I am using a cluster. I will use qsub command to distribute my job, what I want is I can get back the job id so that I can monitor the job.
Basically, I want some thing like this:
#!/bin/bash
JOBID=$( qsub job1 )
# Monitoring base on $JOBID
I found a page http://wiki.ibest.uidaho.edu/index.php/Tutorial:_Submitting_a_job_using_qsub, and it talks about a variable PBS_JOBID
but I don't know how to use it. Does anyone know how to do it?
(My solution now is jobID='qsub task | cut -d ' ' -f 3'
)
The qsub command will submit the script to the server defined by the destination argument. If the destination is a routing queue, the job may be routed by the server to a new destination. If the -q option is not specified, the qsub command will submit the script to the default server.
The qsub command is used to submit jobs to the queue. job, as previously mentioned, is a program or task that may be assigned to run on a cluster system. qsub command is itself simple, however, it to actually run your desired program may be a bit tricky. is because qsub, when used as designed, will only run scripts.
Job submission is accomplished using the qsub command, which takes a number of command line arguments and integrates such into the specified PBS command file. The PBS command file may be specified as a filename on the qsub command line or may be entered via STDIN. The PBS command file does not need to be executable.
PBS_O_WORKDIR the absolute path of the current working directory of the qsub command.
You can use the -terse
:
$ echo sleep 5 | qsub -terse
3543
qsub
has a very predictable output. Many automated submission systems (such as Grid interfaces) simply parse the output from qsub
, looking for the jobid.
An example of parsing is available from the BLAHP project (European grid middleware).
jobID=`${pbs_binpath}/qsub $bls_tmp_file` # actual submission
...
# The job id is actually the first numbers in the string (slurm support)
jobID=`echo $jobID | awk 'match($0,/[0-9]+/){print substr($0, RSTART, RLENGTH)}'`
(source)
This code has been used in production for many years, and has worked for qsub
in both PBS, PBS Pro, and SLURM.
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