[phenixbb] Integrating Phenix with Torque

Thomas C. Terwilliger terwilliger at lanl.gov
Wed Jul 29 08:07:19 PDT 2009

Hi Jeremy,

Phenix.autobuild is set up so that you can specify the number of
processors (nproc) and  the number of batches (nbatch) as you indicated in
your command.  Additionally you will want to set two more parameters:

run_command ="command you use to submit a job to your system"
background=False   # probably false if this is a cluster, true if this is
a multiprocessor machine

If you have a queueing system with 20 nodes, then you probably submit jobs
with something like

"qsub -someflags myjob.csh"   # where someflags are whatever flags you use
(or just "qsub myjob.csh" if no flags)

Then you might use

run_command="qsub -someflags"  background=False nproc=20 nbatch=20

If you have a 20-processor machine instead, then you might say

run_command=csh  background=True nproc=20 nbatch=20

so that it would run your jobs with csh on your machine, and run them all
in the background (i.e., all at one time).

I hope that helps!  I don't have a lot of experience actually using
phenix.autobuild on a queueing system with nproc>1.  Perhaps others would
like to  comment on their experiences.

-Tom T

>> A new user of mine wants to run Phenix on two of our clusters. We use
>> Torque/Maui as our batch scheduler and would like to integrated their
>> usage of Phenix.
>> They want to run something like:
>> phenix.autobuild  data=data.hkl seq_file=seq.dat model=model.pdb
>> multiple_models=True multiple_models_number=20 n_cycle_rebuild_max=5
>> nbatch=20 nproc=20
>> The documentation mentions briefly the ability to use batch schedulers but
>> doesn't give examples of submission scripts.
>> --
>> Jeremy Mann
>> jeremy at biochem.uthscsa.edu
>> University of Texas Health Science Center
>> Bioinformatics Core Facility
>> http://www.bioinformatics.uthscsa.edu
>> Phone: (210) 567-2672
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb

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