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mllg / batchtools

Tools for computation on batch systems
https://mllg.github.io/batchtools/
GNU Lesser General Public License v3.0
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Issue with SLURM #232

Closed rrichmond closed 5 years ago

rrichmond commented 5 years ago

I'm having issues submitting to a SLURM cluster. When I try to submit with batchtools I get the following:

submitJobs(resources = list(walltime = 3600, memory = 1024, ncpus=1))
Submitting 10 jobs in 10 chunks using cluster functions 'Slurm' ...
Error: Fatal error occurred: 101. Command 'sbatch' produced exit code 1. Output: 'sbatch: error: Plase do not specify --ntasks on prince cluster, try to use --nodes and --tasks-per-node together
sbatch: error: Batch job submission failed: Unspecified error'

The template file I'm using (obviously not complete, but I just want to demonstrate the simple issue) is:

#!/bin/bash

#SBATCH --job-name=array
#SBATCH --time=0:05:00
#SBATCH --mem=1024
#SBATCH --cpus-per-task=1
#SBATCH --array=1-4

## Initialize work environment like
module add r/intel/3.6.0

## Run R:
## we merge R output with stdout from SLURM, which gets then logged via --output option
Rscript -e 'batchtools::doJobCollection("<%= uri %>")'

I can rename this from a template to a shell script and submit it to the cluster with sbatch myscript.sh without error (other than the errors in the output files of course). Any suggestions on how to debug this? I've dug through the code of batchtools and didn't find an obvious source of this. Thanks.

rrichmond commented 5 years ago

I'm not sure what I changed, but I've managed to get it to submit now. It seemed like it wasn't reloading the template.