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Add --ntasks-per-node or --exclusive option for your multi-process jobs. #434

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feather-W opened this issue Jan 10, 2024 · 0 comments
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@feather-W
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Hi,
I am running the ATAC-seq pipeline for the first time and encountered some error as follows:

sbatch: error: Please add --ntasks-per-node or --exclusive option for your multi-process jobs.
sbatch: error: Batch job submission failed: Unspecified error

My command as follows:
caper hpc submit /lustre/home/acct-medzy/medzy-pu/Wanggenyu/teacher/ATAC/ENCODE_ATAC_seq_pipeline/atac-seq-pipeline/atac.wdl -i /lustre/home/acct-medzy/medzy-pu/Wanggenyu/teacher/ATAC/ENCODE_ATAC_seq_pipeline/atac-seq-pipeline/example_input_json/ENCSR356KRQ_subsampled.json --conda --leader-job-name ANY_GOOD_LEADER_JOB_NAME

My configuration file as follows:
backend=slurm

SLURM partition. DEFINE ONLY IF REQUIRED BY YOUR CLUSTER'S POLICY.

You must define it for Stanford Sherlock.

slurm-partition=cpu

SLURM account. DEFINE ONLY IF REQUIRED BY YOUR CLUSTER'S POLICY.

You must define it for Stanford SCG.

slurm-account=medzy-pu

Local directory for localized files and Cromwell's intermediate files.

If not defined then Caper will make .caper_tmp/ on CWD or local-out-dir.

/tmp is not recommended since Caper store localized data files here.

local-loc-dir=/lustre/home/acct-medzy/medzy-pu/Wanggenyu/teacher/ATAC/ENCODE_ATAC_seq_pipeline/tmp

cromwell=/lustre/home/acct-medzy/medzy-pu/.caper/cromwell_jar/cromwell-82.jar
womtool=/lustre/home/acct-medzy/medzy-pu/.caper/womtool_jar/womtool-82.jar

So anyone knows how can I add --ntasks-per-node or --exclusive option for my multi-process jobs, and where should I add this parameters?

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