Source Code for Module Biskit.AmberEntropySlave

  1  ## 
  2  ## Biskit, a toolkit for the manipulation of macromolecular structures 
  3  ## Copyright (C) 2004-2006 Raik Gruenberg & Johan Leckner 
  4  ## 
  5  ## This program is free software; you can redistribute it and/or 
  6  ## modify it under the terms of the GNU General Public License as 
  7  ## published by the Free Software Foundation; either version 2 of the 
  8  ## License, or any later version. 
  9  ## 
 10  ## This program is distributed in the hope that it will be useful, 
 11  ## but WITHOUT ANY WARRANTY; without even the implied warranty of 
 12  ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 
 13  ## General Public License for more details. 
 14  ## 
 15  ## You find a copy of the GNU General Public License in the file 
 16  ## license.txt along with this program; if not, write to the Free 
 17  ## Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. 
 18  ## 
 19  ## 
 20  ## $Revision: 2.7 $ 
 21  ## last $Date: 2007/03/05 10:28:21 $ 
 22  ## last $Author: graik $ 
 23   
 24  """ 
 25  Parallellized AmberEntropist calculation. 
 26  """ 
 27   
 28  from Biskit.PVM import JobSlave 
 29  import Biskit.tools as T 
 30  import Biskit.settings as settings 
 31   
 32  from Biskit import LogFile 
 33  from Biskit.AmberEntropist import AmberEntropist 
 34  from Biskit.AmberCrdEntropist import EntropistError 
 35   
 36  import os, time 
 37   
 38 -class AmberEntropySlave( JobSlave ): 
 39      """ 
 40      Collect AmberEntropist jobs from AmberEntropyMaster and return result. 
 41      """ 
 42   
 43 -    def initialize(self, params): 
 44          """ 
 45          expects:: 
 46            {'nice':int, 'ferror':str, .. } 
 47   
 48          @param params: initialisation parameters passed from the master 
 49          @type  params: dict 
 50          """ 
 51          self.__dict__.update( params ) 
 52          self.errorLog = LogFile( self.ferror, mode='a' ) 
 53   
 54   
 55 -    def reportError(self, msg, id ): 
 56          try: 
 57              try: 
 58                  print msg 
 59              except: 
 60                  pass 
 61   
 62              msg = 'trouble with ' + msg 
 63              s = '%s on %s, run %s\n' % (msg, os.uname()[1], id) 
 64              s += '\Error:' + T.lastError() 
 65              s += '\nErrorTrace:\n' + T.lastErrorTrace() + '\n' 
 66              s += '\n' 
 67   
 68              self.errorLog.add( s ) 
 69   
 70          except Exception, why: 
 71              f = open('ErrorReportError_AmberEntropySlave','a') 
 72              f.write( str(type(why)) ) 
 73              try: 
 74                  f.write( T.lastErrorTrace() ) 
 75              except: 
 76                  pass 
 77              f.close() 
 78   
 79   
 80 -    def go(self, jobs): 
 81          """ 
 82          The calculation. 
 83           
 84          @param jobs: dictionary with { int_id : str_protocol } 
 85          @type  jobs: dict 
 86   
 87          @return: result from AmberEntropist.run() 
 88          @rtype: dict 
 89          """ 
 90          result = {} 
 91   
 92          startTime = time.time() 
 93   
 94          for id, protocol in jobs.items(): 
 95   
 96              try: 
 97                  T.flushPrint( "%s " % str(id) ) 
 98   
 99                  protocol.update( {'nice':self.nice} ) 
100   
101                  x = None  ## free memory from previous run 
102   
103                  x = AmberEntropist( **protocol ) 
104   
105                  x.run() 
106   
107                  r = x.result 
108   
109                  if r: 
110                      r['__version_AmberEntropist'] = x.version() 
111   
112                      result[ id ] = r 
113                  else: 
114                      result[ id ] = None 
115   
116              except EntropistError, why: 
117                  self.reportError( str(type(why)), id ) 
118              except IOError, why: 
119                  self.reportError( str(why), id ) 
120              except Exception, why: 
121                  self.reportError( 'ERROR '+str(type(why)), id ) 
122   
123          print "\navg time for last %i jobs: %f s" %\ 
124                ( len(jobs), (time.time()-startTime)/len(jobs)) 
125   
126          return result 
127   
128   
129  if __name__ == '__main__': 
130   
131      import sys 
132   
133      if len(sys.argv) == 2: 
134   
135          nice = int(sys.argv[1]) 
136          os.nice(nice) 
137   
138      slave = AmberEntropySlave() 
139      slave.start() 
140