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authorV3n3RiX <venerix@koprulu.sector>2022-05-12 16:42:50 +0300
committerV3n3RiX <venerix@koprulu.sector>2022-05-12 16:42:50 +0300
commit752d6256e5204b958b0ef7905675a940b5e9172f (patch)
tree330d16e6362a49cbed8875a777fe641a43376cd3 /sci-chemistry/gromacs
parent0c100b7dd2b30e75b799d806df4ef899fd98e1ea (diff)
gentoo resync : 12.05.2022
Diffstat (limited to 'sci-chemistry/gromacs')
-rw-r--r--sci-chemistry/gromacs/Manifest8
-rw-r--r--sci-chemistry/gromacs/gromacs-2019.6-r1.ebuild2
-rw-r--r--sci-chemistry/gromacs/gromacs-2019.6-r2.ebuild2
-rw-r--r--sci-chemistry/gromacs/gromacs-2022.1.ebuild336
4 files changed, 344 insertions, 4 deletions
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 1e530a201c6a..1a86a0ad444f 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -7,6 +7,7 @@ DIST gromacs-2020.4.tar.gz 29149899 BLAKE2B a07c8efd96137d58c1edf4ac9b5aafeb16d9
DIST gromacs-2020.7.tar.gz 29175554 BLAKE2B 98f1aa415946f8eb113febc81105f0c1b0919b96fc3c55a0ab83bf3950ff509b81eade92e645adb0bc2b407df239e20cf3f19828b6e08616437c8693c1fddcc8 SHA512 1d375c44cec38445e56cea252623b5b6c565680268999d4b6c14d6dc38759a27227655b2d29efaab9f9115d3677b446cb555e11cddafa0dc10c4827caaa2477b
DIST gromacs-2021.3.tar.gz 37987972 BLAKE2B d71995c7d5a34978246e33dc637ac3d273e547afcf72d1a107026650f03286ecdf27e4b9a70113b3c3a01af59ad49ac5c813aa6e5d2e8eb29fd05582a7a28d34 SHA512 da420917d06de2e192dfbb4e1b9f46989ed05b5c7e641c657104ed8f2bd8b22509bffd1ecfd7c965c80544eafa6af12d6d0aba7e1e7d9d14a4a88fb3fbf394a5
DIST gromacs-2021.5.tar.gz 38023772 BLAKE2B 45e1f080b86626423e471f06b48b615db1913048f9f6998da8ce45408339b32f829d33dd2af57297a7d307fcffd556c333a58c309ee0f2adb021ca3755619b05 SHA512 56c1b312fc8e52ec6f86e445d2fa2d07107c461b35d4dc8cdf95580f05fd8e6c5fd671d0e72b2b9e74e3232bc8c41db496fe4bcaf2b9a3ae3c2cfa93489a31c5
+DIST gromacs-2022.1.tar.gz 40375423 BLAKE2B fe28ec4c080500d0248bd3d37ec742e8cf51ba3520b5a7c3f640413b232fcf96354940c743e2a54a9fde04c98ecb2fd317863d8c06b008f516fefc0e9e1197dd SHA512 80c98badb7ebad171925486d1676b64e787cf8cbfb8f1b1cf1ccab8cbf8d8340f7fdd084dfb7388afc7a3aef23b95d603265305faf82125324307d86460c6f17
DIST gromacs-2022.tar.gz 40353044 BLAKE2B e9ba72092467c143be7de0739e71181f384a6bb463338c58c60a5d56f30b960651bda60c1df4fa424e237f1ae90d5d7bab19670ec22cd21bba3cb638f8e5b1ba SHA512 f256b032b226c14407ba21c7b825b6bf3f7b3595318b8638594d81ed6346b0b8563098f6ff7005c2ba125447c5d2dff750829b24781c8f1ea266e6465f627db1
DIST manual-2018.8.pdf 10025023 BLAKE2B afb0a6e6a72d78df743fcb57e7c1716848589e571dd35167b957a9b407ca27978ccfb6cb9e0df9c9439b888f352501a00ba32281ed1e0b4193bd606f1d77152e SHA512 b1972f7ce965bfc9377542993c5943ea4868a8ed23a969d4203264746d6bea3a7a65c6379196ece37fd6d68ec7ec80f827bde87d1049284af7082759a124f1d5
