bsub option confused with job arguments

Question

I want to submit a job to LSF using the bsub command. One of the job argument is "-P argument_1". So the overall command looks like

bsub -P project_name -n 4 -W 10:00 my_job -P argument_1

But bsub considers -P argument_1 as the project_name instead of considering as an argument of my_job.

Is there anyway to resolve this issue?

I tried your command in my cluster and it works as expected. Could you provide more details to show why you think that `argument_1` is used as the project name rather than an argument to `my_job`? e.g., provide the output of `bjobs -l` for your job. — Michael Closson, Jan 08 '16 at 16:26

score 0 · Answer 1 · answered Jan 08 '16 at 00:33

0

What version of LSF are you using? You can check by running lsid. Try quoting your command and see if that helps:

bsub -P project_name -n 4 -W 10:00 "my_job -P argument_1"

answered Jan 08 '16 at 00:33

Squirrel

Version of LSF: IBM Platform LSF Advanced 9.1.3.0, Jul 04 2014 – sourav mahmood Jan 08 '16 at 15:17
Could you please append the output of `bjobs -l ` to your question like @Michael Closson suggested? – Squirrel Jan 08 '16 at 20:36

score 0 · Answer 2 · answered Apr 06 '18 at 08:05

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Use a submission script script.sh including my_job -P placeholder_arg1. Then use

sed 's/placeholder_arg1/argument_1/g' < script.sh | bsub

to replace command line argument on-the-fly before submitting the job.

answered Apr 06 '18 at 08:05

gizzmole

2 Answers2