Package Bio :: Package PopGen :: Package FDist :: Module Async
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Source Code for Module Bio.PopGen.FDist.Async

  1  # Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>.  All rights reserved. 
  2  # This code is part of the Biopython distribution and governed by its 
  3  # license.  Please see the LICENSE file that should have been included 
  4  # as part of this package. 
  5   
  6   
  7  """ 
  8  This modules allows for asynchronous execution of Fdist and 
  9    spliting of loads. 
 10   
 11  FDistAsync Allows for the execution of FDist. 
 12   
 13  SplitFDist splits a single Fdist execution in several, taking advantage 
 14      of multi-core architectures. 
 15   
 16  """ 
 17   
 18  import os 
 19  import shutil 
 20  import thread 
 21  from time import sleep 
 22  from Bio.PopGen.Async import Local 
 23  from Bio.PopGen.FDist.Controller import FDistController 
 24   
25 -class FDistAsync(FDistController):
26 """Asynchronous FDist execution. 27 """ 28
29 - def __init__(self, fdist_dir = "", ext = None):
30 """Constructor. 31 32 Parameters: 33 fdist_dir - Where fdist can be found, if = "", then it 34 should be on the path. 35 ext - Extension of binary names (e.g. nothing on Unix, 36 ".exe" on Windows 37 """ 38 FDistController.__init__(self, fdist_dir, ext)
39
40 - def run_job(self, parameters, input_files):
41 """Runs FDist asynchronously. 42 43 Gets typical Fdist parameters from a dictionary and 44 makes a "normal" call. This is run, normally, inside 45 a separate thread. 46 """ 47 npops = parameters['npops'] 48 nsamples = parameters['nsamples'] 49 fst = parameters['fst'] 50 sample_size = parameters['sample_size'] 51 mut = parameters.get('mut', 0) 52 num_sims = parameters.get('num_sims', 20000) 53 data_dir = parameters.get('data_dir', '.') 54 is_dominant = parameters.get('is_dominant', False) 55 theta = parameters.get('theta', 0.06) 56 beta = parameters.get('beta', (0.25, 0.25)) 57 max_freq = parameters.get('max_freq', 0.99) 58 fst = self.run_fdist(npops, nsamples, fst, sample_size, 59 mut, num_sims, data_dir, 60 is_dominant, theta, beta, 61 max_freq) 62 output_files = {} 63 output_files['out.dat'] = open(data_dir + os.sep + 'out.dat', 'r') 64 return fst, output_files
65
66 -class SplitFDist(object):
67 """Splits a FDist run. 68 69 The idea is to split a certain number of simulations in smaller 70 numbers (e.g. 30.000 sims split in 30 packets of 1.000). This 71 allows to run simulations in parallel, thus taking advantage 72 of multi-core CPUs. 73 74 Each SplitFDist object can only be used to run a single FDist 75 simulation. 76 """
77 - def __init__(self, report_fun = None, 78 num_thr = 2, split_size = 1000, fdist_dir = '', ext = None):
79 """Constructor. 80 81 Parameters: 82 report_fun - Function that is called when a single packet is 83 run, it should have a single parameter: Fst. 84 num_thr - Number of desired threads, typically the number 85 of cores. 86 split_size - Size that a full simulation will be split in. 87 ext - Binary extension name (e.g. nothing on Unix, '.exe' on 88 Windows). 89 """ 90 self.async = Local.Local(num_thr) 91 self.async.hooks['fdist'] = FDistAsync(fdist_dir, ext) 92 self.report_fun = report_fun 93 self.split_size = split_size
94 95 #There might be races when reporting...
96 - def monitor(self):
97 """Monitors and reports (using report_fun) execution. 98 99 Every time a partial simulation ends, calls report_fun. 100 IMPORTANT: monitor calls can be concurrent with other 101 events, ie, a tasks might end while report_fun is being 102 called. This means that report_fun should be consider that 103 other events might be happening while it is running (it 104 can call acquire/release if necessary). 105 """ 106 while(True): 107 sleep(1) 108 self.async.access_ds.acquire() 109 keys = self.async.done.keys()[:] 110 self.async.access_ds.release() 111 for done in keys: 112 self.async.access_ds.acquire() 113 fst, files = self.async.done[done] 114 del self.async.done[done] 115 out_dat = files['out.dat'] 116 f = open(self.data_dir + os.sep + 'out.dat','a') 117 f.writelines(out_dat.readlines()) 118 f.close() 119 out_dat.close() 120 self.async.access_ds.release() 121 for file in os.listdir(self.parts[done]): 122 os.remove (self.parts[done] + os.sep + file) 123 os.rmdir(self.parts[done]) 124 #print fst, out_dat 125 if self.report_fun: 126 self.report_fun(fst) 127 self.async.access_ds.acquire() 128 if len(self.async.waiting) == 0 and len(self.async.running) == 0 \ 129 and len(self.async.done) == 0: 130 break 131 self.async.access_ds.release()
132 #print 'R', self.async.running 133 #print 'W', self.async.waiting 134 #print 'R', self.async.running 135
136 - def acquire(self):
137 """Allows the external acquisition of the lock. 138 """ 139 self.async.access_ds.acquire()
140
141 - def release(self):
142 """Allows the external release of the lock. 143 """ 144 self.async.access_ds.release()
145 146 #You can only run a fdist case at a time
147 - def run_fdist(self, npops, nsamples, fst, sample_size, 148 mut = 0, num_sims = 20000, data_dir='.', 149 is_dominant = False, theta = 0.06, beta = (0.25, 0.25), 150 max_freq = 0.99):
151 """Runs FDist. 152 153 Parameters can be seen on FDistController.run_fdist. 154 155 It will split a single execution in several parts and 156 create separated data directories. 157 """ 158 num_parts = num_sims/self.split_size 159 self.parts = {} 160 self.data_dir = data_dir 161 for directory in range(num_parts): 162 full_path = data_dir + os.sep + str(directory) 163 try: 164 os.mkdir(full_path) 165 except OSError: 166 pass #Its ok, if it is already there 167 if "ss_file" in os.listdir(data_dir): 168 shutil.copy(data_dir + os.sep + "ss_file", full_path) 169 id = self.async.run_program('fdist', { 170 'npops' : npops, 171 'nsamples' : nsamples, 172 'fst' : fst, 173 'sample_size' : sample_size, 174 'mut' : mut, 175 'num_sims' : self.split_size, 176 'data_dir' : full_path, 177 'is_dominant' : is_dominant, 178 'theta' : theta, 179 'beta' : beta, 180 'max_freq' : max_freq 181 }, {}) 182 self.parts[id] = full_path 183 thread.start_new_thread(self.monitor, ())
184