| 1 |
commit: 80c324169f08266fd4a384487d7a01ff20a29537 |
| 2 |
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
| 3 |
AuthorDate: Fri Oct 9 21:32:01 2020 +0000 |
| 4 |
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
| 5 |
CommitDate: Fri Oct 9 21:32:01 2020 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=80c32416 |
| 7 |
|
| 8 |
sci-chemistry/gromacs: Version bump |
| 9 |
|
| 10 |
Package-Manager: Portage-3.0.8, Repoman-3.0.1 |
| 11 |
Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org> |
| 12 |
|
| 13 |
sci-chemistry/gromacs/Manifest | 2 + |
| 14 |
sci-chemistry/gromacs/gromacs-2020.4.ebuild | 341 ++++++++++++++++++++++++++++ |
| 15 |
2 files changed, 343 insertions(+) |
| 16 |
|
| 17 |
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest |
| 18 |
index b245b79ba3d..9ff5ce63cab 100644 |
| 19 |
--- a/sci-chemistry/gromacs/Manifest |
| 20 |
+++ b/sci-chemistry/gromacs/Manifest |
| 21 |
@@ -4,6 +4,7 @@ DIST gromacs-2019.6.tar.gz 33446147 BLAKE2B adc21fb6b841b06d499607f8c0166a673645 |
| 22 |
DIST gromacs-2020.1.tar.gz 29153989 BLAKE2B b1c0313da945c57c74040c2bcd50495b238b0e131cc4ebecd74ae0d01465b47d732ea456a52a2f9d998cd37e2bfdb93d52bd15177328c4b7a14e6b1d8bc00117 SHA512 130394ec70e5d75ea451e9fa77c4ea2dd4adb0c51cc7663ac8579972bab7a0b75d9143d0eebb21802fc93305deca8831393a8cb3f51b6d01f9477f3dadece037 |
| 23 |
DIST gromacs-2020.2.tar.gz 29144614 BLAKE2B cd20b031dcec32d9a797d66f2679779077910c184702f12f12093d92e8417d42e07bfb17a8fe63e9d29a889d5f57461b5f86e11adfc26635f8d2b5a5df19473a SHA512 348c80fad93b34e6703906fec97c6c2294c0803c326d6145776b732e1c33cd58e0967ddb2ec4799e3583542c09e7a6a015e4d084d60cf97b81b3a92253cca76c |
| 24 |
DIST gromacs-2020.3.tar.gz 29143950 BLAKE2B ea88fcacc3958f1123c1fe4852f7160a04e4daff15dd2eb87c23197bff2e6379f396df0747b078dc86e7bb909ecbb4b6d98530a34234c989a636dbdb2327562d SHA512 8dbd13f8c6dd9ac337e0bea683aeff38010ee9b4ef438de230beb76e5a54884a5c1eda72f20294b7920758978e247900ac3db32b95c7452350fc1f5ef0a4bcc8 |
| 25 |
+DIST gromacs-2020.4.tar.gz 29149899 BLAKE2B a07c8efd96137d58c1edf4ac9b5aafeb16d9e65234b9459b71471827032654acacb58ed6ae87ec6e0e593a0acd799683cc4461b06cc883b089d740708619345e SHA512 0c56f058741af70660baf0177724ec940dd984c05ea141ede91ee51ce3744f76d00e31bdb5db907e46fa1639de5dca637b3ace26e89f908c2e74c69f0c21ed3a |
| 26 |
DIST manual-2018.8.pdf 10025023 BLAKE2B afb0a6e6a72d78df743fcb57e7c1716848589e571dd35167b957a9b407ca27978ccfb6cb9e0df9c9439b888f352501a00ba32281ed1e0b4193bd606f1d77152e SHA512 b1972f7ce965bfc9377542993c5943ea4868a8ed23a969d4203264746d6bea3a7a65c6379196ece37fd6d68ec7ec80f827bde87d1049284af7082759a124f1d5 |
| 27 |
DIST manual-2019.5.pdf 12702361 BLAKE2B cb80429a59019b190115bf2af689c0df23b0fec6e41a9ebc9eba20977d1b06eed79044c906c41228883767f673140e15d3a5ef947a0c1ec4fe84012089f4fa91 SHA512 baf27961b87e6120c49abc9dc58e25d12a15588b4ac787e1a086748d488692d4a1262229ac66e550d3cca3a6042545fb6ec472a2c98d6a8698b7a18b4397f605 |
| 28 |
