source: issm/trunk/src/py3/classes/clusters/generic.py@ 20500

Last change on this file since 20500 was 20500, checked in by Mathieu Morlighem, 9 years ago

merged trunk-jpl and trunk for revision 20497
File size: 7.8 KB
RevLine 
[19895]1import socket
2import os
3import math
4import subprocess
5from IssmConfig import IssmConfig
6from EnumToString import EnumToString
7from issmdir import issmdir
8from pairoptions import pairoptions
9from issmssh import issmssh
10from issmscpin import issmscpin
11from issmscpout import issmscpout
12import MatlabFuncs as m
13
14class generic(object):
15 """
16 GENERIC cluster class definition
17
18 Usage:
19 cluster=generic('name','astrid','np',3);
20 cluster=generic('name',oshostname(),'np',3,'login','username');
21 """
22
23 def __init__(self,**kwargs): # {{{
24
25 self.name=''
26 self.login=''
27 self.np=1
28 self.port=0
29 self.interactive=1
30 self.codepath=issmdir()+'/bin'
31 self.executionpath=issmdir()+'/execution'
32 self.valgrind=issmdir()+'/externalpackages/valgrind/install/bin/valgrind'
33 self.valgrindlib=issmdir()+'/externalpackages/valgrind/install/lib/libmpidebug.so'
34 self.valgrindsup=issmdir()+'/externalpackages/valgrind/issm.supp'
35
36 #use provided options to change fields
37 options=pairoptions(**kwargs)
38
39 #get name
40 self.name=socket.gethostname()
41
42 #initialize cluster using user settings if provided
43 if os.path.exists(self.name+'_settings.py'):
44 exec(compile(open(self.name+'_settings.py').read(), self.name+'_settings.py', 'exec'),globals())
45
46 #OK get other fields
47 self=options.AssignObjectFields(self)
48 # }}}
49 def __repr__(self): # {{{
50 # display the object
51 s ="class '%s' object '%s' = \n" % (type(self),'self')
52 s+=" name: %s\n" % self.name
53 s+=" login: %s\n" % self.login
54 s+=" np: %i\n" % self.np
55 s+=" port: %i\n" % self.port
56 s+=" codepath: %s\n" % self.codepath
57 s+=" executionpath: %s\n" % self.executionpath
58 s+=" valgrind: %s\n" % self.valgrind
59 s+=" valgrindlib: %s\n" % self.valgrindlib
60 s+=" valgrindsup: %s\n" % self.valgrindsup
61 return s
62 # }}}
63 def checkconsistency(self,md,solution,analyses): # {{{
64 if self.np<1:
65 md = checkmessage(md,'number of processors should be at least 1')
66 if math.isnan(self.np):
67 md = checkmessage(md,'number of processors should not be NaN!')
68
69 return md
70 # }}}
71 def BuildQueueScript(self,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota): # {{{
72
73 executable='issm.exe';
74 if isdakota:
75 version=IssmConfig('_DAKOTA_VERSION_')[0:2]
76 version=float(version)
77 if version>=6:
78 executable='issm_dakota.exe'
79
80 #write queuing script
81 if not m.ispc():
82
83 fid=open(modelname+'.queue','w')
84 fid.write('#!/bin/sh\n')
85 if not isvalgrind:
86 if self.interactive:
87 if IssmConfig('_HAVE_MPI_')[0]:
88 fid.write('mpiexec -np %i %s/%s %s %s/%s %s ' % (self.np,self.codepath,executable,EnumToString(solution)[0],self.executionpath,dirname,modelname))
89 else:
90 fid.write('%s/%s %s %s/%s %s ' % (self.codepath,executable,EnumToString(solution)[0],self.executionpath,dirname,modelname))
91 else:
92 if IssmConfig('_HAVE_MPI_')[0]:
93 fid.write('mpiexec -np %i %s/%s %s %s/%s %s 2> %s.errlog >%s.outlog ' % (self.np,self.codepath,executable,EnumToString(solution)[0],self.executionpath,dirname,modelname,modelname,modelname))
94 else:
95 fid.write('%s/%s %s %s/%s %s 2> %s.errlog >%s.outlog ' % (self.codepath,executable,EnumToString(solution)[0],self.executionpath,dirname,modelname,modelname,modelname))
96 elif isgprof:
97 fid.write('\n gprof %s/%s gmon.out > %s.performance' % (self.codepath,executable,modelname))
98 else:
99 #Add --gen-suppressions=all to get suppression lines
100 fid.write('LD_PRELOAD=%s \\\n' % self.valgrindlib)
101 if IssmConfig('_HAVE_MPI_')[0]:
102 fid.write('mpiexec -np %i %s --leak-check=full --suppressions=%s %s/%s %s %s/%s %s 2> %s.errlog >%s.outlog ' % \
103 (self.np,self.valgrind,self.valgrindsup,self.codepath,executable,EnumToString(solution)[0],self.executionpath,dirname,modelname,modelname,modelname))
104 else:
105 fid.write('%s --leak-check=full --suppressions=%s %s/%s %s %s/%s %s 2> %s.errlog >%s.outlog ' % \
