Integrating Phenix with Torque
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 [email protected] University of Texas Health Science Center Bioinformatics Core Facility http://www.bioinformatics.uthscsa.edu Phone: (210) 567-2672
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 [email protected]
University of Texas Health Science Center Bioinformatics Core Facility http://www.bioinformatics.uthscsa.edu Phone: (210) 567-2672
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participants (2)
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Jeremy Mann -
Thomas C. Terwilliger