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LSF job parameter error #192

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jwtobias opened this issue Apr 6, 2023 · 3 comments
Open

LSF job parameter error #192

jwtobias opened this issue Apr 6, 2023 · 3 comments

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@jwtobias
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jwtobias commented Apr 6, 2023

When I submit an lsf hpc job I get an error because the bsub memory parameter isn't in the form that my system expects. It should get ... "-M 4000" but instead it's getting "-M 4g"

Here is the command that I'm using (default test json) and the error:
$ caper -v
2.2.3
$ echo $INPUT_JSON
https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ_subsampled.json
$ caper hpc submit atac.wdl -i "${INPUT_JSON}" --singularity --leader-job-name JWT_Leader
2023-04-06 10:12:03,243|caper.hpc|INFO| Running shell command: bsub -W 2880 -M 4g -env all -J CAPER_JWT_Leader /home/jtobias/y3v9bq3x.sh
4g: MEMLIMT value should be a positive integer. Job not submitted.

I've also attached my backend conf file which I recovered from a temp directory.

Please let me know what I should modify to work around this problem.

Many thanks!

orig.backend.conf.zip

@leepc12
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leepc12 commented Apr 6, 2023

Please add this to your ~/.caper/default.conf and try again.

lsf-leader-job-resource-param=-W 2880 -M 4000

@jwtobias
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jwtobias commented Apr 7, 2023

I made that change to ~/.caper/default.conf (attached)
default.conf.zip

Now the leader job seems to be put in the queue without error, but simply and immediately disappears. I can't find error logs about why it crashed.

@kmosi0
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kmosi0 commented Jul 10, 2023

I made that change to ~/.caper/default.conf (attached) default.conf.zip

Now the leader job seems to be put in the queue without error, but simply and immediately disappears. I can't find error logs about why it crashed.

I get the same situation too. I think is the some problem in caper. usually we submit job in lsf ,the command should be quote, but cap submit like 'bsub -M 10G -env all -J CAPER_SNPCalling /public/home/al9nwn5e.sh'. it will go wrong "/.lsbatch/1688980273.3800411: line 8: al9nwn5e.sh: command not found"

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