eea786f4e8
- remove the old LGPL license headers from all files in Spack - add SPDX headers to all files - core and most packages are (Apache-2.0 OR MIT) - a very small number of remaining packages are LGPL-2.1-only
79 lines
3.0 KiB
Python
79 lines
3.0 KiB
Python
# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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class Relion(CMakePackage, CudaPackage):
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"""RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a
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stand-alone computer program that employs an empirical Bayesian approach to
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refinement of (multiple) 3D reconstructions or 2D class averages in
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electron cryo-microscopy (cryo-EM)."""
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homepage = "http://http://www2.mrc-lmb.cam.ac.uk/relion"
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git = "https://github.com/3dem/relion.git"
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version('3.0_beta',
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git='https://bitbucket.org/scheres/relion-3.0_beta.git')
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version('2.1', preferred='true', tag='2.1')
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version('2.0.3', tag='2.0.3')
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# relion has no develop branch though pulling from master
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# should be considered the same as develop
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version('develop', branch='master')
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variant('gui', default=True, description="build the gui")
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variant('cuda', default=True, description="enable compute on gpu")
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variant('double', default=True, description="double precision (cpu) code")
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variant('double-gpu', default=False, description="double precision gpu")
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# if built with purpose=cluster then relion will link to gpfs libraries
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# if that's not desirable then use purpose=desktop
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variant('purpose', default='cluster', values=('cluster', 'desktop'),
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description="build relion for use in cluster or desktop")
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variant('build_type', default='RelWithDebInfo',
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description='The build type to build',
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values=('Debug', 'Release', 'RelWithDebInfo',
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'Profiling', 'Benchmarking'))
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depends_on('mpi')
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# relion will not build with newer versions of cmake
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# per https://github.com/3dem/relion/issues/380
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depends_on('cmake@3:3.9.4', type='build')
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depends_on('fftw+float+double')
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depends_on('fltk', when='+gui')
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depends_on('libtiff')
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# relion 3 supports cuda 9
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# relion < 3 does not
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depends_on('cuda', when='+cuda')
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depends_on('cuda@9:', when='@3: +cuda')
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depends_on('cuda@8.0:8.99', when='@:2 +cuda')
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def cmake_args(self):
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carch = self.spec.variants['cuda_arch'].value[0]
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args = [
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'-DCMAKE_C_FLAGS=-g',
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'-DCMAKE_CXX_FLAGS=-g',
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'-DGUI=%s' % ('+gui' in self.spec),
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'-DDoublePrec_CPU=%s' % ('+double' in self.spec),
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'-DDoublePrec_GPU=%s' % ('+double-gpu' in self.spec),
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]
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if '+cuda' in self.spec:
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# relion+cuda requires selecting cuda_arch
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if not carch:
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raise ValueError("select cuda_arch when building with +cuda")
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else:
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args += ['-DCUDA=ON', '-DCudaTexture=ON',
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'-DCUDA_ARCH=%s' % (carch)]
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# these new values were added in relion 3
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# do not seem to cause problems with < 3
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else:
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args += ['-DMKLFFT=ON', '-DFORCE_OWN_TBB=ON', '-DALTCPU=ON']
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return args
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