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sci-chemistry/gromacs: Bump =)

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Package-Manager: Portage-2.3.19, Repoman-2.3.6
This commit is contained in:
Alexey Shvetsov
2018-06-06 23:16:14 +03:00
parent aebb24f158
commit bcebf81201
7 changed files with 2 additions and 1384 deletions
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14
sci-chemistry/gromacs/Manifest
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@@ -1,20 +1,10 @@
DIST gromacs-2016.1.tar.gz 27336258 BLAKE2B 3a255252e789a4260b559ab5ce0676c884c40093f647c4c5b0f5ef143383cdb840a668bafcb921f39a81064e9893ddc3d1f7e481bd40ff88f870e94d232b297d SHA512 d30a4ad5faa6e12c95b8e94acaabc387d9aab3780490f5442c48ccac2f86bef6dca60df5bb6097dbc68ab28e6f1a15e234e1244606afdf12a841b88ece65c97b
DIST gromacs-2016.2.tar.gz 27339623 BLAKE2B c3548f4abdc4c1b09a79a3da99d7ca8060daca7307e4c5b81bd97d54adfb9621fbccf1ea7fd96c3676d6b44c20f9f4cd2168ce131799792512fad3b8b1ac0522 SHA512 f5e74bb8c126823c90d205ac0f0835e61fdd13a4550bc15aa9c972ee9b187f6451cdc90877c17276d2f889d61abb5eaa5ea1b54f7cbf3da67074146c749c1aa6
DIST gromacs-2016.3.tar.gz 27342692 BLAKE2B 3bea357cb672f41dda68c0d4291c06e2ab8bbc91629e25c9e56741223911be7994be10b2427fb1ca1cd41e511d23323851ba3211ee8590f152e23a64b2253095 SHA512 16593df0a52620766fb86cfeb16328793503f860cb07cdbbd503ba7f41e6430efb4848389b7179ca3907b57311162666d05224b454e1afb1b74b220f38498d86
DIST gromacs-2016.4.tar.gz 27368706 BLAKE2B 2a176812fe2a097d72c7148ff5ed4ed7209279cf439af6a969c3aba81157c59a4d9af34d19c7b1da088b0a4ab981b489b84446afbcaf64b20724bda1dc3560ff SHA512 69661d2a7a8a5259be277de35e2baa4b688d1f7bef225fc7d733a9b00c6ee135dcbad517c7c9f751121647c2fbd085f2c9cdf22dbd941c7ebc5d3b09e7e08f1f
DIST gromacs-2016.5.tar.gz 27369491 BLAKE2B 4a8bf1ae3e298ac2e26ec476130720dc3ef00db5d999e3a45fdbfd7fbfe7e94fbc86be6ff0f2f23552769c8bc851ce49c73f6fc1ab13f372523279b93e7794d7 SHA512 9cb8ff88871aa5df0967c60ba303c03296c6fa3c215cd01b26259df7753f0014f04222078ab4b84a66a1f709997837134d5c0f74da19b78322e410010c9d9e10
DIST gromacs-2016.tar.gz 27321561 BLAKE2B cdcf0aa5ac36981e736fd2ecc2f641e99f40146d829c88e5ff973c7b7c3c1ab920f7822c336e9eea87a8605362e723d7477dd07f9154c8a38476a3f6c391d6aa SHA512 756771baaa85a1d16e7d5b8e4c96bbd1c04c7acdc536a253886cff186316330f06d60d206a0159efb15f47f161c779d3757dc5dbceab8c097241c1382d376201
DIST gromacs-2018-rc1.tar.gz 29863602 BLAKE2B 1b8146198aef435d74c57b5a6e42b8107416896fed71444830baf4368604c1b35326a77815c5125e1610a9765cf1d5d51d3a69a04d3679f7c1f3618598258c0a SHA512 f2a56a2d3ce6efd170f22d66dbb9418ae59257aff27853037570d0939582df947c7558aa652626dd911ee22c037ab0cb1b340b5008bc8f40d27d90883100d375
DIST gromacs-2018.tar.gz 29855797 BLAKE2B ff7bfd6a11d8d0fba2a0da405eb264504e18d820179eee234fd2c6e0d6a001aabd601c8a695e14b6d290fbca2253f3fc760a72c6fcaf566f88bb3675612f0bfb SHA512 95c464ec4a0c95b5e7b30571e9693f6be1bce4cd3d6f7d7eeee0f0cd9b8ad43dda4dbb8568e9502706a01d1621f288711227a935060ce524871e6521d53eb902
DIST gromacs-2018.1.tar.gz 29895119 BLAKE2B 45cc674bd78dc7dc56388a899ae50da9f10eb4dc80dad461f7e298894ee845eae744010013e682f3be4b03c1f04624111266e84cd9721415b23f87d544846827 SHA512 d29f152e9f115c7de07881c6af4cc05481e0a5520bd33142a09507e8c4df9f8b6c9d6d96efcb7adaaf4e0127b76ab247421d43918bd7e7779d6e71f5984db715
DIST gromacs-5.0.4.tar.gz 26342095 BLAKE2B 27a2483e23533ad627114c0005fa0d49a311b359c31aed6378bdd768c9dda03c3b19f11d961f0bd3b82a1711737d4b7dce13cad5fc56d058dd0110fe21421ee3 SHA512 bc62b623bf71dcaa948aaf7563a3d3afa973da0702062848a20323db202e862dcee413197dacd1472866ccb40fce7709e283177b1c6c49514064f23e6c46b5ee
