[Bioclusters] cache limit?

[ben]

Justin Powell wrote:

> I've got a small blast cluster which includes a Quad Processor Dell
> (kernel 2.2.16-22enterprise #1 SMP) and a bunch of Dual Athlons (kernel
> 2.4.2-2smp #1).  Repeat BLASTS of the same DB on the Athlons run about 7
> times faster than the first BLAST, I assume this is due to the memory
> mapped dbs being retained in the cache, but this is not the case with the
> Dell.  When I use 'free' to look at memory the cache on the Dell never
> goes above 850MB whereas that on the Athlons happily goes up to 3.5GB
> after identical BLAST jobs.
>
> All systems have 4GB ram.  Are there some obvious parameters which can be
> adjusted to alter the behaviour of the cache under Linux (I can't find
> obvious references to such on Google) or is there some difference in the
> memory management of different versions of the kernel which makes some of
> them less useful for this sort of thing?
>

Yes , there are many , I think . I' m just a newby to linux kernel internals

but I heard that virtual mem management is changed a lot from 2.2 to 2.4
kernels .
At the moment I' m running just 2.4 kernels , thus I don' t know about 2.2 ,

in /proc/sys/vm there are some rw files ...

about 2.4 kernel , I found :

http://www.csn.ul.ie/~mel/projects/vm/guide/html/understand/

contains two documents

1.
http://www.csn.ul.ie/~mel/projects/vm/guide/pdf/understand.pdf

In-depth guide to how the VM in kernel
2.4.20 functions and Linux Memory the major components of it

2. http://www.csn.ul.ie/~mel/projects/vm/guide/pdf/code.pdf

a companion document to the Understanding book
above. It is a detailed code commentary on most of the Linux VM to
help give a detailed understanding of the code and the style

greetings
ben





>
> Justin Powell
> jacp1@mole.bio.cam.ac.uk
>
> _______________________________________________
> Bioclusters maillist  -  Bioclusters@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters

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