Source Code for Module Biskit.default_hosts

  1  ## List of available cluster nodes 
  2  ## 
  3  ## Biskit, a toolkit for the manipulation of macromolecular structures 
  4  ## Copyright (C) 2004-2006 Raik Gruenberg & Johan Leckner 
  5  ## 
  6  ## This program is free software; you can redistribute it and/or 
  7  ## modify it under the terms of the GNU General Public License as 
  8  ## published by the Free Software Foundation; either version 2 of the 
  9  ## License, or any later version. 
 10  ## 
 11  ## This program is distributed in the hope that it will be useful, 
 12  ## but WITHOUT ANY WARRANTY; without even the implied warranty of 
 13  ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 
 14  ## General Public License for more details. 
 15  ## 
 16  ## You find a copy of the GNU General Public License in the file 
 17  ## license.txt along with this program; if not, write to the Free 
 18  ## Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. 
 19  ## 
 20  ## 
 21  ## Adapt this file and save it under biskit/Biskit/hosts.py ! 
 22  ## 
 23  ## last $Date: 2007/02/28 22:37:32 $ 
 24  ## last $Author: graik $ 
 25  ## $Revision: 2.5 $ 
 26   
 27  """ 
 28  List of cluster computers. 
 29   
 30  B{ Each host must be accessible via ssh w/o password. } 
 31   
 32  List and dictionaries describing avaliable hosts:: 
 33   
 34    nodes_* .. lists with one entry per computer 
 35    cpus_*  .. lists with one entry per CPU (usuallly that's the one used) 
 36   
 37    nodes/cpus_own   .. computers reserved for own use, highest priority 
 38    nodes/cpus_shared.. computers shared with others, medium priority 
 39    nodes/cpus_other .. computers mainly used by others, lowest priority 
 40   
 41    nodes/cpus_all   .. all computers in descending priority 
 42    nice_dic         .. nice value for each host 
 43  """ 
 44  import Biskit.mathUtils as MU 
 45  from tools import * 
 46  import os 
 47  import string 
 48   
 49  import ConfigParser 
 50   
 51  ## Read configuration file 
 52  conf = ConfigParser.ConfigParser() 
 53  conf.read( os.path.expanduser('~/.biskit/hosts.dat' ) ) 
 54   
 55   
 56 -def getHosts( section, option ): 
 57      """ 
 58      Get host names from the config file hosts.dat specified bythe 
 59      section and option parameters. 
 60        
 61      @param section: ConfigParser section in ~/.biskit/hosts.dat 
 62      @type  section: str 
 63      @param option: ConfigParser option in ~/.biskit/hosts.dat 
 64      @type  option: str 
 65           
 66      @return: host name taken from hosts.dat or None 
 67      @rtype: str OR None 
 68      """    
 69      if conf.has_option( section, option ): 
 70          setting = conf.get( section, option ) 
 71          ## Strip comment from setting (separator #) 
 72          setting = string.split( setting, '#' ) 
 73          hosts = [] 
 74          ## Split list (separator ,) 
 75          for host in string.split( setting[0], ' ' ): 
 76                  hosts += [ string.strip( host ) ]  
 77          return hosts 
 78      return [] 
 79   
 80   
 81 -def getDict( section, option ): 
 82      """ 
 83      Get host dictionaries from the config file hosts.dat specified by 
 84      the section and option parameters. The dictionary has the host as key 
 85      and the values can be availiable RAM or a nice value.   