DIST manual-2019.6.pdf 12702376 BLAKE2B c350127bc06a9eb3dee73da39037c84daeb89500e23cb131bd19a150bf60602d4dde7611e0c6f0f344af4093e96a899303dac71b4df56fd0c44c3a48a56606b7 SHA512 dfdff67c2c1c9ce1f1c236b7686c5331b0fe86951da6c98eddd6a3e748815e0be0a9653ae4318469fcdd913c4e7c355d64a997cc80b9d9fbe6282ef6d98e61eb
@@ -14,6 +15,7 @@ DIST manual-2020.4.pdf 11851608 BLAKE2B 7b7bdf08e8946fcc448543b08391b94a67fee60a
DIST manual-2020.7.pdf 11850780 BLAKE2B 38594e87993badfbbcf47d6010a7f67d3c3426dab85e1462916b4d62be27b5764953f912cf2b71ee24877e0bfa27b3f74431da2da81b4977d58cb66b2cc795a3 SHA512 4f184f2c90e0bac01a48069cc546cd5b04fa5f543f90dd2d68c6d17be278152fd09456b6a6c5c8236f8fb85a174d6ec7a1c7b44d437b4e6fea5d0ada73cec0f6
DIST manual-2021.3.pdf 12255076 BLAKE2B 6ca516b6832507c9d4100679d1f9bc9e3ab17d226849b050764b0d0626247dc57ce49985f9a7fc0061f3df278923a83faa367ca8ab91c37e5624dc584a51a822 SHA512 5d53798f30ea00fcb4e1b35f7eaa4bebfc05dafa4f2d0c197dcf2b57a624ad3a98b74fd90722e40d0ac13a6fff4ca231f9d6340f52ba94659c827c53c2f1cb16
DIST manual-2021.5.pdf 12253641 BLAKE2B 8850715a2bb21345e1c9735aca1a5dd2ad916e5a18881e7c9f3dda6f055ca12d9d379b74218138999ce50769efd8b9dd6447afbf70bbbefa2564dfb9fb276b91 SHA512 7635108c935e4953d722df6a16ee43edf97eef7e49f047218728f68f61f8f185192ff1d8b13a573b643b040955af211355a7b560c8a894c858d7f71249d41296
+DIST manual-2022.1.pdf 13069337 BLAKE2B fed4d5b5ddc2b91dd2de2873c3efc01f6ce65b033840a79fda471b4481920fa6c5f5d9f23660d97ba4c84e0c7b75dc4c8723ed51413ad55c980818c394e9fde1 SHA512 73455190aec62aaffe760dddac4de26ea148d825f4c2d0e04d38c88b87fe15b7138b5a872bf9757452ac39e68942943c73e19025730ece8052d4a6a1873ca40e
DIST manual-2022.pdf 13060966 BLAKE2B e1684d22e16d2bad878cd0adbac0df74a268f89034756a34374908afc7f2562a05dbdf91b3dcbdb98a45b3d21140b02a2df26e0f997c1f501347e102069f22c2 SHA512 0d9bd1fbe2db122f434df1565ba7c9ea5ad168f73855724a6cb488244eda13d8d47b2d534a6873dc7204012156fbf669bdaf7ca7d03a914745f60950392e6d28
DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb
DIST regressiontests-2019.6.tar.gz 67643195 BLAKE2B 1e054e24b187946f7ea28090d4f20cf8e1d79a26253f57ba07d130e0773d8541b8a1552a38023d31a68ce8bc62d8e0af1d98609234bb3e7d3e6d567307ebb386 SHA512 eacf1c55b982515a305c29459fe80a7cd558a8481e5689962aa956148af542568b1d1ce59c6784ecb0afd4768c2b664afa21e12af2d89ae2b06b1ba61ad72036
@@ -21,15 +23,17 @@ DIST regressiontests-2020.4.tar.gz 48542144 BLAKE2B 1dcde67525d40ababa74d9e8ba2d
DIST regressiontests-2020.7.tar.gz 48541487 BLAKE2B 255608b52158c6c01e7c7c4dcf075128ecf22b2f26d32e8c203de8a4bc69c60ec95f49cf8ccd64abc3073c5e8dca9d6b01daed9dfb8f67bce2dd068ed01acd05 SHA512 2458582f94f3c9f4e1454824ce3940b4f5b6cb2151d06846c42e7a9448296fd2a6df4f53be9624e0d3317d2b59f89bb5348eb8b2970d7b46ac22ca989ef3458a
