def main():
options = parser.parse_args()
if options.logFile:
logging.basicConfig(filename=options.logFile + '-' + str(RANK),
level=logging.DEBUG,
filemode='w',
format='%(asctime)s %(message)s',
datefmt='%m/%d/%Y %H:%M:%S')
logging.info('program started')
logging.info('command line: {}'.format(' '.join(sys.argv)))
data_out = open(options.outputFile, "w")
Drt = options.rtGap/2.0
Dmz = options.mzGap/2.0
idx = index.Index()
logging.info('region: +/- {} sec, +/- {} mz'.format(Drt,Dmz))
count = 0
with open(options.inputFile, "r") as data_in:
for datum in data_in:
# rt, mz, amp, score = (float(v) for v in datum.split(","))
rt, mz, amp, score = [float(v) for v in datum.split(",")][:4]
coord = (rt-Drt, mz-Dmz, rt+Drt, mz+Dmz)
if idx.count(coord) == 0:
idx.insert(count, coord)
print >> data_out, "{}, {}, {}, {}".format(rt, mz, amp, score)
count += 1
print "found {} regions".format(count)
logging.debug('main mem: {}'.format(md_io.memory_usage_resource()))
logging.info('program completed')
def main(MPI=None):
# try parallel
COMM = None
RANK = 0
SIZE = 1
if MPI:
COMM = MPI.COMM_WORLD
RANK = COMM.Get_rank()
SIZE = COMM.Get_size()
status = MPI.Status()
if RANK == 0:
options = parser.parse_args()
else:
options = []
if SIZE > 1:
options = COMM.bcast(options)
if options.logFile:
logging.basicConfig(
filename=options.logFile + "-" + str(RANK),
level=logging.DEBUG,
filemode="w",
format="%(asctime)s %(message)s",
datefmt="%m/%d/%Y %H:%M:%S",
)
logging.info("program started")
logging.info("command line: {}".format(" ".join(sys.argv)))
if RANK == 0:
if options.format == "mzml":
reader = md_io.MZMLtoSpectrum
elif options.format == "mzdata":
# TODO: convert to MPI
reader = md_io.parseMZDATA
else:
exit("Unknown mass spec data format: {}".format(options.format))
# distribute to worker pool
# design
# master | workers
# --------- --------------------------------
# while workers | while !end
# | send result (or None)
# recv result |
# store result |
# get sender |
# read data chunk |
# send to sender |
# | recv data (or None)
# | do work (or end)
#
#
# main split b/w master worker
# read the input data file and extract useful contents
if RANK == 0:
data_out = open(options.outputFile, "w")
half_window = int(math.ceil(options.rtSigma * options.rtWidth / 2.355))
logging.debug("half RT window {}".format(half_window))
if SIZE > 1:
done = 1
else:
done = 0 # only needed for sequential
raw_data = None # only needed for sequential
if not options.noScore:
nextWindow = md_io.nextWindow(reader, options, half_window)
else:
nextWindow = reader(options)
while done < SIZE:
if SIZE > 1:
raw_data, scores = COMM.recv(source=MPI.ANY_SOURCE, status=status)
source = status.Get_source()
if raw_data is not None:
md_io.writeResults(data_out, raw_data, scores)
## Read data chunk
try:
spectra = nextWindow.next()
except StopIteration:
spectra = None
# try removing low values
if options.removeLow > 0 and spectra is not None:
# use the specified low signal
spectra = md_filter.removeLowSignal(spectra, options.removeLow)
if SIZE > 1:
COMM.send(spectra, dest=source)
elif spectra is not None: # do work sequentially
## do work
if not options.noScore:
scores = md_filter.scoreSpectra(spectra, options)
raw_data = spectra[len(spectra) // 2]
else:
scores = None
raw_data = spectra
if spectra is None:
done += 1 # can only ever close each worker once
else: # Worker
scores = None
raw = None
# for stats
send_time = []
recv_time = []
work_time = []
in_mem = md_io.memory_usage_resource()
while True:
t1 = time.time()
COMM.send((raw, scores))
t2 = time.time()
send_time.append(t2 - t1)
raw = None
scores = None
logging.debug("rank {}, mem start, end: {:.1f} {:.1f}".format(RANK, in_mem, md_io.memory_usage_resource()))
in_mem = md_io.memory_usage_resource()
t1 = time.time()
spectra = COMM.recv()
t2 = time.time()
recv_time.append(t2 - t1)
if spectra is not None:
## do work
try:
t1 = time.time()
if not options.noScore:
scores = md_filter.scoreSpectra(spectra, options)
raw = spectra[len(spectra) // 2]
else:
scores = None
raw = spectra
t2 = time.time()
work_time.append(t2 - t1)
spectra = None
except MemoryError:
logging.debug("rank {} Memory Error".format(RANK))
else:
break
logging.info("rank {}, count {}".format(RANK, len(work_time)))
logging.info("rank {}, stats min 10% 25% 50% 75% 90% max".format(RANK))
limits = np.percentile(send_time, [0, 10, 25, 50, 75, 90, 100])
