[phenixbb] nproc for autobuild

Michael Thompson miket at chem.ucla.edu
Tue Nov 8 16:02:49 PST 2011


I apologize if this question seems very basic, but I am new to phenix.autobuild. I would like to set up a series of phenix.autobuild runs on our cluster, and would like to maximize the speed.  I am trying to make single rebuilt models using the command below: 

phenix.autobuild data=data.mtz model=coords.pdb map_file=map_coeffs.mtz multiple_models_number=1 n_cycle_rebuild_max=5 ncycle_refine=5 s_annealing=true refine_with_ncs=True place_waters=True nproc=?? run_command=/home/qsub.sh

The AutoBuild documentation says "if you are using rebuild_in_place=False, then use nproc=4" and "if you are using rebuild_in_place=True, then use nproc=5. (Any more will not make any difference)." My interpretation of the documentation is that for the above AutoBuild run with multiple_models_number=1, I should set nproc=5 (or 4?). Is this correct? Also, if I were to change the command so that multiple_models_number=10, should I then use nproc=50 (i.e. 5 processors per model), or is it still the case that setting nproc>5 doesn't make a difference? 

Thanks in advance for your help!


Michael C. Thompson

Graduate Student

Biochemistry & Molecular Biology Division

Department of Chemistry & Biochemistry

University of California, Los Angeles

miket at chem.ucla.edu

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