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commit: 9f10eb89d0480d7f657a27a24d69337c95e7a2ae |
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Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
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AuthorDate: Tue Feb 8 12:31:53 2022 +0000 |
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Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
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CommitDate: Tue Feb 8 12:32:16 2022 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9f10eb89 |
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|
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sci-chemistry/gromacs: Cleanup 2021 versions |
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|
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Package-Manager: Portage-3.0.30, 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 | 6 - |
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sci-chemistry/gromacs/gromacs-2021.2-r1.ebuild | 360 ------------------------- |
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sci-chemistry/gromacs/gromacs-2021.4.ebuild | 356 ------------------------ |
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sci-chemistry/gromacs/gromacs-2021.5.ebuild | 1 - |
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sci-chemistry/gromacs/gromacs-2021.9999.ebuild | 7 +- |
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5 files changed, 3 insertions(+), 727 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 b04f9954a649..d67ae5817a47 100644 |
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--- a/sci-chemistry/gromacs/Manifest |
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+++ b/sci-chemistry/gromacs/Manifest |
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@@ -2,26 +2,20 @@ DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B 8780032305928067fbfe1559efe9eedc4d47 |
25 |
DIST gromacs-2019.6.tar.gz 33446147 BLAKE2B adc21fb6b841b06d499607f8c0166a673645ef5af0b40bd823d0fff5ea24397e6301c5e1e0070986ae1ce1deba8a42052b66da148b071c1e21f2fe3908fee275 SHA512 7c227a9539e5775d5d128ae9e872a24181d79cdcd2852b86453597987e8d7332ecec371da65d089f6e610c54aafbccc8824ce298743383dd6240719ebee692a8 |
26 |
DIST gromacs-2020.4.tar.gz 29149899 BLAKE2B a07c8efd96137d58c1edf4ac9b5aafeb16d9e65234b9459b71471827032654acacb58ed6ae87ec6e0e593a0acd799683cc4461b06cc883b089d740708619345e SHA512 0c56f058741af70660baf0177724ec940dd984c05ea141ede91ee51ce3744f76d00e31bdb5db907e46fa1639de5dca637b3ace26e89f908c2e74c69f0c21ed3a |
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DIST gromacs-2020.6.tar.gz 29196621 BLAKE2B b350fc62fd8eeb3f2b042fa74a4ed42e43a7b74efd8fddb60ec086a814048a52b8625da65fa5c4cf2cb1e22f8347562bc84d38bf34441fc5ebc6abaa38b0eea0 SHA512 4ce4d6b9ae33e9cd2a1ad3313e80acf63ded21dac897b01dbf87df2e318181796ef64c8a1d3e0a6058b972d8d88d00f710cd0277db12f38fc2c9b29772c98bea |
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-DIST gromacs-2021.2.tar.gz 37976386 BLAKE2B 8818321bbcbdee25356bbf909d9c667f9d7cf180e696a323a61017683234d1269decc8f8d72b8012a8cc207f69e5cd97e2ab48dbbff06d82bbb407bc0578854b SHA512 51b1728f41932274436ab807d569109e2b0e145abcb5cf9c9b7daf6a7396f2f8716dc28fb93cf178c97a7eaeab2a88878d0bc71dd6c6abe7e829d579e7968615 |
29 |
DIST gromacs-2021.3.tar.gz 37987972 BLAKE2B d71995c7d5a34978246e33dc637ac3d273e547afcf72d1a107026650f03286ecdf27e4b9a70113b3c3a01af59ad49ac5c813aa6e5d2e8eb29fd05582a7a28d34 SHA512 da420917d06de2e192dfbb4e1b9f46989ed05b5c7e641c657104ed8f2bd8b22509bffd1ecfd7c965c80544eafa6af12d6d0aba7e1e7d9d14a4a88fb3fbf394a5 |
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-DIST gromacs-2021.4.tar.gz 38023262 BLAKE2B 4e1c9ca23f8bd89a990bac2730f846ce9fd6423aa6934866734272ac8f5ca29cdb51daec440b7ef2af56c68bdbab504c0c1b1a4d5f4af0b16666850bf286c5b2 SHA512 35b26b3df02d151373fab49022281b89e987c867257a998acc926b2b7151f5d4e46f11c398a24f4a174f668dd24a828b07d36594ac5d5506e10e40d4578427a2 |
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DIST gromacs-2021.5.tar.gz 38023772 BLAKE2B 45e1f080b86626423e471f06b48b615db1913048f9f6998da8ce45408339b32f829d33dd2af57297a7d307fcffd556c333a58c309ee0f2adb021ca3755619b05 SHA512 56c1b312fc8e52ec6f86e445d2fa2d07107c461b35d4dc8cdf95580f05fd8e6c5fd671d0e72b2b9e74e3232bc8c41db496fe4bcaf2b9a3ae3c2cfa93489a31c5 |
