Hi Matt,
On Jun 2, 2006, at 8:20 PM, [EMAIL PROTECTED] wrote:
From my browsing of list archives I can only recall seeing advice
that hyperthreading
cannot offer more Gromacs performance. For all I know this remains
true if you're trying
to use MPI to accelerate single calculations on hyperthreaded
processors. However, I
have discovered that it may be possible to increase throughput by
running two
independent jobs on a recent hyperthreaded processor, and I don't
recall seeing this
mentioned on the list before.
My typical job involves ~790 DNA atoms, a few Na+ ions, and
13000-14000 water molecules.
I use Gromacs with the Amber force field ported by the Pande group.
My simulation
machines are 3.2 Ghz Pentium machines with 2 MB of cache (Pentium
640, I think) and 1 GB
RAM.
Typical performance for one of these systems running on an unloaded
machine is 64.3
hours/ns, 1.4 gflop/s. I accidentally started some pairs of
simulations on some of these
machines this week and discovered that the performance of each job
was *not* cut in
half. With two systems running simultaneously, each shows
performance of about 98.8
hours/ns, 908 mflop/s. Running two of these jobs on each machine
thus appears to
increase throughput by about 30%.
If like me you run many independent calculations, throughput is
more important than
turnaround, and you have hyperthreaded machines but have not
previously tried to take
advantage of them, it may be worth testing. I suppose this issue
may have been covered
on the mailing list before, but all I ever remember seeing were
advisements that
hyperthreaded processors won't help performance, or even advice to
disable
hyperthreading in the BIOS. A brief web search indicates that some
[EMAIL PROTECTED]
participants have discovered comparable throughput advantages to
running two client
instances on hyperthreaded processors.
That's certainly good news. I remember trying this when
hyperthreading first appeared, but the early implementations didn't
make any throughput difference whatsoever.
However, it might still lead to significant problems with dual-CPU
systems, where each CPU has hyperthreading enabled. In _theory_ the
Linux scheduler should be able to tell logical from physical CPUs,
but the last time I tried it (which, again, was over a year ago) it
lead to severe load balancing problems.
Cheers,
Erik
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