Thanks for the info.  I ran two instances of phenix which both were able to run at 100%, but ran out of memory after awhile  My guess is the memory is a bigger limit than the processors so I think I'll just stick to running on the one processor.  Thanks for everyone's help!
-Sam

PS: I had trouble attempting an installation from source earlier (and don't have full permissions on this machine).  Since you don't think upping the # of processors will help much, I'm not going to attempt the source installation again.

On Mon, Aug 31, 2009 at 5:22 PM, Nathaniel Echols <NEchols@lbl.gov> wrote:
On Aug 31, 2009, at 1:41 PM, Pavel Afonine wrote:
> phenix.refine cannot use advantage of multiple CPUs. I think the "--
> nproc=4" keyword in your example below is a valid keyword for
> phenix.autobuild, but not for phenix.refine.


Actually, it's just "nproc=4" without the "--".

You can use multiple CPUs for the FFTs in phenix.refine if you compile
from source with OpenMP support (add "--openmp" to the arguments when
running the install script; this requires GCC 4.2 or better, or
Intel's compiler, and perhaps others).  I think it will automatically
use as many CPUs as possible.  It's probably not going to help much,
though.

-------------------
Nathaniel Echols
Lawrence Berkeley Lab
510-486-5136
NEchols@lbl.gov



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