| [20301] | 1 | import subprocess
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| 2 | from fielddisplay import fielddisplay
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| 3 | from pairoptions import pairoptions
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| 4 | from issmssh import issmssh
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| 5 | from issmscpin import issmscpin
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| 6 | from issmscpout import issmscpout
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| 7 | from QueueRequirements import QueueRequirements
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| 8 | import datetime
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| 9 | try:
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| 10 | from vilje_settings import vilje_settings
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| 11 | except ImportError:
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| 12 | print 'You need vilje_settings.py to proceed, check presence and sys.path'
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| 13 |
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| 14 | class vilje(object):
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| 15 | """
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| 16 | Vilje cluster class definition
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| 17 |
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| 18 | Usage:
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| 19 | cluster=vilje();
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| 20 | """
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| 21 |
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| 22 | def __init__(self,*args):
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| 23 | # {{{
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| 24 | self.name = 'vilje'
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| 25 | self.login = ''
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| 26 | self.numnodes = 2
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| 27 | self.cpuspernode = 32
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| [20784] | 28 | self.procspernodes = 16
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| 29 | self.mem = 28
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| [20301] | 30 | self.queue = 'workq'
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| 31 | self.time = 2*60
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| 32 | self.codepath = ''
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| 33 | self.executionpath = ''
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| 34 | self.interactive = 0
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| [20784] | 35 | self.port = []
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| 36 | self.accountname = ''
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| [20301] | 37 |
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| 38 | #use provided options to change fields
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| 39 | options=pairoptions(*args)
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| 40 |
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| 41 | #initialize cluster using user settings if provided
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| 42 | self=vilje_settings(self)
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| 43 | #OK get other fields
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| 44 | self=options.AssignObjectFields(self)
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| [21759] | 45 | self.np=self.numnodes*self.procspernodes
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| [20301] | 46 | # }}}
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| 47 | def __repr__(self):
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| 48 | # {{{
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| 49 | # display the object
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| 50 | s = "class vilje object:"
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| 51 | s = "%s\n%s"%(s,fielddisplay(self,'name','name of the cluster'))
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| 52 | s = "%s\n%s"%(s,fielddisplay(self,'login','login'))
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| 53 | s = "%s\n%s"%(s,fielddisplay(self,'numnodes','number of nodes'))
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| 54 | s = "%s\n%s"%(s,fielddisplay(self,'cpuspernode','number of nodes per CPUs (32)'))
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| 55 | s = "%s\n%s"%(s,fielddisplay(self,'procspernodes','number of mpi procs per nodes'))
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| 56 | s = "%s\n%s"%(s,fielddisplay(self,'mem','node memory'))
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| [21759] | 57 | s = "%s\n%s"%(s,fielddisplay(self,'queue','name of the queue (test is an option, workq the default)'))
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| [20301] | 58 | s = "%s\n%s"%(s,fielddisplay(self,'time','walltime requested in minutes'))
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| 59 | s = "%s\n%s"%(s,fielddisplay(self,'codepath','code path on the cluster'))
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| 60 | s = "%s\n%s"%(s,fielddisplay(self,'executionpath','execution path on the cluster'))
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| 61 | s = "%s\n%s"%(s,fielddisplay(self,'interactive',''))
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| 62 | s = "%s\n%s"%(s,fielddisplay(self,'accountname','your cluster account'))
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| 63 | return s
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| 64 | # }}}
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| 65 | def checkconsistency(self,md,solution,analyses):
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| 66 | # {{{
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| 67 | #Queue dictionarry gives queu name as key and max walltime and cpus as var
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| [21759] | 68 | queuedict = {'workq':[5*24*60, 30],
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| 69 | 'test':[30,4]}
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| [20301] | 70 | QueueRequirements(queuedict,self.queue,self.np,self.time)
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| 71 |
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| 72 | #Miscelaneous
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| 73 | if not self.login:
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| 74 | md = md.checkmessage('login empty')
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| 75 | if not self.codepath:
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| 76 | md = md.checkmessage('codepath empty')
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| 77 | if not self.executionpath:
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| 78 | md = md.checkmessage('executionpath empty')
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| 79 | if self.interactive==1:
