On 18:12 Tue 02 Nov     , Nathaniel Echols wrote:

On Tue, Nov 2, 2010 at 6:02 PM,  <[email protected]> wrote:

I tried a dimer of 4000aa at 3.2A using the following script:

phenix.autobuild data=2VZ8.mtz model=${f}.pdb composite_omit_type=simple_omit

 It took hours and ended up with nothing (probably due to memory leaking).

Is there anyway to make it faster?

This is what the 'nproc' argument does - you should use as many

processors as you have available.  If you can distribute it across a

queuing system, even better.  (The GUI can set this up for you

semi-automatically if you have Sun Grid Engine, but it's possible on

the command line too - check the documentation for details.)  

Now that new versions of SGE will no longer be free thanks to Oracle's
purchase, have you considered adding support for a queueing system that
is free and open-source, such as Torque?

--
Thanks,
Donnie

Donald S. Berkholz, Ph.D.
Research Fellow
James R. Thompson lab, Physiology & Biomedical Engineering
Grazia Isaya lab, Pediatric & Adolescent Medicine
Medical Sciences 2-66
Mayo Clinic College of Medicine
200 First Street SW
Rochester, MN 55905
office: 507-538-6924
cell: 612-991-1321
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