diff options
Diffstat (limited to 'sci-chemistry')
-rw-r--r-- | sci-chemistry/Manifest.gz | bin | 17236 -> 17227 bytes | |||
-rw-r--r-- | sci-chemistry/gromacs/Manifest | 9 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-2016.5.ebuild | 275 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-2019.2.ebuild | 2 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-2019.3.ebuild (renamed from sci-chemistry/gromacs/gromacs-2016.9999.ebuild) | 70 | ||||
-rw-r--r-- | sci-chemistry/molequeue/Manifest | 5 | ||||
-rw-r--r-- | sci-chemistry/molequeue/files/molequeue-0.8.0-cmake.patch | 106 | ||||
-rw-r--r-- | sci-chemistry/molequeue/molequeue-0.8.0.ebuild | 70 | ||||
-rw-r--r-- | sci-chemistry/molequeue/molequeue-0.9.0.ebuild | 9 |
9 files changed, 62 insertions, 484 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz Binary files differindex afcb5812232c..cd635dc327b8 100644 --- a/sci-chemistry/Manifest.gz +++ b/sci-chemistry/Manifest.gz diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 7b4a1c176053..ba4761ab8503 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -1,17 +1,16 @@ -DIST gromacs-2016.5.tar.gz 27369491 BLAKE2B 4a8bf1ae3e298ac2e26ec476130720dc3ef00db5d999e3a45fdbfd7fbfe7e94fbc86be6ff0f2f23552769c8bc851ce49c73f6fc1ab13f372523279b93e7794d7 SHA512 9cb8ff88871aa5df0967c60ba303c03296c6fa3c215cd01b26259df7753f0014f04222078ab4b84a66a1f709997837134d5c0f74da19b78322e410010c9d9e10 DIST gromacs-2018.3.tar.gz 29915626 BLAKE2B 6e6eeafecdd923a25b4a2a78a8e89f793639b57ffbd63f19d133d8474302f9a381041f138a509dadb42b36e25fe508729e860efb6b0c75cdbf01d924b0a8fd83 SHA512 3c4d6eb3942d7b54d01c94c6f6f5ae706e0f5d4f9901ea11a56fde4df97b1a9112007f2cb13feea0f19f30c89f57ae80ff53a8f5203b8cdff103aa903cd0dc8f DIST gromacs-2018.7.tar.gz 29912662 BLAKE2B 0714b28ec2443f3201275fc2fa6db1202a059161362134d4de03a900a3a67fe9d31ba8c058d5ee971198fecd69379fcd389f03d25c61f50b8460c43ba5c564d5 SHA512 fbc3b847b70b1396f412b8f4a1b977268651f8d53a222dcf6349fe563ff6319e096484209a24351e382bc9162a949b3900591f5b469c32dd9effeb894f03c172 DIST gromacs-2019.2.tar.gz 33437869 BLAKE2B bebe4942688dace148856d4491b687b8e0fd2c86d7fbd9eecdb46824d316a0fc3854464ecafa79d8db92327ee8467be204b050c11f1e71132184efd812c3bf09 SHA512 da7ff24e8485774e22d1c2464fbe64675c3305ef0e21a3d17e363201031952e5d4a9b81f572d5284fb6f2596ed99daf62fe78d653387d9d714274f46bc750183 -DIST regressiontests-2016.5.tar.gz 67641413 BLAKE2B 4fcd30c198f3acbbabf1104c040d9a686de49536a97dbeb14732bfa0ed3cf37aa61b1b0f45393668985b993d1f1862a8985e416af819cf9793f5964f3e4f43cc SHA512 31764fd99cc4185d61de5d4443ee482c27b13533451a24aa0e4899997ce275a63685424eafacae38b1a3ffd4ce0d5ebe02a90348953b04c104f91376f0edfdff +DIST gromacs-2019.3.tar.gz 33441419 BLAKE2B 79319dd23982c65c7c4d8e5f633cef0c7fd99a38a4e0cc9030a3ffb0fdfc07a4fbfbcfa942896f23a143b747e044fae645498a3e6992497d1f1a7d966f80b2b0 SHA512 de9f54d095b45ea7efd1043f83a40f6c778a6e3e2067a01f48d1ce843d68d226061933ca28a3edb635b795a8ddd5ef9deb8ed1114aa3235bc8039db8ff7d0218 DIST regressiontests-2018.3.tar.gz 