Frequently Asked Questions

Welcome to the FAQ page for Berzelius!

On this page, you'll find answers to commonly asked questions about our HPC environment. These FAQs are here to provide you with troubleshooting tips and best practices to optimize your experience on our cluster.

• Projects, Accounts, and Quotas FAQs
  • How to resolve the "Disk quota exceeded" error?
• Running Jobs FAQs
  • How to extend the time limit of a job?
• Software FAQs
  • My PyTorch/TensorFlow cannot detect GPU
  • Conda takes too much time for solving environment
• General FAQs
  • How to acknowledge Berzelius in scientific articles and presentations?
  • Can I store sensitive data on Berzelius?

Projects, Accounts, and Quotas FAQs

How to resolve the "Disk quota exceeded" error?

A: This message indicates that your quota is almost full. You can check your quota by nscquota.

You can use ncdu to check which folders are taking the most space.

ncdu /home/username
ncdu /proj/your_proj/users/username

Please note that your /home/username has only a quota of 20 GB. You need to move the large directory from your home directory to your project directory and create a symlink from your project directory pointing to its original location. Please replace your_proj and username in the example command with your actual project name and username.

mv ~/.conda /proj/your_proj/users/username/
ln -s /proj/your_proj/users/username/.conda ~/.conda

Running Jobs FAQs

How to extend the time limit of a job?

A: You can extend the time limit of a running job by using the command nsc-boost-timelimit on the login node. Please read the guide for NSC boost-tools.

Software FAQs

My PyTorch/TensorFlow cannot detect GPU

A: Please make sure that you have installed the GPU version of PyTorch/TensorFlow.

To check the installation info:

# If you installed the package via pip
pip show pytorch
# If you installed the package via conda
conda list pytorch

Conda takes too much time for solving environment

A: Please check out Mamba.

General FAQs

How to acknowledge Berzelius in scientific articles and presentations?

A: The recommended way to acknowledge access to Berzelius is:

"The computations/data handling/[SIMILAR] were/was enabled by the Berzelius resource provided by the Knut and Alice Wallenberg Foundation at the National Supercomputer Centre."

If applicable, also add an acknowledgement for application support: "[NAME] at the National Supercomputer Centre is acknowledged for assistance concerning technical and implementational aspects [OR SIMILAR] in making the code run [OR SIMILAR] on the Berzelius resource."

or

"We thank [NAME] at NSC for [his/her] assistance with [describe tasks such as porting, optimization, etc.], which was made possible through application support provided by National Supercomputer Centre at Linköping University."

Can I store sensitive data on Berzelius?

A: Berzelius is not designed to handle sensitive data. Bianca is currently the only NAISS resource that can be used for sensitive data storage.