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I have a large number of samples (>150) and I was wondering if there is a way of submitting jobs as a bash array. Manually submitting each sample as a loop with 40s of waiting in between is not very practical so I tried submitting jobs as an array. To do this I added these two lines before my predictSV command:
#SBATCH --array=1-16
sleep $(($SLURM_ARRAY_TASK_ID*40))
my predictSV command
This submits 16 jobs for a sample in an array and each predictSV command has a delay of 40 seconds before running. However, the jobs run for some time but fail due to errors related to appropriate lock files not being found. I dont know if the lock files require the jobs to be submitted separately rather than in an array so I was wondering if you can comment on this or recommend a better way of doing this?
I feel using a bash array might generally be a better way of submitting jobs instead of a loop.
Thanks
Thanks
The text was updated successfully, but these errors were encountered:
Hello,
I have a large number of samples (>150) and I was wondering if there is a way of submitting jobs as a bash array. Manually submitting each sample as a loop with 40s of waiting in between is not very practical so I tried submitting jobs as an array. To do this I added these two lines before my predictSV command:
#SBATCH --array=1-16
sleep $(($SLURM_ARRAY_TASK_ID*40))
my predictSV command
This submits 16 jobs for a sample in an array and each predictSV command has a delay of 40 seconds before running. However, the jobs run for some time but fail due to errors related to appropriate lock files not being found. I dont know if the lock files require the jobs to be submitted separately rather than in an array so I was wondering if you can comment on this or recommend a better way of doing this?
I feel using a bash array might generally be a better way of submitting jobs instead of a loop.
Thanks
Thanks
The text was updated successfully, but these errors were encountered: