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# Copyright 2013-2022 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://www2.mrc-lmb.cam.ac.uk/relion"
git = "https://github.com/3dem/relion.git"
url = "https://github.com/3dem/relion/archive/3.1.0.zip"
version('3.1.3', sha256='e67277200b54d1814045cfe02c678a58d88eb8f988091573453c8568bfde90fc')
version('3.1.2', sha256='dcdf6f214f79a03d29f0fed2de58054efa35a9d8401543bdc52bfb177987931f')
version('3.1.1', sha256='63e9b77e1ba9ec239375020ad6ff631424d1a5803cba5c608c09fd44d20b1618')
version('3.1.0', sha256='8a7e751fa6ebcdf9f36046499b3d88e170c4da86d5ff9ad1914b5f3d178867a8')
# 3.0.8 latest release in 3.0 branch
version('3.0.8', sha256='18cdd58e3a612d32413eb37e473fe8fbf06262d2ed72e42da20356f459260973')
version('3.0.7', sha256='a6d37248fc4d0bfc18f4badb7986dc1b6d6849baa2128b0b4dade13cb6991a99')
# relion master contains development code
# contains 3.0 branch code
version('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'))
variant('mklfft', default=True, description='Use MKL rather than FFTW for FFT')
variant('allow_ctf_in_sagd', default=True, description='Allow CTF-modulation in SAGD, as specified in Claim 1 of patent US10,282,513B2')
depends_on('mpi')
depends_on('cmake@3:', type='build')
depends_on('fftw precision=float,double', when='~mklfft')
depends_on('fltk', when='+gui')
depends_on('libtiff')
depends_on('cuda', when='+cuda')
depends_on('cuda@9:', when='@3: +cuda')
depends_on('tbb', when='~cuda')
depends_on('mkl', when='~cuda +mklfft')
patch('0002-Simple-patch-to-fix-intel-mkl-linking.patch', when='@:3.1.1 os=ubuntu18.04')
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),
'-DALLOW_CTF_IN_SAGD=%s' % ('+allow_ctf_in_sagd' 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=%s' % ('+mklfft' in self.spec), '-DALTCPU=ON']
return args
def patch(self):
# Remove flags not recognized by the NVIDIA compilers
if self.spec.satisfies('%nvhpc'):
filter_file('-std=c99', '-c99', 'src/apps/CMakeLists.txt')
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