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commit: becf963f0a75869bd9d6ae48210a1055e32a65c0 |
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Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
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AuthorDate: Fri Jun 18 12:23:39 2021 +0000 |
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Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
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CommitDate: Fri Jun 18 12:23:39 2021 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=becf963f |
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|
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sci-chemistry/gromacs: drop old |
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|
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Package-Manager: Portage-3.0.20, Repoman-3.0.3 |
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Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org> |
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|
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sci-chemistry/gromacs/Manifest | 9 - |
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sci-chemistry/gromacs/gromacs-2020.5.ebuild | 351 ------------------------ |
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sci-chemistry/gromacs/gromacs-2020.9999.ebuild | 351 ------------------------ |
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sci-chemistry/gromacs/gromacs-2021.1.ebuild | 358 ------------------------- |
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sci-chemistry/gromacs/gromacs-2021.ebuild | 355 ------------------------ |
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5 files changed, 1424 deletions(-) |
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|
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diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest |
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index 001d1215733..c60eb6f9145 100644 |
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--- a/sci-chemistry/gromacs/Manifest |
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+++ b/sci-chemistry/gromacs/Manifest |
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@@ -1,24 +1,15 @@ |
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DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B 8780032305928067fbfe1559efe9eedc4d47e27ab2f6ab54d6dba39edfcbeefbee4673d8910009048a850620b5a08ba8feb622db652c439cfa50a149ec5f0015 SHA512 6717895942f2ab7b54019511ed2aebadadde8e96d3c4b7414bb9168ffe418432d2dee330192e199f7b9d2f665c71f5d4f1ef0911aa7243d525a2ca182ef5b122 |
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DIST gromacs-2019.6.tar.gz 33446147 BLAKE2B adc21fb6b841b06d499607f8c0166a673645ef5af0b40bd823d0fff5ea24397e6301c5e1e0070986ae1ce1deba8a42052b66da148b071c1e21f2fe3908fee275 SHA512 7c227a9539e5775d5d128ae9e872a24181d79cdcd2852b86453597987e8d7332ecec371da65d089f6e610c54aafbccc8824ce298743383dd6240719ebee692a8 |
27 |
DIST gromacs-2020.4.tar.gz 29149899 BLAKE2B a07c8efd96137d58c1edf4ac9b5aafeb16d9e65234b9459b71471827032654acacb58ed6ae87ec6e0e593a0acd799683cc4461b06cc883b089d740708619345e SHA512 0c56f058741af70660baf0177724ec940dd984c05ea141ede91ee51ce3744f76d00e31bdb5db907e46fa1639de5dca637b3ace26e89f908c2e74c69f0c21ed3a |
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-DIST gromacs-2020.5.tar.gz 29148909 BLAKE2B ea439ae95d4af67a77d53182f7ddab702799edab8527c1b6ad20625d21a81f3e3c0cc699fa0b656625bffcca0bdd5a1e104aea4f592ee2db92b4f1a460ad0e80 SHA512 fe38fda36d31aef5ce01a3dbc29c9f50d3cc05b20bb34a9a8f10fda5aecde4f93ca8a3f85433139e1bb88fc23d77916a4aff5a292abaa528bd0e6138e84cba18 |
29 |
DIST gromacs-2020.6.tar.gz 29196621 BLAKE2B b350fc62fd8eeb3f2b042fa74a4ed42e43a7b74efd8fddb60ec086a814048a52b8625da65fa5c4cf2cb1e22f8347562bc84d38bf34441fc5ebc6abaa38b0eea0 SHA512 4ce4d6b9ae33e9cd2a1ad3313e80acf63ded21dac897b01dbf87df2e318181796ef64c8a1d3e0a6058b972d8d88d00f710cd0277db12f38fc2c9b29772c98bea |
30 |
-DIST gromacs-2021.1.tar.gz 37971732 BLAKE2B 722a3c21afd9d5ad432b601c99a2d5ebb85012479851d52517559bc113d75424e7509f417fb74f5f935ae6614e01a31e7361e7e673c966964fd73f08621c8415 SHA512 7f9104a3df8aa808940fd380653e43ae716167df717687717d67ddd556a29acc6ba7c2e78ff9b920b145eb521998645bee0b3816438b1398374b6b7a1831513e |
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DIST gromacs-2021.2.tar.gz 37976386 BLAKE2B 8818321bbcbdee25356bbf909d9c667f9d7cf180e696a323a61017683234d1269decc8f8d72b8012a8cc207f69e5cd97e2ab48dbbff06d82bbb407bc0578854b SHA512 51b1728f41932274436ab807d569109e2b0e145abcb5cf9c9b7daf6a7396f2f8716dc28fb93cf178c97a7eaeab2a88878d0bc71dd6c6abe7e829d579e7968615 |
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-DIST gromacs-2021.tar.gz 35061679 BLAKE2B a7d8bd728480455e5c069392e3921a4f788802ec164ee24241cac9bc7c555cee07ef26853efa61e40a787fa87e6d20af35d56b98ac6a3757ef07fc4176679e19 SHA512 10d9d64b3c2329613a18d861589428841f55bede45e1800aec25246258209be1385aabaa0d5b52425c0ac21804c38b401db76448bb539ff3cf25f8b94e09575c |
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DIST manual-2018.8.pdf 10025023 BLAKE2B afb0a6e6a72d78df743fcb57e7c1716848589e571dd35167b957a9b407ca27978ccfb6cb9e0df9c9439b888f352501a00ba32281ed1e0b4193bd606f1d77152e SHA512 b1972f7ce965bfc9377542993c5943ea4868a8ed23a969d4203264746d6bea3a7a65c6379196ece37fd6d68ec7ec80f827bde87d1049284af7082759a124f1d5 |
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DIST manual-2019.6.pdf 12702376 BLAKE2B c350127bc06a9eb3dee73da39037c84daeb89500e23cb131bd19a150bf60602d4dde7611e0c6f0f344af4093e96a899303dac71b4df56fd0c44c3a48a56606b7 SHA512 dfdff67c2c1c9ce1f1c236b7686c5331b0fe86951da6c98eddd6a3e748815e0be0a9653ae4318469fcdd913c4e7c355d64a997cc80b9d9fbe6282ef6d98e61eb |
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DIST manual-2020.4.pdf 11851608 BLAKE2B 7b7bdf08e8946fcc448543b08391b94a67fee60a8c810597c1f09f70443f9d7db817c99622dd0c21c6317f5fdcd6c4a88589ecac57055cb0cd8597d6021026e7 SHA512 928555663c77de36393e625c29d388d4e1c8c1298e7a993d871839e0d4d8d18d190221ad8f1d975bd072bdd6a061e9ea5b9295f2ecf45f24b6523ea5ea290fed |
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-DIST manual-2020.5.pdf 11850797 BLAKE2B b605de81cce385177f278b563526725688b4c2b0326f6f2c22bddc9b455c016365ee82731ad0ef2b2c9522e7d140c4a097b7a25f91552be60741d876bcc4c929 SHA512 0fa81494dbb4cb71c274fa1d1b1ef13bc5be8e69be841d429d06d5e9ef5517158b2130c0120ef6de13e73de5cd8af941c7b983ddba1da8af8214272704ce629e |
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DIST manual-2020.6.pdf 11850850 BLAKE2B 155e4eb9c200dcd0a38e3669b26077fcf310d437b82d9a593d333dada3989c2c8a936d62c642e195f98bb474b1673b8142405c467348fc96a74d57fb12106d76 SHA512 be508ebec597b82a2c4056029f8bb731b22cb8902628a45462ed21af54c554d28e07d5381efaaa96565202b7b47d33aea67950206cd9e8936211ae721b21b3e1 |
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-DIST manual-2021.1.pdf 12252366 BLAKE2B c3f104f3a5c8b784b78bdb027ae3bf818977fd86e15b81760877423805d74f468417df6ad57b240d138f4ee4c567c2e7676c0084911ee1400ebfa7bab2673901 SHA512 8d4468da400abb39c307b1f31f5b4b4ae52152df1fb5bc7059a37072cd2a20136858d7280ea6a7138fe6c18e04821386d72f1ac4ee9a303e359e1d52b5250f12 |
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DIST manual-2021.2.pdf 12252501 BLAKE2B 0dbf9024e1516076b0eeb46e41523b966d1d81f57504fe0501c7bc8575e74fb19e3452ac584757e425bcccbc737367fe83be87fd21a4287f4675cf87184b960b SHA512 14156d3b1017990e0be3ceb7ec055777a1aec4c347ac2e821a042d51c931f84ebca862f60644a90ed7ba4070cb14ff8babcde3e4351e4dbec84df8563e350984 |
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-DIST manual-2021.pdf 12251377 BLAKE2B 6b3c80fedf04b3cdc05ec9b52e0dd78c0c7abf2d9819c00ad29e1d7e2dd829cfc0e61c86c899859ac6af6b631f856737810f05f9c903456805b5b9c9c6c85c16 SHA512 1bd61e4d052ebe4ff293be710159f135013d38f1299557d0b0e5edcf60d288d8534694896a1feebe572f52187f85e890e59b7c71644a0c03bd264cfae6d348bc |
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DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb |
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DIST regressiontests-2019.6.tar.gz 67643195 BLAKE2B 1e054e24b187946f7ea28090d4f20cf8e1d79a26253f57ba07d130e0773d8541b8a1552a38023d31a68ce8bc62d8e0af1d98609234bb3e7d3e6d567307ebb386 SHA512 eacf1c55b982515a305c29459fe80a7cd558a8481e5689962aa956148af542568b1d1ce59c6784ecb0afd4768c2b664afa21e12af2d89ae2b06b1ba61ad72036 |
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DIST regressiontests-2020.4.tar.gz 48542144 BLAKE2B 1dcde67525d40ababa74d9e8ba2dd3fdef1de7d1018491e102edd71d3a622925f213b5a0812e5448882b4cb5fb578317e8e5029bdc4bd53008aa8441a3d9dea1 SHA512 7c71f36a1cef22562f14dcd233e90ad2fe370ae1a7d3b5268727259b374e12d4754253735ac8745d3738bdbc1cc2067780fda5e393be2ff264f632fe4e0c1978 |
