[Bioclusters] Xserve G5 memory

Juan Carlos Perin bioclusters@bioinformatics.org
Tue, 05 Oct 2004 13:09:33 -0400

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