sci-chemistry/gromacs/gromacs-2023.5.ebuild

   1 # Copyright 1999-2024 Gentoo Authors
   2 # Distributed under the terms of the GNU General Public License v2
   3
   4 EAPI=8
   5
   6 CMAKE_MAKEFILE_GENERATOR="ninja"
   7
   8 PYTHON_COMPAT=( python3_{10..12} )
   9
  10 DISTUTILS_OPTIONAL=1
  11 DISTUTILS_USE_PEP517=no
  12 DISTUTILS_SINGLE_IMPL=1
  13
  14 inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils
  15
  16 if [[ ${PV} = *9999* ]]; then
  17         EGIT_REPO_URI="
  18                 https://gitlab.com/gromacs/gromacs.git
  19                 https://github.com/gromacs/gromacs.git
  20                 "
  21         [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
  22         inherit git-r3
  23 else
  24         SRC_URI="
  25                 https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
  26                 doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
  27                 test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
  28         # since 2022 arm support was dropped (but not arm64)
  29         KEYWORDS="amd64 -arm arm64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
  30 fi
  31
  32 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"
  33
  34 DESCRIPTION="The ultimate molecular dynamics simulation package"
  35 HOMEPAGE="https://www.gromacs.org/"
  36
  37 # see COPYING for details
  38 # https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
  39 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
  40 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
  41 SLOT="0/${PV}"
  42 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}"
  43
  44 CDEPEND="
  45         blas? ( virtual/blas )
  46         cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
  47         opencl? ( virtual/opencl )
  48         openmp? (
  49                 sys-devel/gcc[openmp]
  50                 llvm-core/clang-runtime[openmp]
  51         )
  52         fftw? ( sci-libs/fftw:3.0= )
  53         hwloc? ( sys-apps/hwloc:= )
  54         lapack? ( virtual/lapack )
  55         mkl? ( sci-libs/mkl )
  56         mpi? ( virtual/mpi[cxx] )
  57         sci-libs/lmfit:=
  58         >=dev-cpp/muParser-2.3:=
  59         ${PYTHON_DEPS}
  60         "
  61 BDEPEND="${CDEPEND}
  62         virtual/pkgconfig
  63         clang? ( >=llvm-core/clang-6:* )
  64         build-manual? (
  65                 app-text/doxygen
  66                 $(python_gen_cond_dep '
  67                         dev-python/sphinx[${PYTHON_USEDEP}]
  68                         dev-python/sphinx-copybutton[${PYTHON_USEDEP}]
  69                         dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]
  70                         dev-python/sphinx-argparse[${PYTHON_USEDEP}]
  71                         dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}]
  72                 ')
  73                 media-gfx/mscgen
  74                 media-gfx/graphviz
  75                 dev-texlive/texlive-latex
  76                 dev-texlive/texlive-latexextra
  77                 media-gfx/imagemagick
  78         )"
  79 RDEPEND="${CDEPEND}"
  80
  81 REQUIRED_USE="
  82         || ( single-precision double-precision )
  83         doc? ( !build-manual )
  84         cuda? ( single-precision )
  85         opencl? ( single-precision )
  86         cuda? ( !opencl )
  87         clang-cuda? ( clang cuda )
  88         mkl? ( !blas !fftw !lapack )
  89         ${PYTHON_REQUIRED_USE}"
  90
  91 DOCS=( AUTHORS README )
  92
  93 RESTRICT="!test? ( test )"
  94
  95 if [[ ${PV} != *9999 ]]; then
  96         S="${WORKDIR}/${PN}-${PV/_/-}"
  97 fi
  98
  99 pkg_pretend() {
 100         [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
 101 }
 102
 103 pkg_setup() {
 104         [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
 105         python-single-r1_pkg_setup
 106 }
 107
 108 src_unpack() {
 109         if [[ ${PV} != *9999 ]]; then
 110                 default
 111         else
 112                 git-r3_src_unpack
 113                 if use test; then
 114                         EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git" \
 115                         EGIT_BRANCH="${EGIT_BRANCH}" \
 116                         EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
 117                                 git-r3_src_unpack
 118                 fi
 119         fi
 120 }
 121
 122 src_prepare() {
 123         #notes/todos
 124         # -on apple: there is framework support
 125
 126         xdg_environment_reset #591952
 127
 128         # we can use clang as default
 129         if use clang && ! tc-is-clang ; then
 130                 export CC=${CHOST}-clang
 131                 export CXX=${CHOST}-clang++
