DIST gromacs-2016.2.tar.gz 27339623 BLAKE2B c3548f4abdc4c1b09a79a3da99d7ca8060daca7307e4c5b81bd97d54adfb9621fbccf1ea7fd96c3676d6b44c20f9f4cd2168ce131799792512fad3b8b1ac0522 SHA512 f5e74bb8c126823c90d205ac0f0835e61fdd13a4550bc15aa9c972ee9b187f6451cdc90877c17276d2f889d61abb5eaa5ea1b54f7cbf3da67074146c749c1aa6
DIST gromacs-2016.5.tar.gz 27369491 BLAKE2B 4a8bf1ae3e298ac2e26ec476130720dc3ef00db5d999e3a45fdbfd7fbfe7e94fbc86be6ff0f2f23552769c8bc851ce49c73f6fc1ab13f372523279b93e7794d7 SHA512 9cb8ff88871aa5df0967c60ba303c03296c6fa3c215cd01b26259df7753f0014f04222078ab4b84a66a1f709997837134d5c0f74da19b78322e410010c9d9e10
-DIST gromacs-2018.1.tar.gz 29895119 BLAKE2B 45cc674bd78dc7dc56388a899ae50da9f10eb4dc80dad461f7e298894ee845eae744010013e682f3be4b03c1f04624111266e84cd9721415b23f87d544846827 SHA512 d29f152e9f115c7de07881c6af4cc05481e0a5520bd33142a09507e8c4df9f8b6c9d6d96efcb7adaaf4e0127b76ab247421d43918bd7e7779d6e71f5984db715
-DIST gromacs-2018.2.tar.gz 29899294 BLAKE2B a4d7111fdfb2c6919ef7a94aded634c5e14c4ca6ee6411c6c84289a9c88c39d731e89d3b01f14b2370d7de7782964e8db378aa6baabdd85cf46b689504f0738a SHA512 d444b503e24a9875b0ab7622772946ef73ab2c897da6ff45ac908f147ea398ba2404b064a8784996fd34b25e188e36f12a492e0070427e0929f422d934205d28
DIST gromacs-2018.3.tar.gz 29915626 BLAKE2B 6e6eeafecdd923a25b4a2a78a8e89f793639b57ffbd63f19d133d8474302f9a381041f138a509dadb42b36e25fe508729e860efb6b0c75cdbf01d924b0a8fd83 SHA512 3c4d6eb3942d7b54d01c94c6f6f5ae706e0f5d4f9901ea11a56fde4df97b1a9112007f2cb13feea0f19f30c89f57ae80ff53a8f5203b8cdff103aa903cd0dc8f
DIST gromacs-5.0.4.tar.gz 26342095 BLAKE2B 27a2483e23533ad627114c0005fa0d49a311b359c31aed6378bdd768c9dda03c3b19f11d961f0bd3b82a1711737d4b7dce13cad5fc56d058dd0110fe21421ee3 SHA512 bc62b623bf71dcaa948aaf7563a3d3afa973da0702062848a20323db202e862dcee413197dacd1472866ccb40fce7709e283177b1c6c49514064f23e6c46b5ee
DIST gromacs-5.1.3.tar.gz 27095702 BLAKE2B b7fd8fa10e8c4f4368ac551338c59374dc35f85c9fdae5d64eec62929b8f04ea724a084959b3618cd8a151bf3e0a0c84c8f75de953722effca82a4928941ce73 SHA512 9ab26e1b2268f8d567b89b2d99d0b75b937b28edceaec56d17ca3243c76faa31255ffc0c45d762c7c693fe500b00e36ad43b80572d1d7f92dc87f9d2d98c0ba6
DIST regressiontests-2016.2.tar.gz 67095329 BLAKE2B fec8a663845ad67374c8a230d1590fa9e5079460198f41cee3b788aaa1c72e8ec9dcda48bc68a594f15003d11bf6617d46cc1a09c16b7a333587b43904a16ba6 SHA512 e0aceb56d1f38a7e6ab9fdaac5063fd20c5b3a162ffb6eddd0e6dc7dff9b724bfe31363493a9437e9f9d5421a534b375960fcb31e903a4901a0fa94ed8511294
DIST regressiontests-2016.5.tar.gz 67641413 BLAKE2B 4fcd30c198f3acbbabf1104c040d9a686de49536a97dbeb14732bfa0ed3cf37aa61b1b0f45393668985b993d1f1862a8985e416af819cf9793f5964f3e4f43cc SHA512 31764fd99cc4185d61de5d4443ee482c27b13533451a24aa0e4899997ce275a63685424eafacae38b1a3ffd4ce0d5ebe02a90348953b04c104f91376f0edfdff
-DIST regressiontests-2018.1.tar.gz 67859956 BLAKE2B f561eb9373b4e0e5faae2aa91e3cb3911c096c1fce96755fc7a8a7b3a25b53bda88ef90d04d3a6fce414bf9dba44d0933827f080949306d5c98f60e5a1797412 SHA512 81c9a62fca859923c1e27214b32b0cff1dd48224dd4ad9301554036b842ccc400a2729752ba71b284e0c5b6c1769ce7de5fe2c9ba4fc7cf0917fd4ced9883112
-DIST regressiontests-2018.2.tar.gz 67855795 BLAKE2B 32504a7d9315f404b4a57fd45dd59540166b0e73d51ad5938b6a18cafc491cda5c00fe204dedba9c51a3f859759fb1d8c894c0607d71d49701269cf909617584 SHA512 6cc4bd4716f8b7aba69b840facd160f1abb32def2349cc441b89e12bf8df21dc4a4ca23acc4e47bf7ec3ae55b8e3f9a28beab044833b9d8ddfcf5e21d2878a5a
DIST regressiontests-2018.3.tar.gz 67857855 BLAKE2B acd7a05ae79d1b4eb47d0c68a3fec9ee19f028a5019f39c37a033f48cf6da2a468375180ad6ceca9ac4f685a8bead38550663a47d6427b51f84c32a5c810e5f0 SHA512 57980d49efe6dcc3b3d14b5913a30c68fc1de5b679ef986fec1a149c76f67139b0299c3ee2825451461294fab5f345c7ad4f42e90f8991b81aafe9c369f3ff0b