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DIST gromacs-2022-rc1.tar.gz 39674628 BLAKE2B 8943a1e8445aa286305bb786e1303973e58325c01ce86883e5a72075b8ddd57453c61c8a0087a9ec73ea2903b04596109322151d8fadda350a4eace713cd962f SHA512 d6f45e46b653237154fefce95e3799ed2fc96d6a0365d027ef0aabd03cd3c3507108985caca8907c02479f05a10ab833efd3217e7def100897fa845e0ebf029f |
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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 |
35 |
DIST manual-2020.4.pdf 11851608 BLAKE2B 7b7bdf08e8946fcc448543b08391b94a67fee60a8c810597c1f09f70443f9d7db817c99622dd0c21c6317f5fdcd6c4a88589ecac57055cb0cd8597d6021026e7 SHA512 928555663c77de36393e625c29d388d4e1c8c1298e7a993d871839e0d4d8d18d190221ad8f1d975bd072bdd6a061e9ea5b9295f2ecf45f24b6523ea5ea290fed |
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DIST manual-2020.6.pdf 11850850 BLAKE2B 155e4eb9c200dcd0a38e3669b26077fcf310d437b82d9a593d333dada3989c2c8a936d62c642e195f98bb474b1673b8142405c467348fc96a74d57fb12106d76 SHA512 be508ebec597b82a2c4056029f8bb731b22cb8902628a45462ed21af54c554d28e07d5381efaaa96565202b7b47d33aea67950206cd9e8936211ae721b21b3e1 |
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-DIST manual-2021.2.pdf 12252501 BLAKE2B 0dbf9024e1516076b0eeb46e41523b966d1d81f57504fe0501c7bc8575e74fb19e3452ac584757e425bcccbc737367fe83be87fd21a4287f4675cf87184b960b SHA512 14156d3b1017990e0be3ceb7ec055777a1aec4c347ac2e821a042d51c931f84ebca862f60644a90ed7ba4070cb14ff8babcde3e4351e4dbec84df8563e350984 |
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DIST manual-2021.3.pdf 12255076 BLAKE2B 6ca516b6832507c9d4100679d1f9bc9e3ab17d226849b050764b0d0626247dc57ce49985f9a7fc0061f3df278923a83faa367ca8ab91c37e5624dc584a51a822 SHA512 5d53798f30ea00fcb4e1b35f7eaa4bebfc05dafa4f2d0c197dcf2b57a624ad3a98b74fd90722e40d0ac13a6fff4ca231f9d6340f52ba94659c827c53c2f1cb16 |
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-DIST manual-2021.4.pdf 12253232 BLAKE2B 0b859c08a07d5a615ac7a822b61d5a4f4296ca9773d383a07960dc629d6b1df23e1dec51561a4ac26789b84e49cc98b6d7cc10d943c61d7784052664ac1bacf9 SHA512 024f17a670518fc19a2a462186ed2a74f331c5c83b8ba4bbe148a53767515ba19e6af887a1baae3a7770af2095fad5c513784cc54f9d0f881395ad8a89760cba |
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DIST manual-2021.5.pdf 12253641 BLAKE2B 8850715a2bb21345e1c9735aca1a5dd2ad916e5a18881e7c9f3dda6f055ca12d9d379b74218138999ce50769efd8b9dd6447afbf70bbbefa2564dfb9fb276b91 SHA512 7635108c935e4953d722df6a16ee43edf97eef7e49f047218728f68f61f8f185192ff1d8b13a573b643b040955af211355a7b560c8a894c858d7f71249d41296 |
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DIST manual-2022_rc1.pdf 13051892 BLAKE2B 99b0a2110a0a7601d4e2d00f4bb3210fed8e0e4dcc2c3a17fa8e902cc713c8aee90eebbcd9b0cb3fd20fb539be6bcf32414fcd3c35a3f9b4677240877623ca93 SHA512 5ff91b2486792a525fc5fc08bfd31225e3c64018b519592ce899ce0a6f92fb366ea4d1b5df3473d264bc93a651c11583757b6603a855cdcd9ad18ec86e160fdc |
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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-2020.6.tar.gz 48541232 BLAKE2B dbb405bd9168775984de8c9fb9e3fa2398d2790e2e4de23711c51a01dc3ea570d172a35d4924742ad5eda463eb0a885e6924512801e82b241600ceaefd5db70d SHA512 497a9e7d438b0b7b0734a97cf3683baf480ecc056e96b09f1e143c362ff047a4e51e323216750501c954559579716dc024d3c51319bd2c85fa719466ce4330b2 |
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-DIST regressiontests-2021.2.tar.gz 48514312 BLAKE2B 81b007d5e5e1d054349c73dc8bc3589db328752e48a66687c0ad36be87ebe580df9cbd93b193a724669bd5765af06ec306f2e12af00a228af616de03943d6f05 SHA512 b687ddfd3dc6ec1051af2a3253633703ef1c82335d1df23379819ea47e44dfcd417e81e29610cc584d4c5fb1ee1cbc76731a3fd31b529d8cdd0b9c22f432c7ec |
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DIST regressiontests-2021.3.tar.gz 48515038 BLAKE2B ee79d8adddc9c68f7d59d9e568b12bf4d1fe0e44c2810fee846ad6f689bbcacf60f5c266433946329e64e3127bc2d37a3f81f69c070c636b411b38067650c2cf SHA512 e14baa22ef2902a23125bbd9143ae7a9a4810498b321794ff1989f8d044d47db5db41d5225798fda08016c05e5f7f315178b5a6e35cdf01e3b6604670a8ce7a2 |
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-DIST regressiontests-2021.4.tar.gz 48541736 BLAKE2B 37b8e65e333dcfcfc795da631475807ffa4ecc3a85426b4de6dd2ccb50f40a78159149789da13f988340a62d21e7d6b1d4f0c6e7fe69120d4c94ab2252b4c440 SHA512 18663693cf9ce2ca3bd8df0f668e7a0c8236a7f5ae4ee02f621cbe52c139c506b61ac4cab200cc59caab41e9983ea93dfa062d7b52f6558a619096a8d439fb56 |
