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334 lines
9.4 KiB
334 lines
9.4 KiB
# Copyright 1999-2024 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=8
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CMAKE_MAKEFILE_GENERATOR="ninja"
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PYTHON_COMPAT=( python3_{10..12} )
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DISTUTILS_OPTIONAL=1
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DISTUTILS_USE_PEP517=no
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DISTUTILS_SINGLE_IMPL=1
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inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic 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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"
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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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https://ftp.gromacs.org/gromacs/${P}.tar.gz
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doc? ( https://ftp.gromacs.org/manual/manual-${PV}.pdf )
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test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV}.tar.gz )"
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# since 2022 arm support was dropped (but not arm64)
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KEYWORDS="~amd64 -arm ~arm64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
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fi
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ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
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DESCRIPTION="The ultimate molecular dynamics simulation package"
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HOMEPAGE="https://www.gromacs.org/"
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# see COPYING for details
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# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
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# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
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LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
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SLOT="0/${PV}"
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IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
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CDEPEND="
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blas? ( virtual/blas )
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cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
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opencl? ( virtual/opencl )
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fftw? ( sci-libs/fftw:3.0= )
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hwloc? ( sys-apps/hwloc:= )
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lapack? ( virtual/lapack )
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mkl? ( sci-libs/mkl )
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mpi? ( virtual/mpi[cxx] )
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sci-libs/lmfit:=
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>=dev-cpp/muParser-2.3:=
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${PYTHON_DEPS}
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"
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BDEPEND="${CDEPEND}
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virtual/pkgconfig
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clang? ( >=sys-devel/clang-6:* )
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build-manual? (
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app-text/doxygen
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$(python_gen_cond_dep '
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dev-python/sphinx[${PYTHON_USEDEP}]
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')
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media-gfx/mscgen
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media-gfx/graphviz
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dev-texlive/texlive-latex
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dev-texlive/texlive-latexextra
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media-gfx/imagemagick
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)"
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RDEPEND="${CDEPEND}
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<sci-chemistry/dssp-4"
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REQUIRED_USE="
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|| ( single-precision double-precision )
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doc? ( !build-manual )
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cuda? ( single-precision )
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opencl? ( single-precision )
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cuda? ( !opencl )
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clang-cuda? ( clang cuda )
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mkl? ( !blas !fftw !lapack )
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${PYTHON_REQUIRED_USE}"
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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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pkg_pretend() {
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[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
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}
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pkg_setup() {
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[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
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python-single-r1_pkg_setup
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}
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src_unpack() {
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if [[ ${PV} != *9999 ]]; then
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default
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else
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git-r3_src_unpack
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if use test; then
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EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git" \
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EGIT_BRANCH="${EGIT_BRANCH}" \
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EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
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git-r3_src_unpack
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fi
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fi
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}
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src_prepare() {
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#notes/todos
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# -on apple: there is framework support
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xdg_environment_reset #591952
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# we can use clang as default
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if use clang && ! tc-is-clang ; then
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export CC=${CHOST}-clang
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export CXX=${CHOST}-clang++
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else
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tc-export CXX CC
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fi
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# clang-cuda need to filter mfpmath
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if use clang-cuda ; then
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filter-mfpmath sse
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filter-mfpmath i386
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fi
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cmake_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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if use build-manual; then
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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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fi
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}
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src_configure() {
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local mycmakeargs_pre=( ) extra fft_opts=( )
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local acce="AUTO"
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if use custom-cflags; then
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#go from slowest to fastest acceleration
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acce="None"
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if (use amd64 || use x86); then
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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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use cpu_flags_x86_avx512f && acce="AVX_512"
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elif (use arm); then
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use cpu_flags_arm_neon && acce="ARM_NEON"
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elif (use arm64); then
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use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD"
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fi
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else
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strip-flags
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fi
