From 70b82ae359a5538711e103b0e8dfb92654296644 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sat, 27 Oct 2018 12:48:57 +0100 Subject: gentoo resync : 27.10.2018 --- sci-chemistry/gromacs/Manifest | 28 ++- sci-chemistry/gromacs/gromacs-2016.2.ebuild | 4 +- sci-chemistry/gromacs/gromacs-2016.5.ebuild | 8 +- sci-chemistry/gromacs/gromacs-2016.9999.ebuild | 4 +- sci-chemistry/gromacs/gromacs-2018.1.ebuild | 272 ---------------------- sci-chemistry/gromacs/gromacs-2018.2.ebuild | 271 ---------------------- sci-chemistry/gromacs/gromacs-2018.3.ebuild | 8 +- sci-chemistry/gromacs/gromacs-2018.9999.ebuild | 6 +- sci-chemistry/gromacs/gromacs-2019.9999.ebuild | 287 ++++++++++++++++++++++++ sci-chemistry/gromacs/gromacs-2019_beta1.ebuild | 283 +++++++++++++++++++++++ sci-chemistry/gromacs/gromacs-5.1.3.ebuild | 4 +- sci-chemistry/gromacs/gromacs-5.1.9999.ebuild | 4 +- sci-chemistry/gromacs/gromacs-9999.ebuild | 28 ++- sci-chemistry/gromacs/metadata.xml | 2 + 14 files changed, 626 insertions(+), 583 deletions(-) delete mode 100644 sci-chemistry/gromacs/gromacs-2018.1.ebuild delete mode 100644 sci-chemistry/gromacs/gromacs-2018.2.ebuild create mode 100644 sci-chemistry/gromacs/gromacs-2019.9999.ebuild create mode 100644 sci-chemistry/gromacs/gromacs-2019_beta1.ebuild (limited to 'sci-chemistry/gromacs') diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index cc18d9debf2f..51c9344b4905 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -1,28 +1,26 @@ DIST gromacs-2016.2.tar.gz 27339623 BLAKE2B c3548f4abdc4c1b09a79a3da99d7ca8060daca7307e4c5b81bd97d54adfb9621fbccf1ea7fd96c3676d6b44c20f9f4cd2168ce131799792512fad3b8b1ac0522 SHA512 f5e74bb8c126823c90d205ac0f0835e61fdd13a4550bc15aa9c972ee9b187f6451cdc90877c17276d2f889d61abb5eaa5ea1b54f7cbf3da67074146c749c1aa6 DIST gromacs-2016.5.tar.gz 27369491 BLAKE2B 4a8bf1ae3e298ac2e26ec476130720dc3ef00db5d999e3a45fdbfd7fbfe7e94fbc86be6ff0f2f23552769c8bc851ce49c73f6fc1ab13f372523279b93e7794d7 SHA512 9cb8ff88871aa5df0967c60ba303c03296c6fa3c215cd01b26259df7753f0014f04222078ab4b84a66a1f709997837134d5c0f74da19b78322e410010c9d9e10 -DIST gromacs-2018.1.tar.gz 29895119 BLAKE2B 45cc674bd78dc7dc56388a899ae50da9f10eb4dc80dad461f7e298894ee845eae744010013e682f3be4b03c1f04624111266e84cd9721415b23f87d544846827 SHA512 d29f152e9f115c7de07881c6af4cc05481e0a5520bd33142a09507e8c4df9f8b6c9d6d96efcb7adaaf4e0127b76ab247421d43918bd7e7779d6e71f5984db715 -DIST gromacs-2018.2.tar.gz 29899294 BLAKE2B a4d7111fdfb2c6919ef7a94aded634c5e14c4ca6ee6411c6c84289a9c88c39d731e89d3b01f14b2370d7de7782964e8db378aa6baabdd85cf46b689504f0738a SHA512 d444b503e24a9875b0ab7622772946ef73ab2c897da6ff45ac908f147ea398ba2404b064a8784996fd34b25e188e36f12a492e0070427e0929f422d934205d28 DIST gromacs-2018.3.tar.gz 29915626 BLAKE2B 6e6eeafecdd923a25b4a2a78a8e89f793639b57ffbd63f19d133d8474302f9a381041f138a509dadb42b36e25fe508729e860efb6b0c75cdbf01d924b0a8fd83 SHA512 3c4d6eb3942d7b54d01c94c6f6f5ae706e0f5d4f9901ea11a56fde4df97b1a9112007f2cb13feea0f19f30c89f57ae80ff53a8f5203b8cdff103aa903cd0dc8f +DIST gromacs-2019-beta1.tar.gz 33549950 BLAKE2B 667246f9a7cb136efca3fbda21aabe5ab0a759aa42896f8a9ddc86fafbfb1906e31fe46688c98477a5841e8fe5708b960c2a26abe754b8d793046734cd509377 SHA512 9f8bec3671f6f7421dc45cab1b5edb8ba8f2ebc34cd19ebd3d5d534be1f84135a112f49733a3f8c79e93ffc2b09c5053ae0dea31e95832a2b98acaee47f7d1af DIST gromacs-5.0.4.tar.gz 26342095 BLAKE2B 27a2483e23533ad627114c0005fa0d49a311b359c31aed6378bdd768c9dda03c3b19f11d961f0bd3b82a1711737d4b7dce13cad5fc56d058dd0110fe21421ee3 SHA512 bc62b623bf71dcaa948aaf7563a3d3afa973da0702062848a20323db202e862dcee413197dacd1472866ccb40fce7709e283177b1c6c49514064f23e6c46b5ee DIST gromacs-5.1.3.tar.gz 27095702 BLAKE2B b7fd8fa10e8c4f4368ac551338c59374dc35f85c9fdae5d64eec62929b8f04ea724a084959b3618cd8a151bf3e0a0c84c8f75de953722effca82a4928941ce73 SHA512 9ab26e1b2268f8d567b89b2d99d0b75b937b28edceaec56d17ca3243c76faa31255ffc0c45d762c7c693fe500b00e36ad43b80572d1d7f92dc87f9d2d98c0ba6 DIST regressiontests-2016.2.tar.gz 67095329 BLAKE2B fec8a663845ad67374c8a230d1590fa9e5079460198f41cee3b788aaa1c72e8ec9dcda48bc68a594f15003d11bf6617d46cc1a09c16b7a333587b43904a16ba6 SHA512 e0aceb56d1f38a7e6ab9fdaac5063fd20c5b3a162ffb6eddd0e6dc7dff9b724bfe31363493a9437e9f9d5421a534b375960fcb31e903a4901a0fa94ed8511294 DIST regressiontests-2016.5.tar.gz 67641413 BLAKE2B 4fcd30c198f3acbbabf1104c040d9a686de49536a97dbeb14732bfa0ed3cf37aa61b1b0f45393668985b993d1f1862a8985e416af819cf9793f5964f3e4f43cc SHA512 31764fd99cc4185d61de5d4443ee482c27b13533451a24aa0e4899997ce275a63685424eafacae38b1a3ffd4ce0d5ebe02a90348953b04c104f91376f0edfdff -DIST regressiontests-2018.1.tar.gz 67859956 BLAKE2B f561eb9373b4e0e5faae2aa91e3cb3911c096c1fce96755fc7a8a7b3a25b53bda88ef90d04d3a6fce414bf9dba44d0933827f080949306d5c98f60e5a1797412 SHA512 81c9a62fca859923c1e27214b32b0cff1dd48224dd4ad9301554036b842ccc400a2729752ba71b284e0c5b6c1769ce7de5fe2c9ba4fc7cf0917fd4ced9883112 -DIST regressiontests-2018.2.tar.gz 67855795 BLAKE2B 32504a7d9315f404b4a57fd45dd59540166b0e73d51ad5938b6a18cafc491cda5c00fe204dedba9c51a3f859759fb1d8c894c0607d71d49701269cf909617584 SHA512 6cc4bd4716f8b7aba69b840facd160f1abb32def2349cc441b89e12bf8df21dc4a4ca23acc4e47bf7ec3ae55b8e3f9a28beab044833b9d8ddfcf5e21d2878a5a DIST regressiontests-2018.3.tar.gz 67857855 BLAKE2B acd7a05ae79d1b4eb47d0c68a3fec9ee19f028a5019f39c37a033f48cf6da2a468375180ad6ceca9ac4f685a8bead38550663a47d6427b51f84c32a5c810e5f0 SHA512 57980d49efe6dcc3b3d14b5913a30c68fc1de5b679ef986fec1a149c76f67139b0299c3ee2825451461294fab5f345c7ad4f42e90f8991b81aafe9c369f3ff0b +DIST regressiontests-2019-beta1.tar.gz 67604794 BLAKE2B 163046e54206d3406d39e6bd9552dcce5a9a05a73e14249bf371d2432d902a3e336c0caa3e0c83353ac4566d91f4f805724f8eb996a831f8d3b712f65b1d1c42 SHA512 eef7eaacf56ba9358bfb0a3e34da4bc00d2a65564da81d144f57ee8a732081882b8e1c96f7006b966455105b834271715273e7590d3d4310209ee0324e7fa585 DIST regressiontests-5.0.4.tar.gz 65193251 BLAKE2B c5e5f23adcc2639fe652bc252533307c7fda44453d506603242968bd8588c7394028b2c3c7a9252f807a050d40e8f78735e904dfe517d3db8ae962051f4826c1 SHA512 747725fa28c1c9525596bdeeb8809e45268e19036c11dac67d043aa1c51748688ca37eb6014eb7e819eb927a8b9ca2631d0ace4cdff8ed491b08c316c530ab65 DIST regressiontests-5.1.3.tar.gz 66994083 BLAKE2B 7009f65ad0138664ac84e57f8bc7cce5d18a59f99943e56b6642583120bfce279e005ac0bacd2db8904ea477a48e2b938c64de46a65fa5d08fce6009d53583c3 SHA512 486e86eb3b75bae822abe82dac4e1098aa13723bd04214021f835a2f0b847303f015a9ececc33aa5ae63d31a2eeae07e512f22464b6c0e26d1286b0781578022 -EBUILD gromacs-2016.2.ebuild 7971 BLAKE2B 90510b56d31e59f2f7f76e7772b55e4acdb825af6e8df46da40c7aeb6b7d4b986253b10ac71fbd04c749dd3935b1eeb154e7d0aac7b21147859fb03b57e4e687 SHA512 7a85084cc29da0d3da6c9aabf65320edb38cd682146cc1b739120b728c6704c3e20941b9022c846b84a111e3ca88f29ca21cdbcdf4c5b7204989ac194bf15725 -EBUILD gromacs-2016.5.ebuild 7987 BLAKE2B 02bfdcce78718a1e16ad0cdf63e521d656eaa886ddf2ef7016f22abc398b95e240ecb4705a894609f188afbf4ec17c96ee9441ee7510cfaeb02c0ceced4e1b17 SHA512 5d762c0f9212ec0b91fba7565c15787201b1fcd923111b7055d6362b813d92b850f67becff023c57d3846c2f01a7df29e2b5e52d1bd643f797305c59449b1f46 -EBUILD gromacs-2016.9999.ebuild 7987 BLAKE2B 45d8b50b3ee54c8c701eb8c6533c1dc7d680eb0f5c40cdf1a75e81b59bd2d603b4235f6e4942e40211b748b7cf8239c90f8d613b20bdc44fca48d23f9c45ae14 SHA512 ce2b0d2730e87831a517468033cada7097ba431d8a60dcef77a04c9e05bf4cfacb6eb500a5196e378f4c69e5020f8e9f871eac6e61dd2776834aee006ecb167f -EBUILD gromacs-2018.1.ebuild 7899 BLAKE2B f70665f54e2103275dbf7466d15c15ce41593264bb768b542a49eebd76b1764871ac9b82e9eacee5db1a413cac8863a6e87d751cdb2196ff5a431a096c7f6f3f SHA512 3cb7bab30e822420e308b15af997f01ab3ce3072ddefc752d5f0d314040f699febcd804d983cf9af160d1388b38a62e81c9ee6fc7a6647a5d7e199262b3afec9 -EBUILD gromacs-2018.2.ebuild 7859 BLAKE2B 43d1ce476e49201e337c214fa6fcd5fdd83d0f8f209057ee00edffbcbdbfd7cc08177f029702dc26eb111c725b3347e72623a1008857911b1866142395e0d066 SHA512 f080df3b8befb1b6de337f297b561dd76069d15e4053149d1e6e3d98938349ce6e6acab8a73286dd239798be79d0ee9f081b9631aeac5e671de582e68099f574 -EBUILD gromacs-2018.3.ebuild 7859 BLAKE2B 43d1ce476e49201e337c214fa6fcd5fdd83d0f8f209057ee00edffbcbdbfd7cc08177f029702dc26eb111c725b3347e72623a1008857911b1866142395e0d066 SHA512 f080df3b8befb1b6de337f297b561dd76069d15e4053149d1e6e3d98938349ce6e6acab8a73286dd239798be79d0ee9f081b9631aeac5e671de582e68099f574 -EBUILD gromacs-2018.9999.ebuild 7859 BLAKE2B 43d1ce476e49201e337c214fa6fcd5fdd83d0f8f209057ee00edffbcbdbfd7cc08177f029702dc26eb111c725b3347e72623a1008857911b1866142395e0d066 SHA512 f080df3b8befb1b6de337f297b561dd76069d15e4053149d1e6e3d98938349ce6e6acab8a73286dd239798be79d0ee9f081b9631aeac5e671de582e68099f574 +EBUILD gromacs-2016.2.ebuild 7971 BLAKE2B 889ded117d36d17c224bdf65ddc8a2e5fcbdb5cdbf58b5774e308fc45e42a7b3734aae1f87d1d95fb3751c18342025a86317e2bf05a82ffa7f9dfaeb47533e5b SHA512 a2ad66f58d79b03e0832ae0daf9b6cbcdceae2873d25318ee7fb9235a41acc1403708206682848c35d2c347ad2ccb72f75c38df38e8899ba07033040b296eb81 +EBUILD gromacs-2016.5.ebuild 7989 BLAKE2B 1f4673c38c33675dc1e12e84a50d50ca34e04bd0562017a2fcd4b8865313f4de6d3a718ef2809080aef1609d17368cfab8470d743780b8a73b9c77d65337f2f6 SHA512 c2fe28bc3e8483a796ed4ea6cdd31d5fac6f754f2bee9be7014ef0c378f24c9a42bde36f5c4ba0a0715d0312819b49c6998005af127dc3905731a8c9552eee99 +EBUILD gromacs-2016.9999.ebuild 7987 BLAKE2B c048a6f661441fb98bc12cafbbb7194924dda12325195c565045679fb8e3b9a3aa32ec9c3823f307256a0c0679d7dc73dbf0af27e8a34b3d69c94538ee125ded SHA512 6473d8b666f5b99193c3ed4ab49b81b3a3f3e5a34597c382c8f95d32f22447e6c40a481f43a7970c55ffb74ceaa8e27353d0219fec1b7891f0c1c6a828196f8d +EBUILD gromacs-2018.3.ebuild 7840 BLAKE2B 8d78d3b3dbb870f1b21e67143b272734a487d6448a07f619726e97676a774bcbf871c3bf93dda302346359c812adad296743d887152406582776ece827c566e2 SHA512 ea7b38264bb665d3c08268cafd23004a474ddd58a509c7e8be578b157a3ef38cf0790f640e86d0404077f8f8a2304d9c42286d927651ea87cbd990468329ffb4 +EBUILD gromacs-2018.9999.ebuild 7838 BLAKE2B ea4fd716f9de3228df842d3c642ce2cba3b0f2a56c979c328d9a0a6720943b723873b5fa76ac057e869e5cd3273d52a26cb0985319bf6e05301619c92162c3c5 SHA512 4637f96407363bf3eb048de5fc075e7a3df3865641f37e62ed85a7dc5f368c230324f68634729f2ef063a265ca4ae2834853537bb10a616978dc3489b05ed1d1 +EBUILD gromacs-2019.9999.ebuild 8241 BLAKE2B 6892211d932a008b0dadad4ae8d696c882d8ec1f1b76b448e35d727b1f64996e461e4b6e76e4164182fadc707c98167679aa39b282ed0c685f11838a3262929d SHA512 952f5926bd01f66b7f1eae9c16b3bbf5e20896b928c85806b3d39de400418b1b221397ed9107d5a5d958ab15211f6bcd7bc06f1fd963a1495f64aef940440ce5 +EBUILD gromacs-2019_beta1.ebuild 8112 BLAKE2B 56a88efcf6b1b97fe0ba90d8765a83060aa2327e110d1d6be65744e044a7687484e9ae0d21e88711d532df85cec92b8df7cd07f23e6a96c727bd1137304cd093 SHA512 b021200072381da492d37257845e30851e224515438b174361abf15053025c3db600b4719f9dccbc652d276ad7686294bc28d6bba7bf5ef06ef71abcf1ddf01a EBUILD gromacs-4.6.9999.ebuild 8110 BLAKE2B dd8ac9cbc4abfcc75a3a188c59cdbe5111f363404ff5a787f64b05d4bd411deebb50f172f09963800ed87997788b2e678617805e65a523bed19aa6ef18fe2b96 SHA512 2206e257f0b29b6f3a90c5d7739079b9add3e04f2a3acbd58c814811b389b5d51b3594815a94529d1de43deb380504029c302d18fc16d63a81c92727254e863e EBUILD gromacs-5.0.4.ebuild 8429 BLAKE2B c06c423365fa79befd5a4f0b6314e77b96d983c84df776ce84fddc79d35ce735d856d1184e5913af0c8cd3a0c4e9087110af9bd4402e2bce1f014e64a8a585a7 SHA512 d1e91cc25c5f90bd0fbad15060cae9c8bf1235ca45a2b72521b3a4f5f091bdd7d32ec2e6ff2bb22cd3fe165092f11a24ea148ae8000b8517f0b8671f6c2af6f2 EBUILD gromacs-5.0.9999.ebuild 8439 BLAKE2B 33d51254e62593a58c636bd902f43edc553ad11af306d1d022278b223eda15b0772097f26565df74a1118bd5b144e5b93aac09cdb995123ccbae2856889c31b2 SHA512 6756116cdeae9c21b094f74ea1b1d9f41617467dc736878cdcff27fed9f53b338830a608e23e87238d0756884799fbc5d62f02685774ea86c239ecc3e8804814 -EBUILD gromacs-5.1.3.ebuild 7783 BLAKE2B d8154b902324d1f47d4b0d4d316bb0e1154379e3c9e3732e195f269386fe9666ba546ab624df95b201c1dbf63c0d7c24cab0e5be92ac70180c53a362e37e71c9 SHA512 8cf9573ec5dfa09e283b1d50513863214ca216007ad76cce15bc54caa2f1e55de8c992db8bd4b2e4fa95bc3f5d50eef32fce78ca61bc09cae2fe37e35a4cee68 -EBUILD gromacs-5.1.9999.ebuild 7783 BLAKE2B