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sci-chemistry/gromacs: version bump
Package-Manager: Portage-2.3.6, Repoman-2.3.1
This commit is contained in:
Christoph Junghans
@@ -1,12 +1,14 @@
|
||||
DIST gromacs-2016.1.tar.gz 27336258 SHA256 9e7d2892a903777b982bc9ab4306de969d92cb45b51a562f523ec5fe58db41e3 SHA512 d30a4ad5faa6e12c95b8e94acaabc387d9aab3780490f5442c48ccac2f86bef6dca60df5bb6097dbc68ab28e6f1a15e234e1244606afdf12a841b88ece65c97b WHIRLPOOL 4be9c84d99286889dda23d9f1e2dd7b2d87a70740fb686bd58e59155771e897471d0920b02c5ec529a01a4b01428ebb2ca5b27e4d8df9034d2d3b33c5ab1a1ca
|
||||
DIST gromacs-2016.2.tar.gz 27339623 SHA256 b6ac3632b848ab0c19f8f319dd5b58fcd09b8e2005ee7509478606613e5409a5 SHA512 f5e74bb8c126823c90d205ac0f0835e61fdd13a4550bc15aa9c972ee9b187f6451cdc90877c17276d2f889d61abb5eaa5ea1b54f7cbf3da67074146c749c1aa6 WHIRLPOOL 698c4d4e67266483be4f1047eb947b243b5c8caa3c5e30bdab6b5f0dd302bb51ac5aa6e3a3357beab567cf71c1b8ecc1f9684a89754d18f963dd6f5fc90a33f4
|
||||
DIST gromacs-2016.3.tar.gz 27342692 SHA256 7bf00e74a9d38b7cef9356141d20e4ba9387289cbbfd4d11be479ef932d77d27 SHA512 16593df0a52620766fb86cfeb16328793503f860cb07cdbbd503ba7f41e6430efb4848389b7179ca3907b57311162666d05224b454e1afb1b74b220f38498d86 WHIRLPOOL dfe31f212545ae2baf7373fde31f715a8df203d098d3ace915d4269b7bf16d06a1f91ead33ccbf8a17e9e0091b593818d0ce2eff151ce532238a8c27f5e20cda
|
||||
DIST gromacs-2016.4.tar.gz 27368706 SHA256 4be9d3bfda0bdf3b5c53041e0b8344f7d22b75128759d9bfa9442fe65c289264 SHA512 69661d2a7a8a5259be277de35e2baa4b688d1f7bef225fc7d733a9b00c6ee135dcbad517c7c9f751121647c2fbd085f2c9cdf22dbd941c7ebc5d3b09e7e08f1f WHIRLPOOL c1586377d2a27f0b529370efb63e09ecca64cdb3d418fe9bc4f3ea1ff82ff5293d159834f4ed5d0136d801095d6f4085722e0d91bce873776fa4549853497ff7
|
||||
DIST gromacs-2016.tar.gz 27321561 SHA256 aa0a27cd13050a4b70aacfbd169ddce2fe507c7e668f460ecf6cf32afcac5771 SHA512 756771baaa85a1d16e7d5b8e4c96bbd1c04c7acdc536a253886cff186316330f06d60d206a0159efb15f47f161c779d3757dc5dbceab8c097241c1382d376201 WHIRLPOOL 1cc3d3797e1aaf93e1e0cb2e71173896e33fee2bb03f4e97e06be3ab85842e6da3feaf8701425358f1d701e00159ff6ce3b24fa1488d5e8ef70a1acbb914361c
|
||||
DIST gromacs-5.0.4.tar.gz 26342095 SHA256 78068eeccc0b950018ddb45c41280e53c8bedae4639dca48e17c940f8896b23b SHA512 bc62b623bf71dcaa948aaf7563a3d3afa973da0702062848a20323db202e862dcee413197dacd1472866ccb40fce7709e283177b1c6c49514064f23e6c46b5ee WHIRLPOOL d8458d3d563e015e830622ae0c924e896765a6329ffe4cb1a31c7aef3c804f392d29e3f1db5617051e85058403422f7d69a160a6c7cc810564696d88f9d50bd4
|
||||
DIST gromacs-5.1.3.tar.gz 27095702 SHA256 c962d9446939a9ba9905e7ca440c9306fd310f08600da3b744806bfd0eacccde SHA512 9ab26e1b2268f8d567b89b2d99d0b75b937b28edceaec56d17ca3243c76faa31255ffc0c45d762c7c693fe500b00e36ad43b80572d1d7f92dc87f9d2d98c0ba6 WHIRLPOOL bdd9c63ceb5e61963c4edd0af815cc34a3f237d8dee410c834b9b55bb82374de65b437828390a668282e50428b9907b887cd5265caf2a2007fc7673e7ab23733
|
||||
DIST regressiontests-2016.1.tar.gz 67094518 SHA256 10c9f50ff3cb32cf629aa35e35d957965dcfce4af84a6569e6d65a16c4e09eb7 SHA512 fc01c802d81400373a147171881f3b7b9309402e8ffb08287ba393aefbb701ba93bbe0b9549ff6fa264a8befbba445c2d2c7450633063a724f78ec8ca81ae8c9 WHIRLPOOL e8c54164558fcbaa1e65e9280e438882c96bbbaa6c9389a2ee5aed37d70b83b6b36e95dd5141b4e64b303e3799411ee01cf04aa919f25014d172011e49714126
|
||||
