slurm problem submitting DRMAA job

[psteinb]

$ snakemake -j 2 -d /home/steinbac/projects/20180119-prepping-deconvolution-pipeline/cschmied/exampleData --cluster-config ./cluster.json --drmaa " {cluster.slurm_q} {cluster.slurm_extra}"
#...
Submitted DRMAA job (jobid 9701968)
Finished job 11.
1 of 15 steps (7%) done

rule hdf5_xml:
    input: dataset_one_first.xml
    output: dataset_one.xml, dataset_one.h5, dataset_one-00-00.h5_xml, dataset_one-01-00.h5_xml
    log: logs/b1_hdf5_xml.log
    jobid: 12

WorkflowError:
DRMAA Error: code 14: Invalid native specification:  --time=00:45:00 -n 1 -c 3 --mem-per-cpu=7000 (Unsupported option: -c)
Will exit after finishing currently running jobs.
Exiting because a job execution failed. Look above for error message

This needs investigation.

[sommerc]

Hi,

is there any news on this, I have the same problem right now. The -c flag is not supported in the drmaa-slurm native specification. What was it originally intended for?

Cheers,
Chris

[psteinb]

yes, the DRMAA API (even though it's an API) doesn't support -c. It's best to revert to the snakemake cluster CLI for now:

$ snakemake -j 2 -d /home/steinbac/projects/20180119-prepping-deconvolution-pipeline/cschmied/exampleData --cluster-config ./cluster.json --cluster "sbatch {cluster.slurm_q} {cluster.slurm_extra}"