sci-chemistry/gromacs/gromacs-2020.ebuild

   1 # Copyright 1999-2020 Gentoo Authors
   2 # Distributed under the terms of the GNU General Public License v2
   3
   4 EAPI=7
   5
   6 CMAKE_MAKEFILE_GENERATOR="ninja"
   7
   8 PYTHON_COMPAT=( python3_{6,7} )
   9
  10 DISTUTILS_SINGLE_IMPL=1
  11
  12 inherit bash-completion-r1 cmake-utils cuda distutils-r1 eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
  13
  14 if [[ $PV = *9999* ]]; then
  15         EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
  16                 https://gerrit.gromacs.org/gromacs.git
  17                 https://github.com/gromacs/gromacs.git
  18                 https://repo.or.cz/r/gromacs.git"
  19         [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
  20         inherit git-r3
  21 else
  22         SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
  23                 test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
  24         KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
  25 fi
  26
  27 ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
  28
  29 DESCRIPTION="The ultimate molecular dynamics simulation package"
  30 HOMEPAGE="http://www.gromacs.org/"
  31
  32 # see COPYING for details
  33 # https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
  34 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
  35 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
  36 SLOT="0/${PV}"
  37 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}"
  38
  39 CDEPEND="
  40         X? (
  41                 x11-libs/libX11
  42                 x11-libs/libSM
  43                 x11-libs/libICE
  44                 )
  45         blas? ( virtual/blas )
  46         cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 )
  47         opencl? ( virtual/opencl )
  48         fftw? ( sci-libs/fftw:3.0 )
  49         hwloc? ( sys-apps/hwloc )
  50         lapack? ( virtual/lapack )
  51         lmfit? ( sci-libs/lmfit )
  52         mkl? ( sci-libs/mkl )
  53         mpi? ( virtual/mpi )
  54         ${PYTHON_DEPS}
  55         !sci-chemistry/gmxapi
  56         "
  57 BDEPEND="${CDEPEND}
  58         virtual/pkgconfig
  59         doc? (
  60                 app-doc/doxygen
  61                 dev-python/sphinx[${PYTHON_USEDEP}]
  62                 media-gfx/mscgen
  63                 media-gfx/graphviz
  64                 dev-texlive/texlive-latex
  65                 dev-texlive/texlive-latexextra
  66                 media-gfx/imagemagick
  67         )"
  68 RDEPEND="${CDEPEND}"
  69
  70 REQUIRED_USE="
  71         || ( single-precision double-precision )
  72         cuda? ( single-precision )
  73         cuda? ( !opencl )
  74         mkl? ( !blas !fftw !lapack )
  75         ${PYTHON_REQUIRED_USE}"
  76
  77 DOCS=( AUTHORS README )
  78
  79 RESTRICT="!test? ( test )"
  80
  81 if [[ ${PV} != *9999 ]]; then
  82         S="${WORKDIR}/${PN}-${PV/_/-}"
  83 fi
  84
  85 PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" )
  86
  87 pkg_pretend() {
  88         [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
  89         use openmp && ! tc-has-openmp && \
  90                 die "Please switch to an openmp compatible compiler"
  91 }
  92
  93 pkg_setup() {
  94         python-single-r1_pkg_setup
  95 }
  96
  97 src_unpack() {
  98         if [[ ${PV} != *9999 ]]; then
  99                 default
 100         else
 101                 git-r3_src_unpack
 102                 if use test; then
 103                         EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
 104                         EGIT_BRANCH="${EGIT_BRANCH}" \
 105                         EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
 106                                 git-r3_src_unpack
 107                 fi
 108         fi
 109 }
 110
 111 src_prepare() {
 112         #notes/todos
 113         # -on apple: there is framework support
 114
 115         xdg_environment_reset #591952
 116
 117         cmake-utils_src_prepare
 118
 119         use cuda && cuda_src_prepare
 120
 121         GMX_DIRS=""
 122         use single-precision && GMX_DIRS+=" float"
 123         use double-precision && GMX_DIRS+=" double"
 124
 125         if use test; then
 126                 for x in ${GMX_DIRS}; do
 127                         mkdir -p "${WORKDIR}/${P}_${x}" || die
 128                         cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
 129                 done
 130         fi
 131
 132         DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
 133
 134         # try to create policy for imagemagik
 135         mkdir -p ${HOME}/.config/ImageMagick
