I'm trying to run OMA on a cluster that is managed with SLURM. I've used this cluster before for a lot of other things, but I'm not so familiar with job arrays. Although it seems I'm doing things right as far as I can tell, OMA keeps giving only:
"ERROR: Cannot determine total number of jobs in jobarray. requires a range from 1-x"
An example of one of the SLURM scripts I've tried:
#!/bin/sh #SBATCH --partition=standard #SBATCH --time=12:00:00 #SBATCH --nodes=1 #SBATCH --ntasks-per-node=5 #SBATCH --mem-per-cpu=2gb #SBATCH --job-name="OMA_test" #SBATCH --output=output_%A_%a.txt #SBATCH --error=error_%A_%a.txt #SBATCH --array=1-5 ~/OMA/bin/OMA -s
It initializes fine if I don't use SLURM, but I'm working with multiple genomes, so parallelization would be helpful. Additionally, I encountered an edge case when I was trying to run in our debug queue when I specified 10 jobs in the array, but the max simultaneous in debug is 5- so it seemed to group them hierarchically and started executing five tasks properly. Does this mean that perhaps I need to spawn a "parent" job that then submits the array jobs? I couldn't keep it running in debug because it would timeout after an hour, and so I'd probably have to restart it a bunch of times to get the whole job to complete.
The SLURM example in the doc page (http://omabrowser.org/standalone/) does seem to imply that any "parent" task would be necessary, and I didn't come across any way of manually specifying the number of array jobs to OMA manually.
Anyone with some insight on this? Thanks.