$ perl -Mstrict -Mwarnings -Mautodie -le '
    use Tie::File;

    tie my @input_records, "Tie::File", "./pm_1054101_input.txt";

    open my $out_fh, ">", "./pm_1054101_output.txt";

    print $out_fh $input_records[$_] for
        map { $_->[0] }
        sort { $a->[1] <=> $b->[1] || $a->[2] <=> $b->[2] }
        map { [ $_, map { substr $_, 3 } (split " ", $input_records[$_])[0,1] ] }
        0 .. $#input_records;

    close $out_fh;

    untie @input_records;
'

##</code><code>##

$ cat pm_1054101_input.txt
key1  key2  ndnjfgdsjfjjkjjfjf...
key1  key2  kdfkjdfgdfugbjndkfgkjgndkjfjkd
key43 key21 sdkjfhdghdbgbd
key1  key3  jujdejnsduhffnjj
key2  key2  jhzezhdjjf...

##</code><code>##

$ cat pm_1054101_output.txt
key1  key2  ndnjfgdsjfjjkjjfjf...
key1  key2  kdfkjdfgdfugbjndkfgkjgndkjfjkd
key1  key3  jujdejnsduhffnjj
key2  key2  jhzezhdjjf...
key43 key21 sdkjfhdghdbgbd

##</code><code>##

$ ls -l pm_1054101_*
-rw-r--r--  1 ken  staff  159 14 Sep 22:41 pm_1054101_input.txt
-rw-r--r--  1 ken  staff  159 14 Sep 23:04 pm_1054101_output.txt

##</code><code>##

$ perl -Mstrict -Mwarnings -Mautodie -le '
    use Tie::File;

    tie my @input_records, "Tie::File", "./pm_1054101_input.txt";

    my @sorted_record_numbers
        = map { $_->[0] }
          sort { $a->[1] <=> $b->[1] || $a->[2] <=> $b->[2] }
          map { [ $_, map { substr $_, 3 } (split " ", $input_records[$_])[0,1] ] }
          0 .. $#input_records;

    open my $out_fh, ">", "./pm_1054101_output.txt";

    for (@sorted_record_numbers) {
        print $out_fh $input_records[$_];
    }

    close $out_fh;

    untie @input_records;
'