d8154b902324d1f47d4b0d4d316bb0e1154379e3c9e3732e195f269386fe9666ba546ab624df95b201c1dbf63c0d7c24cab0e5be92ac70180c53a362e37e71c9 SHA512 8cf9573ec5dfa09e283b1d50513863214ca216007ad76cce15bc54caa2f1e55de8c992db8bd4b2e4fa95bc3f5d50eef32fce78ca61bc09cae2fe37e35a4cee68 -EBUILD gromacs-9999.ebuild 7710 BLAKE2B efd556f55dc198d8526df775fed3c2aa55fa88794ea9618a222d67886ee46371c19c7ac0b58d37c11b5e0605e08caaeb42de9883db2bdab86c8baacbc372b639 SHA512 a3cb96cf8ada5f278b4b932fafac93659ca2c65ab530337567bf87be53ddea7123e2e03c0c3fefd2faca8bc3ce9494ebf960f1fdf9cff000b548790b5e0c9d81 -MISC metadata.xml 1251 BLAKE2B 324e432ebfca2fea64aa5ec331c51263422f22ef6f326f7034fd0d3e97ff0a408b8bf06e09d488fea89176b2996ec9a7f02597ef5dd65ee718c16c38298d0acb SHA512 b84b070eb8d6e264e036945c9903020cb1b9b8407c9c136ccbac0387f659c2943eb1c3f5c74c2627873bab7eb68d637152da759830f18a996aaa09e63d546e37 +EBUILD gromacs-5.1.3.ebuild 7759 BLAKE2B 77239a47dc1d1a93c4f8a679e0ab3571729b7f69f66eb3a97d1c812ec56289c7b35b14e23e39f47fd2bcdd140eea28bba58353002923b737c9707fddeebfc3ea SHA512 681c76b9224c6a21a443362dbe13fe38a96b0af7349e221b34bab303c8af4401c760fbc8047ad49c932d230ffcebc69d73f90a817efa7585ccadabd6fb62193f +EBUILD gromacs-5.1.9999.ebuild 7759 BLAKE2B 77239a47dc1d1a93c4f8a679e0ab3571729b7f69f66eb3a97d1c812ec56289c7b35b14e23e39f47fd2bcdd140eea28bba58353002923b737c9707fddeebfc3ea SHA512 681c76b9224c6a21a443362dbe13fe38a96b0af7349e221b34bab303c8af4401c760fbc8047ad49c932d230ffcebc69d73f90a817efa7585ccadabd6fb62193f +EBUILD gromacs-9999.ebuild 8105 BLAKE2B a7946a54f0fb54aee44f97f0bf3e6f14cbf842823d7d0dfa6759eb6146deaa3c82771192cb34584340da0bbadf9aa03f7a0b90c217038fdd5cb9e57cf24d619f SHA512 fd8e54b639d355d60269ba4f1a913f38798e33e76359cd75632863725f550d603bf84a444394ab70cf5a65a30f7ee8c394c3f4d13e673883fd23b0831c0d732b +MISC metadata.xml 1378 BLAKE2B 74d5e63ad45455ea441cd4546c2063587be8cff2977f8c0b9e1f92b3ba02481589ca314cf5cba43f61806638e5be336dbc679cc00d5ef96afd6edd0083120791 SHA512 dfbfa2b9199074310d0a959998cdd30def0a32213763aa6e0756b33dbd8d3946981eb8167b68a8669ba9f3799f9c685a786d423014e6b9fcd959a133f8a1b151 diff --git a/sci-chemistry/gromacs/gromacs-2016.2.ebuild b/sci-chemistry/gromacs/gromacs-2016.2.ebuild index 3b371d273088..15acf0b2cf75 100644 --- a/sci-chemistry/gromacs/gromacs-2016.2.ebuild +++ b/sci-chemistry/gromacs/gromacs-2016.2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2018 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -41,7 +41,7 @@ CDEPEND=" blas? ( virtual/blas ) cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) fftw? ( sci-libs/fftw:3.0 ) - hwloc? ( sys-apps/hwloc ) + hwloc? ( =dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) fftw? ( sci-libs/fftw:3.0 ) - hwloc? ( sys-apps/hwloc ) + hwloc? ( "${T}/${n}" || die - newbashcomp "${T}"/"${n}" "${n}" - done - rm "${ED}"usr/bin/gmx-completion*.bash || die - readme.gentoo_create_doc -} - -pkg_postinst() { - einfo - einfo "Please read and cite:" - einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " - einfo "https://dx.doi.org/10.1021/ct700301q" - einfo - readme.gentoo_print_elog -} diff --git a/sci-chemistry/gromacs/gromacs-2018.2.ebuild b/sci-chemistry/gromacs/gromacs-2018.2.ebuild deleted file mode 100644 index d4ea677a994c..000000000000 --- a/sci-chemistry/gromacs/gromacs-2018.2.ebuild +++ /dev/null @@ -1,271 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils - -if [[ $PV = *9999* ]]; then - EGIT_REPO_URI="git://git.gromacs.org/gromacs.git - https://gerrit.gromacs.org/gromacs.git - https://github.com/gromacs/gromacs.git - http://repo.or.cz/r/gromacs.git" - [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" - inherit git-r3 - KEYWORDS="" -else - SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz - test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -fi - -ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" - -DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" - -# see COPYING for details -# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING -# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib -LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" -SLOT="0/${PV}" -IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" - -CDEPEND=" - X? ( - x11-libs/libX11 - x11-libs/libSM - x11-libs/libICE - ) - blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) - opencl? ( virtual/opencl ) - fftw? ( sci-libs/fftw:3.0 ) - hwloc? ( sys-apps/hwloc ) - lapack? ( virtual/lapack ) - mkl? ( sci-libs/mkl ) - mpi? ( virtual/mpi ) - " -DEPEND="${CDEPEND} - virtual/pkgconfig - doc? ( - app-doc/doxygen - dev-texlive/texlive-latex - dev-texlive/texlive-latexextra - media-gfx/imagemagick - )" -RDEPEND="${CDEPEND}" - -REQUIRED_USE=" - || ( single-precision double-precision ) - cuda? ( single-precision ) - cuda? ( !opencl ) - mkl? ( !blas !fftw !lapack )" - -DOCS=( AUTHORS README ) - -if [[ ${PV} != *9999 ]]; then - S="${WORKDIR}/${PN}-${PV/_/-}" -fi - -pkg_pretend() { - [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" - use openmp && ! tc-has-openmp && \ - die "Please switch to an openmp compatible compiler" -} - -src_unpack() { - if [[ ${PV} != *9999 ]]; then - default - else - git-r3_src_unpack - if use test; then - EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ - EGIT_BRANCH="${EGIT_BRANCH}" \ - EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ - git-r3_src_unpack - fi - fi -} - -src_prepare() { - #notes/todos - # -on apple: there is framework support - - xdg_environment_reset #591952 - - cmake-utils_src_prepare - - use cuda && cuda_src_prepare - - GMX_DIRS="" - use single-precision && GMX_DIRS+=" float" - use double-precision && GMX_DIRS+=" double" - - if use test; then - for x in ${GMX_DIRS}; do - mkdir -p "${WORKDIR}/${P}_${x}" || die - cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die - done - fi - - DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" -} - -src_configure() { - local mycmakeargs_pre=( ) extra fft_opts=( ) - - #go from slowest to fastest acceleration - local acce="None" - use cpu_flags_x86_sse2 && acce="SSE2" - use cpu_flags_x86_sse4_1 && acce="SSE4.1" - use cpu_flags_x86_fma4 && acce="AVX_128_FMA" - use cpu_flags_x86_avx && acce="AVX_256" - use cpu_flags_x86_avx2 && acce="AVX2_256" - - #to create man pages, build tree binaries are executed (bug #398437) - [[ ${CHOST} = *-darwin* ]] && \ - extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" - - if use fftw; then - fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${MKLROOT}/include" - -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" - ) - elif use mkl; then - local bits=$(get_libdir) - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" - -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" - ) - else - fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) - fi - - mycmakeargs_pre+=( - "${fft_opts[@]}" - -DGMX_X11=$(usex X) - -DGMX_EXTERNAL_BLAS=$(usex blas) - -DGMX_EXTERNAL_LAPACK=$(usex lapack) - -DGMX_OPENMP=$(usex openmp) - -DGMX_COOL_QUOTES=$(usex offensive) - -DGMX_USE_TNG=$(usex tng) - -DGMX_BUILD_MANUAL=$(usex doc) - -DGMX_HWLOC=$(usex hwloc) - -DGMX_DEFAULT_SUFFIX=off - -DGMX_SIMD="$acce" - -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" - -DBUILD_TESTING=$(usex test) - -DGMX_BUILD_UNITTESTS=$(usex test) - ${extra} - ) - - for x in ${GMX_DIRS}; do - einfo "Configuring for ${x} precision" - local suffix="" - #if we build single and double - double is suffixed - use double-precision && use single-precision && \ - [[ ${x} = "double" ]] && suffix="_d" - local p - [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" - local cuda=( "-DGMX_GPU=OFF" ) - [[ ${x} = "float" ]] && use cuda && \ - cuda=( "-DGMX_GPU=ON" ) - local opencl=( "-DGMX_USE_OPENCL=OFF" ) - use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_MPI=OFF - -DGMX_THREAD_MPI=$(usex threads) - "${opencl[@]}" - "${cuda[@]}" - "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" - -DGMX_BINARY_SUFFIX="${suffix}" - -DGMX_LIBS_SUFFIX="${suffix}" - ) - BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die - use mpi || continue - einfo "Configuring for ${x} precision with