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-DIST regressiontests-2020.5.tar.gz 48541167 BLAKE2B 81f0505090203c970178ca4eba8dfd54d942a20970525cad954833481cd79141fa33fc97e8940ca83cee104ef6b017bc0f7bbed9eddc620a86c818760b3fc261 SHA512 aba67542ed00145cae8de040e4a9074a8a359a529135180e6083b2330934962302349d382d6626bddc6971ae6d44e09c8ea44d5df55ca5fcd038055a1c3e5cc3 |
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DIST regressiontests-2020.6.tar.gz 48541232 BLAKE2B dbb405bd9168775984de8c9fb9e3fa2398d2790e2e4de23711c51a01dc3ea570d172a35d4924742ad5eda463eb0a885e6924512801e82b241600ceaefd5db70d SHA512 497a9e7d438b0b7b0734a97cf3683baf480ecc056e96b09f1e143c362ff047a4e51e323216750501c954559579716dc024d3c51319bd2c85fa719466ce4330b2 |
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-DIST regressiontests-2021.1.tar.gz 48516304 BLAKE2B 61e49e7a3ce0856cd22a6adc360f476bd4978650e21ad64074d3cd8db1d6109fb86cb91bcb161d00d1e912cf3fa40dd83c07e5cc873dc2177a11d7fb304e7ecc SHA512 c1158b7890e2ff94c6600e531fdceee439f19ee2d18093b8be68fbd18064aae4b035c697ebda4e9b74d61c68d905c26515a41c34a2ac9f8dd8a29c5348ecbab1 |
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DIST regressiontests-2021.2.tar.gz 48514312 BLAKE2B 81b007d5e5e1d054349c73dc8bc3589db328752e48a66687c0ad36be87ebe580df9cbd93b193a724669bd5765af06ec306f2e12af00a228af616de03943d6f05 SHA512 b687ddfd3dc6ec1051af2a3253633703ef1c82335d1df23379819ea47e44dfcd417e81e29610cc584d4c5fb1ee1cbc76731a3fd31b529d8cdd0b9c22f432c7ec |
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-DIST regressiontests-2021.tar.gz 48513192 BLAKE2B e27898ef3936495fce111c8debdafbdaafae07cd9b27c8591cc27695f681fddda34f083d427e5b3afd2f318ff41201eabc915025f1fddef61ae29ceb13f37557 SHA512 e33578d32b929d516614592d0bf4aac4e518cc4f18fee4048d5b73b11f4373494c6d8aa43442e4e2be632c12c058657bce1064be82c515787d57b449c1241e48 |
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|
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diff --git a/sci-chemistry/gromacs/gromacs-2020.5.ebuild b/sci-chemistry/gromacs/gromacs-2020.5.ebuild |
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deleted file mode 100644 |
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index 41ac7771497..00000000000 |
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--- a/sci-chemistry/gromacs/gromacs-2020.5.ebuild |
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+++ /dev/null |
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@@ -1,351 +0,0 @@ |
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-# Copyright 1999-2021 Gentoo Authors |
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-# Distributed under the terms of the GNU General Public License v2 |
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- |
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-EAPI=7 |
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- |
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-CMAKE_MAKEFILE_GENERATOR="ninja" |
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- |
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-PYTHON_COMPAT=( python3_{7,8,9} ) |
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- |
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-DISTUTILS_USE_SETUPTOOLS=no |
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-DISTUTILS_SINGLE_IMPL=1 |
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- |
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-inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils |
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- |
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-if [[ ${PV} = *9999* ]]; then |
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- EGIT_REPO_URI=" |
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- https://gitlab.com/gromacs/gromacs.git |
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- https://github.com/gromacs/gromacs.git |
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- git://git.gromacs.org/gromacs.git" |
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- [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" |
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- inherit git-r3 |
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-else |
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- SRC_URI=" |
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- http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz |
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- doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) |
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- test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" |
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- KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
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-fi |
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- |
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-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
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- |
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-DESCRIPTION="The ultimate molecular dynamics simulation package" |
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-HOMEPAGE="http://www.gromacs.org/" |
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- |
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-# see COPYING for details |
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-# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
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-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
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-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
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-SLOT="0/${PV}" |
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-IUSE="X blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" |
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- |
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-CDEPEND=" |
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- X? ( |
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- x11-libs/libX11 |
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- x11-libs/libSM |
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- x11-libs/libICE |
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- ) |
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- blas? ( virtual/blas ) |
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- cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) |
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- opencl? ( virtual/opencl ) |
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- fftw? ( sci-libs/fftw:3.0 ) |
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- hwloc? ( sys-apps/hwloc ) |
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- lapack? ( virtual/lapack ) |
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- lmfit? ( sci-libs/lmfit ) |
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- mkl? ( sci-libs/mkl ) |
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- mpi? ( virtual/mpi ) |
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- ${PYTHON_DEPS} |
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- !sci-chemistry/gmxapi |
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- " |
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-BDEPEND="${CDEPEND} |
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- virtual/pkgconfig |
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- build-manual? ( |
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- app-doc/doxygen |
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- $(python_gen_cond_dep ' |
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- dev-python/sphinx[${PYTHON_MULTI_USEDEP}] |
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- ') |
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- media-gfx/mscgen |
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- media-gfx/graphviz |
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- dev-texlive/texlive-latex |
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- dev-texlive/texlive-latexextra |
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- media-gfx/imagemagick |
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- )" |
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-RDEPEND="${CDEPEND}" |
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- |
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-REQUIRED_USE=" |
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- || ( single-precision double-precision ) |
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- || ( doc build-manual ) |
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- cuda? ( single-precision ) |
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- cuda? ( !opencl ) |