 132         else
 133                 tc-export CXX CC
 134         fi
 135         # clang-cuda need to filter mfpmath
 136         if use clang-cuda ; then
 137                 filter-mfpmath sse
 138                 filter-mfpmath i386
 139         fi
 140
 141         cmake_src_prepare
 142
 143         use cuda && cuda_src_prepare
 144
 145         GMX_DIRS=""
 146         use single-precision && GMX_DIRS+=" float"
 147         use double-precision && GMX_DIRS+=" double"
 148
 149         if use test; then
 150                 for x in ${GMX_DIRS}; do
 151                         mkdir -p "${WORKDIR}/${P}_${x}" || die
 152                         cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
 153                 done
 154         fi
 155
 156         DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
 157         if use build-manual; then
 158                 # try to create policy for imagemagik
 159                 mkdir -p "${HOME}"/.config/ImageMagick
 160                 cat >> "${HOME}"/.config/ImageMagick/policy.xml <<- EOF
 161                 <?xml version="1.0" encoding="UTF-8"?>
 162                 <!DOCTYPE policymap [
 163                 <!ELEMENT policymap (policy)+>
 164                 !ATTLIST policymap xmlns CDATA #FIXED ''>
 165                 <!ELEMENT policy EMPTY>
 166                 <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
 167                         name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
 168                         stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
 169                 ]>
 170                 <policymap>
 171                         <policy domain="coder" rights="read | write" pattern="PS" />
 172                         <policy domain="coder" rights="read | write" pattern="PS2" />
 173                         <policy domain="coder" rights="read | write" pattern="PS3" />
 174                         <policy domain="coder" rights="read | write" pattern="EPS" />
 175                         <policy domain="coder" rights="read | write" pattern="PDF" />
 176                         <policy domain="coder" rights="read | write" pattern="XPS" />
 177                 </policymap>
 178                 EOF
 179         fi
 180 }
 181
 182 src_configure() {
 183         local mycmakeargs_pre=( ) extra fft_opts=( )
 184         local acce="AUTO"
 185
 186         if use custom-cflags; then
 187                 #go from slowest to fastest acceleration
 188                 acce="None"
 189                 if (use amd64 || use x86); then
 190                         use cpu_flags_x86_sse2 && acce="SSE2"
 191                         use cpu_flags_x86_sse4_1 && acce="SSE4.1"
 192                         use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
 193                         use cpu_flags_x86_avx && acce="AVX_256"
 194                         use cpu_flags_x86_avx2 && acce="AVX2_256"
 195                         use cpu_flags_x86_avx512f && acce="AVX_512"
 196                 elif (use arm); then
 197                         use cpu_flags_arm_neon && acce="ARM_NEON"
 198                 elif (use arm64); then
 199                         use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD"
 200                 fi
 201         else
 202                 strip-flags
 203         fi
 204
 205         #to create man pages, build tree binaries are executed (bug #398437)
 206         [[ ${CHOST} = *-darwin* ]] && \
 207                 extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
 208
 209         if use fftw; then
 210                 fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
 211         elif use mkl; then
 212                 local bits=$(get_libdir)
 213                 fft_opts=( -DGMX_FFT_LIBRARY=mkl
 214                         -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
 215                         -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
 216                 )
 217         else
 218                 fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
 219         fi
 220
 221         mycmakeargs_pre+=(
 222                 "${fft_opts[@]}"
 223                 "${lmfit_opts[@]}"
 224                 -DGMX_USE_LMFIT=EXTERNAL
 225                 -DGMX_USE_MUPARSER=EXTERNAL
 226                 -DGMX_EXTERNAL_BLAS=$(usex blas)
 227                 -DGMX_EXTERNAL_LAPACK=$(usex lapack)
 228                 -DGMX_OPENMP=$(usex openmp)
 229                 -DGMX_COOL_QUOTES=$(usex offensive)
 230                 -DGMX_USE_TNG=$(usex tng)
 231                 -DGMX_BUILD_MANUAL=$(usex build-manual)
 232                 -DGMX_HWLOC=$(usex hwloc)
 233                 -DGMX_DEFAULT_SUFFIX=off
