| 1 |
commit: aca2065305ee0a10c63feb64d20d3f82223f210e |
| 2 |
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
| 3 |
AuthorDate: Thu Jan 27 16:01:24 2022 +0000 |
| 4 |
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
| 5 |
CommitDate: Thu Jan 27 16:03:24 2022 +0000 |
| 6 |
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=aca20653 |
| 7 |
|
| 8 |
sci-chemistry/gromacs: Version bump |
| 9 |
|
| 10 |
Package-Manager: Portage-3.0.30, Repoman-3.0.3 |
| 11 |
Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org> |
| 12 |
|
| 13 |
sci-chemistry/gromacs/Manifest | 3 + |
| 14 |
sci-chemistry/gromacs/gromacs-2021.5.ebuild | 356 ++++++++++++++++++++++++++++ |
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2 files changed, 359 insertions(+) |
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|
| 17 |
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest |
| 18 |
index 0788ac6bd4e1..6015e6a4b69e 100644 |
| 19 |
--- a/sci-chemistry/gromacs/Manifest |
| 20 |
+++ b/sci-chemistry/gromacs/Manifest |
| 21 |
@@ -5,6 +5,7 @@ DIST gromacs-2020.6.tar.gz 29196621 BLAKE2B b350fc62fd8eeb3f2b042fa74a4ed42e43a7 |
| 22 |
DIST gromacs-2021.2.tar.gz 37976386 BLAKE2B 8818321bbcbdee25356bbf909d9c667f9d7cf180e696a323a61017683234d1269decc8f8d72b8012a8cc207f69e5cd97e2ab48dbbff06d82bbb407bc0578854b SHA512 51b1728f41932274436ab807d569109e2b0e145abcb5cf9c9b7daf6a7396f2f8716dc28fb93cf178c97a7eaeab2a88878d0bc71dd6c6abe7e829d579e7968615 |
| 23 |
DIST gromacs-2021.3.tar.gz 37987972 BLAKE2B d71995c7d5a34978246e33dc637ac3d273e547afcf72d1a107026650f03286ecdf27e4b9a70113b3c3a01af59ad49ac5c813aa6e5d2e8eb29fd05582a7a28d34 SHA512 da420917d06de2e192dfbb4e1b9f46989ed05b5c7e641c657104ed8f2bd8b22509bffd1ecfd7c965c80544eafa6af12d6d0aba7e1e7d9d14a4a88fb3fbf394a5 |
| 24 |
DIST gromacs-2021.4.tar.gz 38023262 BLAKE2B 4e1c9ca23f8bd89a990bac2730f846ce9fd6423aa6934866734272ac8f5ca29cdb51daec440b7ef2af56c68bdbab504c0c1b1a4d5f4af0b16666850bf286c5b2 SHA512 35b26b3df02d151373fab49022281b89e987c867257a998acc926b2b7151f5d4e46f11c398a24f4a174f668dd24a828b07d36594ac5d5506e10e40d4578427a2 |
| 25 |
+DIST gromacs-2021.5.tar.gz 38023772 BLAKE2B 45e1f080b86626423e471f06b48b615db1913048f9f6998da8ce45408339b32f829d33dd2af57297a7d307fcffd556c333a58c309ee0f2adb021ca3755619b05 SHA512 56c1b312fc8e52ec6f86e445d2fa2d07107c461b35d4dc8cdf95580f05fd8e6c5fd671d0e72b2b9e74e3232bc8c41db496fe4bcaf2b9a3ae3c2cfa93489a31c5 |
| 26 |
DIST gromacs-2022-beta1.tar.gz 39727355 BLAKE2B 2b17684e36f1a2746bd92e4cea2f7eedfcc1770eb127663b7d643a4e9518dc90f788c0f41dcff612d06edb05eeb06a13196810714d5cdf5a8ef5056100d75eb6 SHA512 a311a95b42647819d442be2a6106f4a3bbfa792856ac88ade9ee0793dff3a3bd0e6f2982bfa37d541b3a4673a24358fa72bf9267c3d1743bb01da673d84e0fa8 |
| 27 |
DIST manual-2018.8.pdf 10025023 BLAKE2B afb0a6e6a72d78df743fcb57e7c1716848589e571dd35167b957a9b407ca27978ccfb6cb9e0df9c9439b888f352501a00ba32281ed1e0b4193bd606f1d77152e SHA512 b1972f7ce965bfc9377542993c5943ea4868a8ed23a969d4203264746d6bea3a7a65c6379196ece37fd6d68ec7ec80f827bde87d1049284af7082759a124f1d5 |
| 28 |
DIST manual-2019.6.pdf 12702376 BLAKE2B c350127bc06a9eb3dee73da39037c84daeb89500e23cb131bd19a150bf60602d4dde7611e0c6f0f344af4093e96a899303dac71b4df56fd0c44c3a48a56606b7 SHA512 dfdff67c2c1c9ce1f1c236b7686c5331b0fe86951da6c98eddd6a3e748815e0be0a9653ae4318469fcdd913c4e7c355d64a997cc80b9d9fbe6282ef6d98e61eb |
| 29 |