DIST manual-2019.6.pdf 12702376 BLAKE2B c350127bc06a9eb3dee73da39037c84daeb89500e23cb131bd19a150bf60602d4dde7611e0c6f0f344af4093e96a899303dac71b4df56fd0c44c3a48a56606b7 SHA512 dfdff67c2c1c9ce1f1c236b7686c5331b0fe86951da6c98eddd6a3e748815e0be0a9653ae4318469fcdd913c4e7c355d64a997cc80b9d9fbe6282ef6d98e61eb |
| 29 |
@@ -13,3 +14,4 @@ DIST regressiontests-2019.6.tar.gz 67643195 BLAKE2B 1e054e24b187946f7ea28090d4f2 |
| 30 |
DIST regressiontests-2020.1.tar.gz 48541809 BLAKE2B 0fec2f0fb7fad0ad48bb790d7df6487e2c1931a0a2134795bf7da4a9087f0f2a3743288fc4ec057fa6b22412c2d8f312cfa3af38be8c5bea51d7a06afb5ac9f0 SHA512 664d29ce39629ed218de65179ce4a73e479d73d30bc96f5ae57624d7e4447298c6122dc09e7873b8cad458eaee0530866411fab20e009e46bf39b133e0de47e8 |
| 31 |
DIST regressiontests-2020.2.tar.gz 48539492 BLAKE2B 08222ec18e70f551194fc0a060facda394c0d9999e162dace06029aa5f36e7237aeb2468a80d1198257a45fb076f8f633a7279a85976484900bf4154176aa070 SHA512 3066d92a59dafade78807612681d82a7b8a0bd9b74fa7e8784063a908418c55b4427482dc7feb261ff6981fabb2d64a800d3e90ed647ab45e201f4847347bac7 |
| 32 |
DIST regressiontests-2020.3.tar.gz 48541439 BLAKE2B c8b3840b76b7974e5efd518d02da2be3c8e685a420462962cf4ffb7b234bd5ffec0fb83adc962e4ce4716098667e1431f7bc46911bf5400f369881c697c1d0cb SHA512 84848210b2c4c0387c3f347237d58a114bd28c2d248f359e40a4a5b3557fca7763c431d1e03f167dcf22296a48dd47413a644238d72edc1414e3f830dd732416 |
| 33 |
+DIST regressiontests-2020.4.tar.gz 48542144 BLAKE2B 1dcde67525d40ababa74d9e8ba2dd3fdef1de7d1018491e102edd71d3a622925f213b5a0812e5448882b4cb5fb578317e8e5029bdc4bd53008aa8441a3d9dea1 SHA512 7c71f36a1cef22562f14dcd233e90ad2fe370ae1a7d3b5268727259b374e12d4754253735ac8745d3738bdbc1cc2067780fda5e393be2ff264f632fe4e0c1978 |
| 34 |
|
| 35 |
diff --git a/sci-chemistry/gromacs/gromacs-2020.4.ebuild b/sci-chemistry/gromacs/gromacs-2020.4.ebuild |
| 36 |
new file mode 100644 |
| 37 |
index 00000000000..ba456196edd |
| 38 |
--- /dev/null |
| 39 |
+++ b/sci-chemistry/gromacs/gromacs-2020.4.ebuild |
| 40 |
@@ -0,0 +1,341 @@ |
| 41 |
+# Copyright 1999-2020 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_{6,7,8} ) |
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+ |
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+DISTUTILS_SINGLE_IMPL=1 |
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+ |
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+inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils |
| 53 |
+ |
| 54 |
+if [[ $PV = *9999* ]]; then |
| 55 |
+ EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
| 56 |
+ https://gerrit.gromacs.org/gromacs.git |
| 57 |
+ https://github.com/gromacs/gromacs.git |
| 58 |
+ https://repo.or.cz/r/gromacs.git" |
| 59 |
+ [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" |
| 60 |
+ inherit git-r3 |
| 61 |
+else |
| 62 |
+ SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
| 63 |
+ test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" |
| 64 |
+ KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
| 65 |
+fi |
| 66 |
+ |
| 67 |
+ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
| 68 |
+ |
| 69 |
+DESCRIPTION="The ultimate molecular dynamics simulation package" |
| 70 |
+HOMEPAGE="http://www.gromacs.org/" |
| 71 |
+ |
| 72 |
+# see COPYING for details |
| 73 |
+# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
| 74 |
+# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
| 75 |
+LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
| 76 |
+SLOT="0/${PV}" |
| 77 |
+IUSE="X blas cuda +custom-cflags +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" |
| 78 |
+ |
| 79 |
+CDEPEND=" |
| 80 |
+ X? ( |
| 81 |
+ x11-libs/libX11 |
| 82 |
+ x11-libs/libSM |
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+ x11-libs/libICE |
| 84 |
+ ) |
| 85 |
+ blas? ( virtual/blas ) |
| 86 |
+ cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) |
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+ opencl? ( virtual/opencl ) |
| 88 |
+ fftw? ( sci-libs/fftw:3.0 ) |
| 89 |
+ hwloc? ( sys-apps/hwloc ) |
| 90 |
+ lapack? ( virtual/lapack ) |
| 91 |
+ lmfit? ( sci-libs/lmfit ) |
| 92 |
+ mkl? ( sci-libs/mkl ) |
| 93 |
+ mpi? ( virtual/mpi ) |
| 94 |
+ ${PYTHON_DEPS} |
| 95 |
+ !sci-chemistry/gmxapi |
| 96 |
+ " |
| 97 |
+BDEPEND="${CDEPEND} |
| 98 |
+ virtual/pkgconfig |
| 99 |
+ doc? ( |
| 100 |
+ app-doc/doxygen |
| 101 |
+ $(python_gen_cond_dep ' |
| 102 |
+ dev-python/sphinx[${PYTHON_MULTI_USEDEP}] |
| 103 |
+ ') |
| 104 |
+ media-gfx/mscgen |
| 105 |
+ media-gfx/graphviz |
| 106 |
+ dev-texlive/texlive-latex |
| 107 |
+ dev-texlive/texlive-latexextra |
| 108 |
+ media-gfx/imagemagick |
| 109 |
+ )" |
| 110 |
+RDEPEND="${CDEPEND}" |
| 111 |
+ |
| 112 |
+REQUIRED_USE=" |
| 113 |
+ || ( single-precision double-precision ) |
| 114 |
+ cuda? ( single-precision ) |
| 115 |
+ cuda? ( !opencl ) |
| 116 |
+ mkl? ( !blas !fftw !lapack ) |
| 117 |
+ ${PYTHON_REQUIRED_USE}" |
| 118 |
+ |
| 119 |
+DOCS=( AUTHORS README ) |
| 120 |
+ |
| 121 |
+RESTRICT="!test? ( test )" |
| 122 |
+ |
| 123 |
+if [[ ${PV} != *9999 ]]; then |
| 124 |
+ S="${WORKDIR}/${PN}-${PV/_/-}" |
| 125 |
+fi |
| 126 |
+ |
| 127 |
+PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" ) |
| 128 |
+ |
| 129 |
+pkg_pretend() { |
| 130 |
+ [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
| 131 |
+ use openmp && ! tc-has-openmp && \ |
| 132 |
+ die "Please switch to an openmp compatible compiler" |
| 133 |
+} |
| 134 |
+ |
| 135 |
+pkg_setup() { |
| 136 |
+ python-single-r1_pkg_setup |
| 137 |
+} |
| 138 |
+ |
| 139 |
+src_unpack() { |
| 140 |
+ if [[ ${PV} != *9999 ]]; then |
| 141 |
+ default |
| 142 |
+ else |
| 143 |
+ git-r3_src_unpack |
| 144 |
+ if use test; then |
| 145 |
+ EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
| 146 |
+ EGIT_BRANCH="${EGIT_BRANCH}" \ |
| 147 |
+ EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
| 148 |
+ git-r3_src_unpack |
| 149 |
+ fi |
| 150 |
+ fi |
| 151 |
+} |
| 152 |
+ |
| 153 |
+src_prepare() { |
| 154 |
+ #notes/todos |
| 155 |