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DIST regressiontests-2021.5.tar.gz 48537298 BLAKE2B 860ac34aa8706ecdafab4472162775ce12726d93839079ebf9b7df8c2c6a1b47baa8a635c24cf4cb4551a32237c3de7da3197ec136b5bbf48663edc3943720ad SHA512 3605d04b2602339fb7d33e2776da2ada337ca58a3802472d47f490d4e8dd04249a950bf34608a498eedebf69f344c0311bac8f7fcb58ce0ebbb6d608ee39aa2e |
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DIST regressiontests-2022-rc1.tar.gz 48609151 BLAKE2B b5ec84b9f3f506636136bf9112ea71f7ce5bad8b3dbec6d8c6b21ab13ddab8252a3038f1dd06e1f97cde47f918aff2c62325d09d51bc5632e1db7b84311dbd91 SHA512 a378f724a728fbadbad3b9013f85bf6fb1945e500151d9dacdaea9371f432ce3449dc812f672b77896800c3c46a3893b239101404a1fab63364e62afd7f18097 |
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|
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diff --git a/sci-chemistry/gromacs/gromacs-2021.2-r1.ebuild b/sci-chemistry/gromacs/gromacs-2021.2-r1.ebuild |
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deleted file mode 100644 |
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index 5067010bc65f..000000000000 |
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--- a/sci-chemistry/gromacs/gromacs-2021.2-r1.ebuild |
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+++ /dev/null |
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@@ -1,360 +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_{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 cpu_flags_x86_avx512f cpu_flags_arm_neon" |
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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[profiler] ) |
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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_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/_/-}" |
146 |
-fi |
147 |
- |
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-PATCHES=( |
149 |
- "${FILESDIR}/${PN}-2020-pytest.patch" |
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- "${FILESDIR}/${PN}-2021-nblib.patch" |
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-) |
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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 |
161 |
-} |
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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 |
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- |
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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" |
190 |
- |
191 |
- if use test; then |
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- for x in ${GMX_DIRS}; do |
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- mkdir -p "${WORKDIR}/${P}_${x}" || die |
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- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
195 |
- done |
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- fi |
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- |
198 |
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
199 |
- if use build-manual; then |
200 |
- # try to create policy for imagemagik |
201 |
- mkdir -p ${HOME}/.config/ImageMagick |
202 |
- cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF |
203 |
- <?xml version="1.0" encoding="UTF-8"?> |
204 |
- <!DOCTYPE policymap [ |
205 |
- <!ELEMENT policymap (policy)+> |
206 |
- !ATTLIST policymap xmlns CDATA #FIXED ''> |
207 |
- <!ELEMENT policy EMPTY> |
208 |
- <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED |
209 |
- name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED |
210 |
- stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> |
211 |
- ]> |
212 |
- <policymap> |
213 |
- <policy domain="coder" rights="read | write" pattern="PS" /> |
214 |
- <policy domain="coder" rights="read | write" pattern="PS2" /> |
215 |
- <policy domain="coder" rights="read | write" pattern="PS3" /> |
216 |
- <policy domain="coder" rights="read | write" pattern="EPS" /> |
217 |
- <policy domain="coder" rights="read | write" pattern="PDF" /> |
218 |
- <policy domain="coder" rights="read | write" pattern="XPS" /> |
219 |
- </policymap> |
220 |
- EOF |
221 |
- fi |
222 |
-} |
223 |
- |
224 |
-src_configure() { |
225 |
