From: Ivan Gregoretti (ivangreg_at_gmail.com)
Date: Tue Jul 22 2014 - 08:41:41 CDT
Thank you Jérôme.
On Tue, Jul 22, 2014 at 8:44 AM, Branko <bdrakuli_at_chem.bg.ac.rs> wrote:
> 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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