b/sci-chemistry/gromacs/gromacs-2016.9999.ebuild
index b30ff552e..1ca034301 100644
--- a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2016.9999.ebuild
@@ -18,7 +18,7 @@ if [[ $PV = *9999* ]]; then
KEYWORDS=""
else
SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
+ test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
fi
@@ -32,7 +32,7 @@ HOMEPAGE="http://www.gromacs.org/"
# 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}"
-IUSE="X blas cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
CDEPEND="
X? (
@@ -43,6 +43,7 @@ CDEPEND="
blas? ( virtual/blas )
cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
fftw? ( sci-libs/fftw:3.0 )
+ hwloc? ( sys-apps/hwloc )
lapack? ( virtual/lapack )
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
@@ -149,15 +150,13 @@ src_configure() {
-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-DGMX_OPENMP=$(usex openmp)
-DGMX_COOL_QUOTES=$(usex offensive)
- -DGMX_EXTERNAL_BOOST=$(usex boost)
-DGMX_USE_TNG=$(usex tng)
-DGMX_BUILD_MANUAL=$(usex doc)
+ -DGMX_HWLOC=$(usex hwloc)
-DGMX_DEFAULT_SUFFIX=off
-DGMX_SIMD="$acce"
-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
- -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
- -DGMX_USE_GCC44_BUG_WORKAROUND=OFF
-DBUILD_TESTING=OFF
-DGMX_BUILD_UNITTESTS=OFF
${extra}
@@ -179,7 +178,6 @@ src_configure() {
-DGMX_MPI=OFF
-DGMX_THREAD_MPI=$(usex threads)
"${cuda[@]}"
- -DGMX_OPENMM=OFF
"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-DGMX_BINARY_SUFFIX="${suffix}"
-DGMX_LIBS_SUFFIX="${suffix}"
diff --git a/sci-chemistry/gromacs/gromacs-2016_rc1.ebuild b/sci-chemistry/gromacs/gromacs-2016_rc1.ebuild
new file mode 100644
index 000000000..1ca034301
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-2016_rc1.ebuild
@@ -0,0 +1,266 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs
+
+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"
+ [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}"
+ inherit git-r3
+ KEYWORDS=""
+else
+ SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
+ test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
+ KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+fi
+
+ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+
+# see COPYING for details
+# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
+# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
+LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
+SLOT="0/${PV}"
+IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+
+CDEPEND="
+ X? (
+ x11-libs/libX11
+ x11-libs/libSM
+ x11-libs/libICE
+ )
+ blas? ( virtual/blas )
+ cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
+ fftw? ( sci-libs/fftw:3.0 )
+ hwloc? ( sys-apps/hwloc )
+ lapack? ( virtual/lapack )
+ mkl? ( sci-libs/mkl )
+ mpi? ( virtual/mpi )
+ "
+DEPEND="${CDEPEND}
+ virtual/pkgconfig
+ doc? (
+ app-doc/doxygen
+ dev-texlive/texlive-latex
+ dev-texlive/texlive-latexextra
+ media-gfx/imagemagick
+ )"
+RDEPEND="${CDEPEND}"
+
+REQUIRED_USE="
+ || ( single-precision double-precision )
+ cuda? ( single-precision )
+ mkl? ( !blas !fftw !lapack )"
+
+DOCS=( AUTHORS README )
+
+if [[ ${PV} != *9999 ]]; then
+ S="${WORKDIR}/${PN}-${PV/_/-}"
+fi
+
+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_unpack() {
+ if [[ ${PV} != *9999 ]]; then
+ default
+ else
+ git-r3_src_unpack
+ if use test; then
+ EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
+ EGIT_BRANCH="${EGIT_BRANCH}" \
+ EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
+ git-r3_src_unpack
+ fi
+ fi
+}
+
+src_prepare() {
+ #notes/todos
+ # -on apple: there is framework support
+
+ cmake-utils_src_prepare
+
+ use cuda && cuda_src_prepare
+
+ 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
+
+ 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 cpu_flags_x86_sse2 && acce="SSE2"
+ use cpu_flags_x86_sse4_1 && acce="SSE4.1"
+ use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
+ use cpu_flags_x86_avx && acce="AVX_256"
+ use cpu_flags_x86_avx2 && acce="AVX2_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+=(
+ "${fft_opts[@]}"
+ -DGMX_X11=$(usex X)
+ -DGMX_EXTERNAL_BLAS=$(usex blas)
+ -DGMX_EXTERNAL_LAPACK=$(usex lapack)
+ -DGMX_OPENMP=$(usex openmp)
+ -DGMX_COOL_QUOTES=$(usex offensive)
+ -DGMX_USE_TNG=$(usex tng)
+ -DGMX_BUILD_MANUAL=$(usex doc)
+ -DGMX_HWLOC=$(usex hwloc)
+ -DGMX_DEFAULT_SUFFIX=off
+ -DGMX_SIMD="$acce"
+ -DGMX_LIB_INSTALL_DIR="$(get_libdir)"
+ -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+ -DBUILD_TESTING=OFF
+ -DGMX_BUILD_UNITTESTS=OFF
+ ${extra}
+ )
+
+ for x in ${GMX_DIRS}; do
+ einfo "Configuring for ${x} precision"
+ local suffix=""
+ #if we build single and double - double is suffixed