DIST regressiontests-2021.3.tar.gz 48515038 BLAKE2B ee79d8adddc9c68f7d59d9e568b12bf4d1fe0e44c2810fee846ad6f689bbcacf60f5c266433946329e64e3127bc2d37a3f81f69c070c636b411b38067650c2cf SHA512 e14baa22ef2902a23125bbd9143ae7a9a4810498b321794ff1989f8d044d47db5db41d5225798fda08016c05e5f7f315178b5a6e35cdf01e3b6604670a8ce7a2
DIST regressiontests-2021.5.tar.gz 48537298 BLAKE2B 860ac34aa8706ecdafab4472162775ce12726d93839079ebf9b7df8c2c6a1b47baa8a635c24cf4cb4551a32237c3de7da3197ec136b5bbf48663edc3943720ad SHA512 3605d04b2602339fb7d33e2776da2ada337ca58a3802472d47f490d4e8dd04249a950bf34608a498eedebf69f344c0311bac8f7fcb58ce0ebbb6d608ee39aa2e
+DIST regressiontests-2022.1.tar.gz 48613957 BLAKE2B 57113b1030baed0d4a635c4c4c7123e77640223dddc4e3d7b40d9a2b3805be85fcc3ca0dfc5f3d92f2dce9b962b67ca8732db2c782953c9a5ed1381bf6f02357 SHA512 44633e7497601a4cf11dd6af9d043ca132efe43246b6d924c57f879d2e6f7a6379390d9897e03d7a8f645e7bdbb76a81586b56c5e61846d9f40c137a4de216c2
DIST regressiontests-2022.tar.gz 48616817 BLAKE2B 5d303f365a8b3c4554232ca3e583f0eacc1973dd62faaed769d297efb5d7dde3ca04b8071786ecee992a83d7980aa244965212856f48c8832ca55805af61b1c1 SHA512 4566b76b5eb3bbdcdfed8330d4fcd7ada02eb6802434aa9f2ed4f775da780e4bde7daa35d79a72b3f25c540cb1c2b347aa2e6d504a77c095830da024a933fab5
EBUILD gromacs-2018.8-r1.ebuild 6911 BLAKE2B 7c58e3fd507f54c17e3268bb3dc634f1b708c8c2662d33ae1e125cc2a11591cfefa4a38e6922dee789f63829abe3917a245a12ef06ca43686221c37c65ad9dbe SHA512 f9512b277a696aeb2d287cf1c37f982153889027ef69c3b766519c80049f363a491bd22d0d018f93ca63f41e448fc6b2f93121ac5a66f37c2ef4951bb473b8e8
-EBUILD gromacs-2019.6-r1.ebuild 7250 BLAKE2B 906b6a7c5757f2035600752b8dbbb40c99c68fd441fcaa4e6228cbc04fe93fea40fe42aef37f86804833db25625a16b6b6a52a947ec23fc571915a129dad5658 SHA512 9b32eb868e2b5caffb0d041764350fd45307565246dd0937443ab09d818b51ae4af898d4aaceb2c4fe1673c8c3992d067a89164cb3cf862a21825a0e432ec0dc
-EBUILD gromacs-2019.6-r2.ebuild 7307 BLAKE2B 0105b1602f8fc59d398e24ee5b820916be92962b1e37bb40da03c13641fa02f6fabb484cb6ca481e051c5ec82d446e337e297a8e08004c46634edd586c1399c3 SHA512 058fe35d2b2bfb135f7675d27fa676364c0f6506ca74c8f8a760596d74cc60dac5ac8b95b8886df0c375bc4839c465106e3f7e6af24cfd8a504c2189a4f6e16c
+EBUILD gromacs-2019.6-r1.ebuild 7234 BLAKE2B a1abfa8e110aed2d0c3adfa5e74658ef0635a2851d4d9ecb78e1fbad99efa3d61d8adf8d232b68406927325bb6e23781b0c1f6366d162e6f7adfcf4179c1be50 SHA512 ed17fb00e3609a0adaca74e96236cab544dfea0d264dc46933e292d8d3bd6cd2c49716c7eae7823253523a287466630feb739cabac24fe2f488eadb95901415a
+EBUILD gromacs-2019.6-r2.ebuild 7291 BLAKE2B 8dc60e5521dc7413847d2573ea5fc05e65a4102747c30aaf514d446464ac6707e4b1e65e2b462cfa2099b39578ec50c394db780f060bce7c80e1b6eea69d9fe9 SHA512 02e96e3602295cbe06e7c1c290ea55adee7f4e6f1e9f22b43d1f9f3e561943b3c23bb5e466eeed5a632d4a9d4668b3604a096de64c5618e4f964df3ade27a276
