[Bioclusters] Xserve G5 memory

Joe Landman bioclusters@bioinformatics.org
Tue, 05 Oct 2004 16:01:58 -0400

Unless you are using a memory mapped process reading these same files at 
the same time, it is likely that they are only showing up in buffer 
cache.  OSX probably has a very different cache retention policy as 
compared to AIX and Linux.  This is usually a kernel tunable.

Ask your Apple folks about how to tweak the kernel.

Another very important issue is the size of the file as compared to the 
size of memory (more specifically buffer cache).  If the file overflows 
memory, the mmap mechanism will happily ask the kernel to start paging.  
This is "A Bad Thing(tm)".  You want your database index small enough to 
hold in memory for good performance.  You don't want them too small, as 
you will start to pay some costs associated with increased file activity.

Which database is being used?

Victor M.Ruotti wrote:

> 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.
> Victor
> 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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Joseph Landman, Ph.D
Scalable Informatics LLC,
email: landman@scalableinformatics.com
web  : http://www.scalableinformatics.com
phone: +1 734 612 4615