@@ -13,6 +14,7 @@ DIST manual-2020.6.pdf 11850850 BLAKE2B 155e4eb9c200dcd0a38e3669b26077fcf310d437 |
| 30 |
DIST manual-2021.2.pdf 12252501 BLAKE2B 0dbf9024e1516076b0eeb46e41523b966d1d81f57504fe0501c7bc8575e74fb19e3452ac584757e425bcccbc737367fe83be87fd21a4287f4675cf87184b960b SHA512 14156d3b1017990e0be3ceb7ec055777a1aec4c347ac2e821a042d51c931f84ebca862f60644a90ed7ba4070cb14ff8babcde3e4351e4dbec84df8563e350984 |
| 31 |
DIST manual-2021.3.pdf 12255076 BLAKE2B 6ca516b6832507c9d4100679d1f9bc9e3ab17d226849b050764b0d0626247dc57ce49985f9a7fc0061f3df278923a83faa367ca8ab91c37e5624dc584a51a822 SHA512 5d53798f30ea00fcb4e1b35f7eaa4bebfc05dafa4f2d0c197dcf2b57a624ad3a98b74fd90722e40d0ac13a6fff4ca231f9d6340f52ba94659c827c53c2f1cb16 |
| 32 |
DIST manual-2021.4.pdf 12253232 BLAKE2B 0b859c08a07d5a615ac7a822b61d5a4f4296ca9773d383a07960dc629d6b1df23e1dec51561a4ac26789b84e49cc98b6d7cc10d943c61d7784052664ac1bacf9 SHA512 024f17a670518fc19a2a462186ed2a74f331c5c83b8ba4bbe148a53767515ba19e6af887a1baae3a7770af2095fad5c513784cc54f9d0f881395ad8a89760cba |
| 33 |
+DIST manual-2021.5.pdf 12253641 BLAKE2B 8850715a2bb21345e1c9735aca1a5dd2ad916e5a18881e7c9f3dda6f055ca12d9d379b74218138999ce50769efd8b9dd6447afbf70bbbefa2564dfb9fb276b91 SHA512 7635108c935e4953d722df6a16ee43edf97eef7e49f047218728f68f61f8f185192ff1d8b13a573b643b040955af211355a7b560c8a894c858d7f71249d41296 |
| 34 |
DIST manual-2022_beta1.pdf 13033013 BLAKE2B dda51c931e5b124d0fbd106a73b4f04d6d58374a8590b44d1f64897a2a2c97fb4a682275d2f2bd0907de5faec74d91550642bb505a3a316d2f7e20a84f0c1308 SHA512 ea7c1362fda8a4dc5b21242154daf9d9c66bdd2462d67335c56170189ed6f75a50bf51a0cdf8654886a3c0a537dfc0d364eb57f6602ce0065e4ac8ca106f5544 |
| 35 |
DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb |
| 36 |
DIST regressiontests-2019.6.tar.gz 67643195 BLAKE2B 1e054e24b187946f7ea28090d4f20cf8e1d79a26253f57ba07d130e0773d8541b8a1552a38023d31a68ce8bc62d8e0af1d98609234bb3e7d3e6d567307ebb386 SHA512 eacf1c55b982515a305c29459fe80a7cd558a8481e5689962aa956148af542568b1d1ce59c6784ecb0afd4768c2b664afa21e12af2d89ae2b06b1ba61ad72036 |
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@@ -21,4 +23,5 @@ DIST regressiontests-2020.6.tar.gz 48541232 BLAKE2B dbb405bd9168775984de8c9fb9e3 |
| 38 |
DIST regressiontests-2021.2.tar.gz 48514312 BLAKE2B 81b007d5e5e1d054349c73dc8bc3589db328752e48a66687c0ad36be87ebe580df9cbd93b193a724669bd5765af06ec306f2e12af00a228af616de03943d6f05 SHA512 b687ddfd3dc6ec1051af2a3253633703ef1c82335d1df23379819ea47e44dfcd417e81e29610cc584d4c5fb1ee1cbc76731a3fd31b529d8cdd0b9c22f432c7ec |
| 39 |
DIST regressiontests-2021.3.tar.gz 48515038 BLAKE2B ee79d8adddc9c68f7d59d9e568b12bf4d1fe0e44c2810fee846ad6f689bbcacf60f5c266433946329e64e3127bc2d37a3f81f69c070c636b411b38067650c2cf SHA512 e14baa22ef2902a23125bbd9143ae7a9a4810498b321794ff1989f8d044d47db5db41d5225798fda08016c05e5f7f315178b5a6e35cdf01e3b6604670a8ce7a2 |
| 40 |
DIST regressiontests-2021.4.tar.gz 48541736 BLAKE2B 37b8e65e333dcfcfc795da631475807ffa4ecc3a85426b4de6dd2ccb50f40a78159149789da13f988340a62d21e7d6b1d4f0c6e7fe69120d4c94ab2252b4c440 SHA512 18663693cf9ce2ca3bd8df0f668e7a0c8236a7f5ae4ee02f621cbe52c139c506b61ac4cab200cc59caab41e9983ea93dfa062d7b52f6558a619096a8d439fb56 |
| 41 |
+DIST regressiontests-2021.5.tar.gz 48537298 BLAKE2B 860ac34aa8706ecdafab4472162775ce12726d93839079ebf9b7df8c2c6a1b47baa8a635c24cf4cb4551a32237c3de7da3197ec136b5bbf48663edc3943720ad SHA512 3605d04b2602339fb7d33e2776da2ada337ca58a3802472d47f490d4e8dd04249a950bf34608a498eedebf69f344c0311bac8f7fcb58ce0ebbb6d608ee39aa2e |
