sci-chemistry/gromacs: Beta1

Package-Manager: Portage-2.3.78, Repoman-2.3.17
Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
This commit is contained in:
Alexey Shvetsov
2019-10-24 12:36:32 +03:00
parent 79f226aca7
commit a3f73cefbc
4 changed files with 352 additions and 0 deletions
+2
View File
@@ -3,8 +3,10 @@ DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B 8780032305928067fbfe1559efe9eedc4d47
DIST gromacs-2019.2.tar.gz 33437869 BLAKE2B bebe4942688dace148856d4491b687b8e0fd2c86d7fbd9eecdb46824d316a0fc3854464ecafa79d8db92327ee8467be204b050c11f1e71132184efd812c3bf09 SHA512 da7ff24e8485774e22d1c2464fbe64675c3305ef0e21a3d17e363201031952e5d4a9b81f572d5284fb6f2596ed99daf62fe78d653387d9d714274f46bc750183
DIST gromacs-2019.3.tar.gz 33441419 BLAKE2B 79319dd23982c65c7c4d8e5f633cef0c7fd99a38a4e0cc9030a3ffb0fdfc07a4fbfbcfa942896f23a143b747e044fae645498a3e6992497d1f1a7d966f80b2b0 SHA512 de9f54d095b45ea7efd1043f83a40f6c778a6e3e2067a01f48d1ce843d68d226061933ca28a3edb635b795a8ddd5ef9deb8ed1114aa3235bc8039db8ff7d0218
DIST gromacs-2019.4.tar.gz 33444527 BLAKE2B 5a01ed0e38faade037de701b72e8d52fd5a947a23228f0b5170a170dc963b00068a6b6880dd9a3f6f2a73140a3787952741dcbcc862bc357a8be8bf5640faa16 SHA512 adc6dea187b7f3a3c13fcd39445ae45248d46d56b0102fda47b1850b83ff1fb77a3fec99d4a4124b01ed04646dab6ab67749eae1bec36d1ba6f2205855cd29f8
DIST gromacs-2020-beta1.tar.gz 29019829 BLAKE2B 1884e0984aa6cd8a6bf7d9c692c5f465247ed3c396a0b12fa67c1fc763d84dbeaee23905c95e902e9befe1af8617fc9dc46d7280140ce09ba1915bef58a86d0a SHA512 8992dbdd560fa5227d19f59d9a360cd9e5f0c3a1df435f43293bb044ca6414f177e04a4933b8c0f19d5121a44244a4c9c95d026f6c817fd4ba5b0e4f7b3a01a0
DIST regressiontests-2018.7.tar.gz 67856738 BLAKE2B 955ae8b5e74f90fec704cf41fbd00bd8c09d754f950551fe0adfcd407db6fdb4491a3815149ea37d36c747316c79d462e823b9f6b26f2376bf90d87aad95731b SHA512 c2ff390750bd99faebcd8d5dd8ad6dbf2b00113ed888bddddf985dbf95d7f347093adb67f3c396547b3e2990de330fddb7efe83ded91a72cf97c82a1dac7e826
DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb
DIST regressiontests-2019.2.tar.gz 67643003 BLAKE2B 4178de5d62f194a81f97e442c10f123dc59c5e63f2078f7f07135709f3f6e530e0d237bf40264b285c084519d5ace75dfcbcddc16dc740c4f17233dc33542e45 SHA512 c1f25bc770d3f0a873c887d5563c1cd88179e81211b70ce6f5015696e6fa0b6931a8da7a449f2b223f3105b9e2e7eca67248e96fbfc2a7fd5fb360ba616f22ff
DIST regressiontests-2019.3.tar.gz 67640462 BLAKE2B ed6c176a144e0407be66585be5d6090c31c047498bc5f48f59685108de91f2f9ddb2d22b291a15e6ffa1db848aae19b94a79c8c3d34b1067680f759a179953dd SHA512 822e905fb488ce308eb9324d93f78106da5252c773c7941d49c6162e73bdff109aeca1f0d57216c6dd6536a4c41d80013fa1cee2f5206b0c4160a3e5b4a31315
DIST regressiontests-2019.4.tar.gz 67639728 BLAKE2B aba912863669a4a6a6a74e385f9b0974d0c0aa30d3aea7834d77c8bb3f4f59effcbe10a480e74e7aa31fe32d64ba6628d67703ca1894839ce7ddfc8da93902dc SHA512 45de03d368da4e6e5c647f3fea61d64defe6d1cbc1c4219eeac2db27559e3cea7f15f9acb3e56ab934b44ca3ae4ce199b4e4969f704776bb9f0b23f1a34ff56d
DIST regressiontests-2020-beta1.tar.gz 48263088 BLAKE2B 2c5cacb0ff7d5b31e639388bebc755355837242643ad6dc48b7722918328214c8271f894d956960743641eb9cd4ec9df0013ad8490b73f2006b75fc8ebefcb51 SHA512 fba198e5560c01e6239bcddaa8d574c79062684b3f94f71b06436d83da9b9efd865998cea3a1b9369938e8fec69383d3fd6278c22c7a1a72eb50cc282f4b42c2
@@ -0,0 +1,12 @@
diff -urN gromacs-2020-beta1/python_packaging/src/CMakeLists.txt gromacs-2020-beta1-py/python_packaging/src/CMakeLists.txt
--- gromacs-2020-beta1/python_packaging/src/CMakeLists.txt 2019-09-12 05:48:57.000000000 +0300
+++ gromacs-2020-beta1-py/python_packaging/src/CMakeLists.txt 2019-10-09 17:01:30.845304765 +0300
