QSub Generating module
Copyright © 2006 Richard J. Edwards - See source code for GNU License Notice
This module is designed to make a job file and call it with qsub. Walltime and depend commands are included.
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.
© 2015 RJ Edwards. Contact: firstname.lastname@example.org.