charmm scalability on 2.4 kernels

[David van der Spoel]

On Tue, 8 Jan 2002, Josip Loncaric wrote:

>Actually, Linux kernel 2.4 incorporates an improved yet very different
>TCP stack where my TCP fixes do not help much in my usual test case
>(point-to-point streaming of small messages).  However, Steve's
>scalability problems with the stock 2.4 TCP are very interesting, since
>they involve many machines, i.e. a completely different communication
>pattern from my usual point-to-point tests.
>
>Old 2.2+fix combination was pretty efficient at aggregating small
>messages into larger TCP packets before sending, in fact better than
>stock 2.4.  Packet aggregation is something that depends on delicate
>timing of congestion control events on both sender and receiver; this is
>very sensitive to the application's communication pattern.  Perhaps a
>2.4 TCP fix would need to be developed after all...

Actually for molecular dynamics I think the problem is mainly latency.
Scali/Myrinet is a big win for large number of processors (see
www.gromacs.org/benchmarks/scaling.php for my own benchmarks).
However for me it also helped quite a bit to increase the TCP and Shared
memory short message size for LAM (I use 512 kb). Apparently short and
long messages are treated differently.


Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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