|
18
|
1 #!/usr/bin/env python
|
|
|
2
|
|
|
3 ## @file
|
|
|
4 # Clean the cluster nodes after REPET was used.
|
|
|
5 #
|
|
|
6 # usage: CleanClusterNodesAfterRepet.py [ options ]
|
|
|
7 # options:
|
|
|
8 # -h: this help
|
|
|
9 # -n: node to clean (otherwise all nodes will be cleaned)
|
|
|
10 # -t: temporary directory (e.g. '/tmp')
|
|
|
11 # -p: pattern (e.g. 'DmelChr4*')
|
|
|
12 # -v: verbosity level (default=0/1/2)
|
|
|
13
|
|
|
14 import os
|
|
|
15 import sys
|
|
|
16 import getopt
|
|
|
17
|
|
|
18 class CleanClusterNodesAfterRepet( object ):
|
|
|
19 """
|
|
|
20 Clean the cluster nodes after REPET was used.
|
|
|
21 """
|
|
|
22
|
|
|
23 def __init__( self ):
|
|
|
24 """
|
|
|
25 Constructor.
|
|
|
26 """
|
|
|
27 self._lNodes = []
|
|
|
28 self._tmpDir = ""
|
|
|
29 self._pattern = ""
|
|
|
30 self._verbose = 0
|
|
|
31 self._lNodesToExcept = ["compute-2-46", "compute-2-47"]
|
|
|
32
|
|
|
33 def help( self ):
|
|
|
34 """
|
|
|
35 Display the help on stdout.
|
|
|
36 """
|
|
|
37 print
|
|
|
38 print "usage: %s.py [ options ]" % ( type(self).__name__ )
|
|
|
39 print "options:"
|
|
|
40 print " -h: this help"
|
|
|
41 print " -n: node to clean (otherwise all nodes will be cleaned)"
|
|
|
42 print " -t: temporary directory (e.g. '/tmp')"
|
|
|
43 print " -p: pattern (e.g. 'DmelChr4*')"
|
|
|
44 print " -v: verbosity level (default=0/1/2)"
|
|
|
45 print
|
|
|
46
|
|
|
47 def setAttributesFromCmdLine( self ):
|
|
|
48 """
|
|
|
49 Set the attributes from the command-line.
|
|
|
50 """
|
|
|
51 try:
|
|
|
52 opts, args = getopt.getopt(sys.argv[1:],"hi:n:t:p:v:")
|
|
|
53 except getopt.GetoptError, err:
|
|
|
54 print str(err); self.help(); sys.exit(1)
|
|
|
55 for o,a in opts:
|
|
|
56 if o == "-h":
|
|
|
57 self.help(); sys.exit(0)
|
|
|
58 elif o == "-n":
|
|
|
59 self.setLNodes( a.split(" ") )
|
|
|
60 elif o == "-t":
|
|
|
61 self.setTempDirectory( a )
|
|
|
62 elif o == "-p":
|
|
|
63 self.setPattern( a )
|
|
|
64 elif o == "-v":
|
|
|
65 self.setVerbosityLevel( a )
|
|
|
66
|
|
|
67 def setLNodes( self, a ):
|
|
|
68 self._lNodes = a
|
|
|
69
|
|
|
70 def setTempDirectory( self, a ):
|
|
|
71 if a[-1] == "/":
|
|
|
72 self._tmpDir = a[:-1]
|
|
|
73 else:
|
|
|
74 self._tmpDir = a
|
|
|
75
|
|
|
76 def setPattern( self, a ):
|
|
|
77 self._pattern = a
|
|
|
78
|
|
|
79 def setVerbosityLevel( self, verbose ):
|
|
|
80 self._verbose = int(verbose)
|
|
|
81
|
|
|
82 def checkAttributes( self ):
|
|
|
83 """
|
|
|
84 Before running, check the required attributes are properly filled.
|
|
|
85 """
|
|
|
86 if self._tmpDir == "":
|
|
|
87 print "ERROR: need a valid temporary directory"
|
|
|
88 self.help(); sys.exit(1)
|
|
|
89
|
|
|
90 def getAllNodesList( self ):
|
|
|
91 """
