Having profiled you code line by line two different ways, it seems that almost all of the time is spent performing IO. Either reading from or writing to files. The only executable line that shows any significant cpu ot elapsed time usage is the the line

92:         my @array = split(" ", $in);

Which I don't see any easy way to optimise.

Of course, the IO charecteristics of my system may be significantly different from the system you are running on, though I notice you are on a Win32 sytem too, so it shouldn't be so different.

As for why the FORTRAN program is so much faster, assuming that it is doing the same processing,IO and running on the same hardware (which is an open question?), then my best guess is that the FORTRAN IO uses larger buffers and asynchronous reads and writes. I know of at least one PC-based FORTRAN compiler that does this.

It is possible to use threads and other techniques to acheive this using perl without radically altering the structure of your existing program, but it isn't trivial to do. Whether you would come close to getting the kind of speed up you would need is very speculative.

This is the output from using Devel::SmallProf on your code. I've massaged the output to just show the significant lines in decreasing order of cpu usage.

cpu/iter    iters   wall s    cpu s  line
0.4281          1 0.428139 0.000000    19:close FAIL_FLAG_QUAD4;
0.0034        296 0.999800 0.110000   121:       print FAIL_FLAG_QUAD4
+ ("$Element_ID
0.0011        888 0.999800 0.191000   112:      $Flag_for_elem_id_line
+ = 0;
0.0003       3257 0.999800 0.623000    62:   if (($in =~ /^1/) && ($in
+ =~ /MSC/) &&
0.0003      30192 8.998197 6.425000    92:         my @array = split("
+ ", $in);
0.0003      13912 3.999199 3.344000   115:      print Q4CE_IN ("$Eleme
+nt_ID
0.0003      13912 3.999199 2.245000   116:      $Flag_for_long_line = 
+0;
0.0003      13912 3.999199 3.103000   118:      print Q4FI_IN ("$Eleme
+nt_Id_Line
0.0003      13912 3.999199 2.973000   120:      if( ($size == 2) && ( 
+(defined
0.0002      31672 5.998798 6.290000    88:          $in = (<FILE>);
0.0002      31672 4.998999 5.005000    89:          chomp($in);
0.0002      30192 5.998798 4.405000    93:         my $size = @array;
0.0002      30192 6.998598 5.549000    95:         if($size == 5){
0.0002      13912 2.999399 2.341000   103:      $Ply_Id = $array[0];
0.0001      13912 1.999599 2.293000   104:      $Failure_Index_1 = $ar
+ray[1];
0.0001      13912 0.999800 2.935000   106:      $Flag_for_long_line = 
+1;
0.0000          1 0.000000 0.000000     5:my @FileArray = ("junk.txt")
+;
0.0000          1 0.000000 0.000000     7:open(Q4FI_IN, ">QUAD4FI.txt"
+) or die "Unable
0.0000          1 0.000000 0.010000     9:open(Q4CE_IN, ">QUAD4CE.txt"
+) or die "Unable
[download]

I noticed a couple of errors in your code, but these have been noted above.

One question? Are you guys paid by the keystoke? :^)

Those have to be the longest variable names I've come across in a while.