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| 80 | md = md.checkmessage('interactive mode not implemented')
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| 81 | return self
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| 82 | # }}}
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| [21759] | 83 | def BuildQueueScript(self,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling):
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| [20301] | 84 | # {{{
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| 85 |
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| 86 | executable='issm.exe'
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| 87 | if isdakota:
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| 88 | version=IssmConfig('_DAKOTA_VERSION_')[0:2]
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| 89 | version=float(version)
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| 90 | if version>=6:
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| 91 | executable='issm_dakota.exe'
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| [21759] | 92 | if isoceancoupling:
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| 93 | executable='issm_ocean.exe'
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| [20301] | 94 |
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| 95 | #write queuing script
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| [20784] | 96 | shortname=modelname[0:min(12,len(modelname))]
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| [20301] | 97 | fid=open(modelname+'.queue','w')
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| 98 | fid.write('#PBS -S /bin/bash\n')
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| 99 | fid.write('#PBS -N %s \n' % shortname)
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| 100 | fid.write('#PBS -q %s \n' % self.queue)
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| 101 | fid.write('#PBS -l select=%i:ncpus=%i:mpiprocs=%s\n' % (self.numnodes,self.cpuspernode,self.procspernodes))
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| [21759] | 102 | timeobj=datetime.timedelta(minutes=self.time)
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| 103 | m,s=divmod(timeobj.total_seconds(), 60)
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| 104 | h,m=divmod(m, 60)
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| 105 | timestring="%02d:%02d:%02d" % (h, m, s)
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| [20301] | 106 | fid.write('#PBS -l walltime=%s\n' % timestring) #walltime is hh:mm:ss
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| 107 | #fid.write('#PBS -l mem=%igb\n' % self.mem)
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| 108 | fid.write('#PBS -A %s\n' % self.accountname)
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| 109 | fid.write('#PBS -o %s/%s/%s.outlog \n' % (self.executionpath,dirname,modelname))
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| 110 | fid.write('#PBS -e %s/%s/%s.errlog \n\n' % (self.executionpath,dirname,modelname))
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| 111 | fid.write('export ISSM_DIR="%s/../"\n' % self.codepath)
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| [21759] | 112 | fid.write('module load intelcomp/17.0.0\n')
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| 113 | fid.write('module load mpt/2.14\n')
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| 114 | fid.write('module load petsc/3.7.4d\n')
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| 115 | fid.write('module load parmetis/4.0.3\n')
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| 116 | fid.write('module load mumps/5.0.2\n')
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| [20301] | 117 | fid.write('cd %s/%s/\n\n' % (self.executionpath,dirname))
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| [21234] | 118 | fid.write('mpiexec_mpt -np %i %s/%s %s %s/%s %s\n' % (self.np,self.codepath,executable,str(solution),self.executionpath,dirname,modelname))
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| [20301] | 119 | fid.close()
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| 120 |
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| [21759] | 121 | # }}}
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| [20301] | 122 | def UploadQueueJob(self,modelname,dirname,filelist):
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| [20784] | 123 | # {{{
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| [20301] | 124 | #compress the files into one zip.
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| 125 | compressstring='tar -zcf %s.tar.gz ' % dirname
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| 126 | for file in filelist:
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| [20784] | 127 | compressstring += ' %s' % file
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| [20301] | 128 | subprocess.call(compressstring,shell=True)
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| 129 |
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| 130 | print 'uploading input file and queueing script'
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| 131 | issmscpout(self.name,self.executionpath,self.login,self.port,[dirname+'.tar.gz'])
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| 132 |
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| 133 | # }}}
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| 134 | def LaunchQueueJob(self,modelname,dirname,filelist,restart,batch):
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| [20784] | 135 | # {{{
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| [20301] | 136 |
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| 137 | print 'launching solution sequence on remote cluster'
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| 138 | if restart:
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| 139 | launchcommand='cd %s && cd %s && qsub %s.queue' % (self.executionpath,dirname,modelname)
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| 140 | else:
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| 141 | launchcommand='cd %s && rm -rf ./%s && mkdir %s && cd %s && mv ../%s.tar.gz ./ && tar -zxf %s.tar.gz && qsub %s.queue' % (self.executionpath,dirname,dirname,dirname,dirname,dirname,modelname)
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| 142 | issmssh(self.name,self.login,self.port,launchcommand)
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| 143 |
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| 144 | # }}}
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| 145 | def Download(self,dirname,filelist):
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| 146 | # {{{
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| 147 |
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| 148 | #copy files from cluster to current directory
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| 149 | directory='%s/%s/' % (self.executionpath,dirname)
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| 150 | issmscpin(self.name,self.login,self.port,directory,filelist)
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| 151 | # }}}
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