So I have this Perl program reading a very large file, building hashes and keeping line number counters.

Sounds to me like you should put the data into a DB and use the DB to make these histograms. The data set is so large that using Perl in memory hashes is not the best solution. A good DB will spawn multiple threads to handle a big requests and you will be able to control the amount of memory that the DB has available to it.

Having multiple workers reading separate parts of a single disk file typically doesn't help because the bottleneck is the maximum bandwidth of reading the single hard disk. Having multiple workers doesn't magically make new physical memory appear.

Update: If you are doing significant bio work, then a machine with 16GB RAM is WAY, WAY under powered. Seriously think about buying more hardware with more RAM, a lot more RAM and SSD disks instead of the spinning kind.

In reply to Re: MCE: How to access variables globally by Marshall
in thread MCE: How to access variables globally by biohisham

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