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- mkl? ( !blas !fftw !lapack ) |
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- ${PYTHON_REQUIRED_USE}" |
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- |
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-DOCS=( AUTHORS README ) |
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- |
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-RESTRICT="!test? ( test )" |
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- |
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-if [[ ${PV} != *9999 ]]; then |
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- S="${WORKDIR}/${PN}-${PV/_/-}" |
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-fi |
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- |
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-PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" ) |
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- |
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-pkg_pretend() { |
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- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
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- use openmp && ! tc-has-openmp && \ |
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- die "Please switch to an openmp compatible compiler" |
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-} |
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- |
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-pkg_setup() { |
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- python-single-r1_pkg_setup |
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-} |
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- |
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-src_unpack() { |
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- if [[ ${PV} != *9999 ]]; then |
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- default |
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- else |
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- git-r3_src_unpack |
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- if use test; then |
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- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
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- EGIT_BRANCH="${EGIT_BRANCH}" \ |
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- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
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- git-r3_src_unpack |
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- fi |
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- fi |
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-} |
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- |
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-src_prepare() { |
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- #notes/todos |
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- # -on apple: there is framework support |
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- |
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- xdg_environment_reset #591952 |
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- |
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- cmake_src_prepare |
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- |
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- use cuda && cuda_src_prepare |
181 |
- |
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- GMX_DIRS="" |
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- use single-precision && GMX_DIRS+=" float" |
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- use double-precision && GMX_DIRS+=" double" |
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- |
186 |
- if use test; then |
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- for x in ${GMX_DIRS}; do |
188 |
- mkdir -p "${WORKDIR}/${P}_${x}" || die |
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- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
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- done |
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- fi |
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- |
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- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
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- if use build-manual; then |
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- # try to create policy for imagemagik |
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- mkdir -p ${HOME}/.config/ImageMagick |
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- cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF |
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- <?xml version="1.0" encoding="UTF-8"?> |
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- <!DOCTYPE policymap [ |
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- <!ELEMENT policymap (policy)+> |
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- !ATTLIST policymap xmlns CDATA #FIXED ''> |
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- <!ELEMENT policy EMPTY> |
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- <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED |
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- name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED |
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- stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> |
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- ]> |
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- <policymap> |
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- <policy domain="coder" rights="read | write" pattern="PS" /> |
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- <policy domain="coder" rights="read | write" pattern="PS2" /> |
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- <policy domain="coder" rights="read | write" pattern="PS3" /> |
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- <policy domain="coder" rights="read | write" pattern="EPS" /> |
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- <policy domain="coder" rights="read | write" pattern="PDF" /> |
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- <policy domain="coder" rights="read | write" pattern="XPS" /> |
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- </policymap> |
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- EOF |
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- fi |
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-} |
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- |
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-src_configure() { |
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- local mycmakeargs_pre=( ) extra fft_opts=( ) |
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- |
222 |
- if use custom-cflags; then |
223 |
- #go from slowest to fastest acceleration |
224 |
- local acce="None" |
225 |
- use cpu_flags_x86_sse2 && acce="SSE2" |
226 |
- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
227 |
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
228 |
- use cpu_flags_x86_avx && acce="AVX_256" |
229 |
- use cpu_flags_x86_avx2 && acce="AVX2_256" |
230 |
- else |
231 |
- strip-flags |
232 |
- fi |
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- |
234 |
- #to create man pages, build tree binaries are executed (bug #398437) |
235 |
- [[ ${CHOST} = *-darwin* ]] && \ |
236 |
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
237 |
- |
238 |
- if use fftw; then |
239 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
240 |
- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
241 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
242 |
- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
243 |
- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
244 |
- ) |
245 |
- elif use mkl; then |
246 |
- local bits=$(get_libdir) |
247 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
248 |
- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
249 |
- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
250 |
- ) |
251 |
- else |
252 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
253 |
- fi |
254 |
- |
255 |
- if use lmfit; then |
256 |
- local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) |
257 |
- else |
258 |
- local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) |
259 |
- fi |
260 |
- |
261 |
- mycmakeargs_pre+=( |
262 |
- "${fft_opts[@]}" |
263 |
- "${lmfit_opts[@]}" |
264 |
- -DGMX_X11=$(usex X) |
265 |
- -DGMX_EXTERNAL_BLAS=$(usex blas) |
266 |
- -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
267 |
- -DGMX_OPENMP=$(usex openmp) |
268 |
- -DGMX_COOL_QUOTES=$(usex offensive) |
269 |
- -DGMX_USE_TNG=$(usex tng) |
