Re: Cost of a colvar calculation

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Wed Jul 23 2014 - 07:45:31 CDT

Great George,

Additional just check how fast is communication between nodes (probably
you use cluster with infiniband),
  maybe you can gain something more on sped-up of whole calculation

Branko

On 7/23/2014 8:33 AM, George Patargias wrote:
> Thank you so much Jerome, Aron, Axel and Jo for these so enlightening
> comments!
>
> Indeed, halving the number of C-alpha atoms included in the RMSD
> calculation improved the benchmark times by a factor of 3.5!
>
>
>> This isn't surprising, there are two factors leading to your poorer than
>> average results:
>>
>> 1) The RMSD colvar is a particularly computationally intensive one, since
>> it not only requires the calculation of the RMSD, but also the alignment
>> to
>> the reference at every step. If you redo this test with a simpler colvar
>> like distance, or something intermediate like radius of gyration, you'll
>> get much less slow-down.
>>
>> 2) You are using a lot of cores. The colvar calculation occurs (at least
>> the last time I looked into these things) on a single core, so its speed
>> is
>> more or less set and is a kind of upper limit on what you can expect. So
>> when you add cores to the rest of the calculation, you eventually hit the
>> wall at how long the colvar calculation takes.
>>
>> If you want to improve things, don't use so many atoms in the colvar. For
>> instance, you could use just the C-alphas, or even every other or every
>> third C-alpha. This will likely give you a dramatic improvement.
>>
>>
>>
>>
>> On Tue, Jul 22, 2014 at 9:41 AM, Ivan Gregoretti <ivangreg_at_gmail.com>
>> wrote:
>>
>>> Thank you J?r?me.
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> 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 J?r?me,
>>>>>
>>>>> Could you expand your answer a little bit?
>>>>>
>>>>> Thank you,
>>>>>
>>>>> Ivan
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Tue, Jul 22, 2014 at 7:56 AM, J?r?me H?nin <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
>>>>>>>
>>>
>>
>> --
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo
>>
>
> 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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