sgeenviron.pl

#!/usr/bin/perl

# *  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.
# *  
# * 

use strict;

   my $index;
#  Get SGE environment variable TMPDIR

   my $tmpdir=$ENV{TMPDIR};

#  define a scratchfile

   my $scratch1 ='/scratchxxx';

   if (!defined($tmpdir)) {
      print "Failed to get environment variable TMPDIR \n";
      $tmpdir='/work';
   }

   print "TMPDIR is $tmpdir \n";

#  This is the full file path for scratch

   my $filepath=$tmpdir . $scratch1;

   print "Scratch file path is $filepath \n";

# Now Open the file for writing

   open (OUTFILE, ">$filepath") || die ("Can't open $filepath for writing\n");
   for ($index = 1; $index <= 10; $index++) {
       print OUTFILE " $index \n";
   }
   close (OUTFILE);

# Now Open the file for reading

   open (INFILE, "<$filepath") || die ("Can't open $filepath for reading\n");
   while (<INFILE>) {
     print $_;
   }
   close (INFILE);
   unlink($filepath);
   exit;