Re: Cost of a colvar calculation

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Tue Jul 22 2014 - 07:44:04 CDT

George.

I never observed such drastic difference when I have used colvars (most
often distance and rgyr in NAMD 2.8 and 2.9). It is advisable to check
your input and the scalability of system with and without colvars So do
not check just benchmark time, but also wallclock and CPU time after
some short simulation. Generally 256 processors with 258000 atoms could
be too much...

Branko

On 7/22/2014 2:33 PM, Ivan Gregoretti wrote:
> Hi Jérôme,
>
> Could you expand your answer a little bit?
>
> Thank you,
>
> Ivan
>
>
>
>
>
>
> On Tue, Jul 22, 2014 at 7:56 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
>> That is completely dependent on what variables you define, how many atoms
>> are involved, and the biases.
>>
>> Jerome
>>
>>
>>
>>
>> On 22 July 2014 13:27, George Patargias <gpat_at_bioacademy.gr> wrote:
>>> Hello,
>>>
>>> I am comparing the Benchmark times for a given system (~258,000 atoms)
>>> using
>>> NAMD_CVS-2014-06-02_Source version with and without the colvar module on.
>>>
>>> When the colvar module is *off* (equilibrium MD), I get something like
>>>
>>> Benchmark time: 256 CPUs 0.0268481 s/step 0.155371 days/ns 540.59 MB
>>> memory
>>>
>>> When the colvar module is *on* (moving harmonic restraint on an RMSD
>>> colvar calculated from 1981 C-alpha atoms), I get
>>>
>>> Benchmark time: 256 CPUs 0.320515 s/step 1.85483 days/ns 569.555 MB memory
>>>
>>> which is 11-12 times slower.
>>>
>>> Is this the actual computational cost of a colvar calculation?
>>>
>>> Also the scaling of this particular colvar calculation is not good:
>>>
>>> Benchmark time: 48 CPUs 0.331787 s/step 1.92006 days/ns
>>> Benchmark time: 128 CPUs 0.322472 s/step 1.86616 days/ns
>>> Benchmark time: 256 CPUs 0.320515 s/step 1.85483 days/ns
>>>
>>> Thanks in advance!
>>>
>>> George
>>>
>>> Dr. George Patargias
>>> Postdoctoral Research Fellow
>>> Biomedical Research Foundation
>>> Academy of Athens
>>> 4, Soranou Ephessiou
>>> 115 27
>>> Athens
>>> Greece
>>>
>>> Office: +302106597568
>>>

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