LSF - Get ID of submitted job

问题:

Say I submit a job using something like bsub pwd. Now I would like to get the job ID of that job in order to build a dependency for the next job. Is there some way I can get bsub to return the job ID?

回答1:

Nils and Andrey have the answers to this specific question in shell and C/C++ environments respectively. For the purposes of building dependencies, you can also name your job with -J then build the dependency based on the job name:

bsub -J "job1" <cmd1>
bsub -J "job2" <cmd2>
bsub -w "done(job1) && done(job2)" <cmd>

There's a bit more info here.

This also works with job arrays:

bsub -J "ArrayA[1-10]" <cmd1>
bsub -J "ArrayB[1-10]" <cmd2>
bsub -w "done(ArrayA[3]) && done(ArrayB[5])" <cmd>

You can even do element-by-element dependency. The following job's i-th element will only run when the corresponding element in ArrayB reaches DONE status:

bsub -w "done(ArrayB[*])" -J "ArrayC[1-10]" <cmd3>

You can find more info on the various things you can specify in -w here.

回答2:

Just as a reference, this is the best solution I could come up with so far. It takes advantage of the fact that bsub write a line containing the ID to STDOUT.

function nk_jobid {
    output=$($*)
    echo $output | head -n1 | cut -d'<' -f2 | cut -d'>' -f1
}

Usage:

jobid=$(nk_jobid bsub pwd)

回答3:

In case you are using C++, you can use the lsblib, LSF C API to submit jobs. The input and the output are structs. In particular, the output struct contains the job id.

#include <lsf/lsbatch.h>    
LS_LONG_INT lsb_submit (struct submit *jobSubReq, struct submitReply *jobSubReply)

回答4:

$jobid = "0"
bsub pwd > $jobid
cat $jobid

回答5:

If you just want to view the JOBID after submission, most of the time I will just use bhist or bhist -l to view the running jobs and details.

$ bhist
Summary of time in seconds spent in various states:
JOBID   USER    JOB_NAME  PEND    PSUSP   RUN     USUSP   SSUSP   UNKWN   TOTAL
8664    F14r3   sample       2       0    187954  0       0       0       187956