67857855 BLAKE2B acd7a05ae79d1b4eb47d0c68a3fec9ee19f028a5019f39c37a033f48cf6da2a468375180ad6ceca9ac4f685a8bead38550663a47d6427b51f84c32a5c810e5f0 SHA512 57980d49efe6dcc3b3d14b5913a30c68fc1de5b679ef986fec1a149c76f67139b0299c3ee2825451461294fab5f345c7ad4f42e90f8991b81aafe9c369f3ff0b DIST regressiontests-2018.7.tar.gz 67856738 BLAKE2B 955ae8b5e74f90fec704cf41fbd00bd8c09d754f950551fe0adfcd407db6fdb4491a3815149ea37d36c747316c79d462e823b9f6b26f2376bf90d87aad95731b SHA512 c2ff390750bd99faebcd8d5dd8ad6dbf2b00113ed888bddddf985dbf95d7f347093adb67f3c396547b3e2990de330fddb7efe83ded91a72cf97c82a1dac7e826 DIST regressiontests-2019.2.tar.gz 67643003 BLAKE2B 4178de5d62f194a81f97e442c10f123dc59c5e63f2078f7f07135709f3f6e530e0d237bf40264b285c084519d5ace75dfcbcddc16dc740c4f17233dc33542e45 SHA512 c1f25bc770d3f0a873c887d5563c1cd88179e81211b70ce6f5015696e6fa0b6931a8da7a449f2b223f3105b9e2e7eca67248e96fbfc2a7fd5fb360ba616f22ff -EBUILD gromacs-2016.5.ebuild 7973 BLAKE2B 72b0552595f3187c91bfff89cbe49ac5dbfa1396d82f32428e1519e98aff243f5a68e1c7679386abc8eb0bbb62f40f594def4fa2bf8460134631f5c9e734c456 SHA512 a269b5bc8a484bd27b75f0301267d432d1d0ffa3389f190779acf474410401f8b81fd5ae4fec286472c99e75076da592f06566a777773518b25f2b2b29f9967c -EBUILD gromacs-2016.9999.ebuild 7976 BLAKE2B 24237f4e253faef5df7600baafa01ac9db0e7eacee6c4a5cef6e9e17961e159c701ef8573b3cea4703511f759d7659c5bbd925c8739c1bcf172f9fdf296c7cb2 SHA512 80307361e6b22dcf182bf77c587c31089eb1e85cbda69276bcc90fd85f10a143f69b2568b4ace41104d602793de3fd7219271ca28228ae0b621e23e7c7b58227 +DIST regressiontests-2019.3.tar.gz 67640462 BLAKE2B ed6c176a144e0407be66585be5d6090c31c047498bc5f48f59685108de91f2f9ddb2d22b291a15e6ffa1db848aae19b94a79c8c3d34b1067680f759a179953dd SHA512 822e905fb488ce308eb9324d93f78106da5252c773c7941d49c6162e73bdff109aeca1f0d57216c6dd6536a4c41d80013fa1cee2f5206b0c4160a3e5b4a31315 EBUILD gromacs-2018.3.ebuild 7824 BLAKE2B cc5ec314f5338c269d00bb8ec7af34f38134c59dd7009fc593cfa559cc68e69753f17bd8b77f5156f08999a83980d1e1c5684fd9ed489386af309f1babf850aa SHA512 d47c8c6e1e4c1dc5cd2429e5c77f04af822b5995cdd1f93a1331442dfe95d0192bda5565d3837575100f2fe841f1006cd38698ced727525c716d1925c0e65579 EBUILD gromacs-2018.7.ebuild 7825 BLAKE2B 8ec9d3451720801d0249a6964b3df6dfd774e66a6ec790a0ebaba967d9d9fa23785ed5c229e8821de40f663d6adfaaab1c056ac36b78ebb1ce8213b0bffee7f7 SHA512 5e39cf72d8344c4690161a1ce4a6961ff2fa492167d4dc768de623c3ead7bb40d42a808f5a20386c39530bc33e9d74feca69181929a387c2fb1d41e69dfe7f91 EBUILD gromacs-2018.9999.ebuild 7827 BLAKE2B 97a2437061a55854dd2799c8bdbec6a342586fc480785ea52de8d6b612c747ace1fba0a1fc3dbec9904cafcb3abdabd363ba0d6285cfc44f60964047c52f5b74 SHA512 975f2bcfdd93df006ec2a8f439a2a90e4c9079c58209ec2828b5647d96c29f7eef7fd0c79da844cc8d4e449b573a75884b19c951649c0028133d3fa87b03934c -EBUILD gromacs-2019.2.ebuild 9113 BLAKE2B 9e111d428ab09ddabe000b17e645a1d35de5efb88cfc3989a2119be9e3533eb8c4c3d8df9e396e0dc8140081e6cdfa8e70323e32e0a56c8b88e39b5d27482fc0 SHA512 