From 6b933047f46efec1aa747570f945344254227457 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Fri, 15 Dec 2017 17:25:28 +0000 Subject: gentoo resync : 15.12.2017 --- sci-chemistry/gromacs/Manifest | 35 ++- .../gromacs/files/gromacs-2018-fix-build.patch | 71 ------ sci-chemistry/gromacs/gromacs-2018_beta1.ebuild | 276 --------------------- sci-chemistry/gromacs/gromacs-2018_beta2.ebuild | 272 ++++++++++++++++++++ 4 files changed, 289 insertions(+), 365 deletions(-) delete mode 100644 sci-chemistry/gromacs/files/gromacs-2018-fix-build.patch delete mode 100644 sci-chemistry/gromacs/gromacs-2018_beta1.ebuild create mode 100644 sci-chemistry/gromacs/gromacs-2018_beta2.ebuild (limited to 'sci-chemistry/gromacs') diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index f8cd6987508d..0b1437c19d14 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -1,20 +1,19 @@ -AUX gromacs-2018-fix-build.patch 2797 BLAKE2B 410cf7dd4fe6f47dcdc0ce828884accc8c9f6e973ea130f20a9bf74b153e1ce118ac9c808e7305aad01cce947dd7e1546617becc61e0626278f67c6dce6fa454 SHA512 229dfb531d0bc240fca8e4548b5a3afd8280e7ebbe8006f6da9f59108469808b25ba90b7145ceb8f50e99adc93385daafc97f594ebd86ab11bf683f7e8af44c7 -DIST gromacs-2016.1.tar.gz 27336258 SHA256 9e7d2892a903777b982bc9ab4306de969d92cb45b51a562f523ec5fe58db41e3 SHA512 d30a4ad5faa6e12c95b8e94acaabc387d9aab3780490f5442c48ccac2f86bef6dca60df5bb6097dbc68ab28e6f1a15e234e1244606afdf12a841b88ece65c97b WHIRLPOOL 4be9c84d99286889dda23d9f1e2dd7b2d87a70740fb686bd58e59155771e897471d0920b02c5ec529a01a4b01428ebb2ca5b27e4d8df9034d2d3b33c5ab1a1ca -DIST gromacs-2016.2.tar.gz 27339623 SHA256 b6ac3632b848ab0c19f8f319dd5b58fcd09b8e2005ee7509478606613e5409a5 SHA512 f5e74bb8c126823c90d205ac0f0835e61fdd13a4550bc15aa9c972ee9b187f6451cdc90877c17276d2f889d61abb5eaa5ea1b54f7cbf3da67074146c749c1aa6 WHIRLPOOL 698c4d4e67266483be4f1047eb947b243b5c8caa3c5e30bdab6b5f0dd302bb51ac5aa6e3a3357beab567cf71c1b8ecc1f9684a89754d18f963dd6f5fc90a33f4 -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 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53fa9ad062cc3e269fc6186db1ccbb64a93d36c2fa1cafd6433564ba2583c112 SHA512 e0aceb56d1f38a7e6ab9fdaac5063fd20c5b3a162ffb6eddd0e6dc7dff9b724bfe31363493a9437e9f9d5421a534b375960fcb31e903a4901a0fa94ed8511294 WHIRLPOOL 408741abf781ecf880f8f1337590ed81196cabcf25a49d2cd97bbe0596c8495ea866d6aa64a944c6ee0eb209110883dff204f0f52f6aa6e6dd52f50bcbbade66 -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 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27339623 BLAKE2B c3548f4abdc4c1b09a79a3da99d7ca8060daca7307e4c5b81bd97d54adfb9621fbccf1ea7fd96c3676d6b44c20f9f4cd2168ce131799792512fad3b8b1ac0522 SHA512 