Sorry it's a long script so I was trying to give the portion of code that is the problem. This is the subprocedure:

sub processCnfDirectory {
  use Time::HiRes(gettimeofday);
  use File::Basename;
  my($path) = @_;
  my $pid;
  local $SIG{ALRM} = sub {
        $didTimeout=1;
        print OUTPUT "timeout";
        print "process id", $pid, "\n";
        kill 9, $pid;
       die "Timeout\n";
  };

  print( "working in: $path\n" );

  # append a trailing / if it's not there 
  $path .= '/' if($path !~ /\/$/);

  # loop through the files contained in the directory 
  for my $file (glob($path . '*')) {

    # check if the file is a directory 
    if( -d $file)
      # pass the directory to the routine ( recursion )
      processCnfDirectory($file);
    }
    elsif ($file =~ /.*\.cnf/)
    {
      print OUTPUT basename($file), ",";

      # run using the first solver
      $pid = fork;
      eval {
        $didTimeout=0;
        $start1=gettimeofday();
        alarm $timeout;
        #$pid = `$solver1 $file`;
        $result = `$solver1 $file`;
        waitpid($pid, 0);
      };
      alarm 0;
      $end1=gettimeofday();
      if($didTimeout == 0) {
        print OUTPUT $end1 - $start1;
      }
      print OUTPUT ",";

      # run using the second solver
      $pid = fork;
      eval {
        $didTimeout=0;
        $start2=gettimeofday();
        alarm $timeout;
        #$pid = `$solver2 $file`;
        $result = `$solver2 $file`;
        waitpid($pid, 0);
      };
     };
      alarm 0;
      $end2=gettimeofday();
      if($didTimeout == 0) {
        print OUTPUT $end2 - $start2;
      }
      print OUTPUT "\n";
    }
  }
}
[download]

So what it does is it reads in a directory on the command line. It loops through the directory recursively to include subdirectories. Inside a directory it runs a solver on each file. Then it records the amount of time it took to run. The solvers are also command line input.

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