Re: NAMD on TACC (Darter)

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Thu Dec 10 2015 - 10:03:56 CST

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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