parent
bd8e84069f
commit
75fa605441
@ -0,0 +1,2 @@
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DIST gromacs-2020.4.tar.gz 29149899 BLAKE2B a07c8efd96137d58c1edf4ac9b5aafeb16d9e65234b9459b71471827032654acacb58ed6ae87ec6e0e593a0acd799683cc4461b06cc883b089d740708619345e SHA512 0c56f058741af70660baf0177724ec940dd984c05ea141ede91ee51ce3744f76d00e31bdb5db907e46fa1639de5dca637b3ace26e89f908c2e74c69f0c21ed3a
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DIST regressiontests-2020.4.tar.gz 48542144 BLAKE2B 1dcde67525d40ababa74d9e8ba2dd3fdef1de7d1018491e102edd71d3a622925f213b5a0812e5448882b4cb5fb578317e8e5029bdc4bd53008aa8441a3d9dea1 SHA512 7c71f36a1cef22562f14dcd233e90ad2fe370ae1a7d3b5268727259b374e12d4754253735ac8745d3738bdbc1cc2067780fda5e393be2ff264f632fe4e0c1978
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@ -0,0 +1,26 @@
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From e4e1263776844d660c471e3d1203acf54cdc855f Mon Sep 17 00:00:00 2001
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From: Alexey Shvetsov <alexxyum@gmail.com>
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Date: Fri, 23 Apr 2021 13:21:24 +0300
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Subject: [PATCH 2/2] Allow to build python part without build testing enabled
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Signed-off-by: Alexey Shvetsov <alexxyum@gmail.com>
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---
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python_packaging/src/CMakeLists.txt | 6 ++++--
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1 file changed, 4 insertions(+), 2 deletions(-)
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diff --git a/python_packaging/src/CMakeLists.txt b/python_packaging/src/CMakeLists.txt
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index c75549fc82..4f983fdd5f 100644
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--- a/python_packaging/src/CMakeLists.txt
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+++ b/python_packaging/src/CMakeLists.txt
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@@ -252,5 +252,7 @@ endif()
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# to the `check` target. Normal usage is to first install the Python package,
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# then run `pytest` on the `tests` directory. Refer to gmxapi package documentation.
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if(NOT GMXAPI_MASTER_PROJECT)
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- add_subdirectory(test)
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+ if (BUILD_TESTING)
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+ add_subdirectory(test)
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+ endif()
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endif()
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--
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2.31.1
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@ -0,0 +1,342 @@
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# Copyright 1999-2021 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_{7,8,9} )
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DISTUTILS_SINGLE_IMPL=1
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inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
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if [[ ${PV} = *9999* ]]; then
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EGIT_REPO_URI="
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https://gitlab.com/gromacs/gromacs.git
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https://github.com/gromacs/gromacs.git
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git://git.gromacs.org/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="
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http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
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test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
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KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos"
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fi
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ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
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DESCRIPTION="The ultimate molecular dynamics simulation package"
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HOMEPAGE="http://www.gromacs.org/"
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# see COPYING for details
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# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
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# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
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LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
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SLOT="0/${PV}"
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IUSE="X blas cuda +custom-cflags +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
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CDEPEND="
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X? (
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x11-libs/libX11
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x11-libs/libSM
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x11-libs/libICE
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)
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blas? ( virtual/blas )
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cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 )
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opencl? ( virtual/opencl )
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fftw? ( sci-libs/fftw:3.0 )
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hwloc? ( sys-apps/hwloc )
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lapack? ( virtual/lapack )
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lmfit? ( sci-libs/lmfit )
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mkl? ( sci-libs/mkl )
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mpi? ( virtual/mpi )
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${PYTHON_DEPS}
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!sci-chemistry/gmxapi
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"
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BDEPEND="${CDEPEND}
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virtual/pkgconfig
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doc? (
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app-doc/doxygen
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$(python_gen_cond_dep '
