sgeenviron.py

#!/usr/bin/python
# *  Copyright 2010. The Regents of the University of California.
# *  All Rights Reserved.
# *  @author  Prakashan Korambath
# *
# *  Purpose:  Make use of scheduler TMPDIR variable for File I/O.  The scratch space
# *  defined in SGE is often has a faster I/O than NFS file system.  So your codes
# *  may run faster if you use TMPDIR to write scratch files which are not needed
# *  at the end of a run.  The scheduler used on Hoffman2 is Oracle Grid Engine.
# *  In place of TMPDIR any other faster SCRATCH space can be substituted.
# *
# *  This software program and documentation are copyrighted by The Regents
# *  of the University of California. The software program and documentation
# *  are supplied "as is", without any accompanying services from The Regents.
# *  The Regents does not warrant that the operation of the program will be
# *  uninterrupted or error-free. The end-user understands that the program
# *  was developed for research purposes and is advised not to rely exclusively
# *  on the program for any reason.
#
# *  IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY FOR
# *  DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING
# *  LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION,
# *  EVEN IF THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY
# *  OF SUCH DAMAGE. THE UNIVERSITY OF CALIFORNIA SPECIFICALLY DISCLAIMS ANY
# *  WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
# *  MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE PROVIDED
# *  HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF CALIFORNIA HAS NO
# *  OBLIGATIONS TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR
# *  MODIFICATIONS.
# *
# *

import os, string

# * Get SGE TMPDIR environment variable

try: 
   tmpdir=os.environ["TMPDIR"]
except KeyError:
   print 'Failed to get environment variable TMPDIR'
   tmpdir='/work'

print 'TMPDIR is ' + tmpdir

# * scrathc file name.  Do not forget leading / character

scratch1='/scratchxxx'

filepath=tmpdir+scratch1

print 'Full filepath is ' + filepath

usefulData='FirstName' + '\n' +  'LastName' + '\n'

# * open and output file and write something

output_file = open(filepath, 'w')
output_file.write(usefulData)
output_file.close()

# * oepn the same file for reading 

input_file = open(filepath, 'r')
line = input_file.readline()
while line:
  print line.strip()
  line = input_file.readline()

input_file.close()

try:
  os.remove(filepath)
except os.error:
  print filepath + ' could not be deleted'