f5e74bb8c126823c90d205ac0f0835e61fdd13a4550bc15aa9c972ee9b187f6451cdc90877c17276d2f889d61abb5eaa5ea1b54f7cbf3da67074146c749c1aa6 +DIST gromacs-2016.3.tar.gz 27342692 BLAKE2B 3bea357cb672f41dda68c0d4291c06e2ab8bbc91629e25c9e56741223911be7994be10b2427fb1ca1cd41e511d23323851ba3211ee8590f152e23a64b2253095 SHA512 16593df0a52620766fb86cfeb16328793503f860cb07cdbbd503ba7f41e6430efb4848389b7179ca3907b57311162666d05224b454e1afb1b74b220f38498d86 +DIST gromacs-2016.4.tar.gz 27368706 BLAKE2B 2a176812fe2a097d72c7148ff5ed4ed7209279cf439af6a969c3aba81157c59a4d9af34d19c7b1da088b0a4ab981b489b84446afbcaf64b20724bda1dc3560ff SHA512 69661d2a7a8a5259be277de35e2baa4b688d1f7bef225fc7d733a9b00c6ee135dcbad517c7c9f751121647c2fbd085f2c9cdf22dbd941c7ebc5d3b09e7e08f1f +DIST gromacs-2016.tar.gz 27321561 BLAKE2B 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d5a68dd30c92d1ccfd08b7074b41771c08e94be9556524bf5c13517711cc74ec945aa8bb167cdc4f954b12ac214f9c24a2935ceed6a92c6ecd2a0d1cc860fb63 SHA512 2dcacf52220972b0eae03da7e917e2e2bc85acc4cc2adcddefbe5d6176d5a5200eb77aeb55df06942fa88078f25f623c7b3c586fde852d6045b9caa0337d802a +DIST regressiontests-5.0.4.tar.gz 65193251 BLAKE2B c5e5f23adcc2639fe652bc252533307c7fda44453d506603242968bd8588c7394028b2c3c7a9252f807a050d40e8f78735e904dfe517d3db8ae962051f4826c1 SHA512 747725fa28c1c9525596bdeeb8809e45268e19036c11dac67d043aa1c51748688ca37eb6014eb7e819eb927a8b9ca2631d0ace4cdff8ed491b08c316c530ab65 +DIST regressiontests-5.1.3.tar.gz 66994083 BLAKE2B 7009f65ad0138664ac84e57f8bc7cce5d18a59f99943e56b6642583120bfce279e005ac0bacd2db8904ea477a48e2b938c64de46a65fa5d08fce6009d53583c3 SHA512 486e86eb3b75bae822abe82dac4e1098aa13723bd04214021f835a2f0b847303f015a9ececc33aa5ae63d31a2eeae07e512f22464b6c0e26d1286b0781578022 EBUILD gromacs-2016.1.ebuild 7987 BLAKE2B 45d8b50b3ee54c8c701eb8c6533c1dc7d680eb0f5c40cdf1a75e81b59bd2d603b4235f6e4942e40211b748b7cf8239c90f8d613b20bdc44fca48d23f9c45ae14 SHA512 ce2b0d2730e87831a517468033cada7097ba431d8a60dcef77a04c9e05bf4cfacb6eb500a5196e378f4c69e5020f8e9f871eac6e61dd2776834aee006ecb167f EBUILD gromacs-2016.2.ebuild 7971 BLAKE2B 90510b56d31e59f2f7f76e7772b55e4acdb825af6e8df46da40c7aeb6b7d4b986253b10ac71fbd04c749dd3935b1eeb154e7d0aac7b21147859fb03b57e4e687 SHA512 7a85084cc29da0d3da6c9aabf65320edb38cd682146cc1b739120b728c6704c3e20941b9022c846b84a111e3ca88f29ca21cdbcdf4c5b7204989ac194bf15725 EBUILD gromacs-2016.3.ebuild 7974 BLAKE2B ec37b1dbbbbe9c3aab0d7819f48c15e7c29d2855ac9d1b0b43b364bdfd11d8fae675c6ea8b69cee9966c5022f340b139553f58a592eb637c997fd579b3ba97b1 SHA512 9a3415f66fdd5832abf764b6adfe5deccb62b3f233ccd9156e1caac61907835c13623a3772673c43c9a3e9dbe544e83b2f20953a09d9b598c6af0120cfed558d @@ -22,7 +21,7 @@ EBUILD gromacs-2016.4.ebuild 