Hello,

I'm a bit stuck trying to output a series of very large hashes. Using what I thought would be memory-efficient code:

open(AGG, '>', $aggregate_file);

while ( my ($key1, $val1) = each %noninteracting_hash ) {
        while ( my ($key2, $val2) = each %$val1 ) {
                print AGG join(
                        "\t",
                        $key1,
                        $key2,
                        $noninteracting_hash{$key1}{$key2},
                        $interacting_hash{$key1}{$key2},
                        $literature_hash{$key1}{$key2},
                        $predicted_hash{$key1}{$key2}
                        ), "\n";
                }
        }

close(AGG);

[download]

When I say huge hashes, what I mean is that each hash is keyed by a 10-char string and in total there are 3,895,529,794 elements in each entire HoH (e.g. the output to file should contain four-billion rows or so). The program reproducibly crashes after 6.8 million rows (variance in crash point from run to run is about 30 rows).

The specific error is my favourite: Out of memory!

Can anyone see what might be going on here, as I'm kinda lost!

In reply to Outputting Huge Hashes by bernanke01

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