- local mycmakeargs_pre=( ) extra fft_opts=( ) |
226 |
- |
227 |
- if use custom-cflags; then |
228 |
- #go from slowest to fastest acceleration |
229 |
- local acce="None" |
230 |
- if (use amd64 || use x86); then |
231 |
- use cpu_flags_x86_sse2 && acce="SSE2" |
232 |
- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
233 |
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
234 |
- use cpu_flags_x86_avx && acce="AVX_256" |
235 |
- use cpu_flags_x86_avx2 && acce="AVX2_256" |
236 |
- use cpu_flags_x86_avx512f && acce="AVX_512" |
237 |
- elif (use arm); then |
238 |
- use cpu_flags_arm_neon && acce="ARM_NEON" |
239 |
- elif (use arm64); then |
240 |
- use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD" |
241 |
- fi |
242 |
- else |
243 |
- strip-flags |
244 |
- fi |
245 |
- |
246 |
- #to create man pages, build tree binaries are executed (bug #398437) |
247 |
- [[ ${CHOST} = *-darwin* ]] && \ |
248 |
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
249 |
- |
250 |
- if use fftw; then |
251 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
252 |
- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
253 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
254 |
- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
255 |
- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
256 |
- ) |
257 |
- elif use mkl; then |
258 |
- local bits=$(get_libdir) |
259 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
260 |
- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
261 |
- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
262 |
- ) |
263 |
- else |
264 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
265 |
- fi |
266 |
- |
267 |
- if use lmfit; then |
268 |
- local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) |
269 |
- else |
270 |
- local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) |
271 |
- fi |
272 |
- |
273 |
- mycmakeargs_pre+=( |
274 |
- "${fft_opts[@]}" |
275 |
- "${lmfit_opts[@]}" |
276 |
- -DGMX_X11=$(usex X) |
277 |
- -DGMX_EXTERNAL_BLAS=$(usex blas) |
278 |
- -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
279 |
- -DGMX_OPENMP=$(usex openmp) |
280 |
- -DGMX_COOL_QUOTES=$(usex offensive) |
281 |
- -DGMX_USE_TNG=$(usex tng) |
282 |
- -DGMX_BUILD_MANUAL=$(usex build-manual) |
283 |
- -DGMX_HWLOC=$(usex hwloc) |
284 |
- -DGMX_DEFAULT_SUFFIX=off |
285 |
- -DGMX_SIMD="$acce" |
286 |
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
287 |
- -DBUILD_TESTING=$(usex test) |
288 |
- -DGMX_BUILD_UNITTESTS=$(usex test) |
289 |
- -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" |
290 |
- ${extra} |
291 |
- ) |
292 |
- |
293 |
- for x in ${GMX_DIRS}; do |
294 |
- einfo "Configuring for ${x} precision" |
295 |
- local suffix="" |
296 |
- #if we build single and double - double is suffixed |
297 |
- use double-precision && use single-precision && \ |
298 |
- [[ ${x} = "double" ]] && suffix="_d" |
299 |
- local p |
300 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
301 |
- local gpu=( "-DGMX_GPU=OFF" ) |
302 |
- [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) |
303 |
- use opencl && gpu=( "-DGMX_GPU=OPENCL" ) |
304 |
- mycmakeargs=( |
305 |
- ${mycmakeargs_pre[@]} ${p} |
306 |
- -DGMX_MPI=OFF |
307 |
- -DGMX_THREAD_MPI=$(usex threads) |
308 |
- -DGMXAPI=$(usex gmxapi) |
309 |
- -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) |
310 |
- "${gpu[@]}" |
311 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
312 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
313 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
314 |
- -DGMX_PYTHON_PACKAGE=$(usex python) |
315 |
- ) |
316 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure |
317 |
- [[ ${CHOST} != *-darwin* ]] || \ |
318 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
319 |
- use mpi || continue |
320 |
- einfo "Configuring for ${x} precision with mpi" |
321 |
- mycmakeargs=( |
322 |
- ${mycmakeargs_pre[@]} ${p} |
323 |
- -DGMX_THREAD_MPI=OFF |
324 |
- -DGMX_MPI=ON |
325 |
- -DGMX_OPENMM=OFF |
326 |
- -DGMXAPI=OFF |
327 |
- "${opencl[@]}" |
328 |
- "${cuda[@]}" |
329 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
330 |
- -DBUILD_SHARED_LIBS=OFF |
331 |
- -DGMX_BUILD_MANUAL=OFF |
332 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
333 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
334 |
- ) |
