Source Code for Module Biskit.hosts

  1  ## List of available cluster nodes 
  2  ## Adapt this file and save it under biskit/Biskit/hosts.py ! 
  3  ## 
  4  ## last $Date: 2007/02/28 22:37:32 $ 
  5  ## last $Author: graik $ 
  6  """ 
  7  List of cluster computers. 
  8  Each host must be accessible via ssh w/o password:: 
  9   
 10    nodes_* .. lists with one entry per computer 
 11    cpus_*  .. lists with one entry per CPU (usually that's the one used) 
 12   
 13    nodes/cpus_own   .. computers reserved for own use, highest priority 
 14    nodes/cpus_shared.. computers shared with others, medium priority 
 15    nodes/cpus_other .. computers mainly used by others, lowest priority 
 16   
 17    nodes/cpus_all   .. all computers in descending priority 
 18    nice_dic         .. nice value for each host 
 19  """ 
 20  import Biskit.mathUtils as MU 
 21  import os 
 22  import string as S 
 23   
 24  import ConfigParser 
 25   
 26  ## Read configuration file 
 27  conf = ConfigParser.ConfigParser() 
 28  conf.read( os.path.expanduser('~/.biskit/hosts.dat' ) ) 
 29   
 30   
 31 -def getHosts( section, option ): 
 32      """ 
 33      Get a list of hosts from the host list using ConfigParser. 
 34       
 35      @param section: ConfigParser section in ~/.biskit/hosts.dat 
 36      @type  section: str 
 37      @param option: ConfigParser option in ~/.biskit/hosts.dat 
 38      @type  option: str 
 39       
 40      @return: a list of hosts 
 41      @rtype: [str] 
 42      """ 
 43      ## Strip comment from setting (separator #) 
 44      ## Split list (separator 'space') 
 45      if conf.has_option( section, option ): 
 46          setting = conf.get( section, option ) 
 47          setting = S.split( setting, '#' ) 
 48          hosts = [] 
 49          for host in S.split( setting[0], ' ' ): 
 50              if len(host) != 0: 
 51                  hosts += [ S.strip(host) ]  
 52          return hosts 
 53      return [] 
 54   
 55   
 56 -def getDict( section, option ): 
 57      """ 
 58      Get a dictionary with host as key. 
 59   
 60      @param section: ConfigParser section in ~/.biskit/hosts.dat 
 61      @type  section: str 
 62      @param option: ConfigParser option in ~/.biskit/hosts.dat 
 63      @type  option: str 
 64       
 65      @return: a dictionary with host as key and (nice) value as value 
 66      @rtype: dict 
 67      """ 
 68      ## Strip comment from setting (separator: #) 
 69      ## Split entry (separator 'space') 
 70      ## Split value for dictionary (separator :) 
 71      dic = {} 
 72      for i in getHosts( section, option ): 
 73          i = S.split( i, ':' ) 
 74          dic[ S.strip(i[0]) ] =  float( i[1] ) 
 75      return dic 
 76   
 77   
 78  dual = [] 
 79   
 80  ## 
 81  ## computers reserved for own use, highest priority 
 82  ## 
 83  __dual   = getHosts( 'own_hosts', 'dual' ) # dual cpu computers reserved for own use, highest priority, separate with a blank space 
 84  __single = getHosts( 'own_hosts', 'single' ) # single cpu computers reserved for own use, highest priority, separate with space 
 85   
 86  nodes_own = __dual +__single 
 87  cpus_own = __dual * 2 + __single 
 88   
 89  dual += __dual 
 90   
 91   
 92  ## 
 93  ## computers shared with others, medium priority 
 94  ## 
 95  __dual   = getHosts( 'shared_hosts', 'dual' ) # dual cpu computers shared with others, medium priority, separate with space 
 96  __single = getHosts( 'shared_hosts', 'single' ) # single cpu computers shared with others, medium priority, separate with space 
 97   
 98  dual += __dual 
 99   
100  nodes_shared = __dual + __single 
101  cpus_shared = __dual * 2 + __single 
102   
103   
104  ## 
105  ## computers mainly used by others, lowest priority 
106  ## 
107  __dual   = getHosts( 'others_hosts', 'dual' ) # dual cpu computers mainly used by others, lowest priority, separate with space 
108  __single = getHosts( 'others_hosts', 'single' ) # dual cpu computers mainly used by others, lowest priority, separate with space 
109   
110  dual += __dual 
111   
112  nodes_other =  __dual + __single 
113  cpus_other = __dual * 2 + __single 
114   
115   
116  ## 
117  ## all computers in descending priority 
118  ## 
119  nodes_all = nodes_own + nodes_shared + nodes_other 
120  cpus_all = cpus_own + cpus_shared + cpus_other 
121   
122   
123  ## 
124  ## nice value for each computer 
125  ## 
126  nice_dic = { 'default':19 } 
127  for h in nodes_own: 
128      nice_dic[h] = 0 
129  for h in cpus_shared: 
130      nice_dic[h] = 0 
131  for h in cpus_other: 
132      nice_dic[h] = 17 
133   
134  ## 
135  ## temporary fine tuning 
136  ## 
137  own_nice = getDict( 'own_hosts', 'nice' ) # nice value for own computers, default 0, separate hosts with space and values with ":"  
138  shared_nice = getDict( 'shared_hosts', 'nice' ) # nice value shared computers, default 0, separate hosts with space and values with ":" 
139  others_nice = getDict( 'others_hosts', 'nice' ) # nice value others computers, default 17, separate hosts with space and values with ":" 
140   
141  nice_dic.update(own_nice) 
142  nice_dic.update(shared_nice) 
143  nice_dic.update(others_nice) 
144   
145   
146  ## 
147  ## Memory available for each node, in GB 
148  ## 
149  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 ":"  
150  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 ":"  
151  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 ":"  
152   
153  ram_dic = { 'default':0.5 } 
154  for h in dual: 
155      ram_dic[ h ] = 1.0 
156   
157  ram_dic.update(own_ram) 
158  ram_dic.update(shared_ram) 
159  ram_dic.update(others_ram) 
160   
161   
162  ## 
163  ## exclude list, temporarily remove some nodes 
164  ## 
165  nodes_exclude = [] 
166  nodes_exclude += getHosts( 'own_hosts', 'exclude' ) # exclude list, temporarily remove some nodes, separate with space 
167  nodes_exclude += getHosts( 'shared_hosts', 'exclude' ) # exclude list, temporarily remove some nodes, separate with space 
168  nodes_exclude += getHosts( 'others_hosts', 'exclude' ) # exclude list, temporarily remove some nodes, separate with space 
169   
170   
171  ## 
172  ## Switch On / Off temporary removal of nodes  
173  ## Set to 1 to take some nodes out of the list (i.e. don't use them) 
174  ## Set to 0 to let Biskit use all computers 
175  ## 
176  REMOVE = 1 
177   
178  if REMOVE: 
179      for l in [ nodes_all, cpus_all, nodes_own, cpus_own, 
180                 nodes_shared, cpus_shared, nodes_other, cpus_other ]: 
181   
182          MU.removeFromList( l, nodes_exclude, all=1 ) 
183   
184  ############## 
185  ## empty test 
186  ############## 
187  import Biskit.test as BT 
188   
189 -class Test(BT.BiskitTest): 
190      """Mock test, hosts only contains data""" 
191      pass 
192