b8f234c0dfe092a26d86e6ac856fd9c3221dbda55686d2ea341ba42883fa0b29ed188dfee37bb7859ba069a90a83ddaa2ab117f8694c696ceb58350d25fe393f +EBUILD gromacs-2019.2.ebuild 9112 BLAKE2B 54e93c462fec627d154f385ec910c682a3b57fcded8bec082d1dddc73d774e876422d9b24cd50f9984f1a412db7e85e1e862fd94ac295d6e0318d24e07d53a6c SHA512 4c4906a7a982cfe9fffd4375c469b8f637b3e73ea4dde7ce37d517e916b59418a2f80a007ae516be7611b4a6f6379ac444df6946f70968671bccdf0060d85e97 +EBUILD gromacs-2019.3.ebuild 9114 BLAKE2B 9286e7663d622e30ca491577c880827006f3bb2a68d2e3fd9c26fdc97541c12ebef06ab9d3b73ea89e0bbb079e79188c10b387366948920ee631c37da0be4ac5 SHA512 70fd567f7cdb9d8f2c7609b56c4522b5c3cc8094856ace84c001daeae390de788ff3c103987a44f09a11bf9cc6802a071511140bbd881423cefb8e70d1f8189c EBUILD gromacs-2019.9999.ebuild 9114 BLAKE2B 9286e7663d622e30ca491577c880827006f3bb2a68d2e3fd9c26fdc97541c12ebef06ab9d3b73ea89e0bbb079e79188c10b387366948920ee631c37da0be4ac5 SHA512 70fd567f7cdb9d8f2c7609b56c4522b5c3cc8094856ace84c001daeae390de788ff3c103987a44f09a11bf9cc6802a071511140bbd881423cefb8e70d1f8189c EBUILD gromacs-9999.ebuild 8094 BLAKE2B 932061da2ed5e2e20d1ca0c1ef9000fd946bbe3720cea6d585863e4bf2d7821b7e7b934d4d33d20a4c6040865c58c61c11f5bc8ce98812ad4f946a95b1c1fb83 SHA512 e3987a36622751c20e6a5b3fa88d43c94e24a30cd513eb2e9f9375457413c9ad131ec3f3012ec94e7574d50233c00d9edd357a44413ac0873edb88df82487ba0 MISC metadata.xml 1123 BLAKE2B 5e945fdf580821b62aaf40c5b4b3252b366284f2df16f02e7c3cf913e5ad498a6a8548bc2e4275d8b80373f88d9879ab59d401e619595014262dcebfe8660f9f SHA512 bac0c94aee957487d8af8a1e06323cb286c8773cef2070d91aff9fdad63eb1bd55f2678dd58dca21b33d8d3e7110d2526e280abd538e3653aee638f6de72090d diff --git a/sci-chemistry/gromacs/gromacs-2016.5.ebuild b/sci-chemistry/gromacs/gromacs-2016.5.ebuild deleted file mode 100644 index bef5457975aa..000000000000 --- a/sci-chemistry/gromacs/gromacs-2016.5.ebuild +++ /dev/null @@ -1,275 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# 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 - https://repo.or.cz/r/gromacs.git" - [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" - inherit git-r3 -else - SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz - test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="amd64 arm 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 -# https://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 openmp +single-precision test +threads +tng ${ACCE_IUSE}" - -CDEPEND=" - X? ( - x11-libs/libX11 - x11-libs/libSM - x11-libs/libICE - ) - blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) - fftw? ( sci-libs/fftw:3.0 ) - hwloc? ( <sys-apps/hwloc-2 ) - lapack? ( virtual/lapack ) - mkl? ( sci-libs/mkl ) - mpi? ( virtual/mpi ) - " -DEPEND="${CDEPEND} - virtual/pkgconfig - doc? ( - app-doc/doxygen - dev-texlive/texlive-latex - dev-texlive/texlive-latexextra - media-gfx/imagemagick - ) - dev-libs/tinyxml2 - " -RDEPEND="${CDEPEND}" - -REQUIRED_USE=" - || ( single-precision double-precision ) - cuda? ( single-precision ) - 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 && has_version "<sci-libs/mkl-11.3"; 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)" - ) - elif use mkl; then - local bits=$(get_libdir) - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/linux/mkl/include)" - -DMKL_LIBRARIES="$(echo /opt/intel/*/linux/mkl/lib/*${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=OFF - -DGMX_BUILD_UNITTESTS=OFF - -DGMX_EXTERNAL_TINYXML2=ON - ${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 ) - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_MPI=OFF - -DGMX_THREAD_MPI=$(usex threads) - "${cuda[@]}" - "$(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-2019.2.ebuild b/sci-chemistry/gromacs/gromacs-2019.2.ebuild index 066004be22c5..df6c7eaf37ff 100644 --- a/sci-chemistry/gromacs/gromacs-2019.2.ebuild +++ b/sci-chemistry/gromacs/gromacs-2019.2.ebuild @@ -19,7 +19,7 @@ if [[ $PV = *9999* ]]; then else SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="~amd64 ~arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" + KEYWORDS="amd64 ~arm 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" diff --git a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild b/sci-chemistry/gromacs/gromacs-2019.3.ebuild index 937bdf673d2a..dc5c8185316e 100644 --- a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2019.3.ebuild @@ -5,7 +5,9 @@ EAPI=6 CMAKE_MAKEFILE_GENERATOR="ninja" -inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils +PYTHON_COMPAT=( python2_7 ) + +inherit bash-completion-r1 cmake-utils cuda eutils multilib python-single-r1 readme.gentoo-r1 toolchain-funcs xdg-utils if [[ $PV = *9999* ]]; then EGIT_REPO_URI="git://git.gromacs.org/gromacs.git @@ -30,7 +32,7 @@ HOMEPAGE="http://www.gromacs.org/" # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" -IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" X? ( @@ -39,10 +41,12 @@ CDEPEND=" x11-libs/libICE ) blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) + opencl? ( virtual/opencl ) fftw? ( sci-libs/fftw:3.0 ) - hwloc? ( <sys-apps/hwloc-2 ) + hwloc? ( sys-apps/hwloc ) lapack? ( virtual/lapack ) + lmfit? ( sci-libs/lmfit ) mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi ) " @@ -50,17 +54,18 @@ DEPEND="${CDEPEND} virtual/pkgconfig doc? ( app-doc/doxygen + dev-python/sphinx[${PYTHON_USEDEP}] + media-gfx/mscgen dev-texlive/texlive-latex dev-texlive/texlive-latexextra media-gfx/imagemagick - ) - dev-libs/tinyxml2 - " + )" RDEPEND="${CDEPEND}" REQUIRED_USE=" || ( single-precision double-precision ) cuda? ( single-precision ) + cuda? ( !opencl ) mkl? ( !blas !fftw !lapack )" DOCS=( AUTHORS README ) @@ -111,6 +116,28 @@ src_prepare() { fi DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" + + # try to create policy for imagemagik + mkdir -p ${HOME}/.config/ImageMagick + cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF + <?xml version="1.0" encoding="UTF-8"?