EBUILD gromacs-2020.4-r1.ebuild 10081 BLAKE2B 87104c721cab6ac70218d6d7cea6280ecf0c8dfd11118ffc086ad2264ab4c52f9904ae55f4dd67d8a21a9e1b4309c50ecc65fe969fdfd4dc214663c1c56e4b2b SHA512 d2fceb44f67f1f08609d6cfc3f6e4ecdc607c12b7cf3676f7180a3558e91ca2cdddcc449b5ebc7e09dd20f1bfae2fc6d01ecfd7861a196cf36976b23c72ff4f2
EBUILD gromacs-2020.7.ebuild 10086 BLAKE2B a8dbbf44bafe6d8c3c3b8c2faf7976ca8dc34e3e73209c2f34a16e301d62404689a40de03ba78c602d4d99d687bc555428dd7eb13d8badab4ba997de09fc1812 SHA512 ef212496eb06fc88d53ba190a3ea9d4835b0686ce49278ced3eda0eb39ccfda27c72739962d25ba5a504f7125db18389475335a016df945fe296830429609b15
EBUILD gromacs-2021.3-r1.ebuild 10288 BLAKE2B 0a2a11221d22689fbc514c9748b58e9289a2a5ab1628504aab9515b660be38a2f830da6d40c265898e323646275479b49fd08e9101911996dc9c56be9f345f4e SHA512 ac9cecdf06429435077ddba2932e07c6b580aa41a59a738314383a583bdbf49303bf09f8aef37f494abbd4193efddffac7049cded59590ecc6b470dd9a8ed185
EBUILD gromacs-2021.5.ebuild 10293 BLAKE2B c1c9e5b72fdcba071e5bf045e76b0cc0c2bc4297d09287d305611dd922307509f384b9dd32c64de1c78c6acbb0bc824c1b246688d0ea891b45a2f052eb7a4398 SHA512 56e25ae7a1081dfc11c7b88ea62d3f8df145385b9172409c045d1a74de71dfd11010cb18622ec9a0868677044b7c3dd03852f0a4d883ac48bdfd7d0aef309a71
EBUILD gromacs-2021.9999.ebuild 10237 BLAKE2B 68e2da935cbd8985cbfc00aa114c40c906e82ab87e683d837cc79abef9e480bb3edad1675f996a871d3970b7895315bd946195e19e6d2f9393f6e884664143b3 SHA512 2e452a67c43e08fb8fac5b7c0ce0c54f7e6de67936b0812d257f703f0ab9ba4dd66df307da51fe1173301fd53b569d89b34022e0d3b39d1a768edb77c61a6859
+EBUILD gromacs-2022.1.ebuild 9772 BLAKE2B 7003fa53b924757e9a2215116163b67db174bf1bc358be41caf2067d794331f4deead2a83d6429c9e02bd90348b22f20e5a7bf8d57a481eeda4ecaa131e8dc6b SHA512 642e23a6ee26a9acec9ad4bffa4ac101ac932db2c77dde04a72aebb8890cb5705af21b289acfc340ddcb4822a495181839418011b1571bc716d0ded093e60754
EBUILD gromacs-2022.9999.ebuild 9374 BLAKE2B f8ebda163073d2cdd6a11fe096d1d0aa47637ab94a2d64e14929041066cfb84f63a1c17ee7432454c405b92629cfe12824dc29defb18291bca97cc384fafedec SHA512 1aec18c9918aeed944a2bf36660acead13df7b455b9361f70c97f972b3abef44b3ef6c8df707e7f886c6785abe16cd3a4e9b63508e8a8994e3033bd8e98fbc53
EBUILD gromacs-2022.ebuild 9772 BLAKE2B 7003fa53b924757e9a2215116163b67db174bf1bc358be41caf2067d794331f4deead2a83d6429c9e02bd90348b22f20e5a7bf8d57a481eeda4ecaa131e8dc6b SHA512 642e23a6ee26a9acec9ad4bffa4ac101ac932db2c77dde04a72aebb8890cb5705af21b289acfc340ddcb4822a495181839418011b1571bc716d0ded093e60754
EBUILD gromacs-9999.ebuild 9374 BLAKE2B f8ebda163073d2cdd6a11fe096d1d0aa47637ab94a2d64e14929041066cfb84f63a1c17ee7432454c405b92629cfe12824dc29defb18291bca97cc384fafedec SHA512 1aec18c9918aeed944a2bf36660acead13df7b455b9361f70c97f972b3abef44b3ef6c8df707e7f886c6785abe16cd3a4e9b63508e8a8994e3033bd8e98fbc53
