[Bioclusters] Xserve G5 memory

Victor M.Ruotti bioclusters@bioinformatics.org
Tue, 5 Oct 2004 12:20:01 -0500

Hi Juan,
How exactly do you hold your databases in memory. Do you it through 
programming? It may help to describe how exactly this is done. I am 
also curious to know how you do it.

On Oct 5, 2004, at 12:09 PM, Juan Carlos Perin wrote:

> 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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