def test_pipeline(self):
if self.process_filename is None:
return
temp_dir = tempfile.gettempdir()
process_list = ProcessList()
process_list.populate_process_list(self.process_filename)
first_plugin = pu.load_plugin(process_list.process_list[0]['id'])
input_data = tu.get_appropriate_input_data(first_plugin)[0]
try :
process.run_process_list(input_data, process_list, temp_dir)
except ImportError as e:
print("Failed to run plugin test as libraries not available (%s), passing test" % (e))
pass
def test_pipeline(self):
if self.process_filename is None:
return
temp_dir = tempfile.gettempdir()
process_list = ProcessList()
process_list.populate_process_list(self.process_filename)
first_plugin = pu.load_plugin(process_list.process_list[0]['id'])
input_data = tu.get_appropriate_input_data(first_plugin)[0]
try:
process.run_process_list(input_data, process_list, temp_dir)
except ImportError as e:
print(
"Failed to run plugin test as libraries not available (%s), passing test"
% (e))
pass
logging.debug("Rank : %i - Size : %i", RANK, SIZE)
IP = socket.gethostbyname(socket.gethostname())
logging.debug("ip address is : %s", IP)
call_mpi_barrier()
logging.debug("LD_LIBRARY_PATH is %s", os.getenv('LD_LIBRARY_PATH'))
call_mpi_barrier()
process_filename = args[1]
process_list = ProcessList()
process_list.populate_process_list(process_filename)
input_data = pu.load_raw_data(args[0])
process.run_process_list(input_data,
process_list,
args[2],
mpi=True,
processes=ALL_PROCESSES,
process=RANK)
call_mpi_barrier()
logging.info("Python MPI script complete")
sys.exit(3)
if not os.path.exists(args[2]):
print("Output Directory '%s' does not exist" % args[2])
print("Exiting with error code 4 - Output Directory missing")
sys.exit(4)
logger = logging.getLogger()
logger.setLevel(logging.DEBUG)
if options.log2db:
sqlh = SQLiteHandler(db=os.path.join(args[2], 'log.db'))
logger.addHandler(sqlh)
else:
fh = logging.FileHandler(os.path.join(args[2], 'log.txt'), mode='w')
fh.setFormatter(
logging.Formatter('L %(relativeCreated)12d M' +
MACHINE_NUMBER_STRING + ' ' + MACHINE_RANK_NAME +
' %(levelname)-6s %(message)s'))
logger.addHandler(fh)
logging.info("Starting tomo_recon process")
process_filename = options.process_filename
process_list = ProcessList()
process_list.populate_process_list(process_filename)
input_data = pu.load_raw_data(args[0])
process.run_process_list(input_data, process_list, args[2])
MPI.COMM_WORLD.barrier()
logging.info("Starting the test process")
logging.debug("Rank : %i - Size : %i", RANK, SIZE)
IP = socket.gethostbyname(socket.gethostname())
logging.debug("ip address is : %s", IP)
MPI.COMM_WORLD.barrier()
import os
logging.debug(os.getenv('LD_LIBRARY_PATH'))
MPI.COMM_WORLD.barrier()
process_filename = tu.get_test_data_path(options.process_filename)
process_list = ProcessList()
process_list.populate_process_list(process_filename)
first_plugin = pu.load_plugin(process_list.process_list[0]['id'])
input_data = tu.get_appropriate_input_data(first_plugin)[0]
process.run_process_list(input_data, process_list, options.directory,
mpi=True, processes=ALL_PROCESSES,
process=RANK)
MPI.COMM_WORLD.barrier()
logging.debug("Rank : %i - Size : %i", RANK, SIZE)
IP = socket.gethostbyname(socket.gethostname())
logging.debug("ip address is : %s", IP)
call_mpi_barrier()
import os
logging.debug(os.getenv('LD_LIBRARY_PATH'))
call_mpi_barrier()
process_filename = tu.get_test_data_path(options.process_filename)
process_list = ProcessList()
process_list.populate_process_list(process_filename)
first_plugin = pu.load_plugin(process_list.process_list[0]['id'])
input_data = tu.get_appropriate_input_data(first_plugin)[0]
process.run_process_list(input_data,
process_list,
options.directory,
mpi=True,
processes=ALL_PROCESSES,
process=RANK)
call_mpi_barrier()
sys.exit(4)
logger = logging.getLogger()
logger.setLevel(logging.DEBUG)
if options.log2db:
sqlh = SQLiteHandler(db=os.path.join(args[2], "log.db"))
logger.addHandler(sqlh)
else:
fh = logging.FileHandler(os.path.join(args[2], "log.txt"), mode="w")
fh.setFormatter(
logging.Formatter(
"L %(relativeCreated)12d M"
+ MACHINE_NUMBER_STRING
+ " "
+ MACHINE_RANK_NAME
+ " %(levelname)-6s %(message)s"
)
)
logger.addHandler(fh)
logging.info("Starting tomo_recon process")
process_filename = options.process_filename
process_list = ProcessList()
process_list.populate_process_list(process_filename)
input_data = pu.load_raw_data(args[0])
process.run_process_list(input_data, process_list, args[2])
MPI.COMM_WORLD.barrier()
logging.info("Starting the reconstruction pipeline process")
logging.debug("Rank : %i - Size : %i", RANK, SIZE)
IP = socket.gethostbyname(socket.gethostname())
logging.debug("ip address is : %s", IP)
call_mpi_barrier()
logging.debug("LD_LIBRARY_PATH is %s", os.getenv('LD_LIBRARY_PATH'))
call_mpi_barrier()
process_filename = args[1]
process_list = ProcessList()
process_list.populate_process_list(process_filename)
input_data = pu.load_raw_data(args[0])
process.run_process_list(input_data, process_list, args[2],
mpi=True, processes=ALL_PROCESSES,
process=RANK)
call_mpi_barrier()
logging.info("Python MPI script complete")
