[gmx-users] Unusual processing time

[Justin Lemkul]

On 1/3/13 9:39 PM, Xu Dong Huang wrote:
> The average of all my variations contain about 802780 atoms.
>

The general rule of thumb is to aim for a few hundred or maybe a thousand atoms 
per processor.  Given that you have in excess of 130,000 atoms per processor, I 
would say your observation of slow performance is entirely normal.

-Justin

>
> Xu Dong Huang
> Chemical & Biochemical Engineering
> Rutgers School of Engineering
> xudongh at eden.rutgers.edu
>
> On Jan 3, 2013, at 9:36 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 1/3/13 9:33 PM, Xu Dong Huang wrote:
>>> Actually, I correct myself, it's not even a 85x85x85 system, it's a 45x45x45 box system with water solvent + large multiple solutes.
>>>
>>
>> Performance depends mostly on the number of atoms.  You haven't provided that information, so it's hard to judge what you might expect.
>>
>> -Justin
>>
>>> Xu Dong Huang
>>> Chemical & Biochemical Engineering
>>> Rutgers School of Engineering
>>> xudongh at eden.rutgers.edu
>>>
>>> On Jan 3, 2013, at 9:29 PM, Xu Dong Huang <xudongh at eden.rutgers.edu> wrote:
>>>
>>>> Dear gromac users,
>>>>
>>>> I submitted my NPT run into a MPI cluster. The size of my run system is an 85x85x85 box filled with water solvent. and I set NPT steps to be 1000000 (1million) with dt 0.02. The log says It will finish sometime in mid or towards end of february.
>>>>
>>>> Is that normal for a NPT run of that size? Or am I just faced with slow technology. Or am I doing something wrong (I requested 6 cores for my run)
>>>> Please let me know, thanks.
>>>>
>>>> Xu Dong Huang
>>>> Chemical & Biochemical Engineering
>>>> Rutgers School of Engineering
>>>> xudongh at eden.rutgers.edu
>>>>
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>>
>> --
>> ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================