def getCudaLib(environ=None, useMC2=False):
if environ is None:
environ = Environ(os.environ)
if useMC2:
return environ.getFirst((MOTIONCOR2_CUDA_LIB, CUDA_LIB))
else:
return environ.getFirst((MOTIONCORR_CUDA_LIB, CUDA_LIB))
def testInitialVolumeSelector(self):
def _runVolumeSelector(doGpu=False, label=''):
print label
volSelectorProt = self.newProtocol(ProtInitialVolumeSelector,
targetResol=28.32,
numberOfIterations=15,
numberOfMpi=3, numberOfThreads=1)
volSelectorProt.setObjLabel(label)
volSelectorProt.inputParticles.set(self.protImport.outputParticles)
volSelectorProt.inputVolumes.set(self.protImportVol.outputVolumes)
volSelectorProt.doGpu.set(doGpu)
self.launchProtocol(volSelectorProt)
return volSelectorProt
def _checkAsserts(relionProt):
self.assertIsNotNone(relionProt.outputVolumes, "There was a "
"problem with "
"Initial Volume "
"Selector")
environ = Environ(os.environ)
cudaPath = environ.getFirst(('RELION_CUDA_LIB', 'CUDA_LIB'))
if cudaPath is not None and os.path.exists(cudaPath):
volSelGpu = _runVolumeSelector(True, "Run Volume Selector GPU")
_checkAsserts(volSelGpu)
else:
volSelNoGPU = _runVolumeSelector(False, "Volume Selector No GPU")
_checkAsserts(volSelNoGPU)
def getEnviron():
""" Load the environment variables needed for Spider.
If SPIDER_DIR is defined, the bin, man and proc folders will be
defined from it. If not, each of them should be defined separately.
"""
global SPIDER
env = Environ(os.environ)
SPIDER_PATH = env.getFirst((SPIDER_HOME, SPIDER_DIR), mandatory=True) #
# Scipion
# definition
# env.setInstalled(os.path.exists(SPIDER_DIR))
if SPIDER_PATH is None:
errors = ''
for var in [SPBIN_DIR, SPMAN_DIR, SPPROC_DIR]:
if not var in env:
errors += "\n Missing SPIDER variable: '%s'" % var
if len(errors):
print "ERRORS: " + errors
else:
env.update({SPBIN_DIR: join(SPIDER_PATH, 'bin') + '/', # Spider needs this extra slash at the end
SPMAN_DIR: join(SPIDER_PATH, 'man') + '/',
SPPROC_DIR: join(SPIDER_PATH, 'proc') + '/'
})
# Get the executable or 'spider' by default
SPIDER = join(env[SPBIN_DIR], env.get('SPIDER', 'spider_linux_mp_intel64'))
# expand ~ and vars
SPIDER = abspath(os.path.expanduser(os.path.expandvars(SPIDER)))
env.set('PATH', env[SPBIN_DIR], env.END)
return env
def testInitialVolumeSelector(self):
def _runVolumeSelector(doGpu=False, label=''):
print label
volSelectorProt = self.newProtocol(ProtInitialVolumeSelector,
targetResol=28.32,
numberOfIterations=15,
numberOfMpi=3,
numberOfThreads=1)
volSelectorProt.setObjLabel(label)
volSelectorProt.inputParticles.set(self.protImport.outputParticles)
volSelectorProt.inputVolumes.set(self.protImportVol.outputVolumes)
volSelectorProt.doGpu.set(doGpu)
self.launchProtocol(volSelectorProt)
return volSelectorProt
def _checkAsserts(relionProt):
self.assertIsNotNone(
relionProt.outputVolumes, "There was a "
"problem with "
"Initial Volume "
"Selector")
environ = Environ(os.environ)
cudaPath = environ.getFirst(('RELION_CUDA_LIB', 'CUDA_LIB'))
if cudaPath is not None and os.path.exists(cudaPath):
volSelGpu = _runVolumeSelector(True, "Run Volume Selector GPU")
_checkAsserts(volSelGpu)
else:
volSelNoGPU = _runVolumeSelector(False, "Volume Selector No GPU")
_checkAsserts(volSelNoGPU)
def getEnviron():
""" Setup the environment variables needed to launch Relion. """
environ = Environ(os.environ)
relionHome = os.environ[RELION_HOME]
binPath = join(relionHome, 'bin')
libPath = join(relionHome, 'lib') + ":" + join(relionHome, 'lib64')
if not binPath in environ['PATH']:
environ.update({'PATH': binPath,
'LD_LIBRARY_PATH': libPath,
'SCIPION_MPI_FLAGS': os.environ.get('RELION_MPI_FLAGS', ''),
}, position=Environ.BEGIN)
# Take Scipion CUDA library path
cudaLib = environ.getFirst(('RELION_CUDA_LIB', 'CUDA_LIB'))
environ.addLibrary(cudaLib)
return environ
def getEnviron():
""" Load the environment variables needed for Spider.
If SPIDER_DIR is defined, the bin, man and proc folders will be
defined from it. If not, each of them should be defined separately.
"""
global SPIDER
env = Environ(os.environ)
SPIDER_PATH = env.getFirst((SPIDER_HOME, SPIDER_DIR), mandatory=True) #
# Scipion
# definition
# env.setInstalled(os.path.exists(SPIDER_DIR))
if SPIDER_PATH is None:
errors = ''
for var in [SPBIN_DIR, SPMAN_DIR, SPPROC_DIR]:
if not var in env:
errors += "\n Missing SPIDER variable: '%s'" % var
if len(errors):
print "ERRORS: " + errors
else:
env.update({
SPBIN_DIR: join(SPIDER_PATH, 'bin') +
'/', # Spider needs this extra slash at the end
SPMAN_DIR: join(SPIDER_PATH, 'man') + '/',
SPPROC_DIR: join(SPIDER_PATH, 'proc') + '/'
})
# Get the executable or 'spider' by default
SPIDER = join(env[SPBIN_DIR], env.get('SPIDER', 'spider_linux_mp_intel64'))
# expand ~ and vars
SPIDER = abspath(os.path.expanduser(os.path.expandvars(SPIDER)))
env.set('PATH', env[SPBIN_DIR], env.END)
return env
def getImagicHomeDir():
env = Environ(os.environ)
imagicdir = env.getFirst((IMAGIC_HOME, IMAGIC_DIR), mandatory=True) #
# Scipion
# definition
return env, imagicdir
def getImagicHomeDir():
env = Environ(os.environ)
imagicdir = env.getFirst((IMAGIC_HOME, IMAGIC_DIR), mandatory=True) #
# Scipion
# definition
return env, imagicdir
