Re: NAMD on TACC (Darter)

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Thu Dec 10 2015 - 17:35:15 CST

Hi Jim,

That really helped. Thank you so much.

Regards,
Chitrak.

On Thu, Dec 10, 2015 at 11:03 AM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:

>
> You should use the options for PROCSPERNODE 15 or 16:
>
> case 15:
> set SMP = ""
> set APRUNARGS = "-n ${TOTALPROCS} -N 15 -r 1"
> set NAMDARGS = "+pemap 0-14"
> breaksw
> case 16:
> set SMP = ""
> set APRUNARGS = "-n ${TOTALPROCS} -N 16"
> set NAMDARGS = "+pemap 0-15"
> breaksw
>
> Jim
>
>
>
> On Wed, 9 Dec 2015, Chitrak Gupta wrote:
>
> 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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