 136         cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
 137         <?xml version="1.0" encoding="UTF-8"?>
 138         <!DOCTYPE policymap [
 139         <!ELEMENT policymap (policy)+>
 140         !ATTLIST policymap xmlns CDATA #FIXED ''>
 141         <!ELEMENT policy EMPTY>
 142         <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
 143                         name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
 144                         stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
 145         ]>
 146         <policymap>
 147                 <policy domain="coder" rights="read | write" pattern="PS" />
 148                 <policy domain="coder" rights="read | write" pattern="PS2" />
 149                 <policy domain="coder" rights="read | write" pattern="PS3" />
 150                 <policy domain="coder" rights="read | write" pattern="EPS" />
 151                 <policy domain="coder" rights="read | write" pattern="PDF" />
 152                 <policy domain="coder" rights="read | write" pattern="XPS" />
 153         </policymap>
 154         EOF
 155 }
 156
 157 src_configure() {
 158         local mycmakeargs_pre=( ) extra fft_opts=( )
 159
 160         #go from slowest to fastest acceleration
 161         local acce="None"
 162         use cpu_flags_x86_sse2 && acce="SSE2"
 163         use cpu_flags_x86_sse4_1 && acce="SSE4.1"
 164         use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
 165         use cpu_flags_x86_avx && acce="AVX_256"
 166         use cpu_flags_x86_avx2 && acce="AVX2_256"
 167
 168         #to create man pages, build tree binaries are executed (bug #398437)
 169         [[ ${CHOST} = *-darwin* ]] && \
 170                 extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
 171
 172         if use fftw; then
 173                 fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
 174         elif use mkl && has_version "=sci-libs/mkl-10*"; then
 175                 fft_opts=( -DGMX_FFT_LIBRARY=mkl
 176                         -DMKL_INCLUDE_DIR="${MKLROOT}/include"
 177                         -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
 178                 )
 179         elif use mkl; then
 180                 local bits=$(get_libdir)
 181                 fft_opts=( -DGMX_FFT_LIBRARY=mkl
 182                         -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
 183                         -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
 184                 )
 185         else
 186                 fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
 187         fi
 188
 189         if use lmfit; then
 190                 local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL )
 191         else
 192                 local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL )
 193         fi
 194
 195         mycmakeargs_pre+=(
 196                 "${fft_opts[@]}"
 197                 "${lmfit_opts[@]}"
 198                 -DGMX_X11=$(usex X)
 199                 -DGMX_EXTERNAL_BLAS=$(usex blas)
 200                 -DGMX_EXTERNAL_LAPACK=$(usex lapack)
 201                 -DGMX_OPENMP=$(usex openmp)
 202                 -DGMX_COOL_QUOTES=$(usex offensive)
 203                 -DGMX_USE_TNG=$(usex tng)
 204                 -DGMX_BUILD_MANUAL=$(usex doc)
 205                 -DGMX_HWLOC=$(usex hwloc)
 206                 -DGMX_DEFAULT_SUFFIX=off
 207                 -DGMX_SIMD="$acce"
 208                 -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
 209                 -DBUILD_TESTING=$(usex test)
 210                 -DGMX_BUILD_UNITTESTS=$(usex test)
 211                 -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
 212                 ${extra}
 213         )
 214
 215         for x in ${GMX_DIRS}; do
 216                 einfo "Configuring for ${x} precision"
 217                 local suffix=""
 218                 #if we build single and double - double is suffixed
 219                 use double-precision && use single-precision && \
 220                         [[ ${x} = "double" ]] && suffix="_d"
 221                 local p
 222                 [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
 223                 local cuda=( "-DGMX_GPU=OFF" )
 224                 [[ ${x} = "float" ]] && use cuda && \
 225                         cuda=( "-DGMX_GPU=ON" )
 226                 local opencl=( "-DGMX_USE_OPENCL=OFF" )
 227                 use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" )
 228                 mycmakeargs=(
 229                         ${mycmakeargs_pre[@]} ${p}
 230                         -DGMX_MPI=OFF
 231                         -DGMX_THREAD_MPI=$(usex threads)
