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sci-chemistry/gromacs: Version bump
Package-Manager: Portage-2.3.88, Repoman-2.3.20 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
This commit is contained in:
Alexey Shvetsov
@@ -1,8 +1,10 @@
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DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B 8780032305928067fbfe1559efe9eedc4d47e27ab2f6ab54d6dba39edfcbeefbee4673d8910009048a850620b5a08ba8feb622db652c439cfa50a149ec5f0015 SHA512 6717895942f2ab7b54019511ed2aebadadde8e96d3c4b7414bb9168ffe418432d2dee330192e199f7b9d2f665c71f5d4f1ef0911aa7243d525a2ca182ef5b122
|
||||
DIST gromacs-2019.5.tar.gz 33445791 BLAKE2B 1e2e2764b0c8774c878abf4f32c2fa7ddd9b46f464cf1256deb48335433d92ef1b315f5534cdec9f766ae928a71361b5a4dd4a4def638269eb260ff98dbbe8bb SHA512 fdd177e4dfd29629b72bfbb4d61ff7bcdb37279f534883a9df8fd57569212fe1e9f8b8c9cec347fcc607539f31412d604d11ee3c0eb797251960435962b1bec6
|
||||
DIST gromacs-2019.6.tar.gz 33446147 BLAKE2B adc21fb6b841b06d499607f8c0166a673645ef5af0b40bd823d0fff5ea24397e6301c5e1e0070986ae1ce1deba8a42052b66da148b071c1e21f2fe3908fee275 SHA512 7c227a9539e5775d5d128ae9e872a24181d79cdcd2852b86453597987e8d7332ecec371da65d089f6e610c54aafbccc8824ce298743383dd6240719ebee692a8
|
||||
DIST gromacs-2020.1.tar.gz 29153989 BLAKE2B b1c0313da945c57c74040c2bcd50495b238b0e131cc4ebecd74ae0d01465b47d732ea456a52a2f9d998cd37e2bfdb93d52bd15177328c4b7a14e6b1d8bc00117 SHA512 130394ec70e5d75ea451e9fa77c4ea2dd4adb0c51cc7663ac8579972bab7a0b75d9143d0eebb21802fc93305deca8831393a8cb3f51b6d01f9477f3dadece037
|
||||
DIST gromacs-2020.tar.gz 28928068 BLAKE2B 72d4ff8f6b383284e61df9d3b2b53c51300f6961d4c19810670c8ee9ba2f1864d2a325e2774093b9338db785cb91a94461bf93f16cdf4caf0f690298a672d51c SHA512 15f0d58cd8d217eab39ef8e3535dec34127708797eaf6575fb340292cbee2303cd25deb84b3d4417a787076f4ae7be9e4958ec3a347a3aa9aed52ef337a4587c
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DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb
|
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DIST regressiontests-2019.5.tar.gz 67643634 BLAKE2B c4d9535d9a8a650869d67544ad5f367324f45e55325bb5074ece9b010f232f2f0dd97c9af97924d3f2368ed63015ca7330baff1cc681310e1439ec330b70ee8d SHA512 7c0917b76e7db35ab4e3271d523d268e0e2d858091e68ead863bfe6d1e56b381e30fdbf44f479f6e065c029e2eb27cfa0dbaa1b243f185144321aaf5084c55ce
|
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DIST regressiontests-2019.6.tar.gz 67643195 BLAKE2B 1e054e24b187946f7ea28090d4f20cf8e1d79a26253f57ba07d130e0773d8541b8a1552a38023d31a68ce8bc62d8e0af1d98609234bb3e7d3e6d567307ebb386 SHA512 eacf1c55b982515a305c29459fe80a7cd558a8481e5689962aa956148af542568b1d1ce59c6784ecb0afd4768c2b664afa21e12af2d89ae2b06b1ba61ad72036
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DIST regressiontests-2020.1.tar.gz 48541809 BLAKE2B 0fec2f0fb7fad0ad48bb790d7df6487e2c1931a0a2134795bf7da4a9087f0f2a3743288fc4ec057fa6b22412c2d8f312cfa3af38be8c5bea51d7a06afb5ac9f0 SHA512 664d29ce39629ed218de65179ce4a73e479d73d30bc96f5ae57624d7e4447298c6122dc09e7873b8cad458eaee0530866411fab20e009e46bf39b133e0de47e8
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DIST regressiontests-2020.tar.gz 48536146 BLAKE2B 9511db78b5d6a5ea431fdb73782f28dde4b94655139886c0ad519888ef3e435fe81807f158d66c1a4284cb88fe730f62d039ac23549f17d0ce5984764ef35f10 SHA512 5a35aaf6fe2f3b146c7045e9c967dc1c8bf754748cc1f2a7300193ae3f206a9f5058329380ae7b03b181410303bcd434584571e6161a75f99e52bd48f8ba1821
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337
sci-chemistry/gromacs/gromacs-2020.1.ebuild
Normal file
337
sci-chemistry/gromacs/gromacs-2020.1.ebuild
Normal file
@@ -0,0 +1,337 @@
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# Copyright 1999-2020 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=7
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CMAKE_MAKEFILE_GENERATOR="ninja"
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PYTHON_COMPAT=( python3_{6,7} )
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DISTUTILS_SINGLE_IMPL=1
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inherit bash-completion-r1 cmake-utils cuda distutils-r1 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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https://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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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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|
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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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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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# https://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 +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
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|
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CDEPEND="
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X? (
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x11-libs/libX11
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x11-libs/libSM
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x11-libs/libICE
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||||
)
|
||||
blas? ( virtual/blas )
|
||||
cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 )
|
||||
opencl? ( virtual/opencl )
|
||||
fftw? ( sci-libs/fftw:3.0 )
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||||
hwloc? ( sys-apps/hwloc )
|
||||
lapack? ( virtual/lapack )
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||||
lmfit? ( sci-libs/lmfit )
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mkl? ( sci-libs/mkl )
|
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mpi? ( virtual/mpi )
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||||
${PYTHON_DEPS}
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!sci-chemistry/gmxapi
