Re: Running namd on Mac OS

From: Ian Stokes-Rees (
Date: Tue Jul 20 2010 - 13:38:05 CDT

On 7/20/10 1:25 PM, Patargias, George wrote:
> Hi
> I am trying to run namd on two processors on my Mac desktop.
> Is this the correct command:
> namd +p2 <conf>
> The log file reports that namd is running on 2 processors but it seems
> to me (from the top command) that 2 threads are running on a single processor
> (CPU load ~199%)

The short answer is that you are OK. This number has to be interpreted
along with the number of CPUs on the system. For the per-CPU (or
per-core, or even per-virtual-core, in the case of Hyper Threading),
then you need to divide the CPU load by the number of CPUs.

E.g. on my Core i5 Mac Book Pro, OS X sees 4 cores (2 real cores, but
with HT, I get two virtual cores per real core), and namd runs fastest
with +p4 (although, sadly, not twice as fast as +p2!).

For some more details:

"load" has a complicated algorithm that can also take into account I/O
blocking. CPU load, however, should just indicate how busy the CPUs
are. 100% means 1 CPU is fully occupied. 200% on a 1 CPU system (or a
load average of 2.0) would mean that there are 2x as much processing to
be done as CPUs are available. For an 8 core system, the load can get
up to 800% without things having to wait (more or less).


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