mpi" - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_THREAD_MPI=OFF - -DGMX_MPI=ON ${cuda} - -DGMX_OPENMM=OFF - -DGMX_BUILD_MDRUN_ONLY=ON - -DBUILD_SHARED_LIBS=OFF - -DGMX_BUILD_MANUAL=OFF - -DGMX_BINARY_SUFFIX="_mpi${suffix}" - -DGMX_LIBS_SUFFIX="_mpi${suffix}" - ) - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die - done -} - -src_compile() { - for x in ${GMX_DIRS}; do - einfo "Compiling for ${x} precision" - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile - # not 100% necessary for rel ebuilds as available from website - if use doc; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile manual - fi - use mpi || continue - einfo "Compiling for ${x} precision with mpi" - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - cmake-utils_src_compile - done -} - -src_test() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_make check - done -} - -src_install() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake-utils_src_install - if use doc; then - newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" - fi - use mpi || continue - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake-utils_src_install - done - - if use tng; then - insinto /usr/include/tng - doins src/external/tng_io/include/tng/*h - fi - # drop unneeded stuff - rm "${ED}"usr/bin/GMXRC* || die - for x in "${ED}"usr/bin/gmx-completion-*.bash ; do - local n=${x##*/gmx-completion-} - n="${n%.bash}" - cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die - newbashcomp "${T}"/"${n}" "${n}" - done - rm "${ED}"usr/bin/gmx-completion*.bash || die - readme.gentoo_create_doc -} - -pkg_postinst() { - einfo - einfo "Please read and cite:" - einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " - einfo "https://dx.doi.org/10.1021/ct700301q" - einfo - readme.gentoo_print_elog -} diff --git a/sci-chemistry/gromacs/gromacs-2018.3.ebuild b/sci-chemistry/gromacs/gromacs-2018.3.ebuild index d4ea677a994c..4437231ca268 100644 --- a/sci-chemistry/gromacs/gromacs-2018.3.ebuild +++ b/sci-chemistry/gromacs/gromacs-2018.3.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2018 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -14,11 +14,11 @@ if [[ $PV = *9999* ]]; then http://repo.or.cz/r/gromacs.git" [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" inherit git-r3 - KEYWORDS="" + KEYWORDS="x86" else SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" + KEYWORDS="~amd64 ~arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" fi ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" @@ -43,7 +43,7 @@ CDEPEND=" cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) opencl? ( virtual/opencl ) fftw? ( sci-libs/fftw:3.0 ) - hwloc? ( sys-apps/hwloc ) + hwloc? ( "${T}/${n}" || die + newbashcomp "${T}"/"${n}" "${n}" + done + rm "${ED}"usr/bin/gmx-completion*.bash || die + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " + einfo "https://dx.doi.org/10.1021/ct700301q" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-2019_beta1.ebuild b/sci-chemistry/gromacs/gromacs-2019_beta1.ebuild new file mode 100644 index 000000000000..b59d3312f446 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2019_beta1.ebuild @@ -0,0 +1,283 @@ +# Copyright 1999-2018 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils + +if [[ $PV = *9999* ]]; then + EGIT_REPO_URI="git://git.gromacs.org/gromacs.git + https://gerrit.gromacs.org/gromacs.git + https://github.com/gromacs/gromacs.git + http://repo.or.cz/r/gromacs.git" + [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + inherit git-r3 + KEYWORDS="" +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz + test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" + KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" + +# see COPYING for details +# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib +LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" +SLOT="0/${PV}" +IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) + opencl? ( virtual/opencl ) + fftw? ( sci-libs/fftw:3.0 ) + hwloc? ( sys-apps/hwloc ) + lapack? ( virtual/lapack ) + lmfit? ( sci-libs/lmfit ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + " +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + dev-python/sphinx + media-gfx/mscgen + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + )" +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + cuda? ( !opencl ) + mkl? ( !blas !fftw !lapack )" + +DOCS=( AUTHORS README ) + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +pkg_pretend() { + [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" + use openmp && ! tc-has-openmp && \ + die "Please switch to an openmp compatible compiler" +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="${EGIT_BRANCH}" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + xdg_environment_reset #591952 + + cmake-utils_src_prepare + + use cuda && cuda_src_prepare + + GMX_DIRS="" + use single-precision && GMX_DIRS+=" float" + use double-precision && GMX_DIRS+=" double" + + if use test; then + for x in ${GMX_DIRS}; do + mkdir -p "${WORKDIR}/${P}_${x}" || die + cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die + done + fi + + DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + #go from slowest to fastest acceleration + local acce="None" + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + use cpu_flags_x86_avx2 && acce="AVX2_256" + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${MKLROOT}/include" + -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" + ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + if use lmfit; then + local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) + else + local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + "${lmfit_opts[@]}" + -DGMX_X11=$(usex X) + -DGMX_EXTERNAL_BLAS=$(usex blas) + -DGMX_EXTERNAL_LAPACK=$(usex lapack) + -DGMX_OPENMP=$(usex openmp) + -DGMX_COOL_QUOTES=$(usex offensive) + -DGMX_USE_TNG=$(usex tng) + -DGMX_BUILD_MANUAL=$(usex doc) + -DGMX_HWLOC=$(usex hwloc) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DBUILD_TESTING=$(usex test) + -DGMX_BUILD_UNITTESTS=$(usex test) + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local cuda=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && \ + cuda=( "-DGMX_GPU=ON" ) + local opencl=( "-DGMX_USE_OPENCL=OFF" ) + use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + -DGMX_THREAD_MPI=$(usex threads) + -DGMXAPI=$(usex gmxapi) + "${opencl[@]}" + "${cuda[@]}" + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + use mpi || continue + einfo "Configuring for ${x} precision with mpi" + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_THREAD_MPI=OFF + -DGMX_MPI=ON ${cuda} + -DGMX_OPENMM=OFF + -DGMXAPI=OFF + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" + -DGMX_LIBS_SUFFIX="_mpi${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile + # not 100% necessary for rel ebuilds as available from website + #if use doc; then + # BUILD_DIR="${WORKDIR}/${P}_${x}"\ + # cmake-utils_src_compile manual + #fi + use mpi || continue + einfo "Compiling for ${x} precision with mpi" + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake-utils_src_compile + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_make check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install + #if use doc; then + # newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + #fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake-utils_src_install + done + + if use tng; then + insinto /usr/include/tng + doins src/external/tng_io/include/tng/*h + fi + # drop unneeded stuff + rm "${ED}"usr/bin/GMXRC* || die + for x in "${ED}"usr/bin/gmx-completion-*.bash ; do + local n=${x##*/gmx-completion-} + n="${n%.bash}" + cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die + newbashcomp "${T}"/"${n}" "${n}" + done + rm "${ED}"usr/bin/gmx-completion*.bash || die + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " + einfo "https://dx.doi.org/10.1021/ct700301q" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-5.1.3.ebuild b/sci-chemistry/gromacs/gromacs-5.1.3.ebuild index b08ea7c3af7f..eba3bfc8c094 100644 --- a/sci-chemistry/gromacs/gromacs-5.1.3.ebuild +++ b/sci-chemistry/gromacs/gromacs-5.1.3.