DIST regressiontests-2016.2.tar.gz 67095329 SHA256 53fa9ad062cc3e269fc6186db1ccbb64a93d36c2fa1cafd6433564ba2583c112 SHA512 e0aceb56d1f38a7e6ab9fdaac5063fd20c5b3a162ffb6eddd0e6dc7dff9b724bfe31363493a9437e9f9d5421a534b375960fcb31e903a4901a0fa94ed8511294 WHIRLPOOL 408741abf781ecf880f8f1337590ed81196cabcf25a49d2cd97bbe0596c8495ea866d6aa64a944c6ee0eb209110883dff204f0f52f6aa6e6dd52f50bcbbade66
|
||||
DIST regressiontests-2016.3.tar.gz 67093968 SHA256 a3d1b09acfc61820dddd765a381f706190b4657606488f1e676becb859ea7ecc SHA512 ee87df9f339954da0e1f1b4c8b8d4deb574f3b73d174010a295a7a0e8bc462ead7691090ea7cf8ac3d984a6cd70f1cd22c3592fa161b2967061ae5ba2796286b WHIRLPOOL 2e986136f7faf6db108bc79e6fb6db9fe81d05f5af8bc27037b80cd25869f7cd4162d5cabc03994b36c71945910be79a217ff27f61463d1548cbdff6acd99f56
|
||||
DIST regressiontests-2016.4.tar.gz 67643648 SHA256 d58d1a2a53c22c06e2dc03bd98ae1eea0a0d51696a1f20f635dfc394fa3da957 SHA512 367438b897a05e1cc0dcd1d3872fb6a0e9ff6b1146e9448d941d6517dce789f0c478d20cf0a4f3565070f132dc88872441aadb8b499f59efa0e1e4a6dd6a7135 WHIRLPOOL 695a3b7f81915247a90e95c0a83823c0297fba6ae6266195e86c61ec540ca58afd8d01ba236c5ddb3f44b41fb9301ba6a836b15cad1875bae42ba6276670daff
|
||||
DIST regressiontests-2016.tar.gz 66908712 SHA256 30a72362f011fd9e3a8d33004018126f938536c13fcb70f590afc74beaec5406 SHA512 59902c1973c33ea8f003f21a737dc7cc64da3258112322eedc9834b53628134a6817d5ee5b3950c9bfd97a3a0580aef88ddef0609ef2c58693c96c7575651e01 WHIRLPOOL 9d210aed00ddfa57df47733169997ef04dec84c524eb5a9c5c6dd9b05ad9ec2d7f3c8a5a43f2ade9be166d80f35a260c04b1a48ac092f5969a213475bb63ae20
|
||||
DIST regressiontests-5.0.4.tar.gz 65193251 SHA256 89ad9bc067035ac8f340319b538c446983d937b910067e871911d7afe2ecb3f0 SHA512 747725fa28c1c9525596bdeeb8809e45268e19036c11dac67d043aa1c51748688ca37eb6014eb7e819eb927a8b9ca2631d0ace4cdff8ed491b08c316c530ab65 WHIRLPOOL e15ccab0a0beefac41aeff11e2e596e971167f1590eed159ff82c4a8e3aec1d234287be597026951904ecfe6099f30ef3bcd48f2098b9f5201bde62e15fbc4f9
|
||||
DIST regressiontests-5.1.3.tar.gz 66994083 SHA256 fd5797dcfd29f7ae70857a438dcd4200a8006fce222f297892c8e90123993ebc SHA512 486e86eb3b75bae822abe82dac4e1098aa13723bd04214021f835a2f0b847303f015a9ececc33aa5ae63d31a2eeae07e512f22464b6c0e26d1286b0781578022 WHIRLPOOL 6ddb76859ee8fa3aba4d995e397970e6fd270acbdd6cc07ab77de0aebb0bfdbd2bd1107ae39d4410e750641047ae4b75c703eafad95a57ff42deb3bf1c742d08
|
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|
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276
sci-chemistry/gromacs/gromacs-2016.4.ebuild
Normal file
276
sci-chemistry/gromacs/gromacs-2016.4.ebuild
Normal file
@@ -0,0 +1,276 @@
|
||||
# Copyright 1999-2017 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
|
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|
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EAPI=6
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CMAKE_MAKEFILE_GENERATOR="ninja"
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|
||||
inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
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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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||||
https://github.com/gromacs/gromacs.git
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||||
http://repo.or.cz/r/gromacs.git"
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[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
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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="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
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fi