+ # -on apple: there is framework support |
| 156 |
+ |
| 157 |
+ xdg_environment_reset #591952 |
| 158 |
+ |
| 159 |
+ cmake_src_prepare |
| 160 |
+ |
| 161 |
+ use cuda && cuda_src_prepare |
| 162 |
+ |
| 163 |
+ GMX_DIRS="" |
| 164 |
+ use single-precision && GMX_DIRS+=" float" |
| 165 |
+ use double-precision && GMX_DIRS+=" double" |
| 166 |
+ |
| 167 |
+ if use test; then |
| 168 |
+ for x in ${GMX_DIRS}; do |
| 169 |
+ mkdir -p "${WORKDIR}/${P}_${x}" || die |
| 170 |
+ cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
| 171 |
+ done |
| 172 |
+ fi |
| 173 |
+ |
| 174 |
+ DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
| 175 |
+ |
| 176 |
+ # try to create policy for imagemagik |
| 177 |
+ mkdir -p ${HOME}/.config/ImageMagick |
| 178 |
+ cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF |
| 179 |
+ <?xml version="1.0" encoding="UTF-8"?> |
| 180 |
+ <!DOCTYPE policymap [ |
| 181 |
+ <!ELEMENT policymap (policy)+> |
| 182 |
+ !ATTLIST policymap xmlns CDATA #FIXED ''> |
| 183 |
+ <!ELEMENT policy EMPTY> |
| 184 |
+ <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED |
| 185 |
+ name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED |
| 186 |
+ stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> |
| 187 |
+ ]> |
| 188 |
+ <policymap> |
| 189 |
+ <policy domain="coder" rights="read | write" pattern="PS" /> |
| 190 |
+ <policy domain="coder" rights="read | write" pattern="PS2" /> |
| 191 |
+ <policy domain="coder" rights="read | write" pattern="PS3" /> |
| 192 |
+ <policy domain="coder" rights="read | write" pattern="EPS" /> |
| 193 |
+ <policy domain="coder" rights="read | write" pattern="PDF" /> |
| 194 |
+ <policy domain="coder" rights="read | write" pattern="XPS" /> |
| 195 |
+ </policymap> |
| 196 |
+ EOF |
| 197 |
+} |
| 198 |
+ |
| 199 |
+src_configure() { |
| 200 |
+ local mycmakeargs_pre=( ) extra fft_opts=( ) |
| 201 |
+ |
| 202 |
+ if use custom-cflags; then |
| 203 |
+ #go from slowest to fastest acceleration |
| 204 |
+ local acce="None" |
| 205 |
+ use cpu_flags_x86_sse2 && acce="SSE2" |
| 206 |
+ use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
| 207 |
+ use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
| 208 |
+ use cpu_flags_x86_avx && acce="AVX_256" |
| 209 |
+ use cpu_flags_x86_avx2 && acce="AVX2_256" |
| 210 |
+ else |
| 211 |
+ strip-flags |
| 212 |
+ fi |
| 213 |
+ |
| 214 |
+ #to create man pages, build tree binaries are executed (bug #398437) |
| 215 |
+ [[ ${CHOST} = *-darwin* ]] && \ |
| 216 |
+ extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
| 217 |
+ |
| 218 |
+ if use fftw; then |
| 219 |
+ fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
| 220 |
+ elif use mkl && has_version "=sci-libs/mkl-10*"; then |
| 221 |
+ fft_opts=( -DGMX_FFT_LIBRARY=mkl |
| 222 |
+ -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
| 223 |
+ -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
| 224 |
+ ) |
| 225 |
+ elif use mkl; then |
| 226 |
+ local bits=$(get_libdir) |
| 227 |
