def getEnviron(cls, gpuId='0'):
""" Setup the environment variables needed to launch cryocare. """
environ = Environ(os.environ)
if 'PYTHONPATH' in environ:
# this is required for python virtual env to work
del environ['PYTHONPATH']
environ.update({'CUDA_VISIBLE_DEVICES': gpuId})
cudaLib = environ.get(CRYOCARE_CUDA_LIB, pwem.Config.CUDA_LIB)
environ.addLibrary(cudaLib)
return environ
def getEnviron(useMC2=False):
""" Return the environ settings to run motioncorr programs. """
environ = Environ(os.environ)
if exists(MOTIONCORR_PATH) and not useMC2:
environ.update({'PATH': join(os.environ['MOTIONCORR_HOME'], 'bin')},
position=Environ.BEGIN)
if exists(MOTIONCOR2_PATH):
environ.update({'PATH': join(os.environ['MOTIONCOR2_HOME'], 'bin')},
position=Environ.BEGIN)
cudaLib = getCudaLib(environ, useMC2)
environ.addLibrary(cudaLib)
return environ
def getEnviron(useMC2=False):
""" Return the environ settings to run motioncorr programs. """
environ = Environ(os.environ)
if exists(MOTIONCORR_PATH) and not useMC2:
environ.update({'PATH': join(os.environ['MOTIONCORR_HOME'], 'bin')},
position=Environ.BEGIN)
if exists(MOTIONCOR2_PATH):
environ.update({'PATH': join(os.environ['MOTIONCOR2_HOME'], 'bin')},
position=Environ.BEGIN)
cudaLib = getCudaLib(environ, useMC2)
environ.addLibrary(cudaLib)
return environ
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(cls):
""" Setup the environment variables needed to launch Relion. """
environ = Environ(os.environ)
binPath = os.pathsep.join([cls.getHome('bin'), Config.MPI_BINDIR])
libPath = os.pathsep.join([cls.getHome('lib'), cls.getHome('lib64'), pwem.Config.MPI_LIBDIR])
if binPath not in environ['PATH']:
environ.update({'PATH': binPath,
'LD_LIBRARY_PATH': libPath
}, position=Environ.BEGIN)
# Get Relion CUDA library path if defined
cudaLib = cls.getVar(RELIONTOMO_CUDA_LIB, pwem.Config.CUDA_LIB)
environ.addLibrary(cudaLib)
if 'RELION_MPI_LIB' in os.environ:
environ.addLibrary(os.environ['RELION_MPI_LIB'])
if 'RELION_MPI_BIN' in os.environ:
environ.set('PATH', os.environ['RELION_MPI_BIN'],
position=Environ.BEGIN)
return environ
