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# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
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"
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=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('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',
'-DGUI=%s' % ('+gui' in self.spec),
'-DDoublePrec_CPU=%s' % ('+double' in self.spec),
'-DDoublePrec_GPU=%s' % ('+double-gpu' in self.spec),
]
if '+cuda' in self.spec:
# 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
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