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dev-python/sphinx[${PYTHON_MULTI_USEDEP}]
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')
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media-gfx/mscgen
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media-gfx/graphviz
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dev-texlive/texlive-latex
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dev-texlive/texlive-latexextra
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media-gfx/imagemagick
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)"
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RDEPEND="${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 [[ ${PV} != *9999 ]]; then
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S="${WORKDIR}/${PN}-${PV/_/-}"
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fi
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PATCHES=( "${FILESDIR}/${PN}-2020-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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|
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pkg_setup() {
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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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|
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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_src_prepare
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|
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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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|
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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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|
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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"?>
|
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<!DOCTYPE policymap [
|
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<!ELEMENT policymap (policy)+>
|
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!ATTLIST policymap xmlns CDATA #FIXED ''>
|
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<!ELEMENT policy EMPTY>
|
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<!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
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name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
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stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
|
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]>
|
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<policymap>
|
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<policy domain="coder" rights="read | write" pattern="PS" />
|
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<policy domain="coder" rights="read | write" pattern="PS2" />
|
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<policy domain="coder" rights="read | write" pattern="PS3" />
|
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<policy domain="coder" rights="read | write" pattern="EPS" />
|
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<policy domain="coder" rights="read | write" pattern="PDF" />
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<policy domain="coder" rights="read | write" pattern="XPS" />
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</policymap>
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EOF
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}
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src_configure() {
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local mycmakeargs_pre=( ) extra fft_opts=( )
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if use custom-cflags; then
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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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else
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strip-flags
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fi
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|
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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"
|
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-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)"
|
||||
)
|
||||
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}"
|
||||
-DGMX_PYTHON_PACKAGE=$(usex python)
|
||||
)
|
||||
BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_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_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_src_compile
|
||||
if use python; then
|
||||
BUILD_DIR="${WORKDIR}/${P}_${x}"\
|
||||
cmake_src_compile python_packaging/all
|
||||
BUILD_DIR="${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_src_compile manual
|
||||
fi
|
||||
use mpi || continue
|
||||
einfo "Compiling for ${x} precision with mpi"
|
||||
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
|
||||
cmake_src_compile
|
||||
done
|
||||
}
|
||||
|
||||
src_test() {
|
||||
for x in ${GMX_DIRS}; do
|
||||
BUILD_DIR="${WORKDIR}/${P}_${x}"\
|
||||
cmake_src_compile check
|
||||
done
|
||||
}
|
||||
|
||||
src_install() {
|
||||
for x in ${GMX_DIRS}; do
|
||||
BUILD_DIR="${WORKDIR}/${P}_${x}" \
|
||||
cmake_src_install
|
||||
if use python; then
|
||||
BUILD_DIR="${WORKDIR}/${P}_${x}" \
|
||||
cmake_src_install python_packaging/install
|
||||
fi
|
||||
if use doc; then
|
||||
newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
|
||||
fi
|
||||
use mpi || continue
|
||||
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
|
||||
cmake_src_install
|
||||
done
|
||||
|
||||
if use tng; then
|
||||
insinto /usr/include/tng
|
||||
doins src/external/tng_io/include/tng/*h
|
||||
fi
|
||||
# drop unneeded stuff
|
||||
rm "${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
|
||||
}
|
@ -0,0 +1,25 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
|
||||
<pkgmetadata>
|
||||
<maintainer type="person">
|
||||
<email>alexxy@gentoo.org</email>
|
||||
<name>Alexey Shvetsov</name>
|
||||
</maintainer>
|
||||
<maintainer type="project">
|
||||
<email>sci-chemistry@gentoo.org</email>
|
||||
<name>Gentoo Chemistry Project</name>
|
||||
</maintainer>
|
||||
<use>
|
||||
<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>
|
||||
<flag name="single-precision">Single precision version of gromacs (default)</flag>
|
||||
<flag name="tng">Enable new trajectory format - tng</flag>
|
||||
<flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag>
|
||||
<flag name="offensive">Enable gromacs partly offensive quotes</flag>
|
||||
</use>
|
||||
</pkgmetadata>
|
Loading…
Reference in new issue