submitting to cluster not working

[vmkhot]

Hi there,

I've installed dadasnake on our computing server (slurm) and am trying out the trial run using this command:

./dadasnake -c -n "TESTRUN" -r config/config.test.yaml

the error I get is that there's no "--time" variable set for sbatch.:

Any thoughts on how to fix it or how to include the time parameter into the submission?

Your help is greatly appreciated!!

Thanks,

Varada

[a-h-b]

Dear Varada - thanks for reaching out. I have a few questions to pinpoint the problem: Have you selected one (which one?) of slurm or slurm_simple in the VARIABLE_CONFIG file for SCHEDULER ? Best - A

[vmkhot]

Thanks for your reply!

I selected "slurm" in the VARIABLE_CONFIG file. this is what it looks like

SNAKEMAKE_VIA_CONDA true SNAKEMAKE_EXTRA_ARGUMENTS LOADING_MODULES SUBMIT_COMMAND sbatch BIND_JOBS_TO_MAIN false NODENAME_VAR SCHEDULER slurm MAX_THREADS 20 BIGMEM_CORES 10 BIGMEM_MEM_EACH 6G NORMAL_MEM_EACH 6G LOCK_SETTINGS false

thanks,

Varada

[a-h-b]

Dear Varada - can you please change the SCHEDULER value from slurm to slurm_simple? Generally, to change how slurm is called by dadasnake, you can edit the file in the config folder called slurm_simple.config.yaml (config/slurm_simple.config.yaml). For example you can try to change line 5 runtime: "-t" to runtime: "--time" I am not completely certain that this will actually help, because I think the -t is a standard abbreviation for --time in slurm.

If it does not help, can you let me know which rule throws this error, i.e. up to which point did it run? Thanks- A

[vmkhot]

Thanks for the suggestions.

Tried a few things:

I changed it to slurm_simple and ran the command - error I changed runtime: "--time" in slurm_simple.config.yaml - error Tried running with "--time" as an argument on the command line ./dadasnake -c -n "TESTRUN" -r config/config.test.yaml --time=1:00:00 - error I changed runtime: "--time=1:00:00" in slurm_simple.config.yaml - error

It fails right away. this is the error I get everytime: [vmkhot@arc dadasnake]$ ./dadasnake -c -n "TESTRUN" -r config/config.test.yaml --time=1:00:00
Submitting workflow to cluster
sbatch: error: You did not specify the --time argument. sbatch: error: Batch job submission failed: Unspecified error

[a-h-b]

Hi - yes, [vmkhot@arc dadasnake]$ ./dadasnake -c -n "TESTRUN" -r config/config.test.yaml --time=1:00:00 cannot work. But I think I understand your error now. Can you please try to include the --time argument in the VARIABLE_CONFIG field SUBMIT_COMMAND , as in SUBMIT_COMMAND sbatch --time=120:00:00 You may need further sbatch arguments and you can put all of them into that field (there's a tab between SUBMIT_COMMAND and sbatch, of course). Best - A

[a-h-b]

closing for now, I am assuming this is solved