def get_flowgram_distances_on_cluster(
id, flowgram, flowgrams, fc, ids, num_cores,
num_flows, spread, client_sockets=[]):
"""Computes distance scores of flowgram to all flowgrams in parser.
id: The flowgram identifier, also used to name intermediate files
flowgram: This flowgram is used to filter all the other flowgrams
flowgrams: iterable filehandle of flowgram file
fc: a sink of flowgrams, which serves as source in the next round
ids: list of flowgram ids that should be used from flowgrams
num_cores: number of cpus
num_flows: Number of flows in parser
client_sockets: A list of open sockets for client-server communication
spread: historical distribution of processing runtimes
"""
epoch = time()
check_flowgram_ali_exe()
qiime_config = load_qiime_config()
min_per_core = int(qiime_config['denoiser_min_per_core'])
# if using from future import division this has to be checked,
# as we want true integer division here
per_core = max(min_per_core, (num_flows / num_cores) + 1)
names = []
scores = []
# Need to call this here, since we iterate over the same iterator repeatedly.
# Otherwise the call in ifilter will reset the iterator by implicitely calling __iter__.
# test if iter does the same
flowgrams_iter = flowgrams.__iter__()
# prepare input files and commands
# synchronous client-server communication
workload = compute_workload(num_cores, num_flows, spread)
debug_count = 0
for i in range(num_cores):
socket = client_sockets[i]
# send master flowgram to file first
send_flowgram_to_socket(id, flowgram, socket)
if(workload[i] < 1):
# no data left for this poor guy
save_send(socket, "--END--")
continue
else:
# Then add all others which are still valid, i.e. in ids
for (k, f) in (izip(range(workload[i]),
ifilter(lambda f: f.Name in ids, flowgrams_iter))):
fc.add(f)
send_flowgram_to_socket(k, f, socket, trim=False)
names.append(f.Name)
debug_count += 1
# send the termination signal
save_send(socket, "--END--")
# asynchronous client-server communication
# ClientHandlers write data in results
results = [None] * num_cores
timing = [0.0 for x in xrange(num_cores)]
for i in range(num_cores):
socket = client_sockets[i]
ClientHandler(socket, i, results, timing)
loop()
# end asynchronous loop
spread = adjust_processing_time(num_cores, workload, timing, epoch)
# flatten list
scores = [item for list in results for item in list]
if (debug_count != len(scores)):
raise RuntimeError("Something bad has happened! I received less " +
"alignment scores %d than there are flowgrams %d. Most likely this "
% (len(scores), debug_count) +
"means that the alignment program is not setup correctly or corrupted. " +
"Please run the test scripts to figure out the cause of the error.")
return (scores, names, fc)
def get_flowgram_distances_on_cluster(id,
flowgram,
flowgrams,
fc,
ids,
num_cores,
num_flows,
spread,
client_sockets=[]):
"""Computes distance scores of flowgram to all flowgrams in parser.
id: The flowgram identifier, also used to name intermediate files
flowgram: This flowgram is used to filter all the other flowgrams
flowgrams: iterable filehandle of flowgram file
fc: a sink of flowgrams, which serves as source in the next round
ids: list of flowgram ids that should be used from flowgrams
num_cores: number of cpus
num_flows: Number of flows in parser
client_sockets: A list of open sockets for client-server communication
spread: historical distribution of processing runtimes
"""
epoch = time()
check_flowgram_ali_exe()
qiime_config = load_qiime_config()
min_per_core = int(qiime_config['denoiser_min_per_core'])
# if using from future import division this has to be checked,
# as we want true integer division here
per_core = max(min_per_core, (num_flows / num_cores) + 1)
names = []
scores = []
# Need to call this here, since we iterate over the same iterator repeatedly.
# Otherwise the call in ifilter will reset the iterator by implicitely calling __iter__.
# test if iter does the same
flowgrams_iter = flowgrams.__iter__()
# prepare input files and commands
# synchronous client-server communication
workload = compute_workload(num_cores, num_flows, spread)
debug_count = 0
for i in range(num_cores):
socket = client_sockets[i]
# send master flowgram to file first
send_flowgram_to_socket(id, flowgram, socket)
if (workload[i] < 1):
# no data left for this poor guy
save_send(socket, "--END--")
continue
else:
# Then add all others which are still valid, i.e. in ids
for (k,
f) in (izip(range(workload[i]),
ifilter(lambda f: f.Name in ids,
flowgrams_iter))):
fc.add(f)
send_flowgram_to_socket(k, f, socket, trim=False)
names.append(f.Name)
debug_count += 1
# send the termination signal
save_send(socket, "--END--")
# asynchronous client-server communication
# ClientHandlers write data in results
results = [None] * num_cores
timing = [0.0 for x in xrange(num_cores)]
for i in range(num_cores):
socket = client_sockets[i]
ClientHandler(socket, i, results, timing)
loop()
# end asynchronous loop
spread = adjust_processing_time(num_cores, workload, timing, epoch)
# flatten list
scores = [item for list in results for item in list]
if (debug_count != len(scores)):
raise RuntimeError(
"Something bad has happened! I received less " +
"alignment scores %d than there are flowgrams %d. Most likely this "
% (len(scores), debug_count) +
"means that the alignment program is not setup correctly or corrupted. "
+
"Please run the test scripts to figure out the cause of the error."
)
return (scores, names, fc)
