Hello,
On Tue, May 29, 2012 at 3:40 PM, Jonathan Gough
<jonathan.d.gough.gmail.com>wrote:
> Dear all,
>
> I'm new to this and just setting up a new machine. My question is. if you
> have a CPU that allows multi-threading (as most modern cpu's do) do you
> have it enabled or disabled for running amber calculations?
>
> for example a quad core i7 will show 8 cpu's when in actuality it is only
> really 4. The setting is changed in the bios (i know). But wondering if
> and how it matters when setting a machine up to run amber. I know for QM
> calculations (gamess) multi-threading doesn't help and can sometimes hurt,
> and I always keep it turned off.
>
Try a couple of experiments: Look at the performance of 4 pmemd/sander
threads on a simple benchmark with hyperthreading turned on and then again
with hyperthreading turned off. Then, look at the performance difference
of running 4 threads without hyperthreading vs. 8 threads with
hyperthreading, and see how that change impacts performance.
Performance is likely affected by several factors: what 'multithreading'
scheme does your particular processor use? (Wikipedia suggests the
existence of several and some are better than others at certain tasks)
Does your OS effectively recognize the difference between physically
different processing cores and virtual cores -- that is, will it ever
(often?) assign 2 threads to the 2 virtual processors on the same core?
The more it does this, the worse hyperthreading will be.
Another downside of using hyperthreading cores vs. real, distinct cores is
the on-chip cache. This memory is the fastest memory available to the
processor, yet it's also available in the smallest amounts.
Multi-threading cores must share this cache (and all other resources it
has) with all of the threads running on that core, which could increase the
number of delays and slowdowns to the point that overall timing actually
suffers.
All I've really done is provided excuses for why hyperthreading with Amber
may perform poorly, but I don't think anyone can say for certain how your
system will fare unless you actually try it out.
HTH,
Jason
P.S. If you really want to see performance fly, get a non-super-overclocked
GTX 580 ;)
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue May 29 2012 - 18:30:03 PDT
