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(): """ 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