From: Norman Geist (
Date: Tue Feb 14 2012 - 01:18:44 CST



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: [] Im Auftrag
von Ajasja Ljubetic
Gesendet: Montag, 13. Februar 2012 16:09
Cc: Marcel UJI (IMAP);
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,




On Mon, Feb 13, 2012 at 6:44 AM, Nicholas M Glykos <>

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 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> , <> 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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