Re: recent comparison of NAMD to other MD engines

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Jan 23 2014 - 11:14:22 CST

On one of the compute clusters that I use, the performance of NAMD dropped noticeably after a standard quarterly maintenance just this week. The people managing it are working on tracking it down, although itís hard to say what the cause is, as the same hardware, libraries, etc. is being used. My point is though that the performance of these advanced, parallel codes is dependent on an incredible number of variables that trying to draw general conclusions becomes a foolís errand.

Ideally, one would choose the code based on its optimized performance (this requires either a good sys admin or a lot of experience yourself!) on the hardware available. In practice though, we typically just use what we are most comfortable with. :)

Regarding the specific issue in the paper, one idea is that they are using SDR or DDR Infiniband. So then NAMD saturates the network quickly. Since they only say ďInfinibandĒ we canít know for sure without asking.

On Jan 23, 2014, at 5:05 AM, Hannes Loeffler <Hannes.Loeffler_at_stfc.ac.uk> wrote:

> On Wed, 22 Jan 2014 21:38:29 -0500
> Giacomo Fiorin <giacomo.fiorin_at_gmail.com> wrote:
>
>> Without reading the paper in detail (I only saw Figures 6-8), I think
>> you should try to obtain the original input files used for each
>> program, in particular the cutoffs, PME grid resolution, time steps,
>> etc.
>>
>> It is not rare to find that the input files do not necessarily have
>> the same parameters: I once saw a comparison between program X
>> running with a 8 Ň cutoff and 1.5 Ň Ewald grid, vs. program Y running
>> with a 12 Ň cutoff and 0.8 Ň Ewald grid. I'd leave it up to you to
>> judge the accuracy of such comparison.
>>
>> Ultimately, benchmarks should be considered as any other scientific
>> data: they must be reproducible.
>
>
> The paper appears to be completely based on my benchmark suite which is
> readily available with all necessary input files from
> http://www.stfc.ac.uk/CSE/randd/cbg/Benchmark/25241.aspx . So
> reproducibility shouldn't be a problem provided the authors haven't
> changed the input parameters (except probably for the new CHARMM code
> as needed) or documented such. In the associated reports to the suite
> I also tried to make it clear as possible that the user should be
> careful about comparison and try to give advice how performance could
> possibly be improved. There I also encourage the user to carry out
> benchmarks of their own simulation systems on their chosen hardware.
>
> Those benchmarks, in particular Fig 8, may show some weakness of NAMD
> on this particular hardware configuration (the NAMD developers may be
> able to comment on that) or could also show a problem how the
> benchmarks were run. Regarding hardware, the benchmarks may look quite
> different on different hardware, i.e. those benchmarks only tell us how
> the codes performed on the specific hardware the authors have chosen
> (that's certainly a limiting factor and the authors don't tell us too
> much about their hardware). I personally have never seen such a
> "dramatic" (see below for comments on that) drop in performance of NAMD
> as depicted in Fig 8 but then I should probably add that most of my
> benchmarking was done on "super-computers".
>
> It should also be noted that in Fig 8 the absolute performance of NAMD
> at 256 cores is still slightly better than Gromacs at 512 cores.
> We don't see when GROMACS' performance peaks or when it starts to drop.
> Also, at 256 cores NAMD performs twice as fast as Gromacs! If you have
> to pay for your usage you will probably think twice if you want to run
> NAMD or GROMACS on that particular system on that particular
> hardware. You really ought to think how much cores you can afford in
> actual work. Good science work dictates multiple runs for statistical
> purposes/reproducibility (=independent runs) and you probably also have
> to compete for resources with other users, etc. It's interesting to see
> that GROMACS appears to be so badly performing on a per-core basis as
> that's quite the opposite of what I have seen so far.
>
> There is probably much more that I could say here. Partly I have tried
> to discuss this in my benchmark reports. But the summary is that users
> should look very carefully at what benchmark data really mean and in
> particular what in means for their very own personal circumstances.
> Personally, I don't really see that the performance of NAMD in Fig. 8 is
> a problem in practical work. In fact, I would say NAMD looks really
> great.
>
> Cheers,
> Hannes.
>
>
>> On Wed, Jan 22, 2014 at 7:22 PM, Bennion, Brian <Bennion1_at_llnl.gov>
>> wrote:
>>
>>> Hello,
>>>
>>>
>>>
>>> Based on this recent publication
>>> http://onlinelibrary.wiley.com/doi/10.1002/jcc.23501/abstract
>>>
>>> NAMD2.9 stumbles compared with gromacs and an improved version of
>>> charmm on a large system (465404 atoms and 500 cores).
>>>
>>> Any ideas as to the cause of this dramatic difference in speed
>>> between 256 and 400 cores?
>>>
>>>
>>>
>>> Brian
> --
> Scanned by iCritical.

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