 86    
 87      @param section: ConfigParser section in ~/.biskit/hosts.dat 
 88      @type  section: str 
 89      @param option: ConfigParser option in ~/.biskit/hosts.dat 
 90      @type  option: str 
 91           
 92      @return: dictionary with host:value 
 93      @rtype: dict 
 94      """                       
 95      dic = {} 
 96      ## Strip comment from setting (separator: #) 
 97      ## Split entry (separator ,)     
 98      for i in getHosts( section, option ): 
 99          ## Split dictionary (separator :) 
100          if not len(i) == 0: 
101              i = string.split( i, ':' ) 
102              dic[ string.strip(i[0]) ] =  float( i[1] ) 
103      return dic 
104   
105   
106  dual = [] 
107   
108  ## 
109  ## computers reserved for own use, highest priority 
110  ## 
111  __dual   = getHosts( 'own_hosts', 'dual' ) # dual cpu computers reserved for own use, highest priority, separate with a blank space 
112  __single = getHosts( 'own_hosts', 'single' ) # single cpu computers reserved for own use, highest priority, separate with space 
113   
114  nodes_own = __dual +__single 
115  cpus_own = __dual * 2 + __single 
116   
117  dual += __dual 
118   
119   
120  ## 
121  ## computers shared with others, medium priority 
122  ## 
123  __dual   = getHosts( 'shared_hosts', 'dual' ) # dual cpu computers shared with others, medium priority, separate with space 
124  __single = getHosts( 'shared_hosts', 'single' ) # single cpu computers shared with others, medium priority, separate with space 
125   
126  dual += __dual 
127   
128  nodes_shared = __dual + __single 
129  cpus_shared = __dual * 2 + __single 
130   
131   
132  ## 
133  ## computers mainly used by others, lowest priority 
134  ## 
135  __dual   = getHosts( 'others_hosts', 'dual' ) # dual cpu computers mainly used by others, lowest priority, separate with space 
136  __single = getHosts( 'others_hosts', 'single' ) # dual cpu computers mainly used by others, lowest priority, separate with space 
137   
138  dual += __dual 
139   
140  nodes_other =  __dual + __single 
141  cpus_other = __dual * 2 + __single 
142   
143   
144  ## 
145  ## all computers in descending priority 
146  ## 
147  nodes_all = nodes_own + nodes_shared + nodes_other 
148  cpus_all = cpus_own + cpus_shared + cpus_other 
149   
150   
151  ## 
152  ## nice value for each computer 
153  ## 
154  nice_dic = { 'default':19 } 
155  for h in nodes_own: 
156      nice_dic[h] = 0 
157  for h in cpus_shared: 
158      nice_dic[h] = 0 
159  for h in cpus_other: 
160      nice_dic[h] = 17 
161   
162  ## 
163  ## temporary fine tuning 
164  ## 
165  own_nice = getDict( 'own_hosts', 'nice' ) # nice value for own computers, default 0, separate hosts with space and values with ":"  
166  shared_nice = getDict( 'shared_hosts', 'nice' ) # nice value shared computers, default 0, separate hosts with space and values with ":" 
167  others_nice = getDict( 'others_hosts', 'nice' ) # nice value others computers, default 17, separate hosts with space and values with ":" 
168   
169  nice_dic.update(own_nice) 
170  nice_dic.update(shared_nice) 
171  nice_dic.update(others_nice) 
172   
173   
174  ## 
175  ## Memory available for each node, in GB 
176  ## 
177  own_ram = getDict( 'own_hosts', 'ram' ) # installed RAM for own computers in GB, default values 0.5 for single and 1 for dual, separate hosts with space and values with ":"  
178  shared_ram = getDict( 'shared_hosts', 'ram' ) # installed RAM shared computers in GB, default values 0.5 for single and 1 for dual, separate hosts with space and values with ":"  
179  others_ram = getDict( 'others_hosts', 'ram' ) # installed RAM others computers in GB, default values 0.5 for single and 1 for dual, separate hosts with space and values with ":"  
180   
181  ram_dic = { 'default':0.5 } 
182  for h in dual: 
183      ram_dic[ h ] = 1.0 
184   
185  ram_dic.update(own_ram) 
186  ram_dic.update(shared_ram) 
187  ram_dic.update(others_ram) 
188   
189   
190  ## 
191  ## exclude list, temporarily remove some nodes 
192  ## 
193  nodes_exclude = [] 
194  nodes_exclude += getHosts( 'own_hosts', 'exclude' ) # exclude list, temporarily remove some nodes, separate with space 
195  nodes_exclude += getHosts( 'shared_hosts', 'exclude' ) # exclude list, temporarily remove some nodes, separate with space 
196  nodes_exclude += getHosts( 'others_hosts', 'exclude' ) # exclude list, temporarily remove some nodes, separate with space 
197   
198   
199  ## 
200  ## Switch On / Off temporary removal of nodes  
201  ## Set to 1 to take some nodes out of the list (i.e. don't use them) 
202  ## Set to 0 to let Biskit use all computers 
203  ## 
204  REMOVE = 1 
205   
206  if REMOVE: 
207      for l in [ nodes_all, cpus_all, nodes_own, cpus_own, 
208                 nodes_shared, cpus_shared, nodes_other, cpus_other ]: 
209   
210          MU.removeFromList( l, nodes_exclude, all=1 ) 
211   
212  ################ 
213  ## empty test ## 
214   
215  import Biskit.test as BT 
216   
217 -class Test(BT.BiskitTest): 
218      """Mock test, hosts only contains data""" 
219      pass 
220