DIST regressiontests-5.0.4.tar.gz 65193251 BLAKE2B c5e5f23adcc2639fe652bc252533307c7fda44453d506603242968bd8588c7394028b2c3c7a9252f807a050d40e8f78735e904dfe517d3db8ae962051f4826c1 SHA512 747725fa28c1c9525596bdeeb8809e45268e19036c11dac67d043aa1c51748688ca37eb6014eb7e819eb927a8b9ca2631d0ace4cdff8ed491b08c316c530ab65
DIST regressiontests-5.1.3.tar.gz 66994083 BLAKE2B 7009f65ad0138664ac84e57f8bc7cce5d18a59f99943e56b6642583120bfce279e005ac0bacd2db8904ea477a48e2b938c64de46a65fa5d08fce6009d53583c3 SHA512 486e86eb3b75bae822abe82dac4e1098aa13723bd04214021f835a2f0b847303f015a9ececc33aa5ae63d31a2eeae07e512f22464b6c0e26d1286b0781578022
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
blas? ( virtual/blas )
cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
fftw? ( sci-libs/fftw:3.0 )
- hwloc? ( sys-apps/hwloc )
+ hwloc? ( <sys-apps/hwloc-2 )
lapack? ( virtual/lapack )
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
blas? ( virtual/blas )
cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
fftw? ( sci-libs/fftw:3.0 )
- hwloc? ( sys-apps/hwloc )
+ hwloc? ( <sys-apps/hwloc-2 )
lapack? ( virtual/lapack )
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
blas? ( virtual/blas )
cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
fftw? ( sci-libs/fftw:3.0 )
- hwloc? ( sys-apps/hwloc )
+ hwloc? ( <sys-apps/hwloc-2 )
lapack? ( virtual/lapack )
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
+++ /dev/null
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
-
-if [[ $PV = *9999* ]]; then
- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
- https://gerrit.gromacs.org/gromacs.git
- https://github.com/gromacs/gromacs.git
- http://repo.or.cz/r/gromacs.git"
- [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
- inherit git-r3
- KEYWORDS=""
-else
- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
- KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
- X? (
- x11-libs/libX11
- x11-libs/libSM
- x11-libs/libICE
- )
- blas? ( virtual/blas )
- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
- opencl? ( virtual/opencl )
- fftw? ( sci-libs/fftw:3.0 )
- hwloc? ( sys-apps/hwloc )
- lapack? ( virtual/lapack )
- mkl? ( sci-libs/mkl )
- mpi? ( virtual/mpi )
- "
-DEPEND="${CDEPEND}
- virtual/pkgconfig
- doc? (
- app-doc/doxygen
- dev-texlive/texlive-latex
- dev-texlive/texlive-latexextra
- media-gfx/imagemagick
- )"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
- || ( single-precision double-precision )
- cuda? ( single-precision )
- cuda? ( !opencl )
- mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-
-if [[ ${PV} != *9999 ]]; then
- S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
- use openmp && ! tc-has-openmp && \
- die "Please switch to an openmp compatible compiler"
-}
-
-src_unpack() {
- if [[ ${PV} != *9999 ]]; then
- default
- else
- git-r3_src_unpack
- if use test; then
- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
- EGIT_BRANCH="${EGIT_BRANCH}" \
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
- git-r3_src_unpack
- fi
- fi
-}
-
-src_prepare() {
- #notes/todos
- # -on apple: there is framework support
-
- xdg_environment_reset #591952
-
- cmake-utils_src_prepare
-
- use cuda && cuda_src_prepare
-
- GMX_DIRS=""
- use single-precision && GMX_DIRS+=" float"
- use double-precision && GMX_DIRS+=" double"
-
- if use test; then
- for x in ${GMX_DIRS}; do
- mkdir -p "${WORKDIR}/${P}_${x}" || die
- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
- done
- fi
-
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
-
-src_configure() {
- local mycmakeargs_pre=( ) extra fft_opts=( )
-
- #go from slowest to fastest acceleration
- local acce="None"
- use cpu_flags_x86_sse2 && acce="SSE2"
- use cpu_flags_x86_sse4_1 && acce="SSE4.1"
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