DIST gromacs-5.1.3.tar.gz 27095702 BLAKE2B b7fd8fa10e8c4f4368ac551338c59374dc35f85c9fdae5d64eec62929b8f04ea724a084959b3618cd8a151bf3e0a0c84c8f75de953722effca82a4928941ce73 SHA512 9ab26e1b2268f8d567b89b2d99d0b75b937b28edceaec56d17ca3243c76faa31255ffc0c45d762c7c693fe500b00e36ad43b80572d1d7f92dc87f9d2d98c0ba6
DIST regressiontests-2016.1.tar.gz 67094518 BLAKE2B 3ae0132e246f2abcf77495bff69adb32bfe98063a824cc408279fb43022ca5e8e07afaee08f3a255657b8cdfd21ba2ff4cc428c2c3d21958ba5149ce745d436c SHA512 fc01c802d81400373a147171881f3b7b9309402e8ffb08287ba393aefbb701ba93bbe0b9549ff6fa264a8befbba445c2d2c7450633063a724f78ec8ca81ae8c9
DIST regressiontests-2016.2.tar.gz 67095329 BLAKE2B fec8a663845ad67374c8a230d1590fa9e5079460198f41cee3b788aaa1c72e8ec9dcda48bc68a594f15003d11bf6617d46cc1a09c16b7a333587b43904a16ba6 SHA512 e0aceb56d1f38a7e6ab9fdaac5063fd20c5b3a162ffb6eddd0e6dc7dff9b724bfe31363493a9437e9f9d5421a534b375960fcb31e903a4901a0fa94ed8511294
DIST regressiontests-2016.3.tar.gz 67093968 BLAKE2B a644bbd2a0398c1d84f61809a9f4f1cb89d307b0e9952f414e28d18464799e5f49fe810e342768a7b15f1d63b10bf1facb148c1d04ad670c613022302f04ea9d SHA512 ee87df9f339954da0e1f1b4c8b8d4deb574f3b73d174010a295a7a0e8bc462ead7691090ea7cf8ac3d984a6cd70f1cd22c3592fa161b2967061ae5ba2796286b
DIST regressiontests-2016.4.tar.gz 67643648 BLAKE2B 767c3b0ca1002e6ca68fc3346b7164cca3beaa52f9b1c70672b64cf80427cab045e4d924d0b67a4fe4c76e3a1c0a803964e278d2a9b14b87a555f98dd78525d3 SHA512 367438b897a05e1cc0dcd1d3872fb6a0e9ff6b1146e9448d941d6517dce789f0c478d20cf0a4f3565070f132dc88872441aadb8b499f59efa0e1e4a6dd6a7135
DIST regressiontests-2016.5.tar.gz 67641413 BLAKE2B 4fcd30c198f3acbbabf1104c040d9a686de49536a97dbeb14732bfa0ed3cf37aa61b1b0f45393668985b993d1f1862a8985e416af819cf9793f5964f3e4f43cc SHA512 31764fd99cc4185d61de5d4443ee482c27b13533451a24aa0e4899997ce275a63685424eafacae38b1a3ffd4ce0d5ebe02a90348953b04c104f91376f0edfdff
DIST regressiontests-2016.tar.gz 66908712 BLAKE2B 3039b5b46bf99dc2e34a61ed0f47f7355087c260bd1accc119f9ed99bb03c4645d05df41e301cfc6a6de6a9a369b2bf4e01a54852100577e40605e091bbe24e8 SHA512 59902c1973c33ea8f003f21a737dc7cc64da3258112322eedc9834b53628134a6817d5ee5b3950c9bfd97a3a0580aef88ddef0609ef2c58693c96c7575651e01
DIST regressiontests-2018-rc1.tar.gz 67866295 BLAKE2B 1936a4a14d3011e426e0f057d803339a8324e10d087d56f93dc7a497250a973c6b19ed2691b4641d12b7f13de01dbe36a9903a4e10e3792b842319e42ad0331a SHA512 feccf48d6af84abf350e5ad829c600f86b8e8e4f4f3378c34b209daa30965e3f68751058f12bdbb228da6b4ccd0a72c8191956ec5bd184f190000a9c97e581a9
DIST regressiontests-2018.tar.gz 67858633 BLAKE2B 21fe5ca9ad682873c616d6ac46e1408d646ab4620498bd63f94f2719354ea38e3b2ee81330629038e320229079802705393b049d9fbdd91612a54a043a98fbcd SHA512 95d4085bd7d60cd1a40dde25d7a770e549f17f69771a63eb55e95e5735b29ebe76dbfebd5452542fede984e9b3ce0339c166aeb9a42754d36be87b43b6d6b1ec
DIST regressiontests-2018.1.tar.gz 67859956 BLAKE2B f561eb9373b4e0e5faae2aa91e3cb3911c096c1fce96755fc7a8a7b3a25b53bda88ef90d04d3a6fce414bf9dba44d0933827f080949306d5c98f60e5a1797412 SHA512 81c9a62fca859923c1e27214b32b0cff1dd48224dd4ad9301554036b842ccc400a2729752ba71b284e0c5b6c1769ce7de5fe2c9ba4fc7cf0917fd4ced9883112
DIST regressiontests-5.0.4.tar.gz 65193251 BLAKE2B c5e5f23adcc2639fe652bc252533307c7fda44453d506603242968bd8588c7394028b2c3c7a9252f807a050d40e8f78735e904dfe517d3db8ae962051f4826c1 SHA512 747725fa28c1c9525596bdeeb8809e45268e19036c11dac67d043aa1c51748688ca37eb6014eb7e819eb927a8b9ca2631d0ace4cdff8ed491b08c316c530ab65
DIST regressiontests-5.1.3.tar.gz 66994083 BLAKE2B 7009f65ad0138664ac84e57f8bc7cce5d18a59f99943e56b6642583120bfce279e005ac0bacd2db8904ea477a48e2b938c64de46a65fa5d08fce6009d53583c3 SHA512 486e86eb3b75bae822abe82dac4e1098aa13723bd04214021f835a2f0b847303f015a9ececc33aa5ae63d31a2eeae07e512f22464b6c0e26d1286b0781578022

