Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Submitting jobs using bash array #38

Open
re2srm opened this issue Jul 7, 2024 · 0 comments
Open

Submitting jobs using bash array #38

re2srm opened this issue Jul 7, 2024 · 0 comments

Comments

@re2srm
Copy link

re2srm commented Jul 7, 2024

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant