[Bioperl-l] Comparing DB_FILE and SDBM

Lincoln Stein lstein at cshl.edu
Tue Aug 17 13:49:48 EDT 2004

There's been lots of benchmarking of the various DB implementations, 
including some reported in the perl PODs.  I suggest you look them 


On Friday 13 August 2004 02:11 pm, Josh Lauricha wrote:
> On Fri 08/13/04 13:59, Jason Stajich wrote:
> > If you run top when you are doing the indexing are you seeing
> > mostly perl CPU or system CPU - is it disk I/O that is killing
> > you or is it running full tilt in perl?
> I forgot to mention this in my previous mail, but going by his
> `time` output, I'm pretty sure the delay is not due to the perl
> stuff. There was only a few minutes of CPU time used, but quite a
> bit of time from start to finush. That leads me to think its a slow
> disk (or lotsa data, depending on your viewpoint), or the same
> wierdness I got with XML::SAX.

Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724

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