Re: AW: 2CPU+1GPU vs 1CPU+2GPU

From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
Date: Tue Feb 14 2012 - 04:04:20 CST

Dear Marcel, Norman, List,

I'll play devil's advocate, bear with me. Measuring (and demonstrating)
memory errors with memtest does nothing to answer the important question :
Do these errors change the average long-term dehaviour (and derived
quantites) from the simulations, or they just add (as white noise) another
source of chaotropic behaviour in an already chaotic system ? I would
argue that if the memory errors are trully random, then they can not be
correlated with the aim of any given simulation, and, thus, can not be
held responsible for things working out "incredibly great" or otherwise.
If I were to offer an example in support of this thesis, I would probably
quote the results obtained on folding simulations by the Shaw group (the
Science 2010 paper) using the Anton machine which to my knowledge (please
do correct me if I'm wrong) does not use ECC memory. Although I'm not
advocating the incorporation of avoidable errors in calculations, I do
feel that solid evidence for the effect of these errors on the MD-derived
quantities is missing.

My twocents,
Nicholas

On Tue, 14 Feb 2012, Marcel UJI (IMAP) wrote:

> Yes I have found other sources with similar results (see
> http://www.cs.stanford.edu/people/ihaque/talks/resilience-2010.pdf), so
> I think I will finally go for those Tesla cards.
>
> Thank you all for your help!
>
> Marcel
>
> Al 14/02/12 08:18, En/na Norman Geist ha escrit:
> >
> > Hi,
> >
> >
> >
> > I just wanted to add that I was pretty surprised when I first saw the
> > ECC error counters on my Tesla C2050. Well in fact it's the total of
> > double bit and I never investigated their occurrence but I would only
> > go without ECC with some belly aches because everything that doesn't
> > work or behave strange in your simulations, or even what works
> > incredibly great can come due to artifacts of memory errors, that
> > might sound a little overdone, but is possible. For what else, except
> > of reliability, ECC has been developed. But I'm really not sure what
> > influence those errors can really have, but with ecc you have one
> > thing less to survey when problems occur.
> >
> >
> >
> > Best wishes
> >
> >
> >
> > Norman Geist.
> >
> >
> >
> > *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> > Auftrag von *Ajasja Ljubetic
> > *Gesendet:* Montag, 13. Februar 2012 16:09
> > *Cc:* Marcel UJI (IMAP); namd-l_at_ks.uiuc.edu
> > *Betreff:* Re: namd-l: 2CPU+1GPU vs 1CPU+2GPU
> >
> >
> >
> > One final thing. I've done some benchmarking with a AMD 6-core
> > desktop and a GTX-570 and it ends up being about equal (slightly
> > faster) than a 6-core xeon with an M2070. You can buy a 3GB
> > GTX580 for a fraction of the price of a M series card, and an AMD
> > CPU (particularly the 3 GHz 6-core Thubans) will be close to half
> > the price of the intel. While I'm sure the intel chip is
> > generally superior to the AMD one, it doesn't seem to be a factor
> > when running NAMD. So I would say buy two desktops and save
> > yourself money and also gain performance. I know there is the
> > lack of ECC memory with the GTX series, but I'm really not
> > convinced that is a big issue for MD (maybe someone on the list
> > has a different opinion).
> >
> >
> >
> > I'm running my simulations on several GTX 560 Ti for half a year now
> > and it works great! So I would back up this advice.
> >
> >
> >
> > Best regards,
> >
> > Ajasja
> >
> >
> >
> > ~Aron
> >
> >
> >
> >
> >
> > On Mon, Feb 13, 2012 at 6:44 AM, Nicholas M Glykos
> > <glykos_at_mbg.duth.gr <mailto:glykos_at_mbg.duth.gr>> wrote:
> >
> >
> >
> > You will (hopefully) hear from Axel on this, but :
> >
> >
> > > as it would give more speed for our NAMD based simulations
> >
> > Is this an assumption or the result of benchmarking the two hardware
> > configurations with your intended system sizes ? For small (atom-wise)
> > systems, you shouldn't expect much improvement by increasing the
> > number of
> > GPUs (and for tiny systems the 1CPU+2GPU may not scale at all).
> >
> > My twocents,
> > Nicholas
> >
> >
> > --
> >
> >
> > Nicholas M. Glykos, Department of Molecular Biology
> > and Genetics, Democritus University of Thrace, University Campus,
> > Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office)
> > +302551030620 <tel:%2B302551030620>,
> > Ext.77620, Tel (lab) +302551030615 <tel:%2B302551030615>,
> > http://utopia.duth.gr/~glykos/ <http://utopia.duth.gr/%7Eglykos/>
> >
> >
> >
> > --
> > Aron Broom M.Sc
> > PhD Student
> > Department of Chemistry
> > University of Waterloo
> >
> >
> >
>
>

-- 
            Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/

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