logging.info("rank {}, send {}".format(RANK, ", ".join(["{:.2f}".format(i) for i in limits])))
limits = np.percentile(recv_time, [0, 10, 25, 50, 75, 90, 100])
logging.info("rank {}, recv {}".format(RANK, ", ".join(["{:.2f}".format(i) for i in limits])))
limits = np.percentile(work_time, [0, 10, 25, 50, 75, 90, 100])
logging.info("rank {}, work {}".format(RANK, ", ".join(["{:.2f}".format(i) for i in limits])))
logging.debug("main mem: {}".format(md_io.memory_usage_resource()))
logging.info("program completed")
def main(MPI=None):
# try parallel
COMM = None
RANK = 0
SIZE = 1
if MPI:
COMM = MPI.COMM_WORLD
RANK = COMM.Get_rank()
SIZE = COMM.Get_size()
status = MPI.Status()
if RANK == 0:
options = parser.parse_args()
else:
options = []
if SIZE > 1:
options = COMM.bcast(options)
if options.logFile:
logging.basicConfig(filename=options.logFile + '-' + str(RANK),
level=logging.DEBUG,
filemode='w',
format='%(asctime)s %(message)s',
datefmt='%m/%d/%Y %H:%M:%S')
logging.info('program started')
logging.info('command line: {}'.format(' '.join(sys.argv)))
if RANK == 0:
if options.format == 'mzml':
reader = md_io.MZMLtoSpectrum
elif options.format == 'mzdata':
# TODO: convert to MPI
reader = md_io.parseMZDATA
else:
exit("Unknown mass spec data format: {}".format(options.format))
# distribute to worker pool
# design
# master | workers
# --------- --------------------------------
# while workers | while !end
# | send result (or None)
# recv result |
# store result |
# get sender |
# read data chunk |
# send to sender |
# | recv data (or None)
# | do work (or end)
#
#
# main split b/w master worker
# read the input data file and extract useful contents
if RANK == 0:
data_out = open(options.outputFile, "w")
half_window = int(math.ceil(options.rtSigma * options.rtWidth / 2.355))
logging.debug('half RT window {}'.format(half_window))
if SIZE > 1:
done = 1
else:
done = 0 # only needed for sequential
raw_data = None # only needed for sequential
if not options.noScore:
nextWindow = md_io.nextWindow(reader, options, half_window)
else:
nextWindow = reader(options)
while done < SIZE:
if SIZE > 1:
raw_data, scores = COMM.recv(source=MPI.ANY_SOURCE,
status=status)
source = status.Get_source()
if raw_data is not None:
md_io.writeResults(data_out, raw_data, scores)
## Read data chunk
try:
spectra = nextWindow.next()
except StopIteration:
spectra = None
# try removing low values
if options.removeLow > 0 and spectra is not None:
# use the specified low signal
spectra = md_filter.removeLowSignal(spectra, options.removeLow)
if SIZE > 1:
COMM.send(spectra, dest=source)
elif spectra is not None: # do work sequentially
## do work
if not options.noScore:
scores = md_filter.scoreSpectra(spectra, options)
raw_data = spectra[len(spectra) // 2]
else:
scores = None
raw_data = spectra
if spectra is None:
done += 1 # can only ever close each worker once
else: # Worker
scores = None
raw = None
# for stats
send_time = []
recv_time = []
work_time = []
in_mem = md_io.memory_usage_resource()
while True:
t1 = time.time()
COMM.send((raw, scores))
t2 = time.time()
send_time.append(t2 - t1)
raw = None
scores = None
logging.debug('rank {}, mem start, end: {:.1f} {:.1f}'.format(
RANK, in_mem, md_io.memory_usage_resource()))
in_mem = md_io.memory_usage_resource()
t1 = time.time()
spectra = COMM.recv()
t2 = time.time()
recv_time.append(t2 - t1)
if spectra is not None:
## do work
try:
t1 = time.time()
if not options.noScore:
scores = md_filter.scoreSpectra(spectra, options)
raw = spectra[len(spectra) // 2]
else:
scores = None
raw = spectra
t2 = time.time()
work_time.append(t2 - t1)
spectra = None
except MemoryError:
logging.debug('rank {} Memory Error'.format(RANK))
else:
break
logging.info('rank {}, count {}'.format(RANK, len(work_time)))
logging.info('rank {}, stats min 10% 25% 50% 75% 90% max'.format(RANK))
limits = np.percentile(send_time, [0, 10, 25, 50, 75, 90, 100])
logging.info('rank {}, send {}'.format(
RANK, ', '.join(['{:.2f}'.format(i) for i in limits])))
limits = np.percentile(recv_time, [0, 10, 25, 50, 75, 90, 100])
logging.info('rank {}, recv {}'.format(
RANK, ', '.join(['{:.2f}'.format(i) for i in limits])))
limits = np.percentile(work_time, [0, 10, 25, 50, 75, 90, 100])
logging.info('rank {}, work {}'.format(
RANK, ', '.join(['{:.2f}'.format(i) for i in limits])))
logging.debug('main mem: {}'.format(md_io.memory_usage_resource()))
logging.info('program completed')