270 |
- -DGMX_BUILD_MANUAL=$(usex build-manual) |
271 |
- -DGMX_HWLOC=$(usex hwloc) |
272 |
- -DGMX_DEFAULT_SUFFIX=off |
273 |
- -DGMX_SIMD="$acce" |
274 |
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
275 |
- -DBUILD_TESTING=$(usex test) |
276 |
- -DGMX_BUILD_UNITTESTS=$(usex test) |
277 |
- -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" |
278 |
- ${extra} |
279 |
- ) |
280 |
- |
281 |
- for x in ${GMX_DIRS}; do |
282 |
- einfo "Configuring for ${x} precision" |
283 |
- local suffix="" |
284 |
- #if we build single and double - double is suffixed |
285 |
- use double-precision && use single-precision && \ |
286 |
- [[ ${x} = "double" ]] && suffix="_d" |
287 |
- local p |
288 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
289 |
- local cuda=( "-DGMX_GPU=OFF" ) |
290 |
- [[ ${x} = "float" ]] && use cuda && \ |
291 |
- cuda=( "-DGMX_GPU=ON" ) |
292 |
- local opencl=( "-DGMX_USE_OPENCL=OFF" ) |
293 |
- use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) |
294 |
- mycmakeargs=( |
295 |
- ${mycmakeargs_pre[@]} ${p} |
296 |
- -DGMX_MPI=OFF |
297 |
- -DGMX_THREAD_MPI=$(usex threads) |
298 |
- -DGMXAPI=$(usex gmxapi) |
299 |
- -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) |
300 |
- "${opencl[@]}" |
301 |
- "${cuda[@]}" |
302 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
303 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
304 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
305 |
- -DGMX_PYTHON_PACKAGE=$(usex python) |
306 |
- ) |
307 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure |
308 |
- [[ ${CHOST} != *-darwin* ]] || \ |
309 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
310 |
- use mpi || continue |
311 |
- einfo "Configuring for ${x} precision with mpi" |
312 |
- mycmakeargs=( |
313 |
- ${mycmakeargs_pre[@]} ${p} |
314 |
- -DGMX_THREAD_MPI=OFF |
315 |
- -DGMX_MPI=ON |
316 |
- -DGMX_OPENMM=OFF |
317 |
- -DGMXAPI=OFF |
318 |
- "${opencl[@]}" |
319 |
- "${cuda[@]}" |
320 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
321 |
- -DBUILD_SHARED_LIBS=OFF |
322 |
- -DGMX_BUILD_MANUAL=OFF |
323 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
324 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
325 |
- ) |
326 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure |
327 |
- [[ ${CHOST} != *-darwin* ]] || \ |
328 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
329 |
- done |
330 |
-} |
331 |
- |
332 |
-src_compile() { |
333 |
- for x in ${GMX_DIRS}; do |
334 |
- einfo "Compiling for ${x} precision" |
335 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
336 |
- cmake_src_compile |
337 |
- if use python; then |
338 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
339 |
- cmake_src_compile python_packaging/all |
340 |
- BUILD_DIR="${WORKDIR}/${P}" \ |
341 |
- distutils-r1_src_compile |
342 |
- fi |
343 |
- # not 100% necessary for rel ebuilds as available from website |
344 |
- if use build-manual; then |
345 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
346 |
- cmake_src_compile manual |
347 |
- fi |
348 |
- use mpi || continue |
349 |
- einfo "Compiling for ${x} precision with mpi" |
350 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
351 |
- cmake_src_compile |
352 |
- done |
353 |
-} |
354 |
- |
355 |
-src_test() { |
356 |
- for x in ${GMX_DIRS}; do |
357 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
358 |
- cmake_src_compile check |
359 |
- done |
360 |
-} |
361 |
- |
362 |
-src_install() { |
363 |
- for x in ${GMX_DIRS}; do |
364 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
365 |
- cmake_src_install |
366 |
- if use python; then |
367 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
368 |
- cmake_src_install python_packaging/install |
369 |
- fi |
370 |
- if use build-manual; then |
371 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
372 |
- fi |
373 |
- |
374 |
- if use doc; then |
375 |
- newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" |
376 |
- fi |
377 |
- |
378 |
- use mpi || continue |
379 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
380 |
- cmake_src_install |
381 |
- done |
382 |
- |
383 |
- if use tng; then |
384 |
- insinto /usr/include/tng |
385 |
- doins src/external/tng_io/include/tng/*h |
386 |
- fi |
387 |
- # drop unneeded stuff |
388 |
- rm "${ED}"/usr/bin/GMXRC* || die |
389 |
- for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do |
390 |
- local n=${x##*/gmx-completion-} |
391 |
- n="${n%.bash}" |
392 |
- cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
393 |
- newbashcomp "${T}"/"${n}" "${n}" |
394 |
- done |
395 |
- rm "${ED}"/usr/bin/gmx-completion*.bash || die |
396 |
- readme.gentoo_create_doc |
397 |
-} |
398 |
- |
399 |
-pkg_postinst() { |
400 |
- einfo |
401 |
- einfo "Please read and cite:" |
402 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
403 |
- einfo "https://dx.doi.org/10.1021/ct700301q" |
404 |
- einfo |
405 |
- readme.gentoo_print_elog |
406 |
-} |
407 |
|
408 |
diff --git a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild |
409 |
deleted file mode 100644 |
410 |
index 41ac7771497..00000000000 |
411 |
--- a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild |
412 |
+++ /dev/null |
413 |
@@ -1,351 +0,0 @@ |
414 |
-# Copyright 1999-2021 Gentoo Authors |
415 |
-# Distributed under the terms of the GNU General Public License v2 |
416 |
- |
417 |
-EAPI=7 |
418 |
- |
419 |
-CMAKE_MAKEFILE_GENERATOR="ninja" |
420 |
- |
421 |
-PYTHON_COMPAT=( python3_{7,8,9} ) |
422 |
- |
423 |
-DISTUTILS_USE_SETUPTOOLS=no |
424 |
-DISTUTILS_SINGLE_IMPL=1 |
425 |
- |
426 |
-inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils |
427 |
- |
428 |
-if [[ ${PV} = *9999* ]]; then |
429 |
- EGIT_REPO_URI=" |
430 |
- https://gitlab.com/gromacs/gromacs.git |
431 |
- https://github.com/gromacs/gromacs.git |
432 |
- git://git.gromacs.org/gromacs.git" |
433 |
- [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" |
434 |
- inherit git-r3 |
435 |
-else |
436 |
- SRC_URI=" |
437 |
- http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz |
438 |
- doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) |
439 |
- test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" |
440 |
- KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
441 |
-fi |
442 |
- |
443 |
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
444 |
- |
445 |
-DESCRIPTION="The ultimate molecular dynamics simulation package" |
446 |
-HOMEPAGE="http://www.gromacs.org/" |
447 |
- |
448 |
-# see COPYING for details |
449 |
-# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
450 |
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
451 |
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
452 |
-SLOT="0/${PV}" |
453 |
-IUSE="X blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" |
454 |
- |
455 |
-CDEPEND=" |
456 |
- X? ( |
457 |
- x11-libs/libX11 |
458 |
- x11-libs/libSM |
459 |
- x11-libs/libICE |
460 |
- ) |
461 |
- blas? ( virtual/blas ) |
462 |
- cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) |
463 |
- opencl? ( virtual/opencl ) |
464 |
- fftw? ( sci-libs/fftw:3.0 ) |
465 |
- hwloc? ( sys-apps/hwloc ) |
466 |
- lapack? ( virtual/lapack ) |
467 |
- lmfit? ( sci-libs/lmfit ) |
468 |
- mkl? ( sci-libs/mkl ) |
469 |
- mpi? ( virtual/mpi ) |
470 |
- ${PYTHON_DEPS} |
471 |
- !sci-chemistry/gmxapi |
472 |
- " |
473 |
-BDEPEND="${CDEPEND} |
474 |
- virtual/pkgconfig |
475 |
- build-manual? ( |
476 |
- app-doc/doxygen |
477 |
- $(python_gen_cond_dep ' |
478 |
- dev-python/sphinx[${PYTHON_MULTI_USEDEP}] |
479 |
- ') |
480 |
- media-gfx/mscgen |
481 |
- media-gfx/graphviz |
482 |
- dev-texlive/texlive-latex |
483 |
- dev-texlive/texlive-latexextra |
484 |
- media-gfx/imagemagick |
485 |
- )" |
486 |
-RDEPEND="${CDEPEND}" |
487 |
- |
488 |
-REQUIRED_USE=" |
489 |
- || ( single-precision double-precision ) |
490 |
- || ( doc build-manual ) |
491 |
- cuda? ( single-precision ) |
492 |
- cuda? ( !opencl ) |
493 |
- mkl? ( !blas !fftw !lapack ) |
494 |
- ${PYTHON_REQUIRED_USE}" |
495 |
- |
496 |
-DOCS=( AUTHORS README ) |
497 |
- |
498 |
-RESTRICT="!test? ( test )" |
499 |
- |
500 |
-if [[ ${PV} != *9999 ]]; then |
501 |
- S="${WORKDIR}/${PN}-${PV/_/-}" |
502 |
-fi |
503 |
- |
504 |
-PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" ) |
505 |
- |
506 |
-pkg_pretend() { |
507 |
- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
508 |
- use openmp && ! tc-has-openmp && \ |
509 |
- die "Please switch to an openmp compatible compiler" |
510 |
-} |
511 |
- |
512 |
-pkg_setup() { |
513 |
- python-single-r1_pkg_setup |
514 |
-} |
515 |
- |
516 |
-src_unpack() { |
517 |
- if [[ ${PV} != *9999 ]]; then |
518 |
- default |
519 |
- else |
520 |
- git-r3_src_unpack |
521 |
- if use test; then |
522 |
- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
523 |
- EGIT_BRANCH="${EGIT_BRANCH}" \ |
