Karolina supercomputer

On the Karolina supercomputer, the working directory is, by default, created inside your project directory on the shared scratch storage. You can, however, also choose to use the input directory itself as the working directory.

To control where the working directory is created, use the work-dir option (or the equivalent spelling workdir) of the qq submit command:

• --work-dir=scratch – Default option on Karolina. Creates the working directory on the shared scratch storage.
• --work-dir=input_dir – Uses the input directory itself as the working directory. Files are not copied anywhere. If you use this option, it is strongly recommended to submit from the scratch storage.
• --work-dir=job_dir – Same as input_dir.

Recommendation:

• Submit jobs from your project's mounted storage (/mnt/...). With the default --work-dir option, qq automatically copies your data to scratch, executes the job there, and then copies the results back to your input directory.
• The size of the working directory on Karolina is limited by your filesystem quota, so you do not need to specify the work-size option.