diff options
Diffstat (limited to 'sci-chemistry')
| -rw-r--r-- | sci-chemistry/gromacs/Manifest | 2 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/files/gromacs-2018-fix-build.patch | 71 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-2018.9999.ebuild | 272 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-2018_beta1.ebuild | 276 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/metadata.xml | 1 |
5 files changed, 622 insertions, 0 deletions
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index fb80356088ed..8f7e43c56949 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -3,6 +3,7 @@ DIST gromacs-2016.2.tar.gz 27339623 SHA256 b6ac3632b848ab0c19f8f319dd5b58fcd09b8 DIST gromacs-2016.3.tar.gz 27342692 SHA256 7bf00e74a9d38b7cef9356141d20e4ba9387289cbbfd4d11be479ef932d77d27 SHA512 16593df0a52620766fb86cfeb16328793503f860cb07cdbbd503ba7f41e6430efb4848389b7179ca3907b57311162666d05224b454e1afb1b74b220f38498d86 WHIRLPOOL dfe31f212545ae2baf7373fde31f715a8df203d098d3ace915d4269b7bf16d06a1f91ead33ccbf8a17e9e0091b593818d0ce2eff151ce532238a8c27f5e20cda DIST gromacs-2016.4.tar.gz 27368706 SHA256 4be9d3bfda0bdf3b5c53041e0b8344f7d22b75128759d9bfa9442fe65c289264 SHA512 69661d2a7a8a5259be277de35e2baa4b688d1f7bef225fc7d733a9b00c6ee135dcbad517c7c9f751121647c2fbd085f2c9cdf22dbd941c7ebc5d3b09e7e08f1f WHIRLPOOL c1586377d2a27f0b529370efb63e09ecca64cdb3d418fe9bc4f3ea1ff82ff5293d159834f4ed5d0136d801095d6f4085722e0d91bce873776fa4549853497ff7 DIST gromacs-2016.tar.gz 27321561 SHA256 aa0a27cd13050a4b70aacfbd169ddce2fe507c7e668f460ecf6cf32afcac5771 SHA512 756771baaa85a1d16e7d5b8e4c96bbd1c04c7acdc536a253886cff186316330f06d60d206a0159efb15f47f161c779d3757dc5dbceab8c097241c1382d376201 WHIRLPOOL 1cc3d3797e1aaf93e1e0cb2e71173896e33fee2bb03f4e97e06be3ab85842e6da3feaf8701425358f1d701e00159ff6ce3b24fa1488d5e8ef70a1acbb914361c +DIST gromacs-2018-beta1.tar.gz 29857800 BLAKE2B 221ed414c1dc73b59df27dfb6dd22ef094152bba7a8346cd0d0164e9a0aa5463a7d836dfb13e98ac8cdbef2ae4a0503763a5c445a5e1c73815b3592d8b8f97fe SHA512 6e827b7b33589ccc7ef1d237c4e8ce06749a2c47f59956d383fdb59439a34874a9e0e3a3cca1d209425353a7dcf0f963de035dd0281d4c8aad0c921e6bbc7b93 DIST gromacs-5.0.4.tar.gz 26342095 SHA256 78068eeccc0b950018ddb45c41280e53c8bedae4639dca48e17c940f8896b23b SHA512 bc62b623bf71dcaa948aaf7563a3d3afa973da0702062848a20323db202e862dcee413197dacd1472866ccb40fce7709e283177b1c6c49514064f23e6c46b5ee WHIRLPOOL d8458d3d563e015e830622ae0c924e896765a6329ffe4cb1a31c7aef3c804f392d29e3f1db5617051e85058403422f7d69a160a6c7cc810564696d88f9d50bd4 DIST gromacs-5.1.3.tar.gz 27095702 SHA256 c962d9446939a9ba9905e7ca440c9306fd310f08600da3b744806bfd0eacccde SHA512 9ab26e1b2268f8d567b89b2d99d0b75b937b28edceaec56d17ca3243c76faa31255ffc0c45d762c7c693fe500b00e36ad43b80572d1d7f92dc87f9d2d98c0ba6 WHIRLPOOL bdd9c63ceb5e61963c4edd0af815cc34a3f237d8dee410c834b9b55bb82374de65b437828390a668282e50428b9907b887cd5265caf2a2007fc7673e7ab23733 DIST regressiontests-2016.1.tar.gz 67094518 SHA256 10c9f50ff3cb32cf629aa35e35d957965dcfce4af84a6569e6d65a16c4e09eb7 SHA512 fc01c802d81400373a147171881f3b7b9309402e8ffb08287ba393aefbb701ba93bbe0b9549ff6fa264a8befbba445c2d2c7450633063a724f78ec8ca81ae8c9 WHIRLPOOL e8c54164558fcbaa1e65e9280e438882c96bbbaa6c9389a2ee5aed37d70b83b6b36e95dd5141b4e64b303e3799411ee01cf04aa919f25014d172011e49714126 @@ -10,5 +11,6 @@ DIST regressiontests-2016.2.tar.gz 67095329 SHA256 