Hi, I reduced the code to generate the expected output values, but tried to keep some of your code.

#!/usr/bin/perl -w

use strict;
use warnings;
use v5.10;

my $completeDataPtRef;

for my $slot (1 .. 2) {
      my $TestFileName = "Slot". $slot ."Simplex.cfg.data";
      open my $dataFile, '<', "$TestFileName" or die ("Unable to open 
+file $TestFileName: $!\n");
      my $dataSetCnt = 0;
      while (my $dataLine = <$dataFile>)
      {
         $dataLine =~ /^#/ and next;
         my @dataPts = split(/\s+/, $dataLine);
         my $dataSetSize = shift(@dataPts);
         my $totalThroughput = shift(@dataPts);         
         
         push @{$completeDataPtRef->[$dataSetCnt]}, @dataPts;
         ++$dataSetCnt;
     }
     close $dataFile;
}

for my $linevalues (@{$completeDataPtRef})
{
     print "@{$linevalues}\n";
}
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