split(/,,/);

I don't see any ",," in the sample data you gave.

Do realize, 3Gb is a huge amount of data. It's going to take a long time, no matter what. Some things you may want to try out:

• Use a GRT instead of a ST. That will save many million times of entering and leaving a scope -- in fact, for a GRT no Perl code needs to be executed to determine which is "smaller".
• Use an external sort.

Oh, and in your map, you're splitting twice. Instead of writing map {[$_, (split)[0], (split)[2]]}, why not map {[$_, (split)[0,2]]}? But compared to the sort, this will only have a minor effect.

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