335 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure |
336 |
- [[ ${CHOST} != *-darwin* ]] || \ |
337 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
338 |
- done |
339 |
-} |
340 |
- |
341 |
-src_compile() { |
342 |
- for x in ${GMX_DIRS}; do |
343 |
- einfo "Compiling for ${x} precision" |
344 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
345 |
- cmake_src_compile |
346 |
- if use python; then |
347 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
348 |
- cmake_src_compile python_packaging/all |
349 |
- BUILD_DIR="${WORKDIR}/${P}" \ |
350 |
- distutils-r1_src_compile |
351 |
- fi |
352 |
- # not 100% necessary for rel ebuilds as available from website |
353 |
- if use build-manual; then |
354 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
355 |
- cmake_src_compile manual |
356 |
- fi |
357 |
- use mpi || continue |
358 |
- einfo "Compiling for ${x} precision with mpi" |
359 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
360 |
- cmake_src_compile |
361 |
- done |
362 |
-} |
363 |
- |
364 |
-src_test() { |
365 |
- for x in ${GMX_DIRS}; do |
366 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
367 |
- cmake_src_compile check |
368 |
- done |
369 |
-} |
370 |
- |
371 |
-src_install() { |
372 |
- for x in ${GMX_DIRS}; do |
373 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
374 |
- cmake_src_install |
375 |
- if use python; then |
376 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
377 |
- cmake_src_install python_packaging/install |
378 |
- fi |
379 |
- if use build-manual; then |
380 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
381 |
- fi |
382 |
- |
383 |
- if use doc; then |
384 |
- if [[ ${PV} != *9999* ]]; then |
385 |
- newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" |
386 |
- fi |
387 |
- fi |
388 |
- |
389 |
- use mpi || continue |
390 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
391 |
- cmake_src_install |
392 |
- done |
393 |
- |
394 |
- if use tng; then |
395 |
- insinto /usr/include/tng |
396 |
- doins src/external/tng_io/include/tng/*h |
397 |
- fi |
398 |
- # drop unneeded stuff |
399 |
- rm "${ED}"/usr/bin/GMXRC* || die |
400 |
- for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do |
401 |
- local n=${x##*/gmx-completion-} |
402 |
- n="${n%.bash}" |
403 |
- cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
404 |
- newbashcomp "${T}"/"${n}" "${n}" |
405 |
- done |
406 |
- rm "${ED}"/usr/bin/gmx-completion*.bash || die |
407 |
- readme.gentoo_create_doc |
408 |
-} |
409 |
- |
410 |
-pkg_postinst() { |
411 |
- einfo |
412 |
- einfo "Please read and cite:" |
413 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
414 |
- einfo "https://dx.doi.org/10.1021/ct700301q" |
415 |
- einfo |
416 |
- readme.gentoo_print_elog |
417 |
-} |
418 |
|
419 |
diff --git a/sci-chemistry/gromacs/gromacs-2021.4.ebuild b/sci-chemistry/gromacs/gromacs-2021.4.ebuild |
420 |
deleted file mode 100644 |
421 |
index ab6c1d40dd0b..000000000000 |
422 |
--- a/sci-chemistry/gromacs/gromacs-2021.4.ebuild |
423 |
+++ /dev/null |
424 |
@@ -1,356 +0,0 @@ |
425 |
-# Copyright 1999-2021 Gentoo Authors |
426 |
-# Distributed under the terms of the GNU General Public License v2 |
427 |
- |
428 |
-EAPI=8 |
429 |
- |
430 |
-CMAKE_MAKEFILE_GENERATOR="ninja" |
431 |
- |
432 |
-PYTHON_COMPAT=( python3_{8,9} ) |
433 |
- |
434 |
-DISTUTILS_USE_SETUPTOOLS=no |
435 |
-DISTUTILS_SINGLE_IMPL=1 |
436 |
- |
437 |
-inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils |
438 |
- |
439 |
-if [[ ${PV} = *9999* ]]; then |
440 |
- EGIT_REPO_URI=" |
441 |
- https://gitlab.com/gromacs/gromacs.git |
442 |
- https://github.com/gromacs/gromacs.git |
443 |
- git://git.gromacs.org/gromacs.git" |
444 |
- [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" |
445 |
- inherit git-r3 |
446 |
-else |
447 |
- SRC_URI=" |
448 |
- http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz |
449 |
- doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) |
450 |
- test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" |
451 |
- KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
452 |
-fi |
453 |
- |
454 |
-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" |
455 |
- |
456 |
-DESCRIPTION="The ultimate molecular dynamics simulation package" |
457 |
-HOMEPAGE="http://www.gromacs.org/" |
458 |
- |
459 |