 234                 -DGMX_SIMD="$acce"
 235                 -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
 236                 -DBUILD_TESTING=$(usex test)
 237                 -DGMX_BUILD_UNITTESTS=$(usex test)
 238                 -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
 239                 ${extra}
 240         )
 241
 242         for x in ${GMX_DIRS}; do
 243                 einfo "Configuring for ${x} precision"
 244                 local suffix=""
 245                 #if we build single and double - double is suffixed
 246                 use double-precision && use single-precision && \
 247                         [[ ${x} = "double" ]] && suffix="_d"
 248                 local p
 249                 [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
 250                 local gpu=( "-DGMX_GPU=OFF" )
 251                 [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
 252                 [[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" )
 253                 use opencl && gpu=( "-DGMX_GPU=OPENCL" )
 254                 local mycmakeargs=(
 255                         ${mycmakeargs_pre[@]} ${p}
 256                         -DGMX_MPI=$(usex mpi)
 257                         -DGMX_THREAD_MPI=$(usex threads)
 258                         -DGMXAPI=$(usex gmxapi)
 259                         -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
 260                         "${gpu[@]}"
 261                         "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
 262                         -DGMX_BINARY_SUFFIX="${suffix}"
 263                         -DGMX_LIBS_SUFFIX="${suffix}"
 264                         -DGMX_PYTHON_PACKAGE=$(usex python)
 265                 )
 266                 BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
 267                 [[ ${CHOST} != *-darwin* ]] || \
 268                   sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
 269         done
 270 }
 271
 272 src_compile() {
 273         for x in ${GMX_DIRS}; do
 274                 einfo "Compiling for ${x} precision"
 275                 BUILD_DIR="${WORKDIR}/${P}_${x}"\
 276                         cmake_src_compile
 277                 if use python; then
 278                         BUILD_DIR="${WORKDIR}/${P}_${x}"\
 279                                 cmake_src_compile       python_packaging/all
 280                         BUILD_DIR="${WORKDIR}/${P}" \
 281                                 distutils-r1_src_compile
 282                 fi
 283                 # not 100% necessary for rel ebuilds as available from website
 284                 if use build-manual; then
 285                         BUILD_DIR="${WORKDIR}/${P}_${x}"\
 286                                 cmake_src_compile manual
 287                 fi
 288         done
 289 }
 290
 291 src_test() {
 292         for x in ${GMX_DIRS}; do
 293                 BUILD_DIR="${WORKDIR}/${P}_${x}"\
 294                         cmake_src_compile check
 295         done
 296 }
 297
 298 src_install() {
 299         for x in ${GMX_DIRS}; do
 300                 BUILD_DIR="${WORKDIR}/${P}_${x}" \
 301                         cmake_src_install
 302                 if use python; then
 303                         BUILD_DIR="${WORKDIR}/${P}_${x}" \
 304                                 cmake_src_install       python_packaging/install
 305                 fi
 306                 if use build-manual; then
 307                         newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
 308                 fi
 309
 310                 if use doc; then
 311                         if [[ ${PV} != *9999* ]]; then
 312                                 newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
 313                         fi
 314                 fi
 315         done
 316
 317         if use tng; then
 318                 insinto /usr/include/tng
 319                 doins src/external/tng_io/include/tng/*h
 320         fi
 321         # drop unneeded stuff
 322         rm "${ED}"/usr/bin/GMXRC* || die
 323         for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do
 324                 local n=${x##*/gmx-completion-}
 325                 n="${n%.bash}"
 326                 cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
 327                 newbashcomp "${T}"/"${n}" "${n}"
 328         done
 329         rm "${ED}"/usr/bin/gmx-completion*.bash || die
 330         readme.gentoo_create_doc
 331 }
 332
 333 pkg_postinst() {
 334         einfo
 335         einfo  "Please read and cite gromacs related papers from list:"
 336         einfo  "https://www.gromacs.org/articles.html"
 337         einfo
 338         readme.gentoo_print_elog
 339 }