diff --git a/sci-chemistry/gromacs/gromacs-2019.6-r1.ebuild b/sci-chemistry/gromacs/gromacs-2019.6-r1.ebuild
index 7a2a36b88257..cacbc3eef174 100644
--- a/sci-chemistry/gromacs/gromacs-2019.6-r1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.6-r1.ebuild
@@ -5,7 +5,7 @@ EAPI=7
CMAKE_MAKEFILE_GENERATOR="ninja"
-inherit bash-completion-r1 cmake cuda python-utils-r1 readme.gentoo-r1 toolchain-funcs xdg-utils
+inherit bash-completion-r1 cmake cuda readme.gentoo-r1 toolchain-funcs xdg-utils
SRC_URI="
http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
diff --git a/sci-chemistry/gromacs/gromacs-2019.6-r2.ebuild b/sci-chemistry/gromacs/gromacs-2019.6-r2.ebuild
index 15ec95dcc47e..b01b57f54196 100644
--- a/sci-chemistry/gromacs/gromacs-2019.6-r2.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.6-r2.ebuild
@@ -5,7 +5,7 @@ EAPI=7
CMAKE_MAKEFILE_GENERATOR="ninja"
-inherit bash-completion-r1 cmake cuda python-utils-r1 readme.gentoo-r1 toolchain-funcs xdg-utils
+inherit bash-completion-r1 cmake cuda readme.gentoo-r1 toolchain-funcs xdg-utils
SRC_URI="
http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
diff --git a/sci-chemistry/gromacs/gromacs-2022.1.ebuild b/sci-chemistry/gromacs/gromacs-2022.1.ebuild
new file mode 100644
index 000000000000..338c03cc2a11
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-2022.1.ebuild
@@ -0,0 +1,336 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+DISTUTILS_USE_SETUPTOOLS=no
+DISTUTILS_SINGLE_IMPL=1
+
+inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils
+
+if [[ ${PV} = *9999* ]]; then
+ EGIT_REPO_URI="
+ https://gitlab.com/gromacs/gromacs.git
+ https://github.com/gromacs/gromacs.git
+ git://git.gromacs.org/gromacs.git"
+ [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
+ inherit git-r3
+else
+ SRC_URI="
+ http://ftp.gromacs.org/gromacs/${P}.tar.gz
+ doc? ( https://ftp.gromacs.org/manual/manual-${PV}.pdf )
+ test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV}.tar.gz )"
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+fi
+
+ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+
+# see COPYING for details
+# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
+# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
+LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
+SLOT="0/${PV}"
+IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
+
+CDEPEND="
+ blas? ( virtual/blas )
+ cuda? ( >=dev-util/nvidia-cuda-toolkit-11[profiler] )
+ opencl? ( virtual/opencl )
+ fftw? ( sci-libs/fftw:3.0= )
+ hwloc? ( sys-apps/hwloc:= )
+ lapack? ( virtual/lapack )
+ mkl? ( sci-libs/mkl )