-# see COPYING for details |
460 |
-# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
461 |
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
462 |
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
463 |
-SLOT="0/${PV}" |
464 |
-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}" |
465 |
- |
466 |
-CDEPEND=" |
467 |
- X? ( |
468 |
- x11-libs/libX11 |
469 |
- x11-libs/libSM |
470 |
- x11-libs/libICE |
471 |
- ) |
472 |
- blas? ( virtual/blas ) |
473 |
- cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14[profiler] ) |
474 |
- opencl? ( virtual/opencl ) |
475 |
- fftw? ( sci-libs/fftw:3.0= ) |
476 |
- hwloc? ( sys-apps/hwloc:= ) |
477 |
- lapack? ( virtual/lapack ) |
478 |
- lmfit? ( sci-libs/lmfit:= ) |
479 |
- mkl? ( sci-libs/mkl ) |
480 |
- mpi? ( virtual/mpi ) |
481 |
- ${PYTHON_DEPS} |
482 |
- !sci-chemistry/gmxapi |
483 |
- " |
484 |
-BDEPEND="${CDEPEND} |
485 |
- virtual/pkgconfig |
486 |
- build-manual? ( |
487 |
- app-doc/doxygen |
488 |
- $(python_gen_cond_dep ' |
489 |
- dev-python/sphinx[${PYTHON_USEDEP}] |
490 |
- ') |
491 |
- media-gfx/mscgen |
492 |
- media-gfx/graphviz |
493 |
- dev-texlive/texlive-latex |
494 |
- dev-texlive/texlive-latexextra |
495 |
- media-gfx/imagemagick |
496 |
- )" |
497 |
-RDEPEND="${CDEPEND}" |
498 |
- |
499 |
-REQUIRED_USE=" |
500 |
- || ( single-precision double-precision ) |
501 |
- doc? ( !build-manual ) |
502 |
- cuda? ( single-precision ) |
503 |
- cuda? ( !opencl ) |
504 |
- mkl? ( !blas !fftw !lapack ) |
505 |
- ${PYTHON_REQUIRED_USE}" |
506 |
- |
507 |
-DOCS=( AUTHORS README ) |
508 |
- |
509 |
-RESTRICT="!test? ( test )" |
510 |
- |
511 |
-if [[ ${PV} != *9999 ]]; then |
512 |
- S="${WORKDIR}/${PN}-${PV/_/-}" |
513 |
-fi |
514 |
- |
515 |
-pkg_pretend() { |
516 |
- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
517 |
- use openmp && ! tc-has-openmp && \ |
518 |
- die "Please switch to an openmp compatible compiler" |
519 |
-} |
520 |
- |
521 |
-pkg_setup() { |
522 |
- python-single-r1_pkg_setup |
523 |
-} |
524 |
- |
525 |
-src_unpack() { |
526 |
- if [[ ${PV} != *9999 ]]; then |
527 |
- default |
528 |
- else |
529 |
- git-r3_src_unpack |
530 |
- if use test; then |
531 |
- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
532 |
- EGIT_BRANCH="${EGIT_BRANCH}" \ |
533 |
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
534 |
- git-r3_src_unpack |
535 |
- fi |
536 |
- fi |
537 |
-} |
538 |
- |
539 |
-src_prepare() { |
540 |
- #notes/todos |
541 |
- # -on apple: there is framework support |
542 |
- |
543 |
- xdg_environment_reset #591952 |
544 |
- |
545 |
- cmake_src_prepare |
546 |
- |
547 |
- use cuda && cuda_src_prepare |
548 |
- |
549 |
- GMX_DIRS="" |
550 |
- use single-precision && GMX_DIRS+=" float" |
551 |
- use double-precision && GMX_DIRS+=" double" |
552 |
- |
553 |
- if use test; then |
554 |
- for x in ${GMX_DIRS}; do |
555 |
- mkdir -p "${WORKDIR}/${P}_${x}" || die |
556 |
- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
557 |
- done |
558 |
- fi |
559 |
- |
560 |
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
561 |
- if use build-manual; then |
562 |
- # try to create policy for imagemagik |
563 |
- mkdir -p ${HOME}/.config/ImageMagick |
564 |
- cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF |
565 |
- <?xml version="1.0" encoding="UTF-8"?> |
566 |
- <!DOCTYPE policymap [ |
567 |
- <!ELEMENT policymap (policy)+> |
568 |
- !ATTLIST policymap xmlns CDATA #FIXED ''> |
569 |
- <!ELEMENT policy EMPTY> |
570 |
- <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED |
571 |
- name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED |
572 |
- stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> |
573 |
- ]> |
574 |
- <policymap> |
575 |
- <policy domain="coder" rights="read | write" pattern="PS" /> |
576 |
- <policy domain="coder" rights="read | write" pattern="PS2" /> |
577 |
- <policy domain="coder" rights="read | write" pattern="PS3" /> |
578 |
- <policy domain="coder" rights="read | write" pattern="EPS" /> |
579 |
- <policy domain="coder" rights="read | write" pattern="PDF" /> |
580 |
- <policy domain="coder" rights="read | write" pattern="XPS" /> |
581 |
- </policymap> |
582 |
- EOF |
583 |
- fi |
584 |
-} |
585 |
- |
586 |
-src_configure() { |
587 |
- local mycmakeargs_pre=( ) extra fft_opts=( ) |
588 |
- local acce="AUTO" |
589 |
- |
590 |