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"
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BDEPEND="${CDEPEND}
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virtual/pkgconfig
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||||
doc? (
|
||||
app-doc/doxygen
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||||
$(python_gen_cond_dep '
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||||
dev-python/sphinx[${PYTHON_MULTI_USEDEP}]
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||||
')
|
||||
media-gfx/mscgen
|
||||
media-gfx/graphviz
|
||||
dev-texlive/texlive-latex
|
||||
dev-texlive/texlive-latexextra
|
||||
media-gfx/imagemagick
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||||
)"
|
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RDEPEND="${CDEPEND}"
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REQUIRED_USE="
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|| ( single-precision double-precision )
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cuda? ( single-precision )
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cuda? ( !opencl )
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mkl? ( !blas !fftw !lapack )
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||||
${PYTHON_REQUIRED_USE}"
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|
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DOCS=( AUTHORS README )
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||||
|
||||
RESTRICT="!test? ( test )"
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||||
|
||||
if [[ ${PV} != *9999 ]]; then
|
||||
S="${WORKDIR}/${PN}-${PV/_/-}"
|
||||
fi
|
||||
|
||||
PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" )
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pkg_pretend() {
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[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
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use openmp && ! tc-has-openmp && \
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die "Please switch to an openmp compatible compiler"
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}
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|
||||
pkg_setup() {
|
||||
python-single-r1_pkg_setup
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||||
}
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||||
|
||||
src_unpack() {
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||||
if [[ ${PV} != *9999 ]]; then
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||||
default
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else
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git-r3_src_unpack
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if use test; then
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EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
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EGIT_BRANCH="${EGIT_BRANCH}" \
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EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
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git-r3_src_unpack
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fi
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fi
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}
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src_prepare() {
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||||
#notes/todos
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# -on apple: there is framework support
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xdg_environment_reset #591952
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||||
cmake-utils_src_prepare
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use cuda && cuda_src_prepare
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GMX_DIRS=""
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use single-precision && GMX_DIRS+=" float"
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use double-precision && GMX_DIRS+=" double"
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if use test; then
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for x in ${GMX_DIRS}; do
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mkdir -p "${WORKDIR}/${P}_${x}" || die
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cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
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done
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fi
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DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
|
||||
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||||
# try to create policy for imagemagik
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mkdir -p ${HOME}/.config/ImageMagick
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cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
|
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<?xml version="1.0" encoding="UTF-8"?>
|
||||
<!DOCTYPE policymap [
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<!ELEMENT policymap (policy)+>
|
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!ATTLIST policymap xmlns CDATA #FIXED ''>
|
||||
<!ELEMENT policy EMPTY>
|
||||
<!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
|
||||
name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
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stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
|
||||
]>
|
||||
<policymap>
|
||||
<policy domain="coder" rights="read | write" pattern="PS" />
|
||||
<policy domain="coder" rights="read | write" pattern="PS2" />
|
||||
<policy domain="coder" rights="read | write" pattern="PS3" />
|
||||
<policy domain="coder" rights="read | write" pattern="EPS" />
|
||||
<policy domain="coder" rights="read | write" pattern="PDF" />
|
||||
<policy domain="coder" rights="read | write" pattern="XPS" />
|
||||
</policymap>