| 42 |
DIST regressiontests-2022-beta1.tar.gz 48534065 BLAKE2B 4f0dd89b791fa11696460befa4a755dff14546abc10a4801ddb5f0286cee267ca983c082748b0ce9345a98b7fb98bb4a5387054a373acc543ff56b72e0ad9b64 SHA512 aa178a59bc7074e1d50d2cbe4d376f3593e0af6ad2a563627529fa4b0aa6a9bb29248caaace578150ab9e80feba3bf862ab964993eed183a79e35a189d10fecf |
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|
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diff --git a/sci-chemistry/gromacs/gromacs-2021.5.ebuild b/sci-chemistry/gromacs/gromacs-2021.5.ebuild |
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new file mode 100644 |
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index 000000000000..c40fa7838c07 |
| 47 |
--- /dev/null |
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+++ b/sci-chemistry/gromacs/gromacs-2021.5.ebuild |
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@@ -0,0 +1,356 @@ |
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+# Copyright 1999-2022 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=8 |
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+ |
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+CMAKE_MAKEFILE_GENERATOR="ninja" |
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+ |
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+PYTHON_COMPAT=( python3_{8..10} ) |
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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 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 )" |
| 76 |
+ 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" |
| 80 |
+ |
| 81 |
+DESCRIPTION="The ultimate molecular dynamics simulation package" |
| 82 |
+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 |
| 86 |
+# 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 |
| 96 |
+ ) |
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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:= ) |
| 102 |
+ lapack? ( virtual/lapack ) |
| 103 |
+ lmfit? ( sci-libs/lmfit:= ) |
| 104 |
+ mkl? ( sci-libs/mkl ) |
| 105 |
+ mpi? ( virtual/mpi ) |
| 106 |
+ ${PYTHON_DEPS} |
| 107 |
+ !sci-chemistry/gmxapi |
| 108 |
+ " |
| 109 |
+BDEPEND="${CDEPEND} |
| 110 |
+ virtual/pkgconfig |
| 111 |
+ build-manual? ( |
| 112 |
+ app-doc/doxygen |
| 113 |
+ $(python_gen_cond_dep ' |
| 114 |
+ dev-python/sphinx[${PYTHON_USEDEP}] |
| 115 |
+ ') |
| 116 |
+ media-gfx/mscgen |
| 117 |
+ media-gfx/graphviz |
| 118 |
+ dev-texlive/texlive-latex |
| 119 |
+ dev-texlive/texlive-latexextra |
| 120 |
+ media-gfx/imagemagick |
| 121 |
+ )" |
| 122 |
+RDEPEND="${CDEPEND}" |
| 123 |
+ |
| 124 |
+REQUIRED_USE=" |
| 125 |
+ || ( single-precision double-precision ) |
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+ doc? ( !build-manual ) |
| 127 |
+ cuda? ( single-precision ) |
| 128 |
+ cuda? ( !opencl ) |
| 129 |
+ mkl? ( !blas !fftw !lapack ) |
| 130 |
+ ${PYTHON_REQUIRED_USE}" |
| 131 |
+ |
| 132 |
+DOCS=( AUTHORS README ) |
| 133 |
+ |
| 134 |
+RESTRICT="!test? ( test )" |
| 135 |
+ |
| 136 |
+if [[ ${PV} != *9999 ]]; then |
| 137 |
+ S="${WORKDIR}/${PN}-${PV/_/-}" |
| 138 |
+fi |
| 139 |
+ |
| 140 |
+pkg_pretend() { |
| 141 |
+ [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
| 142 |
+ use openmp && ! tc-has-openmp && \ |
