From: George Patargias (gpat_at_bioacademy.gr)
Date: Wed Jul 23 2014 - 01:33:23 CDT
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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