106 (self.valgrind,self.valgrindsup,self.codepath,executable,EnumToString(solution)[0],self.executionpath,dirname,modelname,modelname,modelname))
107
108 if not io_gather: #concatenate the output files:
109 fid.write('\ncat %s.outbin.* > %s.outbin' % (modelname,modelname))
110 fid.close()
111
112 else: # Windows
113
114 fid=open(modelname+'.bat','w')
115 fid.write('@echo off\n')
116 if self.interactive:
117 fid.write('"%s/%s" %s "%s/%s" %s ' % (self.codepath,executable,EnumToString(solution)[0],self.executionpath,dirname,modelname))
118 else:
119 fid.write('"%s/%s" %s "%s/%s" %s 2> %s.errlog >%s.outlog' % \
120 (self.codepath,executable,EnumToString(solution)[0],self.executionpath,dirname,modelname,modelname,modelname))
121 fid.close()
122
123 #in interactive mode, create a run file, and errlog and outlog file
124 if self.interactive:
125 fid=open(modelname+'.errlog','w')
126 fid.close()
127 fid=open(modelname+'.outlog','w')
128 fid.close()
129 # }}}
130 def BuildKrigingQueueScript(self,modelname,solution,io_gather,isvalgrind,isgprof): # {{{
131
132 #write queuing script
133 if not m.ispc():
134
135 fid=open(modelname+'.queue','w')
136 fid.write('#!/bin/sh\n')
137 if not isvalgrind:
138 if self.interactive:
139 fid.write('mpiexec -np %i %s/kriging.exe %s/%s %s ' % (self.np,self.codepath,self.executionpath,modelname,modelname))
140 else:
141 fid.write('mpiexec -np %i %s/kriging.exe %s/%s %s 2> %s.errlog >%s.outlog ' % (self.np,self.codepath,self.executionpath,modelname,modelname,modelname,modelname))
142 elif isgprof:
143 fid.write('\n gprof %s/kriging.exe gmon.out > %s.performance' & (self.codepath,modelname))
144 else:
145 #Add --gen-suppressions=all to get suppression lines
146 fid.write('LD_PRELOAD=%s \\\n' % self.valgrindlib)
147 fid.write('mpiexec -np %i %s --leak-check=full --suppressions=%s %s/kriging.exe %s/%s %s 2> %s.errlog >%s.outlog ' % \
148 (self.np,self.valgrind,self.valgrindsup,self.codepath,self.executionpath,modelname,modelname,modelname,modelname))
149 if not io_gather: #concatenate the output files:
150 fid.write('\ncat %s.outbin.* > %s.outbin' % (modelname,modelname))
151 fid.close()
152
153 else: # Windows
154
155 fid=open(modelname+'.bat','w')
156 fid.write('@echo off\n')
157 if self.interactive:
158 fid.write('"%s/issm.exe" %s "%s/%s" %s ' % (self.codepath,EnumToString(solution)[0],self.executionpath,modelname,modelname))
159 else:
160 fid.write('"%s/issm.exe" %s "%s/%s" %s 2> %s.errlog >%s.outlog' % \
161 (self.codepath,EnumToString(solution)[0],self.executionpath,modelname,modelname,modelname,modelname))
162 fid.close()
163
164 #in interactive mode, create a run file, and errlog and outlog file
165 if self.interactive:
166 fid=open(modelname+'.errlog','w')
167 fid.close()
168 fid=open(modelname+'.outlog','w')
169 fid.close()
170 # }}}
171 def UploadQueueJob(self,modelname,dirname,filelist): # {{{
172
173 #compress the files into one zip.
174 compressstring='tar -zcf %s.tar.gz ' % dirname
175 for file in filelist:
176 compressstring += ' %s' % file
177 if self.interactive:
178 compressstring += ' %s.errlog %s.outlog ' % (modelname,modelname)
179 subprocess.call(compressstring,shell=True)
180
181 print('uploading input file and queueing script')
182 issmscpout(self.name,self.executionpath,self.login,self.port,[dirname+'.tar.gz'])
183
184 # }}}
185 def LaunchQueueJob(self,modelname,dirname,filelist,restart): # {{{
186
187 print('launching solution sequence on remote cluster')
188 if restart:
189 launchcommand='cd %s && cd %s chmod 777 %s.queue && ./%s.queue' % (self.executionpath,dirname,modelname,modelname)
190 else:
191 launchcommand='cd %s && rm -rf ./%s && mkdir %s && cd %s && mv ../%s.tar.gz ./ && tar -zxf %s.tar.gz && chmod 777 %s.queue && ./%s.queue' % \
192 (self.executionpath,dirname,dirname,dirname,dirname,dirname,modelname,modelname)
193 issmssh(self.name,self.login,self.port,launchcommand)
194 # }}}
195 def Download(self,dirname,filelist): # {{{
196
197 if m.ispc():
198 #do nothing
199 return
200
201 #copy files from cluster to current directory
202 directory='%s/%s/' % (self.executionpath,dirname)
203 issmscpin(self.name,self.login,self.port,directory,filelist)
204 # }}}
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