Module: rje_qsub Description: QSub Generating module Version: 1.11.1 Last Edit: 28/05/20

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 (will parse from hostname if blank) ['kman.restech.unsw.edu.au']
- 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 []
- jobwait=T/F : Whether to wait for the job to finish before exiting [False]
- monitor=T/F : Whether to add "-k oed" to enable instant job monitoring. [False]
- startbash=T/F : Whether to add "-S /bin/bash" to qsub command [False]

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.
    # 1.9.3 - Updates the order of the qsub -S /bin/bash flag.
    # 1.9.4 - Updated qsub to use mem flag rather than vmem. Replaced showstart with qsub -T.
    # 1.9.5 - Added "-k oed" to enable instant job monitoring and option to drop -S /bin/bash/. Tidied walltime.
    # 1.9.6 - Updated qsub to use both mem and vmem flags.
    # 1.10.0 - Added jobwait to wait until the job has finished.
    # 1.10.1 - New default dependhpc=X  ['kman.restech.unsw.edu.au']
    # 1.10.2 - Added notification that job is running when jobwait=T.
    # 1.11.0 - Added output of date and time at end of job script too. (Gives a record of total time running.)
    # 1.11.1 - Added job run summary output to end of stdout.