qsub
Format
cg qsub ?options? cmd ...
Summary
submit a command to the cluster (grid engine).
Description
Convenience function to esily run a command as a job on a (grid
engine) cluster
Arguments
- cmd ...
- command (and parameters) to be executed
Options
- -o outputfile (-outputfile)
- Output of the command will be written to the given
outputfile. By default, the filename job_$name.out will be used
- -e errorfile (-errorfile)
- stderr output of the command will be written to the given
errorfile. By default, the filename job_$name.err will be used
- -name name
- specify name to job (default generated based on the command)
- -run run
- specify the run name for the job (default generated based on
the command)
- -lang interpreter
- use cmd as a piece of code to be run with the given
interpreter, e.g. '''-lang python''' or '''-lang R''' (further
arguments after cmd are ignored in this case)
- -mem memorysize
- indication of (maximum) memory needed by the job (on sge: -l
mem_free=$value,virtual_free=$value, where value is corrected by
the system based on -cores)
- -memlimit memorysize
- limit memory use of the job to the given amount (on sge: -l
h_vmem=$value where value is corrected by the system based on
-cores)
- -cores numcores
- give value > 1 if job uses more than 1 core (on sge hard
option: "-pe local $value" if local pe is defined) If
using multiple cores, other requirements on sge are per core! For
memory (-mem) this conversion will be done by the system, and you
must give the total required memory (for the job)
- -time timelimit
- indication of (maximum) time needed by the job (on sge: -l
s_rt=$time)
- -dqueue value
- (only for sge) Use this option if you want to run on another
queue than the default all.q
- -deps ids
- job will only run when the jobs in ids (a comma separated
list of job ids)
- -hard hardlimits
- on sge: extra options passed on as hard limits
- -soft softlimits
- on sge: extra options passed on as soft limits
Category
Dev