[gmx-users] hyperthreading

[Erik Lindahl]

Hi,

Just say no to hyperthreading.

It really only helps for things like web- or fileservers where it is 
common to have hundreds of threads running, although each thread does 
very little computations - most of it is waiting/starting/stopping. And 
even in those cases you would be very lucky to see more than a couple 
of percent performance gain.

A hyperthreaded Intel CPU does not have any extra floating-point or 
integer units. For a code like Gromacs that is completely compute-bound 
you would just end up with two threads competing for the same 
functional units, and above that you have all the overhead of switching 
between the two processes.

Sorry, there's no such thing as a free lunch :-)
>
> simulations? I mean, is it possible to compile an MPI
> version of GROMACS and run it with the option -np 2
> (like 2 processors present)?

Sure, it's no problem technically. If hyperthreading is enabled in your 
bios and you are running an SMP version of the Linux kernel it should 
detect it. Check /proc/cpuinfo to make sure it lists two CPUs (Or four 
if you have a dual-CPU  box).

After that you can just treat it as any other multi-cpu box. I'd love 
to be proven wrong if Intel has done something magical the last year 
and improved it...

Cheers,

Erik