[Bioperl-l] OT: BLAST benchmark?

Fernan Aguero fernan@iib.unsam.edu.ar
Thu, 9 Nov 2000 19:11:38 -0300

Sorry for being OFF-TOPIC,
I am trying to optimize BLAST searches on our machines. Right now I am
trying to decide on the size of databases (i am splitting huge databases
using formatdb's -v option) to avoid swapping to disk. I know that BLAST
will like to have a certain amount of RAM for itself (100-200 Megs) and the
rest (or most of it) will be claimed by the BLAST database size. I thought
that perhaps there is a linux/unix utility that could be of help to analyze
things like i) run time, ii) memory used, iii) CPU used, etc. I can use top
or another similar tool but it only gives me the information for a
particular instant of the whole run. My impression is that this tool must
exist and I am missing it (i don't seem to be able to find anything that
looked like this on my Linux/Unix books).

Thanks in advance for your help,



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