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# Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Asynchronous execution of Fdist and spliting of loads (DEPRECATED).
FDistAsync Allows for the execution of FDist.
SplitFDist splits a single Fdist execution in several, taking advantage
of multi-core architectures.
"""
import os
import shutil
import threading
from time import sleep
from Bio.PopGen.Async import Local
from Bio.PopGen.FDist.Controller import FDistController
class FDistAsync(FDistController):
"""Asynchronous FDist execution.
"""
def __init__(self, fdist_dir="", ext=None):
"""Constructor.
Parameters:
- fdist_dir - Where fdist can be found, if = "", then it
should be on the path.
- ext - Extension of binary names (e.g. nothing on Unix,
".exe" on Windows
"""
FDistController.__init__(self, fdist_dir, ext)
def run_job(self, parameters, input_files):
"""Runs FDist asynchronously.
Gets typical Fdist parameters from a dictionary and
makes a "normal" call. This is run, normally, inside
a separate thread.
"""
npops = parameters['npops']
nsamples = parameters['nsamples']
fst = parameters['fst']
sample_size = parameters['sample_size']
mut = parameters.get('mut', 0)
num_sims = parameters.get('num_sims', 20000)
data_dir = parameters.get('data_dir', '.')
is_dominant = parameters.get('is_dominant', False)
theta = parameters.get('theta', 0.06)
beta = parameters.get('beta', (0.25, 0.25))
max_freq = parameters.get('max_freq', 0.99)
fst = self.run_fdist(npops, nsamples, fst, sample_size,
mut, num_sims, data_dir,
is_dominant, theta, beta,
max_freq)
output_files = {}
output_files['out.dat'] = open(data_dir + os.sep + 'out.dat', 'r')
return fst, output_files
class SplitFDist(object):
"""Splits a FDist run.
The idea is to split a certain number of simulations in smaller
numbers (e.g. 30.000 sims split in 30 packets of 1.000). This
allows to run simulations in parallel, thus taking advantage
of multi-core CPUs.
Each SplitFDist object can only be used to run a single FDist
simulation.
"""
def __init__(self, report_fun=None,
num_thr=2, split_size=1000, fdist_dir='', ext=None):
"""Constructor.
Parameters:
- report_fun - Function that is called when a single packet is
run, it should have a single parameter: Fst.
- num_thr - Number of desired threads, typically the number
of cores.
- split_size - Size that a full simulation will be split in.
- ext - Binary extension name (e.g. nothing on Unix, '.exe' on
Windows).
"""
self.async = Local.Local(num_thr)
self.async.hooks['fdist'] = FDistAsync(fdist_dir, ext)
self.report_fun = report_fun
self.split_size = split_size
# There might be races when reporting...
def monitor(self):
"""Monitors and reports (using report_fun) execution.
Every time a partial simulation ends, calls report_fun.
IMPORTANT: monitor calls can be concurrent with other
events, ie, a tasks might end while report_fun is being
called. This means that report_fun should be consider that
other events might be happening while it is running (it
can call acquire/release if necessary).
"""
while(True):
sleep(1)
self.async.access_ds.acquire()
keys = list(self.async.done.keys()) # copy it
self.async.access_ds.release()
for done in keys:
self.async.access_ds.acquire()
fst, files = self.async.done[done]
del self.async.done[done]
out_dat = files['out.dat']
f = open(self.data_dir + os.sep + 'out.dat', 'a')
f.writelines(out_dat.readlines())
f.close()
out_dat.close()
self.async.access_ds.release()
for file in os.listdir(self.parts[done]):
os.remove(self.parts[done] + os.sep + file)
os.rmdir(self.parts[done])
if self.report_fun:
self.report_fun(fst)
self.async.access_ds.acquire()
if len(self.async.waiting) == 0 and len(self.async.running) == 0 \
and len(self.async.done) == 0:
break
self.async.access_ds.release()
def acquire(self):
"""Allows the external acquisition of the lock.
"""
self.async.access_ds.acquire()
def release(self):
"""Allows the external release of the lock.
"""
self.async.access_ds.release()
# You can only run a fdist case at a time
def run_fdist(self, npops, nsamples, fst, sample_size,
mut=0, num_sims=20000, data_dir='.',
is_dominant=False, theta=0.06, beta=(0.25, 0.25),
max_freq=0.99):
"""Runs FDist.
Parameters can be seen on FDistController.run_fdist.
It will split a single execution in several parts and
create separated data directories.
"""
num_parts = num_sims // self.split_size
self.parts = {}
self.data_dir = data_dir
for directory in range(num_parts):
full_path = data_dir + os.sep + str(directory)
try:
os.mkdir(full_path)
except OSError:
pass # Its ok, if it is already there
if "ss_file" in os.listdir(data_dir):
shutil.copy(data_dir + os.sep + "ss_file", full_path)
id = self.async.run_program('fdist', {
'npops': npops,
'nsamples': nsamples,
'fst': fst,
'sample_size': sample_size,
'mut': mut,
'num_sims': self.split_size,
'data_dir': full_path,
'is_dominant': is_dominant,
'theta': theta,
'beta': beta,
'max_freq': max_freq
}, {})
self.parts[id] = full_path
threading.Thread(target=self.monitor).run()
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