- use cpu_flags_x86_avx && acce="AVX_256"
- use cpu_flags_x86_avx2 && acce="AVX2_256"
-
- #to create man pages, build tree binaries are executed (bug #398437)
- [[ ${CHOST} = *-darwin* ]] && \
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
- if use fftw; then
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
- elif use mkl && has_version "=sci-libs/mkl-10*"; then
- fft_opts=( -DGMX_FFT_LIBRARY=mkl
- -DMKL_INCLUDE_DIR="${MKLROOT}/include"
- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
- )
- elif use mkl; then
- local bits=$(get_libdir)
- fft_opts=( -DGMX_FFT_LIBRARY=mkl
- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
- )
- else
- fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
- fi
-
- mycmakeargs_pre+=(
- "${fft_opts[@]}"
- -DGMX_X11=$(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_LIB_INSTALL_DIR="$(get_libdir)"
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
- -DBUILD_TESTING=$(usex test)
- -DGMX_BUILD_UNITTESTS=$(usex test)
- ${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)
- "${opencl[@]}"
- "${cuda[@]}"
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
- -DGMX_BINARY_SUFFIX="${suffix}"
- -DGMX_LIBS_SUFFIX="${suffix}"
- )
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_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 ${cuda}
- -DGMX_OPENMM=OFF
- -DGMX_BUILD_MDRUN_ONLY=ON
- -DBUILD_SHARED_LIBS=OFF
- -DGMX_BUILD_MANUAL=OFF
- -DGMX_BINARY_SUFFIX="_mpi${suffix}"
- -DGMX_LIBS_SUFFIX="_mpi${suffix}"
- )
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_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-utils_src_compile
- # not 100% necessary for rel ebuilds as available from website
- if use doc; then
- BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_compile manual
- fi
- use mpi || continue
- einfo "Compiling for ${x} precision with mpi"
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
- cmake-utils_src_compile
- done
-}
-
-src_test() {
- for x in ${GMX_DIRS}; do
- BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_make check
- done
-}
-
-src_install() {
- for x in ${GMX_DIRS}; do
- BUILD_DIR="${WORKDIR}/${P}_${x}" \
- cmake-utils_src_install
- 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-utils_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
-}
+++ /dev/null
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
-
-if [[ $PV = *9999* ]]; then
- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
- https://gerrit.gromacs.org/gromacs.git
- https://github.com/gromacs/gromacs.git
- http://repo.or.cz/r/gromacs.git"
- [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
- inherit git-r3
- KEYWORDS=""
-else
- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
- KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
- X? (
- x11-libs/libX11
- x11-libs/libSM
- x11-libs/libICE
- )
- blas? ( virtual/blas )
- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
- opencl? ( virtual/opencl )
- fftw? ( sci-libs/fftw:3.0 )
- hwloc? ( sys-apps/hwloc )
- lapack? ( virtual/lapack )
- mkl? ( sci-libs/mkl )
- mpi? ( virtual/mpi )
- "
-DEPEND="${CDEPEND}
- virtual/pkgconfig
- doc? (
- app-doc/doxygen
- dev-texlive/texlive-latex
- dev-texlive/texlive-latexextra
- media-gfx/imagemagick
- )"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
- || ( single-precision double-precision )
- cuda? ( single-precision )
- cuda? ( !opencl )
- mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-
-if [[ ${PV} != *9999 ]]; then
- S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
- use openmp && ! tc-has-openmp && \
- die "Please switch to an openmp compatible compiler"
-}
-
-src_unpack() {
- if [[ ${PV} != *9999 ]]; then
- default
- else
- git-r3_src_unpack
- if use test; then
- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
