Orientation for New O2 Cluster Users

Owned by Andy Bergman
Last updated: Feb 06, 2024
2 min read

If you have been provisioned with an O2 user account and are just getting started, please read below.

If you still need to request an O2 user account, please submit a request using the online form.

Two-factor authentication on O2

All O2 cluster logins from outside of the HMS network require two-factor authentication. O2 logins require an HMS profile with DUO, which is different than the DUO profile used for Harvard Key. Please see:

Logging In

O2 logins use HMS Account login credentials (formerly known as eCommons ID). If needed, there is a self-service portal to reset your password or unlock your account. Passwords can not be changed from the O2 command line, even if you are ever prompted to do so.

If the self-service portal does not work, please contact the HMS IT Service Desk for assistance.

Please login to O2 using a SSH (secure shell) application. You MUST use only lower case letters in your username for O2 logins!

For step-by-step details, see:   

https://harvardmed.atlassian.net/wiki/spaces/O2/pages/1601700123

Getting Started

To get started using O2, e.g. running jobs and copying your data to the environment, please first review the main O2 documentation page.

This includes a "Basic guide to using the Slurm job scheduler" and other important information for new users.

The O2 Portal web interface

The O2 Portal, powered by OSC Open OnDemand software, is a web interface that allows you to access and use the O2 cluster from your web browser. From the O2 Portal, you can view the status of your jobs, edit and transfer files, start an O2 login shell, run GUI applications such as MATLAB, RStudio, Jupyter, and more. It’s a great tool for researchers who want the power of O2 without having to use a command line interface. 

For information on the O2 Portal, please check our wiki page: https://harvardmed.atlassian.net/wiki/spaces/O2/pages/2230583317

Storage

All cluster users get up to 100 GiB in their home directory.

Beyond this, you can use up to 25 TiB of temporary space under /n/scratch/users
Scratch has NO backups and files get deleted after not modified for 45 days.

Please see this page for creating your scratch directory on O2:

    https://harvardmed.atlassian.net/wiki/spaces/O2/pages/2652045313

Support and Office Hours

  • For future issues or software installations, please submit a request to us by emailing rchelp@hms.harvard.edu . This will open a support request and a member of the Research Computing team will get back to you.

  • While you can contact RC at any time, the team also holds Office Hours every Wednesday, 1 - 3 PM.

  • Please contact us first with a support request before joining office hours so we can better help you! 

  • Service outages and scheduled maintenance, are posted on the O2 Status Page.

You can also follow HMS RC on X (Twitter):

 

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