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rje_qsub V1.9.2

QSub Generating module

Module: rje_qsub
Description: QSub Generating module
Version: 1.9.2
Last Edit: 30/05/18

Copyright © 2006 Richard J. Edwards - See source code for GNU License Notice


Imported modules: rje rje_zen


See SLiMSuite Blog for further documentation. See rje for general commands.

Function

This module is designed to make a job file and call it with qsub. Walltime and depend commands are included.

Commandline

- program=X : Program call for Qsub (and options) [None]
- job=X : Name of job file (.job added) [qsub]
- qpath=PATH : Path to change directory too [current path]
- rjepy=T/F : Whether program is an RJE *.py script (adds python PyPath/) [True]
- pypath=PATH : Path for RJE Python scripts [/rhome/re1u06/Serpentry/]
- nodes=X : Number of nodes to run on [4]
- ppn=X : Processors per node [12]
- walltime=X : Walltime for qsub job (hours) [60]
- depend=LIST : List of job ids to wait for before starting job (dependhpc=X added) []
- pause=X : Wait X seconds before attempting showstart [5]
- report=T/F : Pull out running job IDs and run showstart [False]
- email=X : Email address to email job stats to at end ['']
- mailstart=T/F : Whether to email user at start of run [False]
- hpc=X : Name of HPC system for depend ['IRIDIS4']
- dependhpc=X : Name of HPC system for depend ['blue30.iridis.soton.ac.uk']
- vmem=X : Virtual Memory limit for run (GB) [48]
- modules=LIST : List of modules to add in job file []
- modpurge=T/F : Whether to purge loaded modules in qsub job file prior to loading [True]
- precall=LIST : List of additional commands to run between module loading and program call []

History Module Version History

    # 1.0 - Initial working script.
    # 1.1 - Reworked for running on Iridis.
    # 1.2 - Added showstart.
    # 1.3 - Converted for IRIDIS3.
    # 1.4 - Added showstart pause.
    # 1.5 - Added emailing of job stats after run. Added vmem limit.
    # 1.6 - Added modules=LIST : List of modules to add in job file [clustalo,mafft]
    # 1.6.1 - Added R/3.1.1 to modules.
    # 1.6.2 - Updated module list: blast+/2.2.30,clustalw,clustalo,fsa,mafft,muscle,pagan,R/3.1.1
    # 1.6.3 - Tweaked the showstart command for katana.
    # 1.7.0 - Added option for email when job started
    # 1.8.0 - Added modpurge=T/F : Whether to purge loaded modules in qsub job file prior to loading [True]
    # 1.9.0 - Added precall=LIST  : List of additional commands to run between module loading and program call []
    # 1.9.1 - Removed default module list: causing conflicts. Better to have in INI file.
    # 1.9.2 - Modified qsub() to return job ID.

© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.