+ mpi? ( virtual/mpi[cxx] )
+ sci-libs/lmfit:=
+ >=dev-cpp/muParser-2.3:=
+ ${PYTHON_DEPS}
+ "
+BDEPEND="${CDEPEND}
+ virtual/pkgconfig
+ clang? ( >=sys-devel/clang-6:* )
+ build-manual? (
+ app-doc/doxygen
+ $(python_gen_cond_dep '
+ dev-python/sphinx[${PYTHON_USEDEP}]
+ ')
+ media-gfx/mscgen
+ media-gfx/graphviz
+ dev-texlive/texlive-latex
+ dev-texlive/texlive-latexextra
+ media-gfx/imagemagick
+ )"
+RDEPEND="${CDEPEND}
+ <sci-chemistry/dssp-4"
+
+REQUIRED_USE="
+ || ( single-precision double-precision )
+ doc? ( !build-manual )
+ cuda? ( single-precision )
+ cuda? ( !opencl )
+ clang-cuda? ( clang cuda )
+ mkl? ( !blas !fftw !lapack )
+ ${PYTHON_REQUIRED_USE}"
+
+DOCS=( AUTHORS README )
+
+RESTRICT="!test? ( test )"
+
+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"
+}
+
+pkg_setup() {
+ python-single-r1_pkg_setup
+}
+
+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="${WORKDIR}/regressiontests"\
+ git-r3_src_unpack
+ fi
+ fi
+}
+
+src_prepare() {
+ #notes/todos
+ # -on apple: there is framework support
+
+ xdg_environment_reset #591952
+
+ # we can use clang as default
+ if use clang && ! tc-is-clang ; then
+ export CC=${CHOST}-clang
+ export CXX=${CHOST}-clang++
+ else
+ tc-export CXX CC
+ fi
+ # clang-cuda need to filter mfpmath
+ if use clang-cuda ; then
+ filter-mfpmath sse
+ filter-mfpmath i386
+ fi
+
+ cmake_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"
+ if use build-manual; then
+ # try to create policy for imagemagik
+ mkdir -p ${HOME}/.config/ImageMagick
+ cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!DOCTYPE policymap [
+ <!ELEMENT policymap (policy)+>
+ !ATTLIST policymap xmlns CDATA #FIXED ''>
+ <!ELEMENT policy EMPTY>
+ <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
+ name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
+ stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
+ ]>
+ <policymap>
+ <policy domain="coder" rights="read | write" pattern="PS" />
+ <policy domain="coder" rights="read | write" pattern="PS2" />
+ <policy domain="coder" rights="read | write" pattern="PS3" />
+ <policy domain="coder" rights="read | write" pattern="EPS" />
+ <policy domain="coder" rights="read | write" pattern="PDF" />
+ <policy domain="coder" rights="read | write" pattern="XPS" />
+ </policymap>
+ EOF
+ fi
+}
+
+src_configure() {
+ local mycmakeargs_pre=( ) extra fft_opts=( )
+ local acce="AUTO"
+
+ if use custom-cflags; then
+ #go from slowest to fastest acceleration
+ acce="None"
+ if (use amd64 || use x86); then
+ 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"
+ use cpu_flags_x86_avx512f && acce="AVX_512"
+ elif (use arm); then
+ use cpu_flags_arm_neon && acce="ARM_NEON"
+ elif (use arm64); then
+ use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD"
