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increasing memory usage for running perl script

windows operating system, 64 bit dual core processors



4:14 am on Dec 30, 2009 (gmt 0)

5+ Year Member

I have a rather ponderous script that aligns DNA sequences and assigns penalties for interactions generating a list of low penalty DNA sequences for PCR (polymerase chain reaction) ... the program takes about 5 min to select primers from several thousand bases of DNA ... when i run this script on a windows computer with 16 gByte of RAM it is not any faster than another computer with < 2 gByte of RAM ... both show 98 MB CPU usage ... is there a way to increase the RAM usage for perl scripts?

thanks guys ... happy new year



6:17 am on Dec 30, 2009 (gmt 0)

WebmasterWorld Administrator phranque is a WebmasterWorld Top Contributor of All Time 10+ Year Member Top Contributors Of The Month

oversimplifying here: perl tends to use what it needs for memory so it sounds like you are not memory constrained.
i would suggest you investigate whether your application is suitable for multi-threading and if so start researching "multiprocessor kernel threads".


6:26 am on Dec 30, 2009 (gmt 0)

5+ Year Member

thanks phranque ... will let you know what i learn


9:33 pm on Dec 30, 2009 (gmt 0)

WebmasterWorld Senior Member 5+ Year Member

you can generally use threading (and increase performance!) if you can get work done in parallel, e.g. if you just work through log files and you don't need the results of all the earlier files, you could just run your script multiple times or use threading, where threading gives you a much nicer way to communicate.

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