Re: NAMD on TACC (Darter)

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Tue Dec 08 2015 - 22:19:12 CST

Hi Jim,

Thanks for update. However, I am still confused with the "+ppn 30 +pemap
0-14,16-30 +commap 15" line. Is it trying to use 32 nodes? But doesn't
Darter have only 16?

Regards,
Chitrak.

On Tue, Dec 8, 2015 at 11:15 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:

>
> /nics/b/home/jphillip/NAMD_scripts/runbatch is the current script for
> Darter. There is no runbatch_2.8 in that directory anymore.
>
> PPN is cores per node, PROCSPERNODE is processes per node.
>
> Jim
>
>
> On Tue, 8 Dec 2015, Chitrak Gupta wrote:
>
> Dear NAMD developers,
>>
>> I am trying to run NAMD on TACC (Darter). I am looking at the runbatch
>> script located at
>>
>> /nics/b/home/jphillip/NAMD_scripts/runbatch_2.8
>>
>>
>> on Darter. I got this location from the following page
>>
>> http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdAtNICS
>>
>>
>> Could you verify whether this is updated for the current build on Darter?
>> I
>> am asking because looks like this one is trying to run on 32 nodes
>> although
>> Darter only has 16.
>>
>> Also, what is the difference between $PPN and $PROCSPERNODE variables in
>> this code?
>>
>>
>>
>> Best regards,
>> Chitrak.
>>
>>

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