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+ die "Please switch to an openmp compatible compiler" |
| 144 |
+} |
| 145 |
+ |
| 146 |
+pkg_setup() { |
| 147 |
+ python-single-r1_pkg_setup |
| 148 |
+} |
| 149 |
+ |
| 150 |
+src_unpack() { |
| 151 |
+ if [[ ${PV} != *9999 ]]; then |
| 152 |
+ default |
| 153 |
+ else |
| 154 |
+ git-r3_src_unpack |
| 155 |
+ if use test; then |
| 156 |
+ EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
| 157 |
+ EGIT_BRANCH="${EGIT_BRANCH}" \ |
| 158 |
+ EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
| 159 |
+ git-r3_src_unpack |
| 160 |
+ fi |
| 161 |
+ fi |
| 162 |
+} |
| 163 |
+ |
| 164 |
+src_prepare() { |
| 165 |
+ #notes/todos |
| 166 |
+ # -on apple: there is framework support |
| 167 |
+ |
| 168 |
+ xdg_environment_reset #591952 |
| 169 |
+ |
| 170 |
+ cmake_src_prepare |
| 171 |
+ |
| 172 |
+ use cuda && cuda_src_prepare |
| 173 |
+ |
| 174 |
+ GMX_DIRS="" |
| 175 |
+ use single-precision && GMX_DIRS+=" float" |
| 176 |
+ use double-precision && GMX_DIRS+=" double" |
| 177 |
+ |
| 178 |
+ if use test; then |
| 179 |
+ for x in ${GMX_DIRS}; do |
| 180 |
+ mkdir -p "${WORKDIR}/${P}_${x}" || die |
| 181 |
+ cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
| 182 |
+ done |
| 183 |
+ fi |
| 184 |
+ |
| 185 |
+ DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
| 186 |
+ if use build-manual; then |
| 187 |
+ # try to create policy for imagemagik |
| 188 |
+ mkdir -p ${HOME}/.config/ImageMagick |
| 189 |
+ cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF |
| 190 |
+ <?xml version="1.0" encoding="UTF-8"?> |
| 191 |
+ <!DOCTYPE policymap [ |
| 192 |
+ <!ELEMENT policymap (policy)+> |
| 193 |
+ !ATTLIST policymap xmlns CDATA #FIXED ''> |
| 194 |
+ <!ELEMENT policy EMPTY> |
| 195 |
+ <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED |
| 196 |
+ name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED |
| 197 |
+ stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> |
| 198 |
+ ]> |
| 199 |
+ <policymap> |
| 200 |
+ <policy domain="coder" rights="read | write" pattern="PS" /> |
| 201 |
+ <policy domain="coder" rights="read | write" pattern="PS2" /> |
| 202 |
+ <policy domain="coder" rights="read | write" pattern="PS3" /> |
| 203 |
+ <policy domain="coder" rights="read | write" pattern="EPS" /> |
| 204 |
+ <policy domain="coder" rights="read | write" pattern="PDF" /> |
| 205 |
+ <policy domain="coder" rights="read | write" pattern="XPS" /> |
| 206 |
+ </policymap> |
| 207 |
+ EOF |
| 208 |
+ fi |
| 209 |
+} |
| 210 |
+ |
| 211 |
+src_configure() { |
| 212 |
+ local mycmakeargs_pre=( ) extra fft_opts=( ) |
| 213 |
+ local acce="AUTO" |
| 214 |
+ |
| 215 |
+ if use custom-cflags; then |
| 216 |
+ #go from slowest to fastest acceleration |
| 217 |
+ acce="None" |
| 218 |
+ if (use amd64 || use x86); then |
| 219 |
+ use cpu_flags_x86_sse2 && acce="SSE2" |
| 220 |
+ use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
| 221 |
+ use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
| 222 |
+ use cpu_flags_x86_avx && acce="AVX_256" |
| 223 |
+ use cpu_flags_x86_avx2 && acce="AVX2_256" |
| 224 |
+ use cpu_flags_x86_avx512f && acce="AVX_512" |
| 225 |
+ elif (use arm); then |
| 226 |
+ use cpu_flags_arm_neon && acce="ARM_NEON" |
| 227 |
+ elif (use arm64); then |
| 228 |
+ use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD" |
| 229 |
+ fi |
| 230 |