+ fft_opts=( -DGMX_FFT_LIBRARY=mkl |
| 228 |
+ -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
| 229 |
+ -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
| 230 |
+ ) |
| 231 |
+ else |
| 232 |
+ fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
| 233 |
+ fi |
| 234 |
+ |
| 235 |
+ if use lmfit; then |
| 236 |
+ local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) |
| 237 |
+ else |
| 238 |
+ local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) |
| 239 |
+ fi |
| 240 |
+ |
| 241 |
+ mycmakeargs_pre+=( |
| 242 |
+ "${fft_opts[@]}" |
| 243 |
+ "${lmfit_opts[@]}" |
| 244 |
+ -DGMX_X11=$(usex X) |
| 245 |
+ -DGMX_EXTERNAL_BLAS=$(usex blas) |
| 246 |
+ -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
| 247 |
+ -DGMX_OPENMP=$(usex openmp) |
| 248 |
+ -DGMX_COOL_QUOTES=$(usex offensive) |
| 249 |
+ -DGMX_USE_TNG=$(usex tng) |
| 250 |
+ -DGMX_BUILD_MANUAL=$(usex doc) |
| 251 |
+ -DGMX_HWLOC=$(usex hwloc) |
| 252 |
+ -DGMX_DEFAULT_SUFFIX=off |
| 253 |
+ -DGMX_SIMD="$acce" |
| 254 |
+ -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
| 255 |
+ -DBUILD_TESTING=$(usex test) |
| 256 |
+ -DGMX_BUILD_UNITTESTS=$(usex test) |
| 257 |
+ -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" |
| 258 |
+ ${extra} |
| 259 |
+ ) |
| 260 |
+ |
| 261 |
+ for x in ${GMX_DIRS}; do |
| 262 |
+ einfo "Configuring for ${x} precision" |
| 263 |
+ local suffix="" |
| 264 |
+ #if we build single and double - double is suffixed |
| 265 |
+ use double-precision && use single-precision && \ |
| 266 |
+ [[ ${x} = "double" ]] && suffix="_d" |
| 267 |
+ local p |
| 268 |
+ [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
| 269 |
+ local cuda=( "-DGMX_GPU=OFF" ) |
| 270 |
+ [[ ${x} = "float" ]] && use cuda && \ |
| 271 |
+ cuda=( "-DGMX_GPU=ON" ) |
| 272 |
+ local opencl=( "-DGMX_USE_OPENCL=OFF" ) |
| 273 |
+ use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) |
| 274 |
+ mycmakeargs=( |
| 275 |
+ ${mycmakeargs_pre[@]} ${p} |
| 276 |
+ -DGMX_MPI=OFF |
| 277 |
+ -DGMX_THREAD_MPI=$(usex threads) |
| 278 |
+ -DGMXAPI=$(usex gmxapi) |
| 279 |
+ -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) |
| 280 |
+ "${opencl[@]}" |
| 281 |
+ "${cuda[@]}" |
| 282 |
+ "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
| 283 |
+ -DGMX_BINARY_SUFFIX="${suffix}" |
| 284 |
+ -DGMX_LIBS_SUFFIX="${suffix}" |
| 285 |
+ -DGMX_PYTHON_PACKAGE=$(usex python) |
| 286 |
+ ) |
| 287 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure |
| 288 |
+ [[ ${CHOST} != *-darwin* ]] || \ |
| 289 |
+ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
| 290 |
+ use mpi || continue |
| 291 |
+ einfo "Configuring for ${x} precision with mpi" |
| 292 |
+ mycmakeargs=( |
| 293 |
+ ${mycmakeargs_pre[@]} ${p} |
| 294 |
+ -DGMX_THREAD_MPI=OFF |
| 295 |
+ -DGMX_MPI=ON |
| 296 |
+ -DGMX_OPENMM=OFF |
| 297 |
+ -DGMXAPI=OFF |
| 298 |
+ "${opencl[@]}" |
| 299 |
+ "${cuda[@]}" |
| 300 |
+ -DGMX_BUILD_MDRUN_ONLY=ON |
| 301 |
+ -DBUILD_SHARED_LIBS=OFF |
