charmm scalability on 2.4 kernels

Eray Ozkural (exa) erayo at cs.bilkent.edu.tr
Sat Jan 5 16:55:42 EST 2002


On Saturday 05 January 2002 20:10, Steve Fellini wrote:
> Hi All,
>
> Many of our users run charmm dynamics using Ewald/PME calculations,
> which require 3D FFTs.  When run in parallel on a cluster, these
> calculations scale moderately well to around 2-4 nodes (4-8
> processors) when run on either nodes on a Myrinet network, or on nodes
> running on fast ethernet with Linux 2.2.16 kernels with Josip
> Loncaric's tcp fix (see
> http://biowulf.nih.gov/charmm-bench/image003.gif).
>
> However for nodes running on ethernet with Linux 2.4.12 (i.e., without
> the tcp fix) scalability is very poor - so much so that there's no
> point in running on more than one node (see
> http://biowulf.nih.gov/charmm-bench/image004.gif and image005.gif).
>

This is rather surprising, I'd expect 2.4.x to actually improve upon 2.2.x. 
It was said before on this list that 2.4 already incorporates TCP fixes. Has 
anybody met a similar situation before?

Thanks,

-- 
Eray Ozkural (exa) <erayo at cs.bilkent.edu.tr>
Comp. Sci. Dept., Bilkent University, Ankara
www: http://www.cs.bilkent.edu.tr/~erayo
GPG public key fingerprint: 360C 852F 88B0 A745 F31B  EA0F 7C07 AE16 874D 539C
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