@@ -201,5 +201,7 @@
# to the `check` target. Normal usage is to first install the Python package,
# then run `pytest` on the `tests` directory. Refer to gmxapi package documentation.
if(NOT GMXAPI_MASTER_PROJECT)
- add_subdirectory(test)
+ if (GMX_BUILD_TESTING)
+ add_subdirectory(test)
+ endif()
endif()
@@ -0,0 +1,337 @@
# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
CMAKE_MAKEFILE_GENERATOR="ninja"
PYTHON_COMPAT=( python3_{5,6,7} )
inherit bash-completion-r1 cmake-utils cuda distutils-r1 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
https://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
# https://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 +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +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-6.5.14 )
opencl? ( virtual/opencl )
fftw? ( sci-libs/fftw:3.0 )
hwloc? ( sys-apps/hwloc )
lapack? ( virtual/lapack )
lmfit? ( sci-libs/lmfit )
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
${PYTHON_DEPS}
"
BDEPEND="${CDEPEND}
virtual/pkgconfig
doc? (
app-doc/doxygen
dev-python/sphinx[${PYTHON_USEDEP}]
media-gfx/mscgen
media-gfx/graphviz
dev-texlive/texlive-latex
dev-texlive/texlive-latexextra
media-gfx/imagemagick
)"
RDEPEND="${CDEPEND}"
REQUIRED_USE="
|| ( single-precision double-precision )
cuda? ( single-precision )
cuda? ( !opencl )
mkl? ( !blas !fftw !lapack )
${PYTHON_REQUIRED_USE}"
DOCS=( AUTHORS README )
RESTRICT="!test? ( test )"
if [[ ${PV} != *9999 ]]; then
S="${WORKDIR}/${PN}-${PV/_/-}"
fi
PATCHES=( "${FILESDIR}/${P}-pytest.patch" )
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"
# try to create policy for imagemagik
mkdir -p ${HOME}/.config/ImageMagick
cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE policymap [
<!ELEMENT policymap (policy)+>
!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
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>
EOF
}
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
if use lmfit; then
local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL )
else
local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL )
fi
mycmakeargs_pre+=(
"${fft_opts[@]}"
"${lmfit_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="$acce"
-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-DBUILD_TESTING=$(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"
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}"
)
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
if use python; then
cd python_packaging
distutils-r1_src_configure
cd ..
fi
}
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
if use python; then
cd python_packaging
distutils-r1_src_compile
cd ..
fi
}
src_test() {
for x in ${GMX_DIRS}; do
BUILD_DIR="${WORKDIR}/${P}_${x}"\
cmake-utils_src_make check
done
if use python; then
cd python_packaging
distutils-r1_src_test
cd ..
fi
}
src_install() {
for x in ${GMX_DIRS}; do
BUILD_DIR="${WORKDIR}/${P}_${x}" \
cmake-utils_src_install ${GMX_PYTHON_INSTALL}
if use doc; then
newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
fi
use mpi || continue
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
cmake-utils_src_install
done
if use tng; then
insinto /usr/include/tng
doins src/external/tng_io/include/tng/*h
fi
if use python; then
cd python_packaging
distutils-r1_src_install
cd ..
fi
# drop unneeded stuff
rm "${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
}
+1
View File
@@ -13,6 +13,7 @@
<flag name="cuda">Enable cuda non-bonded kernels</flag>
<flag name="double-precision">More precise calculations at the expense of speed</flag>
<flag name="gmxapi">Add support for gmxapi library</flag>
<flag name="gmxapi-legacy">Enable installing lagacy headers</flag>
<flag name="hwloc">Enable HWLoc lib support</flag>
<flag name="lmfit">Use external <pkg>sci-libs/lmfit</pkg></flag>
<flag name="opencl">Enable opencl non-bonded kernels</flag>