|
|
|
92 Return the list of the names of each node.
|
|
|
93 """
|
|
|
94 lNodes = []
|
|
|
95 log = os.system( "qhost > qhost.txt" )
|
|
|
96 if log != 0: print "ERROR with qhost"; sys.exit(1)
|
|
|
97 inF = open( "qhost.txt", "r" )
|
|
|
98 line = inF.readline()
|
|
|
99 line = inF.readline()
|
|
|
100 line = inF.readline()
|
|
|
101 while True:
|
|
|
102 if line == "":
|
|
|
103 break
|
|
|
104 tokens = line.split()
|
|
|
105 if tokens[3] == "-":
|
|
|
106 line = inF.readline()
|
|
|
107 continue
|
|
|
108 lNodes.append( tokens[0] )
|
|
|
109 line = inF.readline()
|
|
|
110 inF.close()
|
|
|
111 #Remove nodes to avoid from the nodes list
|
|
|
112 for node in self._lNodesToExcept:
|
|
|
113 if node in lNodes:
|
|
|
114 lNodes.remove(node)
|
|
|
115 return lNodes
|
|
|
116
|
|
|
117 def showNodeList( self, lNodes ):
|
|
|
118 print "nb of nodes: %i" % ( len(lNodes) )
|
|
|
119 for i in range(0,len(lNodes)):
|
|
|
120 print " %i: %s" % ( i+1, lNodes[i] )
|
|
|
121
|
|
|
122 def cleanNodes( self):
|
|
|
123 """
|
|
|
124 Connect to each job and clean the temporary directory.
|
|
|
125 """
|
|
|
126 nbNodes = len(self._lNodes)
|
|
|
127 nodeCount = 0
|
|
|
128 for node in self._lNodes:
|
|
|
129 nodeCount += 1
|
|
|
130 if self._verbose > 0:
|
|
|
131 print "connect to node '%s' (%i/%i)..." % ( node, nodeCount, nbNodes )
|
|
|
132 sys.stdout.flush()
|
|
|
133 cmd = "ssh"
|
|
|
134 cmd += " -q %s " % ( node )
|
|
|
135 cmd += "'find %s" % ( self._tmpDir )
|
|
|
136 cmd += " -user %s" % ( os.environ["USER"] )
|
|
|
137 if self._pattern != "":
|
|
|
138 cmd += " -name '%s'" % ( self._pattern )
|
|
|
139 cmd += " 2> /dev/null -exec rm -rf {} \; ; exit'"
|
|
|
140 if self._verbose > 0: print cmd; sys.stdout.flush()
|
|
|
141 os.system( cmd ) # warning, even if everything goes right, ssh returns an error code, i.e. different than 0
|
|
|
142
|
|
|
143 def clean( self ):
|
|
|
144 if os.path.exists( "qhost.txt" ):
|
|
|
145 os.remove( "qhost.txt" )
|
|
|
146
|
|
|
147 def start( self ):
|
|
|
148 """
|
|
|
149 Useful commands before running the program.
|
|
|
150 """
|
|
|
151 if self._verbose > 0:
|
|
|
152 print "START %s" % ( type(self).__name__ ); sys.stdout.flush()
|
|
|
153 self.checkAttributes()
|
|
|
154
|
|
|
155 def end( self ):
|
|
|
156 """
|
|
|
157 Useful commands before ending the program.
|
|
|
158 """
|
|
|
159 self.clean()
|
|
|
160 if self._verbose > 0:
|
|
|
161 print "END %s" % ( type(self).__name__ ); sys.stdout.flush()
|
|
|
162
|
|
|
163 def run( self ):
|
|
|
164 """
|
|
|
165 Run the program.
|
|
|
166 """
|
|
|
167 self.start()
|
|
|
168 if self._lNodes == []:
|
|
|
169 self._lNodes = self.getAllNodesList()
|
|
|
170 if self._verbose > 0: self.showNodeList( self._lNodes )
|
|
|
171 self.cleanNodes()
|
|
|
172 self.end()
|
|
|
173
|
|
|
174 if __name__ == "__main__":
|
|
|
175 i = CleanClusterNodesAfterRepet()
|
|
|
176 i.setAttributesFromCmdLine()
|
|
|
177 i.run()
|