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|
||||
ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
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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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|
||||
# 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 cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
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||||
|
||||
CDEPEND="
|
||||
X? (
|
||||
x11-libs/libX11
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||||
x11-libs/libSM
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||||
x11-libs/libICE
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||||
)
|
||||
blas? ( virtual/blas )
|
||||
cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
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||||
fftw? ( sci-libs/fftw:3.0 )
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||||
hwloc? ( sys-apps/hwloc )
|
||||
lapack? ( virtual/lapack )
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||||
mkl? ( sci-libs/mkl )
|
||||
mpi? ( virtual/mpi )
|
||||
"
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||||
DEPEND="${CDEPEND}
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||||
virtual/pkgconfig
|
||||
doc? (
|
||||
app-doc/doxygen
|
||||
dev-texlive/texlive-latex
|
||||
dev-texlive/texlive-latexextra
|
||||
media-gfx/imagemagick
|
||||
)
|
||||
dev-libs/tinyxml2
|
||||
"
|
||||
RDEPEND="${CDEPEND}"
|
||||
|
||||
REQUIRED_USE="
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||||
|| ( single-precision double-precision )
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||||
cuda? ( single-precision )
|
||||
mkl? ( !blas !fftw !lapack )"
|
||||
|
||||
DOCS=( AUTHORS README )
|
||||
|
||||
if [[ ${PV} != *9999 ]]; then
|
||||
S="${WORKDIR}/${PN}-${PV/_/-}"
|
||||
fi
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||||
|
||||
pkg_pretend() {
|
||||
[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
|
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use openmp && ! tc-has-openmp && \
|
||||
die "Please switch to an openmp compatible compiler"
|
||||
}
|
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|
||||
src_unpack() {
|
||||
if [[ ${PV} != *9999 ]]; then
|
||||
default
|
||||
else
|
||||
git-r3_src_unpack
|
||||
if use test; then
|
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EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
|
||||
EGIT_BRANCH="${EGIT_BRANCH}" \
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||||
EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
|
||||
git-r3_src_unpack
|
||||
fi
|
||||
fi
|
||||
}
|
||||
|
||||
src_prepare() {
|
||||
#notes/todos
|
||||
# -on apple: there is framework support
|
||||
|
||||
xdg_environment_reset #591952
|
||||
|
||||
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 && has_version "<sci-libs/mkl-11.3"; 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)"
|
||||
)
|
||||
elif use mkl; then
|
||||
local bits=$(get_libdir)
|
||||
fft_opts=( -DGMX_FFT_LIBRARY=mkl
|
||||
-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/linux/mkl/include)"
|
||||
-DMKL_LIBRARIES="$(echo /opt/intel/*/linux/mkl/lib/*${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
|
||||
-DGMX_EXTERNAL_TINYXML2=ON
|
||||
${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 "https://dx.doi.org/10.1021/ct700301q"
|
||||
einfo
|
||||
readme.gentoo_print_elog
|
||||
}
|
||||
Reference in New Issue
Block a user