[Bioclusters] Xserve G5 memory

Chris Dwan bioclusters@bioinformatics.org
Tue, 5 Oct 2004 14:27:17 -0400

Collision on the term "database."

BLAST "databases" as described here are really just sets of target data 
stored in flat files.  They have nothing to do with Oracle, unless 
you're doing some really nifty stuff.

-Chris Dwan
  The BioTeam

> I believe one way you can do what you desire is to "PIN" the oracle 
> procedures into your memory and force oracle to make them memory 
> resident..
> Also, possibly increase the SGA oracle instance size on your 
> troublesome box..
> Either way talk to your local DBA
> Dan
> -----Original Message-----
> From: bioclusters-admin@bioinformatics.org
> [mailto:bioclusters-admin@bioinformatics.org]On Behalf Of Juan Carlos
> Perin
> Sent: Tuesday, October 05, 2004 1:10 PM
> To: bioclusters@bioinformatics.org
> Subject: [Bioclusters] Xserve G5 memory
> I have been running benchmarks with blastall on several different 
> machines.
> We've come to realize that one of the biggest differences affecting 
> search
> times is how the machines actually maintain the search databases in 
> memory.
> Eg..  On our IBM 8-way machine, the databases are held in the memory, 
> which
> seems to be an effect of the architecture of the machine, and search 
> times
> become incredibly fast after an initial run, which stores the database 
> in
> memory.  The same effect seems to take place on our Dual Xeon Dell (PE
> 1650), which also outpaces the Xserves significantly after an initial 
> run to
> populate the db in  memory.
> It would appear the the Xserves dump the db from memory after each 
> search,
> even when submitting batch jobs with multiple sequences in a file.  Is
> anyone aware of how this functions, and how this effect might be 
> changed to
> allow the db to stay in memory longer?  Thanks
> Juan Perin
> Child. Hospital of Philadelphia
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