524 |
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
525 |
- git-r3_src_unpack |
526 |
- fi |
527 |
- fi |
528 |
-} |
529 |
- |
530 |
-src_prepare() { |
531 |
- #notes/todos |
532 |
- # -on apple: there is framework support |
533 |
- |
534 |
- xdg_environment_reset #591952 |
535 |
- |
536 |
- cmake_src_prepare |
537 |
- |
538 |
- use cuda && cuda_src_prepare |
539 |
- |
540 |
- GMX_DIRS="" |
541 |
- use single-precision && GMX_DIRS+=" float" |
542 |
- use double-precision && GMX_DIRS+=" double" |
543 |
- |
544 |
- if use test; then |
545 |
- for x in ${GMX_DIRS}; do |
546 |
- mkdir -p "${WORKDIR}/${P}_${x}" || die |
547 |
- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
548 |
- done |
549 |
- fi |
550 |
- |
551 |
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
552 |
- if use build-manual; then |
553 |
- # try to create policy for imagemagik |
554 |
- mkdir -p ${HOME}/.config/ImageMagick |
555 |
- cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF |
556 |
- <?xml version="1.0" encoding="UTF-8"?> |
557 |
- <!DOCTYPE policymap [ |
558 |
- <!ELEMENT policymap (policy)+> |
559 |
- !ATTLIST policymap xmlns CDATA #FIXED ''> |
560 |
- <!ELEMENT policy EMPTY> |
561 |
- <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED |
562 |
- name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED |
563 |
- stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> |
564 |
- ]> |
565 |
- <policymap> |
566 |
- <policy domain="coder" rights="read | write" pattern="PS" /> |
567 |
- <policy domain="coder" rights="read | write" pattern="PS2" /> |
568 |
- <policy domain="coder" rights="read | write" pattern="PS3" /> |
569 |
- <policy domain="coder" rights="read | write" pattern="EPS" /> |
570 |
- <policy domain="coder" rights="read | write" pattern="PDF" /> |
571 |
- <policy domain="coder" rights="read | write" pattern="XPS" /> |
572 |
- </policymap> |
573 |
- EOF |
574 |
- fi |
575 |
-} |
576 |
- |
577 |
-src_configure() { |
578 |
- local mycmakeargs_pre=( ) extra fft_opts=( ) |
579 |
- |
580 |
- if use custom-cflags; then |
581 |
- #go from slowest to fastest acceleration |
582 |
- local acce="None" |
583 |
- use cpu_flags_x86_sse2 && acce="SSE2" |
584 |
- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
585 |
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
586 |
- use cpu_flags_x86_avx && acce="AVX_256" |
587 |
- use cpu_flags_x86_avx2 && acce="AVX2_256" |
588 |
- else |
589 |
- strip-flags |
590 |
- fi |
591 |
- |
592 |
- #to create man pages, build tree binaries are executed (bug #398437) |
593 |
- [[ ${CHOST} = *-darwin* ]] && \ |
594 |
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
595 |
- |
596 |
- if use fftw; then |
597 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
598 |
- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
599 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
600 |
- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
601 |
- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
602 |
- ) |
603 |
- elif use mkl; then |
604 |
- local bits=$(get_libdir) |
605 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
606 |
- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
607 |
- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
608 |
- ) |
609 |
- else |
610 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
611 |
- fi |
612 |
- |
613 |
- if use lmfit; then |
614 |
- local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) |
615 |
- else |
616 |
- local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) |
617 |
- fi |
618 |
- |
619 |
- mycmakeargs_pre+=( |
620 |
- "${fft_opts[@]}" |
621 |
- "${lmfit_opts[@]}" |
622 |
- -DGMX_X11=$(usex X) |
623 |
- -DGMX_EXTERNAL_BLAS=$(usex blas) |
624 |
- -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
625 |
- -DGMX_OPENMP=$(usex openmp) |
626 |
- -DGMX_COOL_QUOTES=$(usex offensive) |
627 |
- -DGMX_USE_TNG=$(usex tng) |
628 |
- -DGMX_BUILD_MANUAL=$(usex build-manual) |
629 |
- -DGMX_HWLOC=$(usex hwloc) |
630 |
- -DGMX_DEFAULT_SUFFIX=off |
631 |
- -DGMX_SIMD="$acce" |
632 |
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
633 |
- -DBUILD_TESTING=$(usex test) |
634 |
- -DGMX_BUILD_UNITTESTS=$(usex test) |
635 |
- -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" |
636 |
- ${extra} |
637 |
- ) |
638 |
- |
639 |
- for x in ${GMX_DIRS}; do |
640 |
- einfo "Configuring for ${x} precision" |
641 |
- local suffix="" |
642 |
- #if we build single and double - double is suffixed |
643 |
- use double-precision && use single-precision && \ |
644 |
- [[ ${x} = "double" ]] && suffix="_d" |
645 |
- local p |
646 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
647 |
- local cuda=( "-DGMX_GPU=OFF" ) |
648 |
- [[ ${x} = "float" ]] && use cuda && \ |
649 |
- cuda=( "-DGMX_GPU=ON" ) |
650 |
- local opencl=( "-DGMX_USE_OPENCL=OFF" ) |
651 |
- use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) |
652 |
- mycmakeargs=( |
653 |
- ${mycmakeargs_pre[@]} ${p} |
654 |
- -DGMX_MPI=OFF |
655 |
- -DGMX_THREAD_MPI=$(usex threads) |
656 |
- -DGMXAPI=$(usex gmxapi) |
657 |
- -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) |
658 |
- "${opencl[@]}" |
659 |
- "${cuda[@]}" |
660 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
661 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
662 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
663 |
- -DGMX_PYTHON_PACKAGE=$(usex python) |
664 |
- ) |
665 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure |
666 |
- [[ ${CHOST} != *-darwin* ]] || \ |
667 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
668 |
- use mpi || continue |
669 |
- einfo "Configuring for ${x} precision with mpi" |
670 |
- mycmakeargs=( |
671 |
- ${mycmakeargs_pre[@]} ${p} |
672 |
- -DGMX_THREAD_MPI=OFF |
673 |
- -DGMX_MPI=ON |
674 |
- -DGMX_OPENMM=OFF |
675 |
- -DGMXAPI=OFF |
676 |
- "${opencl[@]}" |
677 |
- "${cuda[@]}" |
678 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
679 |
- -DBUILD_SHARED_LIBS=OFF |
680 |
- -DGMX_BUILD_MANUAL=OFF |
681 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
682 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
683 |
- ) |
684 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure |
685 |
- [[ ${CHOST} != *-darwin* ]] || \ |
686 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
687 |
- done |
688 |
-} |
689 |
- |
690 |
-src_compile() { |
691 |
- for x in ${GMX_DIRS}; do |
692 |
- einfo "Compiling for ${x} precision" |
693 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
694 |
- cmake_src_compile |
695 |
- if use python; then |
696 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
697 |
- cmake_src_compile python_packaging/all |
698 |
- BUILD_DIR="${WORKDIR}/${P}" \ |
699 |
- distutils-r1_src_compile |
700 |
- fi |
701 |
- # not 100% necessary for rel ebuilds as available from website |
702 |
- if use build-manual; then |
703 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
704 |
- cmake_src_compile manual |
705 |
- fi |
706 |
- use mpi || continue |
707 |
- einfo "Compiling for ${x} precision with mpi" |
708 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
709 |
- cmake_src_compile |
710 |
- done |
711 |
-} |
712 |
- |
713 |
-src_test() { |
714 |
- for x in ${GMX_DIRS}; do |
715 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
716 |
- cmake_src_compile check |
717 |
- done |
718 |
-} |
719 |
- |
720 |
-src_install() { |
721 |
- for x in ${GMX_DIRS}; do |
722 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
723 |
- cmake_src_install |
724 |
- if use python; then |
725 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
726 |
- cmake_src_install python_packaging/install |
727 |
- fi |
728 |
- if use build-manual; then |
729 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
730 |
- fi |
731 |
- |
732 |
- if use doc; then |
733 |
- newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" |
734 |
- fi |
735 |
- |
736 |
- use mpi || continue |
737 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
738 |
- cmake_src_install |
739 |
- done |
740 |
- |
741 |
- if use tng; then |
742 |
- insinto /usr/include/tng |
743 |
- doins src/external/tng_io/include/tng/*h |
744 |
- fi |
745 |
- # drop unneeded stuff |
746 |
- rm "${ED}"/usr/bin/GMXRC* || die |
747 |
- for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do |
748 |
- local n=${x##*/gmx-completion-} |
749 |
- n="${n%.bash}" |
750 |
- cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
751 |
- newbashcomp "${T}"/"${n}" "${n}" |
752 |
- done |
753 |
- rm "${ED}"/usr/bin/gmx-completion*.bash || die |
754 |
- readme.gentoo_create_doc |
755 |
-} |
756 |
- |
757 |
-pkg_postinst() { |
758 |
- einfo |
759 |
- einfo "Please read and cite:" |
760 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
761 |
- einfo "https://dx.doi.org/10.1021/ct700301q" |
762 |
- einfo |