> + <!DOCTYPE policymap [ + <!ELEMENT policymap (policy)+> + !ATTLIST policymap xmlns CDATA #FIXED ''> + <!ELEMENT policy EMPTY> + <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED + name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED + stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> + ]> + <policymap> + <policy domain="coder" rights="read | write" pattern="PS" /> + <policy domain="coder" rights="read | write" pattern="PS2" /> + <policy domain="coder" rights="read | write" pattern="PS3" /> + <policy domain="coder" rights="read | write" pattern="EPS" /> + <policy domain="coder" rights="read | write" pattern="PDF" /> + <policy domain="coder" rights="read | write" pattern="XPS" /> + </policymap> + EOF } src_configure() { @@ -135,24 +162,25 @@ src_configure() { -DMKL_INCLUDE_DIR="${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 && has_version "<sci-libs/mkl-11.3"; then + 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)" ) - elif use mkl; then - local bits=$(get_libdir) - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/linux/mkl/include)" - -DMKL_LIBRARIES="$(echo /opt/intel/*/linux/mkl/lib/*${bits/lib}/libmkl_rt.so)" - ) else fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) fi + if use lmfit; then + local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) + else + local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) + fi + mycmakeargs_pre+=( "${fft_opts[@]}" + "${lmfit_opts[@]}" -DGMX_X11=$(usex X) -DGMX_EXTERNAL_BLAS=$(usex blas) -DGMX_EXTERNAL_LAPACK=$(usex lapack) @@ -163,11 +191,10 @@ src_configure() { -DGMX_HWLOC=$(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=OFF - -DGMX_BUILD_UNITTESTS=OFF - -DGMX_EXTERNAL_TINYXML2=ON + -DBUILD_TESTING=$(usex test) + -DGMX_BUILD_UNITTESTS=$(usex test) + -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" ${extra} ) @@ -181,11 +208,15 @@ src_configure() { [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" local cuda=( "-DGMX_GPU=OFF" ) [[ ${x} = "float" ]] && use cuda && \ - cuda=( -DGMX_GPU=ON ) + 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) + -DGMXAPI=$(usex gmxapi) + "${opencl[@]}" "${cuda[@]}" "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" -DGMX_BINARY_SUFFIX="${suffix}" @@ -201,6 +232,7 @@ src_configure() { -DGMX_THREAD_MPI=OFF -DGMX_MPI=ON ${cuda} -DGMX_OPENMM=OFF + -DGMXAPI=OFF -DGMX_BUILD_MDRUN_ONLY=ON -DBUILD_SHARED_LIBS=OFF -DGMX_BUILD_MANUAL=OFF diff --git a/sci-chemistry/molequeue/Manifest b/sci-chemistry/molequeue/Manifest index 5297d5f0b10b..d70775668870 100644 --- a/sci-chemistry/molequeue/Manifest +++ b/sci-chemistry/molequeue/Manifest @@ -1,7 +1,4 @@ -AUX molequeue-0.8.0-cmake.patch 4285 BLAKE2B 916f0c248f487b6d7c11dd34e20364b5dfb494d2e27e657bc5a13f9d6c3f71ae2ab6818bace7df04c0a1388f6f85c42e3e0ab96fc5d3d892c0a95612532baf28 SHA512 9031fd3e5efe0a9332db4b1f46d82486fc804cef55c9fab35030bc562d1a40f5f16a02a5eb8c31bf4c50c7a0abcf22c11da5bdd4e2a45a37a8b6f4ff994d3ad6 AUX molequeue-0.9.0-qt-5.11b3.patch 6380 BLAKE2B 8d4a66dab1b233880269559cff9b566593ec271fc2b0982a92eec1d60a7c2c42e7186c0007be2afc956200d28c250822b36d3146d1a9ff1fb33b574f97969c60 SHA512 