 232                         -DGMXAPI=$(usex gmxapi)
 233                         -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
 234                         "${opencl[@]}"
 235                         "${cuda[@]}"
 236                         "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
 237                         -DGMX_BINARY_SUFFIX="${suffix}"
 238                         -DGMX_LIBS_SUFFIX="${suffix}"
 239                         -DGMX_PYTHON_PACKAGE=$(usex python)
 240                         )
 241                 BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
 242                 [[ ${CHOST} != *-darwin* ]] || \
 243                   sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
 244                 use mpi || continue
 245                 einfo "Configuring for ${x} precision with mpi"
 246                 mycmakeargs=(
 247                         ${mycmakeargs_pre[@]} ${p}
 248                         -DGMX_THREAD_MPI=OFF
 249                         -DGMX_MPI=ON
 250                         -DGMX_OPENMM=OFF
 251                         -DGMXAPI=OFF
 252                         "${opencl[@]}"
 253                         "${cuda[@]}"
 254                         -DGMX_BUILD_MDRUN_ONLY=ON
 255                         -DBUILD_SHARED_LIBS=OFF
 256                         -DGMX_BUILD_MANUAL=OFF
 257                         -DGMX_BINARY_SUFFIX="_mpi${suffix}"
 258                         -DGMX_LIBS_SUFFIX="_mpi${suffix}"
 259                         )
 260                 BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
 261                 [[ ${CHOST} != *-darwin* ]] || \
 262                   sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
 263         done
 264 }
 265
 266 src_compile() {
 267         for x in ${GMX_DIRS}; do
 268                 einfo "Compiling for ${x} precision"
 269                 BUILD_DIR="${WORKDIR}/${P}_${x}"\
 270                         cmake-utils_src_compile
 271                 if use python; then
 272                         BUILD_DIR="${WORKDIR}/${P}_${x}"\
 273                                 cmake-utils_src_compile python_packaging/all
 274                         BUILD_DIR="${WORKDIR}/${P}" \
 275                                 distutils-r1_src_compile
 276                 fi
 277                 # not 100% necessary for rel ebuilds as available from website
 278                 if use doc; then
 279                         BUILD_DIR="${WORKDIR}/${P}_${x}"\
 280                                 cmake-utils_src_compile manual
 281                 fi
 282                 use mpi || continue
 283                 einfo "Compiling for ${x} precision with mpi"
 284                 BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
 285                         cmake-utils_src_compile
 286         done
 287 }
 288
 289 src_test() {
 290         for x in ${GMX_DIRS}; do
 291                 BUILD_DIR="${WORKDIR}/${P}_${x}"\
 292                         cmake-utils_src_make check
 293         done
 294 }
 295
 296 src_install() {
 297         for x in ${GMX_DIRS}; do
 298                 BUILD_DIR="${WORKDIR}/${P}_${x}" \
 299                         cmake-utils_src_install
 300                 if use python; then
 301                         BUILD_DIR="${WORKDIR}/${P}_${x}" \
 302                                 cmake-utils_src_install python_packaging/install
 303                 fi
 304                 if use doc; then
 305                         newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
 306                 fi
 307                 use mpi || continue
 308                 BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
 309                         cmake-utils_src_install
 310         done
 311
 312         if use tng; then
 313                 insinto /usr/include/tng
 314                 doins src/external/tng_io/include/tng/*h
 315         fi
 316         # drop unneeded stuff
 317         rm "${ED}"/usr/bin/GMXRC* || die
 318         for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do
 319                 local n=${x##*/gmx-completion-}
 320                 n="${n%.bash}"
 321                 cat "${ED}"/usr/bin/gmx-completion-gmx.bash "$x" > "${T}/${n}" || die
 322                 newbashcomp "${T}"/"${n}" "${n}"
 323         done
 324         rm "${ED}"/usr/bin/gmx-completion*.bash || die
 325         readme.gentoo_create_doc
 326 }
 327
 328 pkg_postinst() {
 329         einfo
 330         einfo  "Please read and cite:"
 331         einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
 332         einfo  "https://dx.doi.org/10.1021/ct700301q"
 333         einfo
 334         readme.gentoo_print_elog
 335 }