+ use double-precision && use single-precision && \
+ [[ ${x} = "double" ]] && suffix="_d"
+ local p
+ [[ ${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[@]} ${p}
+ -DGMX_MPI=OFF
+ -DGMX_THREAD_MPI=$(usex threads)
+ "${cuda[@]}"
+ "$(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
+ [[ ${CHOST} != *-darwin* ]] || \
+ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
+ use mpi || continue
+ einfo "Configuring for ${x} precision with mpi"
+ mycmakeargs=(
+ ${mycmakeargs_pre[@]} ${p}
+ -DGMX_THREAD_MPI=OFF
+ -DGMX_MPI=ON ${cuda}
+ -DGMX_OPENMM=OFF
+ -DGMX_BUILD_MDRUN_ONLY=ON
+ -DBUILD_SHARED_LIBS=OFF
+ -DGMX_BUILD_MANUAL=OFF
+ -DGMX_BINARY_SUFFIX="_mpi${suffix}"
+ -DGMX_LIBS_SUFFIX="_mpi${suffix}"
+ )
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+ [[ ${CHOST} != *-darwin* ]] || \
+ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
+ done
+}
+
+src_compile() {
+ for x in ${GMX_DIRS}; do
+ einfo "Compiling for ${x} precision"
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake-utils_src_compile
+ # not 100% necessary for rel ebuilds as available from website
+ if use doc; then
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake-utils_src_compile manual
+ fi
+ use mpi || continue
+ einfo "Compiling for ${x} precision with mpi"
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+ cmake-utils_src_compile
+ done
+}
+
+src_test() {
+ for x in ${GMX_DIRS}; do
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake-utils_src_make check
+ done
+}
+
+src_install() {
+ for x in ${GMX_DIRS}; do
+ BUILD_DIR="${WORKDIR}/${P}_${x}" \
+ cmake-utils_src_install
+ if use doc; then
+ newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
+ fi
+ use mpi || continue
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+ cmake-utils_src_install
+ done
+
+ if use tng; then
+ insinto /usr/include/tng
+ doins src/external/tng_io/include/tng/*h
+ fi
+ # drop unneeded stuff
+ rm "${ED}"usr/bin/GMXRC* || die
+ for x in "${ED}"usr/bin/gmx-completion-*.bash ; do
+ local n=${x##*/gmx-completion-}
+ n="${n%.bash}"
+ cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
+ newbashcomp "${T}"/"${n}" "${n}"
+ done
+ rm "${ED}"usr/bin/gmx-completion*.bash || die
+ readme.gentoo_create_doc
+}
+
+pkg_postinst() {
+ einfo
+ einfo "Please read and cite:"
+ einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
+ einfo "http://dx.doi.org/10.1021/ct700301q"
+ einfo
+ readme.gentoo_print_elog
+}
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index b30ff552e..1ca034301 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -18,7 +18,7 @@ if [[ $PV = *9999* ]]; then
KEYWORDS=""
else
SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
+ test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
fi
@@ -32,7 +32,7 @@ HOMEPAGE="http://www.gromacs.org/"
# 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}"
-IUSE="X blas cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
CDEPEND="
X? (
@@ -43,6 +43,7 @@ CDEPEND="
blas? ( virtual/blas )
cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
fftw? ( sci-libs/fftw:3.0 )
+ hwloc? ( sys-apps/hwloc )
lapack? ( virtual/lapack )
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
@@ -149,15 +150,13 @@ src_configure() {
-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-DGMX_OPENMP=$(usex openmp)
-DGMX_COOL_QUOTES=$(usex offensive)
- -DGMX_EXTERNAL_BOOST=$(usex boost)
-DGMX_USE_TNG=$(usex tng)
-DGMX_BUILD_MANUAL=$(usex doc)
+ -DGMX_HWLOC=$(usex hwloc)
-DGMX_DEFAULT_SUFFIX=off
-DGMX_SIMD="$acce"
-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
- -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
- -DGMX_USE_GCC44_BUG_WORKAROUND=OFF
-DBUILD_TESTING=OFF
-DGMX_BUILD_UNITTESTS=OFF
${extra}
@@ -179,7 +178,6 @@ src_configure() {
-DGMX_MPI=OFF
-DGMX_THREAD_MPI=$(usex threads)
"${cuda[@]}"
- -DGMX_OPENMM=OFF
"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-DGMX_BINARY_SUFFIX="${suffix}"
-DGMX_LIBS_SUFFIX="${suffix}"
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 0c7b1076f..e98cd51fc 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -17,7 +17,8 @@
<flag name="cuda">Enable cuda non-bonded kernels</flag>
<flag name="double-precision">More precise calculations at the expense of speed</flag>
<flag name="single-precision">Single precision version of gromacs (default)</flag>
- <flag name="boost">Enable external boost library</flag>
+ <flag name="boost">Enable external boost library</flag>
+ <flag name="hwloc">Enable HWLoc lib support</flag>
<flag name="tng">Enable new trajectory format - tng</flag>
<flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag>
<!-- acceleration optimization flags -->