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||||
EOF
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||||
}
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||||
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src_configure() {
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local mycmakeargs_pre=( ) extra fft_opts=( )
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#go from slowest to fastest acceleration
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local acce="None"
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use cpu_flags_x86_sse2 && acce="SSE2"
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use cpu_flags_x86_sse4_1 && acce="SSE4.1"
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use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
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use cpu_flags_x86_avx && acce="AVX_256"
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use cpu_flags_x86_avx2 && acce="AVX2_256"
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|
||||
#to create man pages, build tree binaries are executed (bug #398437)
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[[ ${CHOST} = *-darwin* ]] && \
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extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
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|
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if use fftw; then
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fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
|
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elif use mkl && has_version "=sci-libs/mkl-10*"; then
|
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fft_opts=( -DGMX_FFT_LIBRARY=mkl
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-DMKL_INCLUDE_DIR="${MKLROOT}/include"
|
||||
-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
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)
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elif use mkl; then
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local bits=$(get_libdir)
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fft_opts=( -DGMX_FFT_LIBRARY=mkl
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-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
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||||
-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
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)
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else
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fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
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fi
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||||
if use lmfit; then
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local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL )
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else
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local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL )
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fi
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||||
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||||
mycmakeargs_pre+=(
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"${fft_opts[@]}"
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"${lmfit_opts[@]}"
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-DGMX_X11=$(usex X)
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||||
-DGMX_EXTERNAL_BLAS=$(usex blas)
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-DGMX_EXTERNAL_LAPACK=$(usex lapack)
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||||
-DGMX_OPENMP=$(usex openmp)
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||||
-DGMX_COOL_QUOTES=$(usex offensive)
|
||||
-DGMX_USE_TNG=$(usex tng)
|
||||
-DGMX_BUILD_MANUAL=$(usex doc)
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||||
-DGMX_HWLOC=$(usex hwloc)
|
||||
-DGMX_DEFAULT_SUFFIX=off
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||||
-DGMX_SIMD="$acce"
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||||
-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
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||||
-DBUILD_TESTING=$(usex test)
|
||||
-DGMX_BUILD_UNITTESTS=$(usex test)
|
||||
-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
|
||||
${extra}
|
||||
)
|
||||
|
||||
for x in ${GMX_DIRS}; do
|
||||
einfo "Configuring for ${x} precision"
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||||
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)
|
||||
-DGMXAPI=$(usex gmxapi)
|
||||
-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
|
||||
"${opencl[@]}"
|
||||
"${cuda[@]}"
|
||||
"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
|
||||
-DGMX_BINARY_SUFFIX="${suffix}"
|
||||
-DGMX_LIBS_SUFFIX="${suffix}"
|
||||
-DGMX_PYTHON_PACKAGE=$(usex python)
|
||||
)
|
||||
BUILD_DIR="${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[@]} ${p}
|
||||
-DGMX_THREAD_MPI=OFF
|
||||
-DGMX_MPI=ON
|
||||
-DGMX_OPENMM=OFF
|
||||
-DGMXAPI=OFF
|
||||
"${opencl[@]}"
|
||||
"${cuda[@]}"
|
||||
-DGMX_BUILD_MDRUN_ONLY=ON
|
||||
-DBUILD_SHARED_LIBS=OFF
|
||||
-DGMX_BUILD_MANUAL=OFF
|
||||
-DGMX_BINARY_SUFFIX="_mpi${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
|
||||
if use python; then
|
||||
BUILD_DIR="${WORKDIR}/${P}_${x}"\
|
||||
cmake-utils_src_compile python_packaging/all
|
||||
BUILD_DIR="${WORKDIR}/${P}" \
|
||||
distutils-r1_src_compile
|
||||
fi
|
||||
# not 100% necessary for rel ebuilds as available from website
|
||||
if use doc; then
|
||||
BUILD_DIR="${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 python; then
|
||||
BUILD_DIR="${WORKDIR}/${P}_${x}" \
|
||||
cmake-utils_src_install python_packaging/install
|
||||
fi
|
||||
if use doc; then
|
||||
newdoc "${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-gmx.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