From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jul 22 2014 - 11:02:47 CDT
On Tue, Jul 22, 2014 at 11:56 AM, Aron Broom <broomsday_at_gmail.com> wrote:
> 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.
yup. one cannot repeat the lessons of amdahl's law often enough. it is
not the parallel part of a program that decides its maximal speed when
run in parallel, but the serial parts.
http://en.wikipedia.org/wiki/Amdahl%27s_law
>
> 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 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
>> >>>>
>> >
>>
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:01 CST