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mjarvis |
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#!/usr/bin/env python
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import errno
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import os
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import os.path
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import commands
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import re
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import sys
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from copy import deepcopy
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header_eq="="*50
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header_dash="-"*50
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def chunks(l, n):
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for i in xrange(0, len(l), n):
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yield l[i:i+n]
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# def ensure_dir(f):
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# d = os.path.dirname(f)
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# if not os.path.exists(d):
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# os.makedirs(d)
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def ensure_dir(path):
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try:
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os.makedirs(path)
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except OSError as exc: # Python >2.5
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if exc.errno == errno.EEXIST:
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pass
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else: raise
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YourSusyDir = commands.getoutput('echo $SUSY_WORKING_SW_DIR') #Get the susy working Dir
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print YourSusyDir
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YourScriptsDir = commands.getoutput('pwd')
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def BatchRun(samples,analysis,config,outputDir,nFilesPerJob):
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print header_eq
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print "Running Batch Analysis"
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print header_eq
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print "On %d sample(s):" % len(samples)
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for sample in samples:
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print "\t%s " % (sample.Name)
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print header_eq
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#copy contents of file
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folder = YourScriptsDir+"/tmp/"
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ensure_dir(folder) # where we'll put all our files
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filename = sys.argv[0]
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file = open(filename,"r")
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code = file.read()
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#re for things we need to change
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p = re.compile('samples\s?=\s?\[*?.*?\]', re.DOTALL)
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q = re.compile('BatchRun\(*?.*?\)')
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#loop over each suplied sample, then fragment in to subsamples each of 10 files
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for sample in samples:
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tmpSamplePset = deepcopy(sample)
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filesList = list(chunks(sample.File,nFilesPerJob))
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#Loop over fragments of samples
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for files,i in zip(filesList,range(len(filesList))) :
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fragName = sample.Name +"_part"+str(i)
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print "submitting " + folder + fragName + " to batch queue."
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#replace samples in copy of file to fragment samples
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tmpSamplePset.Name = "\"" + fragName + "\""
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tmpSamplePset.File = files
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string = "sample = PSet("
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for (k,v) in tmpSamplePset._flatten().iteritems() :
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string += "\n\t%s = %s ,"% (k,v)
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string +="\n)"
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string += "\nsamples=[sample]"
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newCode = p.sub(string, code)
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ensure_dir(outputDir+"/"+sample.Name)
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#replace batch run with normal "a.run()"
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mjarvis |
1.2 |
string = analysis+".Run( \""+outputDir +sample.Name +"/\"," +config +", samples)"
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mjarvis |
1.1 |
newCode = q.sub(string, newCode)
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#write .py
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temp = open(folder+filename[:-3]+analysis+"_"+fragName+".py", 'w')
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temp.write(newCode)
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temp.close()
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#write .sh that we will submit to batch
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temp = open(folder+filename[:-3]+analysis+"_"+fragName+".sh", 'w')
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script = '\n'.join([
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'#!/bin/sh',
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'source '+YourSusyDir+'/setup.sh',#Need to be changed to be more portable
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'cd '+ YourScriptsDir+"/tmp/",# There is a $SUSY_WORKING_DIR path, " how to make python expand this"
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filename[:-3]+analysis+"_"+fragName+".py"
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])
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temp.write(script)
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temp.close()
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#make executable
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os.chmod(folder+filename[:-3]+analysis+"_"+fragName+".py",0777)
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#Submit
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output = commands.getstatusoutput("qsub -q hep.q " + folder+filename[:-3]+analysis+"_"+fragName+".sh")
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#Succesful?
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if output[0] != 0 :
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print "\tError occured:"
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print output
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break
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else :
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print output[1]
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#make clean up script that
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#hadd root files
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#deletes fragments of root files
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#deletes .py and .sh
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