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

--slurm-extra-param: expected one argument #202

Open
OrangeyO2 opened this issue Dec 6, 2023 · 1 comment
Open

--slurm-extra-param: expected one argument #202

OrangeyO2 opened this issue Dec 6, 2023 · 1 comment

Comments

@OrangeyO2
Copy link

Hello

I am trying to run the pipeline in a hpc cluster setting and I want to pass some extra parameters to sbatch.
My command is
caper hpc submit ...
--slurm-extra-param " --mail-type=END --mail-type=FAIL --mail-user=email@address"

As per previous issue #27 I included a space in front of the first dash inside the double quotes.

The command works fine without the --slurm-extra-param but as soon as I include that last bit, I instantly get an error with the usage listed as well as the "expected one argument" error.

usage: caper run [-h] [-c CONF] [-D]
...
caper run: error: argument --slurm-extra-param: expected one argument

It would be great if I could get some help on this, thank you!

@OrangeyO2
Copy link
Author

OrangeyO2 commented Dec 6, 2023

I think I got it to work by defining it in the default.conf file.

slurm-extra-param="--mail-type=END --mail-type=FAIL --mail-user=email@address"

Waiting for the pipeline to finish running to see if I indeed will receive an email notification.

Why did it not work in the command line though...?

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