1. Modified code

$totalscoreinv{$key1}{key2}= $totalscore;

foreach $keyscore (keys %totalscoreinv){
 print OUT "\n\nFirst key:$keyscore\n";
  foreach my $keyscore2 (sort by_score keys %{$totalscoreinv{$keyscore
+}}){
    printf(OUT "%30s %s\n", "$keyscore2= ", "$totalscoreinv{$keyscore}
+{$keyscore2}");
 }
}

sub by_score {
 $totalscoreinv{$keyscore}{$b}<=>$totalscoreinv{$keyscore}{$a};
}
[download]

2. well..as simple as it is not sorting at all. Here an excerpt of my results

 First key:700200
-----------------------------------------------------------
                523261=  -509.711586526694
                523237=  -494.393864137596
                523246=  -438.024029240629
                523424=  -521.488541326437
                523247=  -470.547762535975
[download]

Thanks