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# Copyright 1999-2023 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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EAPI=8
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CMAKE_MAKEFILE_GENERATOR="ninja"
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inherit bash-completion-r1 cmake cuda readme.gentoo-r1 toolchain-funcs xdg-utils
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PYTHON_COMPAT=( python3_{9..11} )
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SRC_URI="
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https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.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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KEYWORDS="amd64 arm ~x86 ~amd64-linux ~x86-linux ~x64-macos"
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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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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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https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.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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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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# 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 +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}"
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IUSE="X blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
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CDEPEND="
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X? (
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"
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BDEPEND="${CDEPEND}
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virtual/pkgconfig
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"
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build-manual? (
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app-doc/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="${CDEPEND}"
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REQUIRED_USE="
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|| ( single-precision double-precision )
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doc? ( !build-manual )
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cuda? ( single-precision )
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opencl? ( single-precision )
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cuda? ( !opencl )
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RESTRICT="!test? ( test )"
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S="${WORKDIR}/${PN}-${PV/_/-}"
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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=( "${FILESDIR}/${P}-missing-include.patch" )
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PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" )
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pkg_pretend() {
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[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
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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 [[ ${PV} != *9999 ]]; then
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default
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else
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git-r3_src_unpack
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if use test; then
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EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
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EGIT_BRANCH="${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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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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#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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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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#to create man pages, build tree binaries are executed (bug #398437)
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[[ ${CHOST} = *-darwin* ]] && \
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-DGMX_OPENMP=$(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="$acce"
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-DGMX_MPI=OFF
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-DGMX_THREAD_MPI=$(usex threads)
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-DGMXAPI=$(usex gmxapi)
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-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
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"${opencl[@]}"
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"${cuda[@]}"
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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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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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use mpi || continue
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einfo "Compiling for ${x} precision with mpi"
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BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
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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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newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
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if [[ ${PV} != *9999* ]]; then
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newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf"
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fi
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fi
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use mpi || continue
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BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
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cmake_src_install
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