+ fi
+ else
+ strip-flags
+ fi
+
+ #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+=(
+ "${fft_opts[@]}"
+ "${lmfit_opts[@]}"
+ -DGMX_USE_LMFIT=EXTERNAL
+ -DGMX_USE_MUPARSER=EXTERNAL
+ -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 build-manual)
+ -DGMX_HWLOC=$(usex hwloc)
+ -DGMX_DEFAULT_SUFFIX=off
+ -DGMX_SIMD="$acce"
+ -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+ -DGMX_DSSP_PROGRAM_PATH="${EPREFIX}/usr/bin/dssp"
+ -DBUILD_TESTING=$(usex test)
+ -DGMX_BUILD_UNITTESTS=$(usex test)
+ -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
+ ${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 gpu=( "-DGMX_GPU=OFF" )
+ [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
+ [[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" )
+ use opencl && gpu=( "-DGMX_GPU=OPENCL" )
+ mycmakeargs=(
+ ${mycmakeargs_pre[@]} ${p}
+ -DGMX_MPI=$(usex mpi)
+ -DGMX_THREAD_MPI=$(usex threads)
+ -DGMXAPI=$(usex gmxapi)
+ -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
+ "${gpu[@]}"
+ "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
+ -DGMX_BINARY_SUFFIX="${suffix}"
+ -DGMX_LIBS_SUFFIX="${suffix}"
+ -DGMX_PYTHON_PACKAGE=$(usex python)
+ )
+ BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
+ [[ ${CHOST} != *-darwin* ]] || \
+ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
+ done
+}
+
+src_compile() {
+ for x in ${GMX_DIRS}; do
+ einfo "Compiling for ${x} precision"
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake_src_compile
+ if use python; then
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake_src_compile python_packaging/all
+ BUILD_DIR="${WORKDIR}/${P}" \
+ distutils-r1_src_compile
+ fi
+ # not 100% necessary for rel ebuilds as available from website
+ if use build-manual; then
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake_src_compile manual
+ fi
+ done
+}
+
+src_test() {
+ for x in ${GMX_DIRS}; do
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake_src_compile check
+ done
+}
+
+src_install() {
+ for x in ${GMX_DIRS}; do
+ BUILD_DIR="${WORKDIR}/${P}_${x}" \
+ cmake_src_install
+ if use python; then
+ BUILD_DIR="${WORKDIR}/${P}_${x}" \
+ cmake_src_install python_packaging/install
+ fi
+ if use build-manual; then
+ newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
+ fi
+
+ if use doc; then
+ if [[ ${PV} != *9999* ]]; then
+ newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf"
+ fi
+ fi
+ done
+
+ if use tng; then
+ insinto /usr/include/tng
+ doins src/external/tng_io/include/tng/*h
+ fi
+ # drop unneeded stuff
+ rm "${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 gromacs related papers from list:"
+ einfo "https://www.gromacs.org/Gromacs_papers"
+ einfo
+ readme.gentoo_print_elog
+}