From: Zeki Zeybek (zeki.zeybek_at_bilgiedu.net)
Date: Mon Feb 06 2017 - 02:59:51 CST
In NAMD relasing notes (http://www.ks.uiuc.edu/Research/namd/2.9/ug/node88.html) it is recommended to add the +idlepoll line, I don't know whether they are equivalent or not.
________________________________
From: Francesco Pietra <chiendarret_at_gmail.com>
Sent: 06 February 2017 11:37:33
To: NAMD; Norman Geist
Cc: Zeki Zeybek
Subject: Re: namd-l: ++idlepoll
Hello:
what about
"nvidia-smi -pm 1"
that I command with a single node linux box before launching namd2 ... +idlepoll.....?
Also, is "+idlepoll" equivalent to "++idlepoll"?
thanks
francesco pietra
On Mon, Feb 6, 2017 at 9:15 AM, Norman Geist <norman.geist_at_uni-greifswald.de<mailto:norman.geist_at_uni-greifswald.de>> wrote:
In simple words:
In distributed parallel implementations, two or more endpoints that share some kind of network connection exchange messages. In the case of GPU acceleration this network is the PCIE bus and the endpoints are the CPU and the GPU. The CPU puts work to the GPU and must wait for the GPU to return back the result. Since the CPU can't know when the GPU will be finished, it must frequently ask the GPU if it has finished, this is called polling. Such polling without a wait time in-between is very CPU intensive (++idlepoll), but with a wait time of N, there's always a chance of getting the results N time too late, so this would waste time and increase latency. Therefore using ++idlepoll is absolutely recommended, and even forced for GPU runs.
Norman Geist
Von: owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> [mailto:owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>] Im Auftrag von Zeki Zeybek
Gesendet: Montag, 6. Februar 2017 08:21
An: namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>
Betreff: namd-l: ++idlepoll
Hi!
I was just wondering what is the rationale behind adding this command in order to run a simulation on GPU. Simply I did not really understand what the statement `you should add +idlepoll to the command line in order to poll the GPU for results rather than sleeping while idle` means. Sorry for my ignorance on the matter. I would appreciate any sort of detailed info on the matter. Thank you in advance
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