- EGIT_BRANCH="${EGIT_BRANCH}" \
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
- git-r3_src_unpack
- fi
- fi
-}
-
-src_prepare() {
- #notes/todos
- # -on apple: there is framework support
-
- xdg_environment_reset #591952
-
- cmake-utils_src_prepare
-
- use cuda && cuda_src_prepare
-
- GMX_DIRS=""
- use single-precision && GMX_DIRS+=" float"
- use double-precision && GMX_DIRS+=" double"
-
- if use test; then
- for x in ${GMX_DIRS}; do
- mkdir -p "${WORKDIR}/${P}_${x}" || die
- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
- done
- fi
-
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
-
-src_configure() {
- local mycmakeargs_pre=( ) extra fft_opts=( )
-
- #go from slowest to fastest acceleration
- local acce="None"
- use cpu_flags_x86_sse2 && acce="SSE2"
- use cpu_flags_x86_sse4_1 && acce="SSE4.1"
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
- use cpu_flags_x86_avx && acce="AVX_256"
- use cpu_flags_x86_avx2 && acce="AVX2_256"
-
- #to create man pages, build tree binaries are executed (bug #398437)
- [[ ${CHOST} = *-darwin* ]] && \
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
- if use fftw; then
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
- elif use mkl && has_version "=sci-libs/mkl-10*"; then
- fft_opts=( -DGMX_FFT_LIBRARY=mkl
- -DMKL_INCLUDE_DIR="${MKLROOT}/include"
- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
- )
- elif use mkl; then
- local bits=$(get_libdir)
- fft_opts=( -DGMX_FFT_LIBRARY=mkl
- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
- )
- else
- fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
- fi
-
- mycmakeargs_pre+=(
- "${fft_opts[@]}"
- -DGMX_X11=$(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)
- ${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)
- "${opencl[@]}"
- "${cuda[@]}"
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
- -DGMX_BINARY_SUFFIX="${suffix}"
- -DGMX_LIBS_SUFFIX="${suffix}"
- )
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_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 ${cuda}
- -DGMX_OPENMM=OFF
- -DGMX_BUILD_MDRUN_ONLY=ON
- -DBUILD_SHARED_LIBS=OFF
- -DGMX_BUILD_MANUAL=OFF
- -DGMX_BINARY_SUFFIX="_mpi${suffix}"
- -DGMX_LIBS_SUFFIX="_mpi${suffix}"
- )
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_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-utils_src_compile
- # not 100% necessary for rel ebuilds as available from website
- if use doc; then
- BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_compile manual
- fi
- use mpi || continue
- einfo "Compiling for ${x} precision with mpi"
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
- cmake-utils_src_compile
- done
-}
-
-src_test() {
- for x in ${GMX_DIRS}; do
- BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_make check
- done
-}
-
-src_install() {
- for x in ${GMX_DIRS}; do
- BUILD_DIR="${WORKDIR}/${P}_${x}" \
- cmake-utils_src_install
- 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-utils_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
-}
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
opencl? ( virtual/opencl )
fftw? ( sci-libs/fftw:3.0 )
- hwloc? ( sys-apps/hwloc )
+ hwloc? ( <sys-apps/hwloc-2 )
lapack? ( virtual/lapack )
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
opencl? ( virtual/opencl )
fftw? ( sci-libs/fftw:3.0 )
- hwloc? ( sys-apps/hwloc )
+ hwloc? ( <sys-apps/hwloc-2 )
lapack? ( virtual/lapack )
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
blas? ( virtual/blas )
cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
fftw? ( sci-libs/fftw:3.0 )
- hwloc? ( sys-apps/hwloc )
+ hwloc? ( <sys-apps/hwloc-2 )
lapack? ( virtual/lapack )
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
projects / gentoo.git / commitdiff