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

From: (malrot13_at_gmail.com)
Date: Sat Dec 14 2013 - 07:55:47 CST

I have changed my switch from 3Com Switch 2824 to IP-Com G1024(a low-end
gigabit switch brrowed from reseller). To my suprise, there is neither any
performance improvement nor deterioration. The benchmark result is totally
the same as before within a reasonable error range. I guess it's not only
an "old-switch" problem.
Any help would be appreciated!

Neil

2013/12/10 Norman Geist <norman.geist_at_uni-greifswald.de>

> Jeah, something like that. I guess relative comparison is the best
> choice in your case. Thats why I gave you a reference model. Otherwise,
> look for some support from resellers.
>
>
>
> Norman Geist.
>
>
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *???
>
> *Gesendet:* Dienstag, 10. Dezember 2013 13:52
> *An:* Norman Geist
> *Cc:* Namd Mailing List
> *Betreff:* Re: namd-l: 50% system CPU usage when parallel running NAMD on
> Rocks cluster
>
>
>
> Your suggestion is very helpful. We are looking for some "better scale"
> switch. But here comes another question: what feature represent the
> "switching-latency" or "switching-capacity" of one switch? Is it "packet
> forwarding speed" or something else? Thanks again!
>
>
>
> Neil
>
>
>
> 2013/12/9 Norman Geist <norman.geist_at_uni-greifswald.de>
>
> Maybe a little. Theres lots you can try on the software side of the
> problem, but all this will only try to circumvent the real problem or
> lessen the impact. The most comfortable and likely successful solution, is
> buying another switch. So the keywords are switching-latency and
> switching-capacity. Take the model I posted as a reference, but notice,
> that 16 cores per node is really heavy for 1Gbit/s Ethernet and you might
> want to consider spending some money into a HPC network like Infiniband or
> at least 10Gbit/s Ethernet.
>
>
>
> Norman Geist.
>
>
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *???
>
>
> *Gesendet:* Sonntag, 8. Dezember 2013 16:12
> *An:* Norman Geist
> *Cc:* Namd Mailing List
>
> *Betreff:* Re: namd-l: 50% system CPU usage when parallel running NAMD on
> Rocks cluster
>
>
>
> 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 ok scaling. You can temporarily improve
> the situation by trying the tcp congestion control algorithm highspeed.
> 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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