From: Ivan Gregoretti (ivangreg_at_gmail.com)
Date: Tue Jul 22 2014 - 07:33:14 CDT
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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