From 99abbc5e5a6ecd3fc981b45646fd8cb5d320377b Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sat, 24 Feb 2018 19:58:07 +0000 Subject: gentoo resync : 24.02.2018 --- sci-chemistry/gromacs/Manifest | 3 + sci-chemistry/gromacs/gromacs-2016.5.ebuild | 276 ++++++++++++++++++++++++++++ 2 files changed, 279 insertions(+) create mode 100644 sci-chemistry/gromacs/gromacs-2016.5.ebuild (limited to 'sci-chemistry/gromacs') diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index a366b73cb338..021a84b14bbe 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -2,6 +2,7 @@ DIST gromacs-2016.1.tar.gz 27336258 BLAKE2B 3a255252e789a4260b559ab5ce0676c884c4 DIST gromacs-2016.2.tar.gz 27339623 BLAKE2B c3548f4abdc4c1b09a79a3da99d7ca8060daca7307e4c5b81bd97d54adfb9621fbccf1ea7fd96c3676d6b44c20f9f4cd2168ce131799792512fad3b8b1ac0522 SHA512 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9cb8ff88871aa5df0967c60ba303c03296c6fa3c215cd01b26259df7753f0014f04222078ab4b84a66a1f709997837134d5c0f74da19b78322e410010c9d9e10 DIST gromacs-2016.tar.gz 27321561 BLAKE2B cdcf0aa5ac36981e736fd2ecc2f641e99f40146d829c88e5ff973c7b7c3c1ab920f7822c336e9eea87a8605362e723d7477dd07f9154c8a38476a3f6c391d6aa SHA512 756771baaa85a1d16e7d5b8e4c96bbd1c04c7acdc536a253886cff186316330f06d60d206a0159efb15f47f161c779d3757dc5dbceab8c097241c1382d376201 DIST gromacs-2018-rc1.tar.gz 29863602 BLAKE2B 1b8146198aef435d74c57b5a6e42b8107416896fed71444830baf4368604c1b35326a77815c5125e1610a9765cf1d5d51d3a69a04d3679f7c1f3618598258c0a SHA512 f2a56a2d3ce6efd170f22d66dbb9418ae59257aff27853037570d0939582df947c7558aa652626dd911ee22c037ab0cb1b340b5008bc8f40d27d90883100d375 DIST gromacs-2018.tar.gz 29855797 BLAKE2B ff7bfd6a11d8d0fba2a0da405eb264504e18d820179eee234fd2c6e0d6a001aabd601c8a695e14b6d290fbca2253f3fc760a72c6fcaf566f88bb3675612f0bfb SHA512 95c464ec4a0c95b5e7b30571e9693f6be1bce4cd3d6f7d7eeee0f0cd9b8ad43dda4dbb8568e9502706a01d1621f288711227a935060ce524871e6521d53eb902 @@ -11,6 +12,7 @@ DIST regressiontests-2016.1.tar.gz 67094518 BLAKE2B 3ae0132e246f2abcf77495bff69a DIST regressiontests-2016.2.tar.gz 67095329 BLAKE2B fec8a663845ad67374c8a230d1590fa9e5079460198f41cee3b788aaa1c72e8ec9dcda48bc68a594f15003d11bf6617d46cc1a09c16b7a333587b43904a16ba6 SHA512 e0aceb56d1f38a7e6ab9fdaac5063fd20c5b3a162ffb6eddd0e6dc7dff9b724bfe31363493a9437e9f9d5421a534b375960fcb31e903a4901a0fa94ed8511294 DIST regressiontests-2016.3.tar.gz 67093968 BLAKE2B a644bbd2a0398c1d84f61809a9f4f1cb89d307b0e9952f414e28d18464799e5f49fe810e342768a7b15f1d63b10bf1facb148c1d04ad670c613022302f04ea9d SHA512 ee87df9f339954da0e1f1b4c8b8d4deb574f3b73d174010a295a7a0e8bc462ead7691090ea7cf8ac3d984a6cd70f1cd22c3592fa161b2967061ae5ba2796286b DIST regressiontests-2016.4.tar.gz 67643648 BLAKE2B 767c3b0ca1002e6ca68fc3346b7164cca3beaa52f9b1c70672b64cf80427cab045e4d924d0b67a4fe4c76e3a1c0a803964e278d2a9b14b87a555f98dd78525d3 SHA512 367438b897a05e1cc0dcd1d3872fb6a0e9ff6b1146e9448d941d6517dce789f0c478d20cf0a4f3565070f132dc88872441aadb8b499f59efa0e1e4a6dd6a7135 +DIST regressiontests-2016.5.tar.gz 67641413 BLAKE2B 4fcd30c198f3acbbabf1104c040d9a686de49536a97dbeb14732bfa0ed3cf37aa61b1b0f45393668985b993d1f1862a8985e416af819cf9793f5964f3e4f43cc SHA512 31764fd99cc4185d61de5d4443ee482c27b13533451a24aa0e4899997ce275a63685424eafacae38b1a3ffd4ce0d5ebe02a90348953b04c104f91376f0edfdff DIST regressiontests-2016.tar.gz 66908712 BLAKE2B 3039b5b46bf99dc2e34a61ed0f47f7355087c260bd1accc119f9ed99bb03c4645d05df41e301cfc6a6de6a9a369b2bf4e01a54852100577e40605e091bbe24e8 SHA512 59902c1973c33ea8f003f21a737dc7cc64da3258112322eedc9834b53628134a6817d5ee5b3950c9bfd97a3a0580aef88ddef0609ef2c58693c96c7575651e01 