Re: Namd benchmark problem

From: Nicholas M Glykos (
Date: Mon Oct 26 2009 - 09:14:36 CDT

Hi Axel,

> > I should add as a side note that -at least to my experience- there is no
> > single optimal way of tuning the operating system, such that it performs
> > best for all possible problem sizes and protocols. If you tune the OS
> > using the ApoA1 system, you shouldn't be surprised if it turns-out that it
> > is not optimal for, say, a peptide simulation. For large centralised
> > clusters, of course, you do not have a choice (which usually is a relief ;-)
> if you have a software on your operating system, that is _that_
> sensitive to two different systems in the same code, then there
> is something wrong with the OS software that needs to be tweaked.

Ok. An example then. Take PCI bus and a network card sitting on it:
changing the PCI latency of the card will decrease the latency, but will
also reduce maximum throughput. For a small MD system, the messages
exchanged are short, the bottleneck is definitely latency, and you are
better-off zeroing it (as seen on lspci). But for, say, a very large
system with a small number of nodes, the bottleneck may well be
throughput, in which case you want the card to hold-on to the bus for
longer (higher value in lspci).

> if one operates a machine for multiple purposes, the best option
> is usually to first characterize the dominant usage and tune a
> machine for that and then make sure the machine is usable and
> the performance does not degrade too badly for other uses.

Completely agree on that.


          Dr Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615,

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