I have had no luck building pmemd.cuda on Mac OS X.
HTH,
Jason
On Tue, May 29, 2012 at 7:25 PM, Jonathan Gough
<jonathan.d.gough.gmail.com>wrote:
> I just set up an i7-920 machine with 12GB of RAM. and a tesla 1060 running
> ubuntu 12.04. I'll give it a shot and see how it goes. i also set up a
> hackentosh with a GTX 560, although i have been having issues compiling
> amber on it...
>
> On Tue, May 29, 2012 at 9:25 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 - 20:00:02 PDT