53fa9ad062cc3e269fc6186db1ccb DIST regressiontests-2016.3.tar.gz 67093968 SHA256 a3d1b09acfc61820dddd765a381f706190b4657606488f1e676becb859ea7ecc SHA512 ee87df9f339954da0e1f1b4c8b8d4deb574f3b73d174010a295a7a0e8bc462ead7691090ea7cf8ac3d984a6cd70f1cd22c3592fa161b2967061ae5ba2796286b WHIRLPOOL 2e986136f7faf6db108bc79e6fb6db9fe81d05f5af8bc27037b80cd25869f7cd4162d5cabc03994b36c71945910be79a217ff27f61463d1548cbdff6acd99f56 DIST regressiontests-2016.4.tar.gz 67643648 SHA256 d58d1a2a53c22c06e2dc03bd98ae1eea0a0d51696a1f20f635dfc394fa3da957 SHA512 367438b897a05e1cc0dcd1d3872fb6a0e9ff6b1146e9448d941d6517dce789f0c478d20cf0a4f3565070f132dc88872441aadb8b499f59efa0e1e4a6dd6a7135 WHIRLPOOL 695a3b7f81915247a90e95c0a83823c0297fba6ae6266195e86c61ec540ca58afd8d01ba236c5ddb3f44b41fb9301ba6a836b15cad1875bae42ba6276670daff DIST regressiontests-2016.tar.gz 66908712 SHA256 30a72362f011fd9e3a8d33004018126f938536c13fcb70f590afc74beaec5406 SHA512 59902c1973c33ea8f003f21a737dc7cc64da3258112322eedc9834b53628134a6817d5ee5b3950c9bfd97a3a0580aef88ddef0609ef2c58693c96c7575651e01 WHIRLPOOL 9d210aed00ddfa57df47733169997ef04dec84c524eb5a9c5c6dd9b05ad9ec2d7f3c8a5a43f2ade9be166d80f35a260c04b1a48ac092f5969a213475bb63ae20 +DIST regressiontests-2018-beta1.tar.gz 67870909 BLAKE2B e9aff43331394c4a50cbc626d0327498f1571cf457e6b924f0cfe8eb688a9cd8d2b66c13c900da8737b124861fb567f9129aff840a294e92233b9a2214ff20d7 SHA512 509175cbbb8528d9bb1394c726c6e89291c2077880a3c4bf99a330ff457ca233ae74e771b8a753b0c94bba8de02840b1e5460b7c226e177742b1dee289833c0f DIST regressiontests-5.0.4.tar.gz 65193251 SHA256 89ad9bc067035ac8f340319b538c446983d937b910067e871911d7afe2ecb3f0 SHA512 747725fa28c1c9525596bdeeb8809e45268e19036c11dac67d043aa1c51748688ca37eb6014eb7e819eb927a8b9ca2631d0ace4cdff8ed491b08c316c530ab65 WHIRLPOOL e15ccab0a0beefac41aeff11e2e596e971167f1590eed159ff82c4a8e3aec1d234287be597026951904ecfe6099f30ef3bcd48f2098b9f5201bde62e15fbc4f9 DIST regressiontests-5.1.3.tar.gz 66994083 SHA256 fd5797dcfd29f7ae70857a438dcd4200a8006fce222f297892c8e90123993ebc SHA512 486e86eb3b75bae822abe82dac4e1098aa13723bd04214021f835a2f0b847303f015a9ececc33aa5ae63d31a2eeae07e512f22464b6c0e26d1286b0781578022 WHIRLPOOL 6ddb76859ee8fa3aba4d995e397970e6fd270acbdd6cc07ab77de0aebb0bfdbd2bd1107ae39d4410e750641047ae4b75c703eafad95a57ff42deb3bf1c742d08 diff --git a/sci-chemistry/gromacs/files/gromacs-2018-fix-build.patch b/sci-chemistry/gromacs/files/gromacs-2018-fix-build.patch new file mode 100644 index 000000000000..2ed6a19f31b0 --- /dev/null +++ b/sci-chemistry/gromacs/files/gromacs-2018-fix-build.patch @@ -0,0 +1,71 @@ +From 81e68584512b21ec572d2561c25a1b19982aa0be Mon Sep 17 00:00:00 2001 +From: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru> +Date: Fri, 1 Dec 2017 17:12:36 +0300 +Subject: [PATCH] Fix build with cmake 3.10 on Linux + +Without this fix cmake will fail with + +-- Detecting CXX compiler ABI info - done +-- Detecting CXX compile features +-- Detecting CXX compile features - done +CMake Error at cmake/gmxCTestUtilities.cmake:56 (file): + file STRINGS file + "/var/tmp/portage/sci-chemistry/gromacs-2018_beta1/work/gromacs-2018_beta1_float/DartConfiguration.tcl" + cannot be read. +Call Stack (most recent call first): + CMakeLists.txt:89 (gmx_ctest_init) + +-- Performing Test CXXFLAG_STD_CXX0X +-- Performing Test CXXFLAG_STD_CXX0X - Success +-- Performing Test CXX11_SUPPORTED +-- Performing Test CXX11_SUPPORTED - Success +.... +.... +.... +-- Looking for inttypes.h +-- Looking for inttypes.h - found +-- <<< Gentoo configuration >>> +Build type Gentoo +Install path /usr +Compiler flags: +C -march=core-avx2 -O2 -pipe -march=native -mtune=native -mfpmath=sse -mavx2 +C++ -march=core-avx2 -O2 -pipe -march=native -mtune=native -mfpmath=sse -mavx2 -std=c++11 +Linker flags: +Executable -Wl,-O1 -Wl,--as-needed +Module -Wl,-O1 -Wl,--as-needed +Shared -Wl,-O1 -Wl,--as-needed + +-- Configuring incomplete, errors occurred! +See also "/var/tmp/portage/sci-chemistry/gromacs-2018_beta1/work/gromacs-2018_beta1_float/CMakeFiles/CMakeOutput.log". +See also "/var/tmp/portage/sci-chemistry/gromacs-2018_beta1/work/gromacs-2018_beta1_float/CMakeFiles/CMakeError.log". + +Change-Id: Ie04c2e5f5884f05c3648fed7289157e73fd8d81f +Signed-off-by: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru> +--- + cmake/gmxCTestUtilities.cmake | 10 ++++++---- + 1 file changed, 6 insertions(+), 4 deletions(-) + +diff --git a/cmake/gmxCTestUtilities.cmake b/cmake/gmxCTestUtilities.cmake +index 89715f910..3685df648 100644 +--- a/cmake/gmxCTestUtilities.cmake ++++ b/cmake/gmxCTestUtilities.cmake +@@ -50,10 +50,12 @@ macro (gmx_ctest_init) + set(MEMORYCHECK_TYPE "AddressSanitizer") + endif() + include(CTest) +- # At least with CMake 3.4.1 on OS X, AddressSanitizer support in CTest +- # does not work without this... +- set(_ctest_config_file "${PROJECT_BINARY_DIR}/DartConfiguration.tcl") +- file(STRINGS ${_ctest_config_file} _existing REGEX "^CMakeCommand: ") ++ if(APPLE) ++ # At least with CMake 3.4.1 on OS X, AddressSanitizer support in CTest ++ # does not work without this... ++ set(_ctest_config_file "${PROJECT_BINARY_DIR}/DartConfiguration.tcl") ++ file(STRINGS ${_ctest_config_file} _existing REGEX "^CMakeCommand: ") ++ endif() + if (NOT _existing) + file(APPEND ${_ctest_config_file} "\nCMakeCommand: ${CMAKE_COMMAND}\n") + endif() +-- +2.15.0 + diff --git a/sci-chemistry/gromacs/gromacs-2018.9999.ebuild b/sci-chemistry/gromacs/gromacs-2018.9999.ebuild new file mode 100644 index 000000000000..315835fdc606 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2018.9999.ebuild @@ -0,0 +1,272 @@ +# Copyright 1999-2017 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 +} diff --git a/sci-chemistry/gromacs/gromacs-2018_beta1.ebuild b/sci-chemistry/gromacs/gromacs-2018_beta1.ebuild new file mode 100644 index 000000000000..3e0dd9b80bc9 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2018_beta1.ebuild @@ -0,0 +1,276 @@ +# Copyright 1999-2017 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="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + cuda? ( !opencl ) + mkl? ( !blas !fftw !lapack )" + +DOCS=( AUTHORS README ) + +PATCHES=( + "${FILESDIR}/${PN}-2018-fix-build.patch" + ) + +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 +} diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml index c9beb4a5a326..844b34dd014b 100644 --- a/sci-chemistry/gromacs/metadata.xml +++ b/sci-chemistry/gromacs/metadata.xml @@ -15,6 +15,7 @@ </maintainer> <use> <flag name="cuda">Enable cuda non-bonded kernels</flag> + <flag name="opencl">Enable opencl non-bonded kernels</flag> <flag name="double-precision">More precise calculations at the expense of speed</flag> <flag name="single-precision">Single precision version of gromacs (default)</flag> <flag name="boost">Enable external boost library</flag> |