763 |
- readme.gentoo_print_elog |
764 |
-} |
765 |
|
766 |
diff --git a/sci-chemistry/gromacs/gromacs-2021.1.ebuild b/sci-chemistry/gromacs/gromacs-2021.1.ebuild |
767 |
deleted file mode 100644 |
768 |
index e8ea613693f..00000000000 |
769 |
--- a/sci-chemistry/gromacs/gromacs-2021.1.ebuild |
770 |
+++ /dev/null |
771 |
@@ -1,358 +0,0 @@ |
772 |
-# Copyright 1999-2021 Gentoo Authors |
773 |
-# Distributed under the terms of the GNU General Public License v2 |
774 |
- |
775 |
-EAPI=7 |
776 |
- |
777 |
-CMAKE_MAKEFILE_GENERATOR="ninja" |
778 |
- |
779 |
-PYTHON_COMPAT=( python3_{7,8,9} ) |
780 |
- |
781 |
-DISTUTILS_USE_SETUPTOOLS=no |
782 |
-DISTUTILS_SINGLE_IMPL=1 |
783 |
- |
784 |
-inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils |
785 |
- |
786 |
-if [[ ${PV} = *9999* ]]; then |
787 |
- EGIT_REPO_URI=" |
788 |
- https://gitlab.com/gromacs/gromacs.git |
789 |
- https://github.com/gromacs/gromacs.git |
790 |
- git://git.gromacs.org/gromacs.git" |
791 |
- [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" |
792 |
- inherit git-r3 |
793 |
-else |
794 |
- SRC_URI=" |
795 |
- http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz |
796 |
- doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) |
797 |
- test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" |
798 |
- KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
799 |
-fi |
800 |
- |
801 |
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" |
802 |
- |
803 |
-DESCRIPTION="The ultimate molecular dynamics simulation package" |
804 |
-HOMEPAGE="http://www.gromacs.org/" |
805 |
- |
806 |
-# see COPYING for details |
807 |
-# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
808 |
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
809 |
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
810 |
-SLOT="0/${PV}" |
811 |
-IUSE="X blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" |
812 |
- |
813 |
-CDEPEND=" |
814 |
- X? ( |
815 |
- x11-libs/libX11 |
816 |
- x11-libs/libSM |
817 |
- x11-libs/libICE |
818 |
- ) |
819 |
- blas? ( virtual/blas ) |
820 |
- cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) |
821 |
- opencl? ( virtual/opencl ) |
822 |
- fftw? ( sci-libs/fftw:3.0 ) |
823 |
- hwloc? ( sys-apps/hwloc ) |
824 |
- lapack? ( virtual/lapack ) |
825 |
- lmfit? ( sci-libs/lmfit ) |
826 |
- mkl? ( sci-libs/mkl ) |
827 |
- mpi? ( virtual/mpi ) |
828 |
- ${PYTHON_DEPS} |
829 |
- !sci-chemistry/gmxapi |
830 |
- " |
831 |
-BDEPEND="${CDEPEND} |
832 |
- virtual/pkgconfig |
833 |
- build-manual? ( |
834 |
- app-doc/doxygen |
835 |
- $(python_gen_cond_dep ' |
836 |
- dev-python/sphinx[${PYTHON_MULTI_USEDEP}] |
837 |
- ') |
838 |
- media-gfx/mscgen |
839 |
- media-gfx/graphviz |
840 |
- dev-texlive/texlive-latex |
841 |
- dev-texlive/texlive-latexextra |
842 |
- media-gfx/imagemagick |
843 |
- )" |
844 |
-RDEPEND="${CDEPEND}" |
845 |
- |
846 |
-REQUIRED_USE=" |
847 |
- || ( single-precision double-precision ) |
848 |
- || ( doc build-manual ) |
849 |
- cuda? ( single-precision ) |
850 |
- cuda? ( !opencl ) |
851 |
- mkl? ( !blas !fftw !lapack ) |
852 |
- ${PYTHON_REQUIRED_USE}" |
853 |
- |
854 |
-DOCS=( AUTHORS README ) |
855 |
- |
856 |
-RESTRICT="!test? ( test )" |
857 |
- |
858 |
-if [[ ${PV} != *9999 ]]; then |
859 |
- S="${WORKDIR}/${PN}-${PV/_/-}" |
860 |
-fi |
861 |
- |
862 |
-PATCHES=( |
863 |
- "${FILESDIR}/${PN}-2020-pytest.patch" |
864 |
- "${FILESDIR}/${PN}-2021-nblib.patch" |
865 |
-) |
866 |
- |
867 |
-pkg_pretend() { |
868 |
- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
869 |
- use openmp && ! tc-has-openmp && \ |
870 |
- die "Please switch to an openmp compatible compiler" |
871 |
-} |
872 |
- |
873 |
-pkg_setup() { |
874 |
- python-single-r1_pkg_setup |
875 |
-} |
876 |
- |
877 |
-src_unpack() { |
878 |
- if [[ ${PV} != *9999 ]]; then |
879 |
- default |
880 |
- else |
881 |
- git-r3_src_unpack |
882 |
- if use test; then |
883 |
- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
884 |
- EGIT_BRANCH="${EGIT_BRANCH}" \ |
885 |
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
886 |
- git-r3_src_unpack |
887 |
- fi |
888 |
- fi |
889 |
-} |
890 |
- |
891 |
-src_prepare() { |
892 |
- #notes/todos |
893 |
- # -on apple: there is framework support |
894 |
- |
895 |
- xdg_environment_reset #591952 |
896 |
- |
897 |
- cmake_src_prepare |
898 |
- |
899 |
- use cuda && cuda_src_prepare |
900 |
- |
901 |
- GMX_DIRS="" |
902 |
- use single-precision && GMX_DIRS+=" float" |
903 |
- use double-precision && GMX_DIRS+=" double" |
904 |
- |
905 |
- if use test; then |
906 |
- for x in ${GMX_DIRS}; do |
907 |
- mkdir -p "${WORKDIR}/${P}_${x}" || die |
908 |
- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
909 |
- done |
910 |
- fi |
911 |
- |
912 |
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
913 |
- if use build-manual; then |
914 |
- # try to create policy for imagemagik |
915 |
- mkdir -p ${HOME}/.config/ImageMagick |
916 |
- cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF |
917 |
- <?xml version="1.0" encoding="UTF-8"?> |
918 |
- <!DOCTYPE policymap [ |
919 |
- <!ELEMENT policymap (policy)+> |
920 |
- !ATTLIST policymap xmlns CDATA #FIXED ''> |
921 |
- <!ELEMENT policy EMPTY> |
922 |
- <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED |
923 |
- name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED |
924 |
- stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> |
925 |
- ]> |
926 |
- <policymap> |
927 |
- <policy domain="coder" rights="read | write" pattern="PS" /> |
928 |
- <policy domain="coder" rights="read | write" pattern="PS2" /> |
929 |
- <policy domain="coder" rights="read | write" pattern="PS3" /> |
930 |
- <policy domain="coder" rights="read | write" pattern="EPS" /> |
931 |
- <policy domain="coder" rights="read | write" pattern="PDF" /> |
932 |
- <policy domain="coder" rights="read | write" pattern="XPS" /> |
933 |
- </policymap> |
934 |
- EOF |
935 |
- fi |
936 |
-} |
937 |
- |
938 |
-src_configure() { |
939 |
- local mycmakeargs_pre=( ) extra fft_opts=( ) |
940 |
- |
941 |
- if use custom-cflags; then |
942 |
- #go from slowest to fastest acceleration |
943 |
- local acce="None" |
944 |
- if (use amd64 || use x86); then |
945 |
- use cpu_flags_x86_sse2 && acce="SSE2" |
946 |
- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
947 |
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
948 |
- use cpu_flags_x86_avx && acce="AVX_256" |
949 |
- use cpu_flags_x86_avx2 && acce="AVX2_256" |
950 |
- use cpu_flags_x86_avx512f && acce="AVX_512" |
951 |
- elif (use arm); then |
952 |
- use cpu_flags_arm_neon && acce="ARM_NEON" |
953 |
- elif (use arm64); then |
954 |
- use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD" |
955 |
- fi |
956 |
- else |
957 |
- strip-flags |
958 |
- fi |
959 |
- |
960 |
- #to create man pages, build tree binaries are executed (bug #398437) |
961 |
- [[ ${CHOST} = *-darwin* ]] && \ |
962 |
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
963 |
- |
964 |
- if use fftw; then |
965 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
966 |
- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
967 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
968 |
- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
969 |
- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
970 |
- ) |
971 |
- elif use mkl; then |
972 |
- local bits=$(get_libdir) |
973 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
974 |
- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
975 |
- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
976 |
- ) |
977 |
- else |
978 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
979 |
- fi |
980 |
- |
981 |
- if use lmfit; then |
982 |
- local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) |
983 |
- else |
984 |
- local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) |
985 |
- fi |
986 |
- |
987 |
- mycmakeargs_pre+=( |
988 |
- "${fft_opts[@]}" |
989 |
- "${lmfit_opts[@]}" |
990 |
- -DGMX_X11=$(usex X) |
991 |
- -DGMX_EXTERNAL_BLAS=$(usex blas) |
992 |
- -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
993 |
- -DGMX_OPENMP=$(usex openmp) |
994 |
- -DGMX_COOL_QUOTES=$(usex offensive) |
995 |
- -DGMX_USE_TNG=$(usex tng) |
996 |
- -DGMX_BUILD_MANUAL=$(usex build-manual) |
997 |
- -DGMX_HWLOC=$(usex hwloc) |
998 |
- -DGMX_DEFAULT_SUFFIX=off |
999 |
- -DGMX_SIMD="$acce" |
1000 |
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
1001 |
- -DBUILD_TESTING=$(usex test) |
1002 |
- -DGMX_BUILD_UNITTESTS=$(usex test) |
1003 |
- -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" |
1004 |
- ${extra} |
1005 |
- ) |
1006 |
- |
1007 |
- for x in ${GMX_DIRS}; do |
1008 |
- einfo "Configuring for ${x} precision" |
1009 |
- local suffix="" |
1010 |
- #if we build single and double - double is suffixed |
1011 |
