lindahl at csb.stanford.edu
Wed Jan 28 16:29:01 CET 2004
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...
More information about the gromacs.org_gmx-users