09429566422a1490c2621fd895238d4aeba3c324563cab411290a60942c749e9fa967dd6399f4f4efdc635fa77c339d08824def3e6a175aadc1061893df7df9c -DIST molequeue-0.8.0.tar.gz 643072 BLAKE2B c9ba0a93e4dac3027de1aeb5ae6c62fc3e4229786973d6c3b56af4b70476b0ed54a563837d489912a40c76b9ce0013e13633a327eb314c34305ba17d7f0b4cf7 SHA512 b9539d2ad2c67188ad254f186c1d67c122a15a32047801c632a1613a4f9c887f38baf2da1bb80cb123391948c2a44604fb1082e475ca6de1e683fbe51266ac84 DIST molequeue-0.9.0.tar.gz 604015 BLAKE2B 37e7f404a0fefb40defb198295659372121fbe770269c2f9fb92e856aceb8222bec5e83939ecea061b76f925c0cbde1be0a854db41f992a92a2b2b9e0651f2e1 SHA512 87ddd8ca59227cab60c0ce2643e5bd435d9ac7e23b929659b95f190478734a5b71d4935f37d03eeadbc39939cbffb3604e0a283d50b0a23a1a000b57c1fce335 -EBUILD molequeue-0.8.0.ebuild 1613 BLAKE2B 21ddbe84fb9ad674cc796330ee2a26f5fdcfc7f6187869d2775e5679bbb2bf2dc147d80c79617867f9b1424bf07eb797315fb5cab3cb59359c39171315cf353c SHA512 6971db16063f3c1dfad7a780adae7aaf438c2957f46698a1739a65ac3d658ccac501f687db18eddc1305a4e6a220cac206d781f5783cdcb0d38b4e952c550ed7 -EBUILD molequeue-0.9.0.ebuild 1471 BLAKE2B ace497ea7a4c5ebaae14755f27ac18348fc7190246f7292318d50d2f1b120152fb626af0efd735f27b9d1aed4d615912261f304b589f4f947f3461d6989f26cb SHA512 05afccaad6d36c69a8838278a9e4d5af3257aff61c99467958fd62074c7e4823100d15e80c86521e626fc3625d1333c5cdaea78a16f51fa3ed9a166f34ea3325 +EBUILD molequeue-0.9.0.ebuild 1479 BLAKE2B f00bb04fa08a720367daa464399daa71f47c4fe34263dc699811cc9ea0683a065d06a30e8be9d0ccd46071329829cae739a8c3fa5773998c1c3b8fb6d53653a1 SHA512 a6a5643849c85231652e9d1ff1c93e599a539eca0cc5572bab8ae9b837cc2f6ad8f5c04d96774493187f3f3cb216f163e7990a9d62abb60caefcde9ad610aedb MISC metadata.xml 1257 BLAKE2B 181f9234f11d0cb14fd6b93b42ef153c089d4df8dcb7cf72bc710dbee11bf4bb573f37ea703d02dbe17fa1f39c0aaf591c6d28ad1429abced5108b9ce39f2030 SHA512 10e3dd48ec1e54bc0d47d4c2f0aca427875cc0ceb59a93ab41ab2734607aa6474e80f3ae622e45fa319753591f16439118dd0b301068cb3e16fd79ff11a4f058 diff --git a/sci-chemistry/molequeue/files/molequeue-0.8.0-cmake.patch b/sci-chemistry/molequeue/files/molequeue-0.8.0-cmake.patch deleted file mode 100644 index 3fd8a9db76be..000000000000 --- a/sci-chemistry/molequeue/files/molequeue-0.8.0-cmake.patch +++ /dev/null @@ -1,106 +0,0 @@ -From 45cbc9f167d1158bc73e87618cc08ede2e3f2911 Mon Sep 17 00:00:00 2001 -From: "Marcus D. Hanwell" <marcus.hanwell@kitware.com> -Date: Thu, 1 Jun 2017 13:17:20 -0400 -Subject: [PATCH] Removed GenerateExportHeader, bumped CMake min - -Removed the GenerateExportHeader copy we had, use CMake's, and bump the -minimum to ensure it has the features we expect. ---- - CMakeLists.txt | 2 +- - cmake/GenerateExportHeader.cmake | 375 --------------------------------------- - cmake/exportheader.cmake.in | 35 ---- - 3 files changed, 1 insertion(+), 411 deletions(-) - delete mode 100644 cmake/GenerateExportHeader.cmake - delete mode 100644 cmake/exportheader.cmake.in - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index df93bc8..a107c8f 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -1,4 +1,4 @@ --cmake_minimum_required(VERSION 2.8.8 FATAL_ERROR) -+cmake_minimum_required(VERSION 3.3 FATAL_ERROR) - - project(MoleQueue) - -From aae92632d10fe98728c3e73bfd891e502e8712fd Mon Sep 17 00:00:00 2001 -From: "Marcus D. Hanwell" <marcus.hanwell@kitware.com> -Date: Thu, 16 Nov 2017 15:10:25 -0500 -Subject: [PATCH] Remove deprecated calls for export flags - -Move them to the project default variables in the top level. ---- - CMakeLists.txt | 8 ++++++++ - molequeue/client/CMakeLists.txt | 1 - - molequeue/servercore/CMakeLists.txt | 1 - - molequeue/zeromq/CMakeLists.txt | 1 - - thirdparty/qt5json/CMakeLists.txt | 1 - - 5 files changed, 8 insertions(+), 4 deletions(-) - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index a107c8f..e68d81f 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -4,6 +4,14 @@ project(MoleQueue) - - set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake) - -+# Request C++11 standard, using new CMake variables. -+set(CMAKE_CXX_STANDARD 11) -+set(CMAKE_CXX_STANDARD_REQUIRED True) -+set(CMAKE_CXX_EXTENSIONS False) -+# Set symbol visibility defaults for all targets. -+set(CMAKE_CXX_VISIBILITY_PRESET "hidden") -+set(CMAKE_VISIBILITY_INLINES_HIDDEN True) -+ - include(BuildType) - include(BuildLocation) - include(CompilerFlags) -diff --git a/molequeue/client/CMakeLists.txt b/molequeue/client/CMakeLists.txt -index 674f91a..8cb131a 100644 ---- a/molequeue/client/CMakeLists.txt -+++ b/molequeue/client/CMakeLists.txt -@@ -20,7 +20,6 @@ set_target_properties(MoleQueueClient PROPERTIES AUTOMOC TRUE) - include(GenerateExportHeader) - generate_export_header(MoleQueueClient EXPORT_FILE_NAME molequeueclientexport.h) - list(APPEND headers "${CMAKE_CURRENT_BINARY_DIR}/molequeueclientexport.h") --add_compiler_export_flags(molequeue_export_flags) - set_property(TARGET MoleQueueClient APPEND - PROPERTY COMPILE_FLAGS ${molequeue_export_flags}) - -diff --git a/molequeue/servercore/CMakeLists.txt b/molequeue/servercore/CMakeLists.txt -index 8d4f7ee..aab0bec 100644 ---- a/molequeue/servercore/CMakeLists.txt -+++ b/molequeue/servercore/CMakeLists.txt -@@ -30,7 +30,6 @@ set(hdrs - generate_export_header(MoleQueueServerCore - EXPORT_FILE_NAME molequeueservercoreexport.h) - include_directories(${CMAKE_CURRENT_BINARY_DIR}) --add_compiler_export_flags(molequeue_export_flags) - set_property(TARGET MoleQueueServerCore APPEND - PROPERTY COMPILE_FLAGS ${molequeue_export_flags}) - -diff --git a/molequeue/zeromq/CMakeLists.txt b/molequeue/zeromq/CMakeLists.txt -index bc1e893..188f437 100644 ---- a/molequeue/zeromq/CMakeLists.txt -+++ b/molequeue/zeromq/CMakeLists.txt -@@ -20,7 +20,6 @@ target_link_libraries(MoleQueueZeroMq MoleQueueServerCore ${ZeroMQ_LIBRARIES}) - generate_export_header(MoleQueueZeroMq - EXPORT_FILE_NAME molequeuezeromqexport.h) - include_directories(${CMAKE_CURRENT_BINARY_DIR}) --add_compiler_export_flags(molequeue_export_flags) - set_property(TARGET MoleQueueZeroMq APPEND - PROPERTY COMPILE_FLAGS ${molequeue_export_flags}) - -diff --git a/thirdparty/qt5json/CMakeLists.txt b/thirdparty/qt5json/CMakeLists.txt -index 6d00685..52f5df2 100644 ---- a/thirdparty/qt5json/CMakeLists.txt -+++ b/thirdparty/qt5json/CMakeLists.txt -@@ -54,7 +54,6 @@ include(GenerateExportHeader) - generate_export_header(${QT5_JSON_LIBRARY_NAME} - EXPORT_FILE_NAME qt5jsonexport.h - EXPORT_MACRO_NAME QT5JSON_EXPORT) --add_compiler_export_flags(qt5json_export_flags) - - set_property(TARGET ${QT5_JSON_LIBRARY_NAME} APPEND - PROPERTY COMPILE_FLAGS ${qt5json_export_flags}) diff --git a/sci-chemistry/molequeue/molequeue-0.8.0.ebuild b/sci-chemistry/molequeue/molequeue-0.8.0.ebuild deleted file mode 100644 index 2c20c0bfeeac..000000000000 --- a/sci-chemistry/molequeue/molequeue-0.8.0.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit cmake-utils python-single-r1 versionator virtualx - -DESCRIPTION="Abstract, manage and coordinate execution of tasks" -HOMEPAGE="https://www.openchemistry.org/projects/molequeue/" -SRC_URI="https://github.com/OpenChemistry/molequeue/archive/${PV}.tar.gz -> ${P}.tar.gz" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="+client doc server test +zeromq" - -REQUIRED_USE="${PYTHON_REQUIRED_USE} - server? ( client ) - test? ( server )" - -RDEPEND="${PYTHON_DEPS} - dev-qt/qtcore:5 - dev-qt/qtgui:5 - dev-qt/qtnetwork:5 - dev-qt/qtwidgets:5 - zeromq? ( net-libs/cppzmq:0= )" -DEPEND="${RDEPEND} - doc? ( app-doc/doxygen )" - -PATCHES=( "${FILESDIR}"/${P}-cmake.patch ) - -src_prepare() { - cmake-utils_src_prepare - - rm cmake/{GenerateExportHeader.cmake,exportheader.cmake.in} || die - - # delete bundled Qt5Json library - rm -r thirdparty || die -} - -src_configure() { - local mycmakeargs=( - -DBUILD_DOCUMENTATION=$(usex doc) - -DMoleQueue_BUILD_CLIENT=$(usex client) - -DoleQueue_BUILD_APPLICATION=$(usex server) - -DENABLE_TESTING=$(usex test) - -DUSE_ZERO_MQ=$(usex zeromq) - -DINSTALL_LIBRARY_DIR=$(get_libdir) - ) - use zeromq && \ - mycmakeargs+=( -DZeroMQ_ROOT_DIR=\"${EPREFIX}/usr\" ) - - cmake-utils_src_configure -} - -src_compile() { - cmake-utils_src_compile all $(usex doc documentation "") -} - -src_test() { - VIRTUALX_COMMAND=cmake-utils_src_test - virtualmake -} - -src_install() { - use doc && HTML_DOCS=( "${BUILD_DIR}"/docs/html/. ) - cmake-utils_src_install -} diff --git a/sci-chemistry/molequeue/molequeue-0.9.0.ebuild b/sci-chemistry/molequeue/molequeue-0.9.0.ebuild index 1f484848233a..71e253b4283a 100644 --- a/sci-chemistry/molequeue/molequeue-0.9.0.ebuild +++ b/sci-chemistry/molequeue/molequeue-0.9.0.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 PYTHON_COMPAT=( python2_7 ) @@ -20,14 +20,15 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE} server? ( client ) test? ( server )" +BDEPEND=" + doc? ( app-doc/doxygen )" RDEPEND="${PYTHON_DEPS} dev-qt/qtcore:5 dev-qt/qtgui:5 dev-qt/qtnetwork:5 dev-qt/qtwidgets:5 zeromq? ( net-libs/cppzmq:0= )" -DEPEND="${RDEPEND} - doc? ( app-doc/doxygen )" +DEPEND="${RDEPEND}" PATCHES=( "${FILESDIR}"/${P}-qt-5.11b3.patch ) |