+ else |
| 231 |
+ strip-flags |
| 232 |
+ fi |
| 233 |
+ |
| 234 |
+ #to create man pages, build tree binaries are executed (bug #398437) |
| 235 |
+ [[ ${CHOST} = *-darwin* ]] && \ |
| 236 |
+ extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
| 237 |
+ |
| 238 |
+ if use fftw; then |
| 239 |
+ fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
| 240 |
+ elif use mkl && has_version "=sci-libs/mkl-10*"; then |
| 241 |
+ fft_opts=( -DGMX_FFT_LIBRARY=mkl |
| 242 |
+ -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
| 243 |
+ -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
| 244 |
+ ) |
| 245 |
+ elif use mkl; then |
| 246 |
+ local bits=$(get_libdir) |
| 247 |
+ fft_opts=( -DGMX_FFT_LIBRARY=mkl |
| 248 |
+ -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
| 249 |
+ -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
| 250 |
+ ) |
| 251 |
+ else |
| 252 |
+ fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
| 253 |
+ fi |
| 254 |
+ |
| 255 |
+ if use lmfit; then |
| 256 |
+ local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) |
| 257 |
+ else |
| 258 |
+ local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) |
| 259 |
+ fi |
| 260 |
+ |
| 261 |
+ mycmakeargs_pre+=( |
| 262 |
+ "${fft_opts[@]}" |
| 263 |
+ "${lmfit_opts[@]}" |
| 264 |
+ -DGMX_X11=$(usex X) |
| 265 |
+ -DGMX_EXTERNAL_BLAS=$(usex blas) |
| 266 |
+ -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
| 267 |
+ -DGMX_OPENMP=$(usex openmp) |
| 268 |
+ -DGMX_COOL_QUOTES=$(usex offensive) |
| 269 |
+ -DGMX_USE_TNG=$(usex tng) |
| 270 |
+ -DGMX_BUILD_MANUAL=$(usex build-manual) |
| 271 |
+ -DGMX_HWLOC=$(usex hwloc) |
| 272 |
+ -DGMX_DEFAULT_SUFFIX=off |
| 273 |
+ -DGMX_SIMD="$acce" |
| 274 |
+ -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
| 275 |
+ -DBUILD_TESTING=$(usex test) |
| 276 |
+ -DGMX_BUILD_UNITTESTS=$(usex test) |
| 277 |
+ -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" |
| 278 |
+ ${extra} |
| 279 |
+ ) |
| 280 |
+ |
| 281 |
+ for x in ${GMX_DIRS}; do |
| 282 |
+ einfo "Configuring for ${x} precision" |
| 283 |
+ local suffix="" |
| 284 |
+ #if we build single and double - double is suffixed |
| 285 |
+ use double-precision && use single-precision && \ |
| 286 |
+ [[ ${x} = "double" ]] && suffix="_d" |
| 287 |
+ local p |
| 288 |
+ [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
| 289 |
+ local gpu=( "-DGMX_GPU=OFF" ) |
| 290 |
+ [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) |
| 291 |
+ use opencl && gpu=( "-DGMX_GPU=OPENCL" ) |
| 292 |
+ mycmakeargs=( |
| 293 |
+ ${mycmakeargs_pre[@]} ${p} |
| 294 |
+ -DGMX_MPI=OFF |
| 295 |
+ -DGMX_THREAD_MPI=$(usex threads) |
| 296 |
+ -DGMXAPI=$(usex gmxapi) |
| 297 |
+ -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) |
| 298 |
+ "${gpu[@]}" |
| 299 |
+ "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
| 300 |
+ -DGMX_BINARY_SUFFIX="${suffix}" |
| 301 |
+ -DGMX_LIBS_SUFFIX="${suffix}" |
| 302 |
+ -DGMX_PYTHON_PACKAGE=$(usex python) |
| 303 |
+ ) |
| 304 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure |
| 305 |
+ [[ ${CHOST} != *-darwin* ]] || \ |
| 306 |
+ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
| 307 |
+ use mpi || continue |
| 308 |
+ einfo "Configuring for ${x} precision with mpi" |
| 309 |
+ mycmakeargs=( |
| 310 |
+ ${mycmakeargs_pre[@]} ${p} |
| 311 |
+ -DGMX_THREAD_MPI=OFF |
| 312 |
+ -DGMX_MPI=ON |