- use double-precision && use single-precision && \ |
1012 |
- [[ ${x} = "double" ]] && suffix="_d" |
1013 |
- local p |
1014 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
1015 |
- local gpu=( "-DGMX_GPU=OFF" ) |
1016 |
- [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) |
1017 |
- use opencl && gpu=( "-DGMX_GPU=OPENCL" ) |
1018 |
- mycmakeargs=( |
1019 |
- ${mycmakeargs_pre[@]} ${p} |
1020 |
- -DGMX_MPI=OFF |
1021 |
- -DGMX_THREAD_MPI=$(usex threads) |
1022 |
- -DGMXAPI=$(usex gmxapi) |
1023 |
- -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) |
1024 |
- "${gpu[@]}" |
1025 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
1026 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
1027 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
1028 |
- -DGMX_PYTHON_PACKAGE=$(usex python) |
1029 |
- ) |
1030 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure |
1031 |
- [[ ${CHOST} != *-darwin* ]] || \ |
1032 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
1033 |
- use mpi || continue |
1034 |
- einfo "Configuring for ${x} precision with mpi" |
1035 |
- mycmakeargs=( |
1036 |
- ${mycmakeargs_pre[@]} ${p} |
1037 |
- -DGMX_THREAD_MPI=OFF |
1038 |
- -DGMX_MPI=ON |
1039 |
- -DGMX_OPENMM=OFF |
1040 |
- -DGMXAPI=OFF |
1041 |
- "${opencl[@]}" |
1042 |
- "${cuda[@]}" |
1043 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
1044 |
- -DBUILD_SHARED_LIBS=OFF |
1045 |
- -DGMX_BUILD_MANUAL=OFF |
1046 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
1047 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
1048 |
- ) |
1049 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure |
1050 |
- [[ ${CHOST} != *-darwin* ]] || \ |
1051 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
1052 |
- done |
1053 |
-} |
1054 |
- |
1055 |
-src_compile() { |
1056 |
- for x in ${GMX_DIRS}; do |
1057 |
- einfo "Compiling for ${x} precision" |
1058 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1059 |
- cmake_src_compile |
1060 |
- if use python; then |
1061 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1062 |
- cmake_src_compile python_packaging/all |
1063 |
- BUILD_DIR="${WORKDIR}/${P}" \ |
1064 |
- distutils-r1_src_compile |
1065 |
- fi |
1066 |
- # not 100% necessary for rel ebuilds as available from website |
1067 |
- if use build-manual; then |
1068 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1069 |
- cmake_src_compile manual |
1070 |
- fi |
1071 |
- use mpi || continue |
1072 |
- einfo "Compiling for ${x} precision with mpi" |
1073 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
1074 |
- cmake_src_compile |
1075 |
- done |
1076 |
-} |
1077 |
- |
1078 |
-src_test() { |
1079 |
- for x in ${GMX_DIRS}; do |
1080 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1081 |
- cmake_src_compile check |
1082 |
- done |
1083 |
-} |
1084 |
- |
1085 |
-src_install() { |
1086 |
- for x in ${GMX_DIRS}; do |
1087 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
1088 |
- cmake_src_install |
1089 |
- if use python; then |
1090 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
1091 |
- cmake_src_install python_packaging/install |
1092 |
- fi |
1093 |
- if use build-manual; then |
1094 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
1095 |
- fi |
1096 |
- |
1097 |
- if use doc; then |
1098 |
- newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" |
1099 |
- fi |
1100 |
- |
1101 |
- use mpi || continue |
1102 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
1103 |
- cmake_src_install |
1104 |
- done |
1105 |
- |
1106 |
- if use tng; then |
1107 |
- insinto /usr/include/tng |
1108 |
- doins src/external/tng_io/include/tng/*h |
1109 |
- fi |
1110 |
- # drop unneeded stuff |
1111 |
- rm "${ED}"/usr/bin/GMXRC* || die |
1112 |
- for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do |
1113 |
- local n=${x##*/gmx-completion-} |
1114 |
- n="${n%.bash}" |
1115 |
- cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
1116 |
- newbashcomp "${T}"/"${n}" "${n}" |
1117 |
- done |
1118 |
- rm "${ED}"/usr/bin/gmx-completion*.bash || die |
1119 |
- readme.gentoo_create_doc |
1120 |
-} |
1121 |
- |
1122 |
-pkg_postinst() { |
1123 |
- einfo |
1124 |
- einfo "Please read and cite:" |
1125 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
1126 |
- einfo "https://dx.doi.org/10.1021/ct700301q" |
1127 |
- einfo |
1128 |
- readme.gentoo_print_elog |
1129 |
-} |
1130 |
|
1131 |
diff --git a/sci-chemistry/gromacs/gromacs-2021.ebuild b/sci-chemistry/gromacs/gromacs-2021.ebuild |
1132 |
deleted file mode 100644 |
1133 |
index a4fdab0dfaf..00000000000 |
1134 |
--- a/sci-chemistry/gromacs/gromacs-2021.ebuild |
1135 |
+++ /dev/null |
1136 |
@@ -1,355 +0,0 @@ |
1137 |
-# Copyright 1999-2021 Gentoo Authors |
1138 |
-# Distributed under the terms of the GNU General Public License v2 |
1139 |
- |
1140 |
-EAPI=7 |
1141 |
- |
1142 |
-CMAKE_MAKEFILE_GENERATOR="ninja" |
1143 |
- |
1144 |
-PYTHON_COMPAT=( python3_{7,8,9} ) |
1145 |
- |
1146 |
-DISTUTILS_USE_SETUPTOOLS=no |
1147 |
-DISTUTILS_SINGLE_IMPL=1 |
1148 |
- |
1149 |
-inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils |
1150 |
- |
1151 |
-if [[ ${PV} = *9999* ]]; then |
1152 |
- EGIT_REPO_URI=" |
1153 |
- https://gitlab.com/gromacs/gromacs.git |
1154 |
- https://github.com/gromacs/gromacs.git |
1155 |
- git://git.gromacs.org/gromacs.git" |
1156 |
- [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" |
1157 |
- inherit git-r3 |
1158 |
-else |
1159 |
- SRC_URI=" |
1160 |
- http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz |
1161 |
- doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) |
1162 |
- test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" |
1163 |
- KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
1164 |
-fi |
1165 |
- |
1166 |
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" |
1167 |
- |
1168 |
-DESCRIPTION="The ultimate molecular dynamics simulation package" |
1169 |
-HOMEPAGE="http://www.gromacs.org/" |
1170 |
- |
1171 |
-# see COPYING for details |
1172 |
-# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
1173 |
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
1174 |
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
1175 |
-SLOT="0/${PV}" |
1176 |
-IUSE="X blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" |
1177 |
- |
1178 |
-CDEPEND=" |
1179 |
- X? ( |
1180 |
- x11-libs/libX11 |
1181 |
- x11-libs/libSM |
1182 |
- x11-libs/libICE |
1183 |
- ) |
1184 |
- blas? ( virtual/blas ) |
1185 |
- cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) |
1186 |
- opencl? ( virtual/opencl ) |
1187 |
- fftw? ( sci-libs/fftw:3.0 ) |
1188 |
- hwloc? ( sys-apps/hwloc ) |
1189 |
- lapack? ( virtual/lapack ) |
1190 |
- lmfit? ( sci-libs/lmfit ) |
1191 |
- mkl? ( sci-libs/mkl ) |
1192 |
- mpi? ( virtual/mpi ) |
1193 |
- ${PYTHON_DEPS} |
1194 |
- !sci-chemistry/gmxapi |
1195 |
- " |
1196 |
-BDEPEND="${CDEPEND} |
1197 |
- virtual/pkgconfig |
1198 |
- build-manual? ( |
1199 |
- app-doc/doxygen |
1200 |
- $(python_gen_cond_dep ' |
1201 |
- dev-python/sphinx[${PYTHON_MULTI_USEDEP}] |
1202 |
- ') |
1203 |
- media-gfx/mscgen |
1204 |
- media-gfx/graphviz |
1205 |
- dev-texlive/texlive-latex |
1206 |
- dev-texlive/texlive-latexextra |
1207 |
- media-gfx/imagemagick |
1208 |
- )" |
1209 |
-RDEPEND="${CDEPEND}" |
1210 |
- |
1211 |
-REQUIRED_USE=" |
1212 |
- || ( single-precision double-precision ) |
1213 |
- || ( doc build-manual ) |
1214 |
- cuda? ( single-precision ) |
1215 |
- cuda? ( !opencl ) |
1216 |
- mkl? ( !blas !fftw !lapack ) |
1217 |
- ${PYTHON_REQUIRED_USE}" |
1218 |
- |
1219 |
-DOCS=( AUTHORS README ) |
1220 |
- |
1221 |
-RESTRICT="!test? ( test )" |
1222 |
- |
1223 |
-if [[ ${PV} != *9999 ]]; then |
1224 |
- S="${WORKDIR}/${PN}-${PV/_/-}" |
1225 |
-fi |
1226 |
- |
1227 |
-PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" ) |
1228 |
- |
1229 |
-pkg_pretend() { |
1230 |
- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
1231 |
- use openmp && ! tc-has-openmp && \ |
1232 |
- die "Please switch to an openmp compatible compiler" |
1233 |
-} |
1234 |
- |
1235 |
-pkg_setup() { |
1236 |
- python-single-r1_pkg_setup |
1237 |
-} |
1238 |
- |
1239 |
-src_unpack() { |
1240 |
- if [[ ${PV} != *9999 ]]; then |
1241 |
- default |
1242 |
- else |
1243 |
- git-r3_src_unpack |
1244 |
- if use test; then |
1245 |
- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
1246 |
- EGIT_BRANCH="${EGIT_BRANCH}" \ |
1247 |
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
1248 |
- git-r3_src_unpack |
1249 |
- fi |
1250 |
- fi |
1251 |
-} |
1252 |
- |
1253 |
-src_prepare() { |
1254 |
- #notes/todos |
1255 |
- # -on apple: there is framework support |
1256 |
- |
1257 |
- xdg_environment_reset #591952 |
1258 |
- |
1259 |
- cmake_src_prepare |
1260 |
- |
1261 |
- use cuda && cuda_src_prepare |
1262 |
- |
1263 |
- GMX_DIRS="" |
1264 |
- use single-precision && GMX_DIRS+=" float" |
