CODEWITHSUNDEEP
lsf
Nils
Nils

Reputation: 1996

LSF - Get ID of submitted job

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?

Upvotes: 12

Views: 11133

Answers (6)

kdubs
kdubs

Reputation: 1722

you can put the job id into the name of the log file.

bsub -oo '%J' <rest of your command>

a log file will appear in the current directory that is the job id. You can then do what you want.

there are other values you can use besides %J. have a look at the bsub man page.

simple example:

> for job in {1..4} ; do bsub -oo '%J' sleep 1s ; done
> bjobs -o 'id cresreq' *
JOBID COMBINED_RESREQ
13217166 select[(type = any ) && (hi&&type == any )] order[r15s:pg]
13217167 select[(type = any ) && (hi&&type == any )] order[r15s:pg]
13217169 select[(type = any ) && (hi&&type == any )] order[r15s:pg]
13217170 select[(type = any ) && (hi&&type == any )] order[r15s:pg]

Upvotes: 0

Squirrel
Squirrel

Reputation: 2282

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.

Upvotes: 9

F14r3
F14r3

Reputation: 41

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

Upvotes: 1

Andrey Rubshtein
Andrey Rubshtein

Reputation: 20915

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)

Upvotes: 4

me_an
me_an

Reputation: 509

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

Upvotes: 0

Nils
Nils

Reputation: 1996

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)

Upvotes: 8

Related Questions