| 313 |
+ -DGMX_OPENMM=OFF |
| 314 |
+ -DGMXAPI=OFF |
| 315 |
+ "${opencl[@]}" |
| 316 |
+ "${cuda[@]}" |
| 317 |
+ -DGMX_BUILD_MDRUN_ONLY=ON |
| 318 |
+ -DBUILD_SHARED_LIBS=OFF |
| 319 |
+ -DGMX_BUILD_MANUAL=OFF |
| 320 |
+ -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
| 321 |
+ -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
| 322 |
+ ) |
| 323 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure |
| 324 |
+ [[ ${CHOST} != *-darwin* ]] || \ |
| 325 |
+ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
| 326 |
+ done |
| 327 |
+} |
| 328 |
+ |
| 329 |
+src_compile() { |
| 330 |
+ for x in ${GMX_DIRS}; do |
| 331 |
+ einfo "Compiling for ${x} precision" |
| 332 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| 333 |
+ cmake_src_compile |
| 334 |
+ if use python; then |
| 335 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| 336 |
+ cmake_src_compile python_packaging/all |
| 337 |
+ BUILD_DIR="${WORKDIR}/${P}" \ |
| 338 |
+ distutils-r1_src_compile |
| 339 |
+ fi |
| 340 |
+ # not 100% necessary for rel ebuilds as available from website |
| 341 |
+ if use build-manual; then |
| 342 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| 343 |
+ cmake_src_compile manual |
| 344 |
+ fi |
| 345 |
+ use mpi || continue |
| 346 |
+ einfo "Compiling for ${x} precision with mpi" |
| 347 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
| 348 |
+ cmake_src_compile |
| 349 |
+ done |
| 350 |
+} |
| 351 |
+ |
| 352 |
+src_test() { |
| 353 |
+ for x in ${GMX_DIRS}; do |
| 354 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| 355 |
+ cmake_src_compile check |
| 356 |
+ done |
| 357 |
+} |
| 358 |
+ |
| 359 |
+src_install() { |
| 360 |
+ for x in ${GMX_DIRS}; do |
| 361 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
| 362 |
+ cmake_src_install |
| 363 |
+ if use python; then |
| 364 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
| 365 |
+ cmake_src_install python_packaging/install |
| 366 |
+ fi |
| 367 |
+ if use build-manual; then |
| 368 |
+ newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
| 369 |
+ fi |
| 370 |
+ |
| 371 |
+ if use doc; then |
| 372 |
+ if [[ ${PV} != *9999* ]]; then |
| 373 |
+ newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" |
| 374 |
+ fi |
| 375 |
+ fi |
| 376 |
+ |
| 377 |
+ use mpi || continue |
| 378 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
| 379 |
+ cmake_src_install |
| 380 |
+ done |
| 381 |
+ |
| 382 |
+ if use tng; then |
| 383 |
+ insinto /usr/include/tng |
| 384 |
+ doins src/external/tng_io/include/tng/*h |
| 385 |
+ fi |
| 386 |
+ # drop unneeded stuff |
| 387 |
+ rm "${ED}"/usr/bin/GMXRC* || die |
| 388 |
+ for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do |
| 389 |
+ local n=${x##*/gmx-completion-} |
| 390 |
+ n="${n%.bash}" |
| 391 |
+ cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
| 392 |
+ newbashcomp "${T}"/"${n}" "${n}" |
| 393 |
+ done |
| 394 |
+ rm "${ED}"/usr/bin/gmx-completion*.bash || die |
| 395 |
+ readme.gentoo_create_doc |
| 396 |
+} |
| 397 |
+ |
| 398 |
+pkg_postinst() { |
| 399 |
+ einfo |
| 400 |
+ einfo "Please read and cite:" |
| 401 |
+ einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
| 402 |
+ einfo "https://dx.doi.org/10.1021/ct700301q" |
| 403 |
+ einfo |
| 404 |
+ readme.gentoo_print_elog |
| 405 |
+} |
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