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#to create man pages, build tree binaries are executed (bug #398437)
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[[ ${CHOST} = *-darwin* ]] && \
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extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
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if use fftw; then
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fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
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elif use mkl; then
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local bits=$(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/*${bits/lib}/libmkl_rt.so)"
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)
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else
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fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
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fi
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mycmakeargs_pre+=(
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"${fft_opts[@]}"
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"${lmfit_opts[@]}"
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-DGMX_USE_LMFIT=EXTERNAL
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-DGMX_USE_MUPARSER=EXTERNAL
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-DGMX_EXTERNAL_BLAS=$(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=$(usex offensive)
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-DGMX_USE_TNG=$(usex tng)
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-DGMX_BUILD_MANUAL=$(usex build-manual)
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-DGMX_HWLOC=$(usex hwloc)
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-DGMX_DEFAULT_SUFFIX=off
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-DGMX_SIMD="$acce"
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-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
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-DGMX_DSSP_PROGRAM_PATH="${EPREFIX}/usr/bin/dssp"
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-DBUILD_TESTING=$(usex test)
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-DGMX_BUILD_UNITTESTS=$(usex test)
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-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
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${extra}
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)
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for x in ${GMX_DIRS}; do
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einfo "Configuring for ${x} precision"
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local suffix=""
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#if we build single and double - double is suffixed
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use double-precision && use single-precision && \
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[[ ${x} = "double" ]] && suffix="_d"
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local p
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[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
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local gpu=( "-DGMX_GPU=OFF" )
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[[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
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[[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" )
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use opencl && gpu=( "-DGMX_GPU=OPENCL" )
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local mycmakeargs=(
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${mycmakeargs_pre[@]} ${p}
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-DGMX_MPI=$(usex mpi)
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-DGMX_THREAD_MPI=$(usex threads)
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-DGMXAPI=$(usex gmxapi)
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-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
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"${gpu[@]}"
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"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
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-DGMX_BINARY_SUFFIX="${suffix}"
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-DGMX_LIBS_SUFFIX="${suffix}"
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-DGMX_PYTHON_PACKAGE=$(usex python)
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)
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BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
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[[ ${CHOST} != *-darwin* ]] || \
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sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
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done
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}
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src_compile() {
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for x in ${GMX_DIRS}; do
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einfo "Compiling for ${x} precision"
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BUILD_DIR="${WORKDIR}/${P}_${x}"\
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cmake_src_compile
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if use python; then
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BUILD_DIR="${WORKDIR}/${P}_${x}"\
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cmake_src_compile python_packaging/all
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BUILD_DIR="${WORKDIR}/${P}" \
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distutils-r1_src_compile
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fi
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# not 100% necessary for rel ebuilds as available from website
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if use build-manual; then
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BUILD_DIR="${WORKDIR}/${P}_${x}"\
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cmake_src_compile manual
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fi
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done
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}
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src_test() {
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for x in ${GMX_DIRS}; do
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BUILD_DIR="${WORKDIR}/${P}_${x}"\
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cmake_src_compile check
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done
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}
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src_install() {
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for x in ${GMX_DIRS}; do
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BUILD_DIR="${WORKDIR}/${P}_${x}" \
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cmake_src_install
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if use python; then
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BUILD_DIR="${WORKDIR}/${P}_${x}" \
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cmake_src_install python_packaging/install
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fi
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if use build-manual; then
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newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
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fi
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if use doc; then
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if [[ ${PV} != *9999* ]]; then
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newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf"
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fi
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fi
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done
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if use tng; then
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insinto /usr/include/tng
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doins src/external/tng_io/include/tng/*h
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fi
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# drop unneeded stuff
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rm "${ED}"/usr/bin/GMXRC* || die
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for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do
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local n=${x##*/gmx-completion-}
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n="${n%.bash}"
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cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
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newbashcomp "${T}"/"${n}" "${n}"
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done
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rm "${ED}"/usr/bin/gmx-completion*.bash || die
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readme.gentoo_create_doc
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}
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pkg_postinst() {
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einfo
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einfo "Please read and cite gromacs related papers from list:"
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einfo "https://www.gromacs.org/articles.html"
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einfo
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readme.gentoo_print_elog
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}
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