Re: for the isntall and run NAMD soft on 8 core (dual quad-core Xeons) system

From: Ilya Chorny (ichorny_at_gmail.com)
Date: Thu Sep 27 2007 - 20:48:10 CDT

Victor,

What kind of scaling do you get? Mine is not very good. I think 8
processors per nic is a bottle neck.

Ilya Chorny Ph.D.

On Sep 27, 2007, at 5:11 PM, Victor Ovchinnikov <ovchinnv_at_MIT.EDU>
wrote:

> Shulin,
> The existing 64 bit binaries compiled for AMD processors (both TCP/
> UDP)
> work fine (as also suggested by previous posts on this topic). I
> have a
> cluster of dual 4-core Xeons that I've tried this on.
>
> The execution command is unchanged (essentially as you describe)
>
> One thing that I don't know, and wonder if others have any
> information,
> is how NAMD scales with the number of these 8-cpu babies connected by
> myrinet/infiniband. I have Gbit ethernet, and so the scaling is
> decent
> for big systems only (>100,000 atoms) and only up to around 4 nodes
>
> Victor
>
> On Wed, 2007-09-26 at 15:08 -0700, Shulin Zhuang wrote:
>> Dear All,
>>
>> I want to ask a basic problem.
>>
>> Our lab plans to buy a 8 core (dual quad-core Xeons) to run parallel
>> NAMD. Can NAMD be directly run on it or shoud I recompile it.
>>
>> For the parallel run, after set the nodelist file, should I also use
>> the command: charmrun namd2 +p8 config file >outfile ?
>>
>> Great thanks
>>
>> Best regards
>>
>> Shulin
>

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