DIST regressiontests-2018-rc1.tar.gz 67866295 BLAKE2B 1936a4a14d3011e426e0f057d803339a8324e10d087d56f93dc7a497250a973c6b19ed2691b4641d12b7f13de01dbe36a9903a4e10e3792b842319e42ad0331a SHA512 feccf48d6af84abf350e5ad829c600f86b8e8e4f4f3378c34b209daa30965e3f68751058f12bdbb228da6b4ccd0a72c8191956ec5bd184f190000a9c97e581a9 DIST regressiontests-2018.tar.gz 67858633 BLAKE2B 21fe5ca9ad682873c616d6ac46e1408d646ab4620498bd63f94f2719354ea38e3b2ee81330629038e320229079802705393b049d9fbdd91612a54a043a98fbcd SHA512 95d4085bd7d60cd1a40dde25d7a770e549f17f69771a63eb55e95e5735b29ebe76dbfebd5452542fede984e9b3ce0339c166aeb9a42754d36be87b43b6d6b1ec @@ -20,6 +22,7 @@ EBUILD gromacs-2016.1.ebuild 7987 BLAKE2B 45d8b50b3ee54c8c701eb8c6533c1dc7d680eb EBUILD gromacs-2016.2.ebuild 7971 BLAKE2B 90510b56d31e59f2f7f76e7772b55e4acdb825af6e8df46da40c7aeb6b7d4b986253b10ac71fbd04c749dd3935b1eeb154e7d0aac7b21147859fb03b57e4e687 SHA512 7a85084cc29da0d3da6c9aabf65320edb38cd682146cc1b739120b728c6704c3e20941b9022c846b84a111e3ca88f29ca21cdbcdf4c5b7204989ac194bf15725 EBUILD gromacs-2016.3.ebuild 7974 BLAKE2B ec37b1dbbbbe9c3aab0d7819f48c15e7c29d2855ac9d1b0b43b364bdfd11d8fae675c6ea8b69cee9966c5022f340b139553f58a592eb637c997fd579b3ba97b1 SHA512 9a3415f66fdd5832abf764b6adfe5deccb62b3f233ccd9156e1caac61907835c13623a3772673c43c9a3e9dbe544e83b2f20953a09d9b598c6af0120cfed558d EBUILD gromacs-2016.4.ebuild 7987 BLAKE2B 45d8b50b3ee54c8c701eb8c6533c1dc7d680eb0f5c40cdf1a75e81b59bd2d603b4235f6e4942e40211b748b7cf8239c90f8d613b20bdc44fca48d23f9c45ae14 SHA512 ce2b0d2730e87831a517468033cada7097ba431d8a60dcef77a04c9e05bf4cfacb6eb500a5196e378f4c69e5020f8e9f871eac6e61dd2776834aee006ecb167f +EBUILD gromacs-2016.5.ebuild 7987 BLAKE2B 02bfdcce78718a1e16ad0cdf63e521d656eaa886ddf2ef7016f22abc398b95e240ecb4705a894609f188afbf4ec17c96ee9441ee7510cfaeb02c0ceced4e1b17 SHA512 5d762c0f9212ec0b91fba7565c15787201b1fcd923111b7055d6362b813d92b850f67becff023c57d3846c2f01a7df29e2b5e52d1bd643f797305c59449b1f46 EBUILD gromacs-2016.9999.ebuild 7987 BLAKE2B 45d8b50b3ee54c8c701eb8c6533c1dc7d680eb0f5c40cdf1a75e81b59bd2d603b4235f6e4942e40211b748b7cf8239c90f8d613b20bdc44fca48d23f9c45ae14 SHA512 ce2b0d2730e87831a517468033cada7097ba431d8a60dcef77a04c9e05bf4cfacb6eb500a5196e378f4c69e5020f8e9f871eac6e61dd2776834aee006ecb167f EBUILD gromacs-2016.ebuild 7968 BLAKE2B c0ba44661dce5ccda3c2378fad57e88ca90d15cb1914d6214ee4559e8ebd6c6c700624b32abf168a4a653cc5794fac9fab71024a9b7bc5464d404d768ac74ef1 SHA512 3ca5d4ae9b01a106b279bc828e42366a017b9517a450b773b944c6d12dce64199e3a80d280e4c475c637c70009a1a0fd1ca74f99b03f08067a10d9e9ad450d8f EBUILD gromacs-2018.9999.ebuild 7899 BLAKE2B 8053de4c12e2201d37e8d0a077d33fc0b103b79d73379488c46bc638ba763b55ebf69ae53180ffd850e4b860fc03a1c3ec57049f1b257e04e0322ed482afcd51 SHA512 734710474160c6a55206b332e5370bd9e2d0092aed19c4c1ccab7f5d9567eac2a47d163a50aa607f8c7e8e2ccc6eadeb9b394e9f638ac85eafe5f74ced68fd02 diff --git a/sci-chemistry/gromacs/gromacs-2016.5.ebuild b/sci-chemistry/gromacs/gromacs-2016.5.ebuild new file mode 100644 index 000000000000..e86fdf946c7c --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2016.5.ebuild @@ -0,0 +1,276 @@ +# 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="~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 +# 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 openmp +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + fftw? ( sci-libs/fftw:3.0 ) + hwloc? ( sys-apps/hwloc ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + " +DEPEND="${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 " "${T}/${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 +} -- cgit v1.2.3