sub fill_matrix {
    my ($in) = @_;
    open my $IN, '<', $in or die $!;

    my @index = (0);
    push @index, tell $IN while <$IN>;
    pop @index;

    for my $line_no (0 .. $#index) {
        print STDERR "$line_no\r";
        for my $idx (0 .. $line_no - 1) {
            seek $IN, $index[$idx], 0;
            my $line = <$IN>;
            print +(split ' ', $line, $line_no + 2)[$line_no], ' ';
        }
        seek $IN, $index[$line_no], 0;
        my $line = <$IN>;
        print +(split ' ', $line, $line_no + 1)[-1];
    }
}
[download]

but it was much slower: 28s for SIZE 1000, 280s for SIZE 2000.

($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,
[download]