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Diffstat (limited to 'var/spack/repos/builtin/packages/relion/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/relion/package.py | 80 |
1 files changed, 46 insertions, 34 deletions
diff --git a/var/spack/repos/builtin/packages/relion/package.py b/var/spack/repos/builtin/packages/relion/package.py index ba006b9b43..eb092b6fa1 100644 --- a/var/spack/repos/builtin/packages/relion/package.py +++ b/var/spack/repos/builtin/packages/relion/package.py @@ -1,56 +1,59 @@ -############################################################################## -# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. +# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. # -# This file is part of Spack. -# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/spack/spack -# Please also see the NOTICE and LICENSE files for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU Lesser General Public License (as -# published by the Free Software Foundation) version 2.1, February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + from spack import * -class Relion(CMakePackage): +class Relion(CMakePackage, CudaPackage): """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).""" homepage = "http://http://www2.mrc-lmb.cam.ac.uk/relion" - url = "https://github.com/3dem/relion" + git = "https://github.com/3dem/relion.git" - version('develop', git='https://github.com/3dem/relion.git') + version('3.0_beta', + git='https://bitbucket.org/scheres/relion-3.0_beta.git') + version('2.1', preferred='true', tag='2.1') + version('2.0.3', tag='2.0.3') + # relion has no develop branch though pulling from master + # should be considered the same as develop + version('develop', branch='master') variant('gui', default=True, description="build the gui") - variant('cuda', default=False, description="enable compute on gpu") - variant('double', default=False, description="double precision (cpu) code") - variant('double-gpu', default=False, description="double precision (gpu) code") + variant('cuda', default=True, description="enable compute on gpu") + variant('double', default=True, description="double precision (cpu) code") + variant('double-gpu', default=False, description="double precision gpu") + # if built with purpose=cluster then relion will link to gpfs libraries + # if that's not desirable then use purpose=desktop + variant('purpose', default='cluster', values=('cluster', 'desktop'), + description="build relion for use in cluster or desktop") variant('build_type', default='RelWithDebInfo', description='The build type to build', values=('Debug', 'Release', 'RelWithDebInfo', 'Profiling', 'Benchmarking')) depends_on('mpi') + # relion will not build with newer versions of cmake + # per https://github.com/3dem/relion/issues/380 + depends_on('cmake@3:3.9.4', type='build') depends_on('fftw+float+double') depends_on('fltk', when='+gui') - depends_on('cuda@8.0:8.99', when='+cuda') + depends_on('libtiff') + + # relion 3 supports cuda 9 + # relion < 3 does not + depends_on('cuda', when='+cuda') + depends_on('cuda@9:', when='@3: +cuda') + depends_on('cuda@8.0:8.99', when='@:2 +cuda') def cmake_args(self): + + carch = self.spec.variants['cuda_arch'].value[0] + args = [ '-DCMAKE_C_FLAGS=-g', '-DCMAKE_CXX_FLAGS=-g', @@ -58,9 +61,18 @@ class Relion(CMakePackage): '-DDoublePrec_CPU=%s' % ('+double' in self.spec), '-DDoublePrec_GPU=%s' % ('+double-gpu' in self.spec), ] + if '+cuda' in self.spec: - args += [ - '-DCUDA=on', - '-DCUFFT=on', - ] + # relion+cuda requires selecting cuda_arch + if not carch: + raise ValueError("select cuda_arch when building with +cuda") + else: + args += ['-DCUDA=ON', '-DCudaTexture=ON', + '-DCUDA_ARCH=%s' % (carch)] + + # these new values were added in relion 3 + # do not seem to cause problems with < 3 + else: + args += ['-DMKLFFT=ON', '-DFORCE_OWN_TBB=ON', '-DALTCPU=ON'] + return args |