Re: 50% system CPU usage when parallel running NAMD on Rocks cluster

From: 周昵昀 (malrot13_at_gmail.com)
Date: Sun Dec 08 2013 - 09:11:31 CST

Thanks for your reply! 16 cores per node are physical, HT was closed before
NAMD was tested. I'll consider buying a new switch.

BTW, will it scale better if I compile a UDP version NAMD?

Neil Zhou

2013/12/3 Norman Geist <norman.geist_at_uni-greifswald.de>

> Your switch is too slow in switching. Try something like the netgear
> gs748t, not that expensive and 搊k scaling. You can temporarily improve
> the situation by trying the tcp congestion control algorithm 揾ighspeed.
> Set it via sysconfig on all the nodes.
>
>
>
> Additionally, are these 16 cores per node physical or logical (HT). If it
> is HT, leave them out, no speed gain, only more network load.
>
>
>
> Norman Geist.
>
>
>
>

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