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2018 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -18,7 +18,7 @@ if [[ $PV = *9999* ]]; then else SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" - KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" + KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" fi ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" diff --git a/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild index b08ea7c3af7f..eba3bfc8c094 100644 --- a/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2018 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -18,7 +18,7 @@ if [[ $PV = *9999* ]]; then else SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" - KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" + KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" fi ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild index b38e62cc3e58..8a643e0fb30d 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2018 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -18,7 +18,7 @@ if [[ $PV = *9999* ]]; then else SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" + KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" fi ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" @@ -31,7 +31,7 @@ HOMEPAGE="http://www.gromacs.org/" # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" -IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" X? ( @@ -40,10 +40,12 @@ CDEPEND=" x11-libs/libICE ) blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) + opencl? ( virtual/opencl ) fftw? ( sci-libs/fftw:3.0 ) hwloc? ( sys-apps/hwloc ) lapack? ( virtual/lapack ) + lmfit? ( sci-libs/lmfit ) mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi ) " @@ -51,6 +53,8 @@ DEPEND="${CDEPEND} virtual/pkgconfig doc? ( app-doc/doxygen + dev-python/sphinx + media-gfx/mscgen dev-texlive/texlive-latex dev-texlive/texlive-latexextra media-gfx/imagemagick @@ -60,6 +64,7 @@ RDEPEND="${CDEPEND}" REQUIRED_USE=" || ( single-precision double-precision ) cuda? ( single-precision ) + cuda? ( !opencl ) mkl? ( !blas !fftw !lapack )" DOCS=( AUTHORS README ) @@ -144,8 +149,15 @@ src_configure() { fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) fi + if use lmfit; then + local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) + else + local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) + fi + mycmakeargs_pre+=( "${fft_opts[@]}" + "${lmfit_opts[@]}" -DGMX_X11=$(usex X) -DGMX_EXTERNAL_BLAS=$(usex blas) -DGMX_EXTERNAL_LAPACK=$(usex lapack) @@ -156,7 +168,6 @@ src_configure() { -DGMX_HWLOC=$(usex hwloc) -DGMX_DEFAULT_SUFFIX=off -DGMX_SIMD="$acce" - -DGMX_LIB_INSTALL_DIR="$(get_libdir)" -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" -DBUILD_TESTING=$(usex test) -DGMX_BUILD_UNITTESTS=$(usex test) @@ -173,11 +184,15 @@ src_configure() { [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" local cuda=( "-DGMX_GPU=OFF" ) [[ ${x} = "float" ]] && use cuda && \ - cuda=( -DGMX_GPU=ON ) + cuda=( "-DGMX_GPU=ON" ) + local opencl=( "-DGMX_USE_OPENCL=OFF" ) + use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF -DGMX_THREAD_MPI=$(usex threads) + -DGMXAPI=$(usex gmxapi) + "${opencl[@]}" "${cuda[@]}" "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" -DGMX_BINARY_SUFFIX="${suffix}" @@ -193,6 +208,7 @@ src_configure() { -DGMX_THREAD_MPI=OFF -DGMX_MPI=ON ${cuda} -DGMX_OPENMM=OFF + -DGMXAPI=OFF -DGMX_BUILD_MDRUN_ONLY=ON -DBUILD_SHARED_LIBS=OFF -DGMX_BUILD_MANUAL=OFF diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml index 844b34dd014b..0dcc6a6c4d7f 100644 --- a/sci-chemistry/gromacs/metadata.xml +++ b/sci-chemistry/gromacs/metadata.xml @@ -22,6 +22,8 @@ Enable HWLoc lib support Enable new trajectory format - tng Create symbolic links for pre-5.0 binary names + Use external sci-libs/lmfit + Add support for gmxapi library Enable gromacs partly offensive quotes Use sci-libs/mkl for fft, blas, lapack routines -- cgit v1.2.3