- if use custom-cflags; then |
591 |
- #go from slowest to fastest acceleration |
592 |
- acce="None" |
593 |
- if (use amd64 || use x86); then |
594 |
- use cpu_flags_x86_sse2 && acce="SSE2" |
595 |
- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
596 |
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
597 |
- use cpu_flags_x86_avx && acce="AVX_256" |
598 |
- use cpu_flags_x86_avx2 && acce="AVX2_256" |
599 |
- use cpu_flags_x86_avx512f && acce="AVX_512" |
600 |
- elif (use arm); then |
601 |
- use cpu_flags_arm_neon && acce="ARM_NEON" |
602 |
- elif (use arm64); then |
603 |
- use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD" |
604 |
- fi |
605 |
- else |
606 |
- strip-flags |
607 |
- fi |
608 |
- |
609 |
- #to create man pages, build tree binaries are executed (bug #398437) |
610 |
- [[ ${CHOST} = *-darwin* ]] && \ |
611 |
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
612 |
- |
613 |
- if use fftw; then |
614 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
615 |
- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
616 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
617 |
- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
618 |
- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
619 |
- ) |
620 |
- elif use mkl; then |
621 |
- local bits=$(get_libdir) |
622 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
623 |
- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
624 |
- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
625 |
- ) |
626 |
- else |
627 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
628 |
- fi |
629 |
- |
630 |
- if use lmfit; then |
631 |
- local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) |
632 |
- else |
633 |
- local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) |
634 |
- fi |
635 |
- |
636 |
- mycmakeargs_pre+=( |
637 |
- "${fft_opts[@]}" |
638 |
- "${lmfit_opts[@]}" |
639 |
- -DGMX_X11=$(usex X) |
640 |
- -DGMX_EXTERNAL_BLAS=$(usex blas) |
641 |
- -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
642 |
- -DGMX_OPENMP=$(usex openmp) |
643 |
- -DGMX_COOL_QUOTES=$(usex offensive) |
644 |
- -DGMX_USE_TNG=$(usex tng) |
645 |
- -DGMX_BUILD_MANUAL=$(usex build-manual) |
646 |
- -DGMX_HWLOC=$(usex hwloc) |
647 |
- -DGMX_DEFAULT_SUFFIX=off |
648 |
- -DGMX_SIMD="$acce" |
649 |
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
650 |
- -DBUILD_TESTING=$(usex test) |
651 |
- -DGMX_BUILD_UNITTESTS=$(usex test) |
652 |
- -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" |
653 |
- ${extra} |
654 |
- ) |
655 |
- |
656 |
- for x in ${GMX_DIRS}; do |
657 |
- einfo "Configuring for ${x} precision" |
658 |
- local suffix="" |
659 |
- #if we build single and double - double is suffixed |
660 |
- use double-precision && use single-precision && \ |
661 |
- [[ ${x} = "double" ]] && suffix="_d" |
662 |
- local p |
663 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
664 |
- local gpu=( "-DGMX_GPU=OFF" ) |
665 |
- [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) |
666 |
- use opencl && gpu=( "-DGMX_GPU=OPENCL" ) |
667 |
- mycmakeargs=( |
668 |
- ${mycmakeargs_pre[@]} ${p} |
669 |
- -DGMX_MPI=OFF |
670 |
- -DGMX_THREAD_MPI=$(usex threads) |
671 |
- -DGMXAPI=$(usex gmxapi) |
672 |
- -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) |
673 |
- "${gpu[@]}" |
674 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
675 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
676 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
677 |
- -DGMX_PYTHON_PACKAGE=$(usex python) |
678 |
- ) |
679 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure |
680 |
- [[ ${CHOST} != *-darwin* ]] || \ |
681 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
682 |
- use mpi || continue |
683 |
- einfo "Configuring for ${x} precision with mpi" |
684 |
- mycmakeargs=( |
685 |
- ${mycmakeargs_pre[@]} ${p} |
686 |
- -DGMX_THREAD_MPI=OFF |
687 |
- -DGMX_MPI=ON |
688 |
- -DGMX_OPENMM=OFF |
689 |
- -DGMXAPI=OFF |
690 |
- "${opencl[@]}" |
691 |
- "${cuda[@]}" |
692 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
693 |
- -DBUILD_SHARED_LIBS=OFF |
694 |
- -DGMX_BUILD_MANUAL=OFF |
695 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
696 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
697 |
- ) |
698 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure |
699 |