| 302 |
+ -DGMX_BUILD_MANUAL=OFF |
| 303 |
+ -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
| 304 |
+ -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
| 305 |
+ ) |
| 306 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure |
| 307 |
+ [[ ${CHOST} != *-darwin* ]] || \ |
| 308 |
+ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
| 309 |
+ done |
| 310 |
+} |
| 311 |
+ |
| 312 |
+src_compile() { |
| 313 |
+ for x in ${GMX_DIRS}; do |
| 314 |
+ einfo "Compiling for ${x} precision" |
| 315 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| 316 |
+ cmake_src_compile |
| 317 |
+ if use python; then |
| 318 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| 319 |
+ cmake_src_compile python_packaging/all |
| 320 |
+ BUILD_DIR="${WORKDIR}/${P}" \ |
| 321 |
+ distutils-r1_src_compile |
| 322 |
+ fi |
| 323 |
+ # not 100% necessary for rel ebuilds as available from website |
| 324 |
+ if use doc; then |
| 325 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| 326 |
+ cmake_src_compile manual |
| 327 |
+ fi |
| 328 |
+ use mpi || continue |
| 329 |
+ einfo "Compiling for ${x} precision with mpi" |
| 330 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
| 331 |
+ cmake_src_compile |
| 332 |
+ done |
| 333 |
+} |
| 334 |
+ |
| 335 |
+src_test() { |
| 336 |
+ for x in ${GMX_DIRS}; do |
| 337 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| 338 |
+ cmake_src_make check |
| 339 |
+ done |
| 340 |
+} |
| 341 |
+ |
| 342 |
+src_install() { |
| 343 |
+ for x in ${GMX_DIRS}; do |
| 344 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
| 345 |
+ cmake_src_install |
| 346 |
+ if use python; then |
| 347 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
| 348 |
+ cmake_src_install python_packaging/install |
| 349 |
+ fi |
| 350 |
+ if use doc; then |
| 351 |
+ newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
| 352 |
+ fi |
| 353 |
+ use mpi || continue |
| 354 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
| 355 |
+ cmake_src_install |
| 356 |
+ done |
| 357 |
+ |
| 358 |
+ if use tng; then |
| 359 |
+ insinto /usr/include/tng |
| 360 |
+ doins src/external/tng_io/include/tng/*h |
| 361 |
+ fi |
| 362 |
+ # drop unneeded stuff |
| 363 |
+ rm "${ED}"/usr/bin/GMXRC* || die |
| 364 |
+ for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do |
| 365 |
+ local n=${x##*/gmx-completion-} |
| 366 |
+ n="${n%.bash}" |
| 367 |
+ cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
| 368 |
+ newbashcomp "${T}"/"${n}" "${n}" |
| 369 |
+ done |
| 370 |
+ rm "${ED}"/usr/bin/gmx-completion*.bash || die |
| 371 |
+ readme.gentoo_create_doc |
| 372 |
+} |
| 373 |
+ |
| 374 |
+pkg_postinst() { |
| 375 |
+ einfo |
| 376 |
+ einfo "Please read and cite:" |
| 377 |
+ einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
| 378 |
+ einfo "https://dx.doi.org/10.1021/ct700301q" |
| 379 |
+ einfo |
| 380 |
+ readme.gentoo_print_elog |
| 381 |
+} |
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