1265 |
- use double-precision && GMX_DIRS+=" double" |
1266 |
- |
1267 |
- if use test; then |
1268 |
- for x in ${GMX_DIRS}; do |
1269 |
- mkdir -p "${WORKDIR}/${P}_${x}" || die |
1270 |
- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
1271 |
- done |
1272 |
- fi |
1273 |
- |
1274 |
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
1275 |
- if use build-manual; then |
1276 |
- # try to create policy for imagemagik |
1277 |
- mkdir -p ${HOME}/.config/ImageMagick |
1278 |
- cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF |
1279 |
- <?xml version="1.0" encoding="UTF-8"?> |
1280 |
- <!DOCTYPE policymap [ |
1281 |
- <!ELEMENT policymap (policy)+> |
1282 |
- !ATTLIST policymap xmlns CDATA #FIXED ''> |
1283 |
- <!ELEMENT policy EMPTY> |
1284 |
- <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED |
1285 |
- name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED |
1286 |
- stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> |
1287 |
- ]> |
1288 |
- <policymap> |
1289 |
- <policy domain="coder" rights="read | write" pattern="PS" /> |
1290 |
- <policy domain="coder" rights="read | write" pattern="PS2" /> |
1291 |
- <policy domain="coder" rights="read | write" pattern="PS3" /> |
1292 |
- <policy domain="coder" rights="read | write" pattern="EPS" /> |
1293 |
- <policy domain="coder" rights="read | write" pattern="PDF" /> |
1294 |
- <policy domain="coder" rights="read | write" pattern="XPS" /> |
1295 |
- </policymap> |
1296 |
- EOF |
1297 |
- fi |
1298 |
-} |
1299 |
- |
1300 |
-src_configure() { |
1301 |
- local mycmakeargs_pre=( ) extra fft_opts=( ) |
1302 |
- |
1303 |
- if use custom-cflags; then |
1304 |
- #go from slowest to fastest acceleration |
1305 |
- local acce="None" |
1306 |
- if (use amd64 || use x86); then |
1307 |
- use cpu_flags_x86_sse2 && acce="SSE2" |
1308 |
- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
1309 |
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
1310 |
- use cpu_flags_x86_avx && acce="AVX_256" |
1311 |
- use cpu_flags_x86_avx2 && acce="AVX2_256" |
1312 |
- use cpu_flags_x86_avx512f && acce="AVX_512" |
1313 |
- elif (use arm); then |
1314 |
- use cpu_flags_arm_neon && acce="ARM_NEON" |
1315 |
- elif (use arm64); then |
1316 |
- use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD" |
1317 |
- fi |
1318 |
- else |
1319 |
- strip-flags |
1320 |
- fi |
1321 |
- |
1322 |
- #to create man pages, build tree binaries are executed (bug #398437) |
1323 |
- [[ ${CHOST} = *-darwin* ]] && \ |
1324 |
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
1325 |
- |
1326 |
- if use fftw; then |
1327 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
1328 |
- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
1329 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
1330 |
- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
1331 |
- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
1332 |
- ) |
1333 |
- elif use mkl; then |
1334 |
- local bits=$(get_libdir) |
1335 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
1336 |
- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
1337 |
- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
1338 |
- ) |
1339 |
- else |
1340 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
1341 |
- fi |
1342 |
- |
1343 |
- if use lmfit; then |
1344 |
- local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) |
1345 |
- else |
1346 |
- local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) |
1347 |
- fi |
1348 |
- |
1349 |
- mycmakeargs_pre+=( |
1350 |
- "${fft_opts[@]}" |
1351 |
- "${lmfit_opts[@]}" |
1352 |
- -DGMX_X11=$(usex X) |
1353 |
- -DGMX_EXTERNAL_BLAS=$(usex blas) |
1354 |
- -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
1355 |
- -DGMX_OPENMP=$(usex openmp) |
1356 |
- -DGMX_COOL_QUOTES=$(usex offensive) |
1357 |
- -DGMX_USE_TNG=$(usex tng) |
1358 |
- -DGMX_BUILD_MANUAL=$(usex build-manual) |
1359 |
- -DGMX_HWLOC=$(usex hwloc) |
1360 |
- -DGMX_DEFAULT_SUFFIX=off |
1361 |
- -DGMX_SIMD="$acce" |
1362 |
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
1363 |
- -DBUILD_TESTING=$(usex test) |
1364 |
- -DGMX_BUILD_UNITTESTS=$(usex test) |
1365 |
- -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" |
1366 |
- ${extra} |
1367 |
- ) |
1368 |
- |
1369 |
- for x in ${GMX_DIRS}; do |
1370 |
- einfo "Configuring for ${x} precision" |
1371 |
- local suffix="" |
1372 |
- #if we build single and double - double is suffixed |
1373 |
- use double-precision && use single-precision && \ |
1374 |
- [[ ${x} = "double" ]] && suffix="_d" |
1375 |
- local p |
1376 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
1377 |
- local gpu=( "-DGMX_GPU=OFF" ) |
1378 |
- [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) |
1379 |
- use opencl && gpu=( "-DGMX_GPU=OPENCL" ) |
1380 |
- mycmakeargs=( |
1381 |
- ${mycmakeargs_pre[@]} ${p} |
1382 |
- -DGMX_MPI=OFF |
1383 |
- -DGMX_THREAD_MPI=$(usex threads) |
1384 |
- -DGMXAPI=$(usex gmxapi) |
1385 |
- -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) |
1386 |
- "${gpu[@]}" |
1387 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
1388 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
1389 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
1390 |
- -DGMX_PYTHON_PACKAGE=$(usex python) |
1391 |
- ) |
1392 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure |
1393 |
- [[ ${CHOST} != *-darwin* ]] || \ |
1394 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
1395 |
- use mpi || continue |
1396 |
- einfo "Configuring for ${x} precision with mpi" |
1397 |
- mycmakeargs=( |
1398 |
- ${mycmakeargs_pre[@]} ${p} |
1399 |
- -DGMX_THREAD_MPI=OFF |
1400 |
- -DGMX_MPI=ON |
1401 |
- -DGMX_OPENMM=OFF |
1402 |
- -DGMXAPI=OFF |
1403 |
- "${opencl[@]}" |
1404 |
- "${cuda[@]}" |
1405 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
1406 |
- -DBUILD_SHARED_LIBS=OFF |
1407 |
- -DGMX_BUILD_MANUAL=OFF |
1408 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
1409 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
1410 |
- ) |
1411 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure |
1412 |
- [[ ${CHOST} != *-darwin* ]] || \ |
1413 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
1414 |
- done |
1415 |
-} |
1416 |
- |
1417 |
-src_compile() { |
1418 |
- for x in ${GMX_DIRS}; do |
1419 |
- einfo "Compiling for ${x} precision" |
1420 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1421 |
- cmake_src_compile |
1422 |
- if use python; then |
1423 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1424 |
- cmake_src_compile python_packaging/all |
1425 |
- BUILD_DIR="${WORKDIR}/${P}" \ |
1426 |
- distutils-r1_src_compile |
1427 |
- fi |
1428 |
- # not 100% necessary for rel ebuilds as available from website |
1429 |
- if use build-manual; then |
1430 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1431 |
- cmake_src_compile manual |
1432 |
- fi |
1433 |
- use mpi || continue |
1434 |
- einfo "Compiling for ${x} precision with mpi" |
1435 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
1436 |
- cmake_src_compile |
1437 |
- done |
1438 |
-} |
1439 |
- |
1440 |
-src_test() { |
1441 |
- for x in ${GMX_DIRS}; do |
1442 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1443 |
- cmake_src_compile check |
1444 |
- done |
1445 |
-} |
1446 |
- |
1447 |
-src_install() { |
1448 |
- for x in ${GMX_DIRS}; do |
1449 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
1450 |
- cmake_src_install |
1451 |
- if use python; then |
1452 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
1453 |
- cmake_src_install python_packaging/install |
1454 |
- fi |
1455 |
- if use build-manual; then |
1456 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
1457 |
- fi |
1458 |
- |
1459 |
- if use doc; then |
1460 |
- newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" |
1461 |
- fi |
1462 |
- |
1463 |
- use mpi || continue |
1464 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
1465 |
- cmake_src_install |
1466 |
- done |
1467 |
- |
1468 |
- if use tng; then |
1469 |
- insinto /usr/include/tng |
1470 |
- doins src/external/tng_io/include/tng/*h |
1471 |
- fi |
1472 |
- # drop unneeded stuff |
1473 |
- rm "${ED}"/usr/bin/GMXRC* || die |
1474 |
- for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do |
1475 |
- local n=${x##*/gmx-completion-} |
1476 |
- n="${n%.bash}" |
1477 |
- cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
1478 |
- newbashcomp "${T}"/"${n}" "${n}" |
1479 |
- done |
1480 |
- rm "${ED}"/usr/bin/gmx-completion*.bash || die |
1481 |
- readme.gentoo_create_doc |
1482 |
-} |
1483 |
- |
1484 |
-pkg_postinst() { |
1485 |
- einfo |
1486 |
- einfo "Please read and cite:" |
1487 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
1488 |
- einfo "https://dx.doi.org/10.1021/ct700301q" |
1489 |
- einfo |
1490 |
- readme.gentoo_print_elog |
1491 |
-} |