- [[ ${CHOST} != *-darwin* ]] || \ |
700 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
701 |
- done |
702 |
-} |
703 |
- |
704 |
-src_compile() { |
705 |
- for x in ${GMX_DIRS}; do |
706 |
- einfo "Compiling for ${x} precision" |
707 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
708 |
- cmake_src_compile |
709 |
- if use python; then |
710 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
711 |
- cmake_src_compile python_packaging/all |
712 |
- BUILD_DIR="${WORKDIR}/${P}" \ |
713 |
- distutils-r1_src_compile |
714 |
- fi |
715 |
- # not 100% necessary for rel ebuilds as available from website |
716 |
- if use build-manual; then |
717 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
718 |
- cmake_src_compile manual |
719 |
- fi |
720 |
- use mpi || continue |
721 |
- einfo "Compiling for ${x} precision with mpi" |
722 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
723 |
- cmake_src_compile |
724 |
- done |
725 |
-} |
726 |
- |
727 |
-src_test() { |
728 |
- for x in ${GMX_DIRS}; do |
729 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
730 |
- cmake_src_compile check |
731 |
- done |
732 |
-} |
733 |
- |
734 |
-src_install() { |
735 |
- for x in ${GMX_DIRS}; do |
736 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
737 |
- cmake_src_install |
738 |
- if use python; then |
739 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
740 |
- cmake_src_install python_packaging/install |
741 |
- fi |
742 |
- if use build-manual; then |
743 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
744 |
- fi |
745 |
- |
746 |
- if use doc; then |
747 |
- if [[ ${PV} != *9999* ]]; then |
748 |
- newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" |
749 |
- fi |
750 |
- fi |
751 |
- |
752 |
- use mpi || continue |
753 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
754 |
- cmake_src_install |
755 |
- done |
756 |
- |
757 |
- if use tng; then |
758 |
- insinto /usr/include/tng |
759 |
- doins src/external/tng_io/include/tng/*h |
760 |
- fi |
761 |
- # drop unneeded stuff |
762 |
- rm "${ED}"/usr/bin/GMXRC* || die |
763 |
- for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do |
764 |
- local n=${x##*/gmx-completion-} |
765 |
- n="${n%.bash}" |
766 |
- cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
767 |
- newbashcomp "${T}"/"${n}" "${n}" |
768 |
- done |
769 |
- rm "${ED}"/usr/bin/gmx-completion*.bash || die |
770 |
- readme.gentoo_create_doc |
771 |
-} |
772 |
- |
773 |
-pkg_postinst() { |
774 |
- einfo |
775 |
- einfo "Please read and cite:" |
776 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
777 |
- einfo "https://dx.doi.org/10.1021/ct700301q" |
778 |
- einfo |
779 |
- readme.gentoo_print_elog |
780 |
-} |
781 |
|
782 |
diff --git a/sci-chemistry/gromacs/gromacs-2021.5.ebuild b/sci-chemistry/gromacs/gromacs-2021.5.ebuild |
783 |
index c40fa7838c07..69016d2eab59 100644 |
784 |
--- a/sci-chemistry/gromacs/gromacs-2021.5.ebuild |
785 |
+++ b/sci-chemistry/gromacs/gromacs-2021.5.ebuild |
786 |
@@ -55,7 +55,6 @@ CDEPEND=" |
787 |
mkl? ( sci-libs/mkl ) |
788 |
mpi? ( virtual/mpi ) |
789 |
${PYTHON_DEPS} |
790 |
- !sci-chemistry/gmxapi |
791 |
" |
792 |
BDEPEND="${CDEPEND} |
793 |
virtual/pkgconfig |
794 |
|
795 |
diff --git a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild |
796 |
index c135dc43d747..30f361601b7b 100644 |
797 |
--- a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild |
798 |
+++ b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild |
799 |
@@ -1,16 +1,16 @@ |
800 |
-# Copyright 1999-2021 Gentoo Authors |
801 |
+# Copyright 1999-2022 Gentoo Authors |
802 |
# Distributed under the terms of the GNU General Public License v2 |
803 |
|
804 |
EAPI=7 |
805 |
|
806 |
CMAKE_MAKEFILE_GENERATOR="ninja" |
807 |
|
808 |
-PYTHON_COMPAT=( python3_{8,9} ) |
809 |
+PYTHON_COMPAT=( python3_{8..10} ) |
810 |
|
811 |
DISTUTILS_USE_SETUPTOOLS=no |
812 |
DISTUTILS_SINGLE_IMPL=1 |
813 |
|
814 |
-inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils |
815 |
+inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils |
816 |
|
817 |
if [[ ${PV} = *9999* ]]; then |
818 |
EGIT_REPO_URI=" |
819 |
@@ -55,7 +55,6 @@ CDEPEND=" |
820 |
mkl? ( sci-libs/mkl ) |
821 |
mpi? ( virtual/mpi ) |
822 |
${PYTHON_DEPS} |
823 |
- !sci-chemistry/gmxapi |
824 |
" |
825 |
BDEPEND="${CDEPEND} |
826 |
virtual/pkgconfig |