7987 BLAKE2B 45d8b50b3ee54c8c701eb8c6533c1dc7d680eb 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 -EBUILD gromacs-2018_beta1.ebuild 7955 BLAKE2B c26e1b835fa94c9e7531a292a6aa79a3a0659fea032085a02b1aff77ce71388017760a4be5bd72bc5a41cf688489ba78e5d6ab134b4c086300e2c0c2f9b36f01 SHA512 5c14d982e7db5ec1727df4d4a8578c5b28cbc0d8f192d20fd18cc88efdf2bf3f26ead61c08136227d8f043f726967a84bc5f252a2da830852cf8c396a3bd1d98 +EBUILD gromacs-2018_beta2.ebuild 7899 BLAKE2B 8053de4c12e2201d37e8d0a077d33fc0b103b79d73379488c46bc638ba763b55ebf69ae53180ffd850e4b860fc03a1c3ec57049f1b257e04e0322ed482afcd51 SHA512 734710474160c6a55206b332e5370bd9e2d0092aed19c4c1ccab7f5d9567eac2a47d163a50aa607f8c7e8e2ccc6eadeb9b394e9f638ac85eafe5f74ced68fd02 EBUILD gromacs-4.6.9999.ebuild 8110 BLAKE2B dd8ac9cbc4abfcc75a3a188c59cdbe5111f363404ff5a787f64b05d4bd411deebb50f172f09963800ed87997788b2e678617805e65a523bed19aa6ef18fe2b96 SHA512 2206e257f0b29b6f3a90c5d7739079b9add3e04f2a3acbd58c814811b389b5d51b3594815a94529d1de43deb380504029c302d18fc16d63a81c92727254e863e EBUILD gromacs-5.0.4.ebuild 8429 BLAKE2B c06c423365fa79befd5a4f0b6314e77b96d983c84df776ce84fddc79d35ce735d856d1184e5913af0c8cd3a0c4e9087110af9bd4402e2bce1f014e64a8a585a7 SHA512 d1e91cc25c5f90bd0fbad15060cae9c8bf1235ca45a2b72521b3a4f5f091bdd7d32ec2e6ff2bb22cd3fe165092f11a24ea148ae8000b8517f0b8671f6c2af6f2 EBUILD gromacs-5.0.9999.ebuild 8439 BLAKE2B 33d51254e62593a58c636bd902f43edc553ad11af306d1d022278b223eda15b0772097f26565df74a1118bd5b144e5b93aac09cdb995123ccbae2856889c31b2 SHA512 6756116cdeae9c21b094f74ea1b1d9f41617467dc736878cdcff27fed9f53b338830a608e23e87238d0756884799fbc5d62f02685774ea86c239ecc3e8804814 diff --git a/sci-chemistry/gromacs/files/gromacs-2018-fix-build.patch b/sci-chemistry/gromacs/files/gromacs-2018-fix-build.patch deleted file mode 100644 index 2ed6a19f31b0..000000000000 --- a/sci-chemistry/gromacs/files/gromacs-2018-fix-build.patch +++ /dev/null @@ -1,71 +0,0 @@ -From 81e68584512b21ec572d2561c25a1b19982aa0be Mon Sep 17 00:00:00 2001 -From: Alexey Shvetsov -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 ---- - 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_beta1.ebuild b/sci-chemistry/gromacs/gromacs-2018_beta1.ebuild deleted file mode 100644 index 3e0dd9b80bc9..000000000000 --- a/sci-chemistry/gromacs/gromacs-2018_beta1.ebuild +++ /dev/null @@ -1,276 +0,0 @@ -# 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/gromacs-2018_beta2.ebuild b/sci-chemistry/gromacs/gromacs-2018_beta2.ebuild new file mode 100644 index 000000000000..315835fdc606 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2018_beta2.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 +} -- cgit v1.2.3