From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Wed Dec 09 2015 - 07:49:53 CST
Hi Jim,
Ok, I guess I am getting this now. Basically I have built my own version of
NAMD on Darter, which is non-smp. Should I remove the NAMDARGS variable
from my aprun command?
Regards,
Chitrak.
On Tue, Dec 8, 2015 at 11:41 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
>
> Sorry, the "-j 2" in the APRUNARGS enables hyperthreads, so there are 32
> "cpus" per node. In my tests this was faster for smp runs (1 or 2
> processes per node). Non-smp runs are faster with hyperthreads disabled.
>
>
> Jim
>
> On Tue, 8 Dec 2015, Chitrak Gupta wrote:
>
> 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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