276
sci-chemistry/gromacs/gromacs-2016.1.ebuild
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@@ -1,276 +0,0 @@
# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
CMAKE_MAKEFILE_GENERATOR="ninja"
inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
if [[ $PV = *9999* ]]; then
EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
https://gerrit.gromacs.org/gromacs.git
https://github.com/gromacs/gromacs.git
http://repo.or.cz/r/gromacs.git"
[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
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="~amd64 ~arm ~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
)
dev-libs/tinyxml2
"
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
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
}

275
sci-chemistry/gromacs/gromacs-2016.3.ebuild
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@@ -1,275 +0,0 @@
# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
CMAKE_MAKEFILE_GENERATOR="ninja"
inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
if [[ $PV = *9999* ]]; then
EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
https://gerrit.gromacs.org/gromacs.git
https://github.com/gromacs/gromacs.git
http://repo.or.cz/r/gromacs.git"
[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
inherit git-r3
else
SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
KEYWORDS="~amd64 ~arm ~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
)
dev-libs/tinyxml2
"
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
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
}

276
sci-chemistry/gromacs/gromacs-2016.4.ebuild
View File

@@ -1,276 +0,0 @@
# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
CMAKE_MAKEFILE_GENERATOR="ninja"
inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
if [[ $PV = *9999* ]]; then
EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
https://gerrit.gromacs.org/gromacs.git
https://github.com/gromacs/gromacs.git
http://repo.or.cz/r/gromacs.git"
[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
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="~amd64 ~arm ~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
)
dev-libs/tinyxml2
"
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
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
}

273
sci-chemistry/gromacs/gromacs-2016.ebuild
View File

@@ -1,273 +0,0 @@
# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
CMAKE_MAKEFILE_GENERATOR="ninja"
inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
if [[ $PV = *9999* ]]; then
EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
https://gerrit.gromacs.org/gromacs.git
https://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
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
${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
}

0
sci-chemistry/gromacs/gromacs-2018.ebuild → sci-chemistry/gromacs/gromacs-2018.1.ebuild
View File

272
sci-chemistry/gromacs/gromacs-2018_rc1.ebuild
View File

@@ -1,272 +0,0 @@
# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
CMAKE_MAKEFILE_GENERATOR="ninja"
inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
if [[ $PV = *9999* ]]; then
EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
https://gerrit.gromacs.org/gromacs.git
https://github.com/gromacs/gromacs.git
http://repo.or.cz/r/gromacs.git"
[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
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 opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}"
CDEPEND="
X? (
x11-libs/libX11
x11-libs/libSM
x11-libs/libICE
)
blas? ( virtual/blas )
cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
opencl? ( virtual/opencl )
fftw? ( sci-libs/fftw:3.0 )
hwloc? ( sys-apps/hwloc )
lapack? ( virtual/lapack )
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
"
DEPEND="${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 )
cuda? ( !opencl )
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
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; 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/$(get_libdir)/vmd/plugins/*/molfile/"
-DBUILD_TESTING=$(usex test)
-DGMX_BUILD_UNITTESTS=$(usex test)
${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" )
local opencl=( "-DGMX_USE_OPENCL=OFF" )
use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" )
mycmakeargs=(
${mycmakeargs_pre[@]} ${p}
-DGMX_MPI=OFF
-DGMX_THREAD_MPI=$(usex threads)
"${opencl[@]}"
"${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
}