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Snakemake-Profiles / lsf

Snakemake profile for running jobs on an LSF cluster
MIT License
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BsubInvocation Error #63

Closed suhridbuddha closed 4 months ago

suhridbuddha commented 4 months ago

I am trying to select some specific nodes on lsf cluster by making a new cluster.json file:

{
    "__default__": {
        "queue": "normal",
        "nodes": "lz-gpu lf-gpu ln-gpu lx-gpu ly-gpu ll-gpu",
        "extra": "",
        "threads": 4  # Default thread count, can be overridden per rule
    }
}

But i am getting this error?

File "/home/ryanr2/data/anaconda3/envs/sopa/lib/python3.10/subprocess.py", line 526, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command 'bsub -M 200 -n 1 -R 'select[mem>200] rusage[mem=200] span[hosts=1]' -W 300 -o "logs/cluster/patch_segmentation_baysor/index=53/jobid55_6637d0e7-670b-4ba2-ad88-3580dba86228.out" -e "logs/cluster/patch_segmentation_baysor/index=53/jobid55_6637d0e7-670b-4ba2-ad88-3580dba86228.err" -J "patch_segmentation_baysor.index=53" -q normal /lila/data/chanjlab/ryanr2/sopa/workflow/.snakemake/tmp.5z0azw4k/snakejob.patch_segmentation_baysor.55.sh' returned non-zero exit status 255.

any idea?

mbhall88 commented 4 months ago

The cluster.json functionality has been deprecated for a long time. Please follow these instructions to achieve what you're trying.

dlaehnemann commented 4 months ago

Also, for more flexibility with regard to resource specifications, I can recommend switching to snakemake >=8.10.7 and the new lsf remote executor plugin.