NOTICE: FULL O2 Cluster Outage, January 3 - January 10th

O2 will be completely offline for a planned HMS IT data center relocation from Friday, Jan 3, 6:00 PM, through Friday, Jan 10

  • on Jan 3 (5:30-6:00 PM): O2 login access will be turned off.
  • on Jan 3 (6:00 PM): O2 systems will start being powered off.

This project will relocate existing services, consolidate servers, reduce power consumption, and decommission outdated hardware to improve efficiency, enhance resiliency, and lower costs.

Specifically:

  • The O2 Cluster will be completely offline, including O2 Portal.
  • All data on O2 will be inaccessible.
  • Any jobs still pending when the outage begins will need to be resubmitted after O2 is back online.
  • Websites on O2 will be completely offline, including all web content.

More details at: https://harvardmed.atlassian.net/l/cp/1BVpyGqm & https://it.hms.harvard.edu/news/upcoming-data-center-relocation

Scratch Storage

Owned by Raffaele Potami
Last updated: Jan 03, 2024 by Kathleen Chappell
2 min read

 

Scratch is a storage location on O2 for temporary data. In summary:

  • THE SCRATCH SPACE IS NOT BACKED UP!

  • Files are AUTOMATICALLY DELETED 45 days after they are last modified.

    • Modification time indicates when a file’s content was last changed, not merely accessed.

  • There are NO SNAPSHOTS available for recovering deleted data from scratch folders.

  • O2 users can have up to 25 TiB and 2.5 million files/directories under the /n/scratch filesystem.

  • Use this space for intermediate files in a longer workflow or for extra output that doesn't matter much.

To reiterate, if you delete a file on purpose or by accident or just leave it sitting for 45 days, it is GONE. You can't get it back, and Research Computing can't get it back for you. Using this model lets us provide cost-effective, high-end storage to many more users than would be possible with permanent and backed-up files. But it is important that you understand the risks of using it.

Important - Artificially modifying file modification times is against policy and may result in losing your access to scratch.

Scratch Overview

A scratch space is available on O2, mounted at /n/scratch.

Users cannot write files directly under /n/scratch itself.

If you don't have a scratch directory, then you must use the scratch create directory script.

Scratch Directories: Users

On scratch, user directories are found under:

  • /n/scratch/users/<first_hms_id_char>/<HMSID>

Where "<first_hms_id_char>" is the first character of your HMS ID (formerly eCommons ID), and  "<HMSID>" is your HMS ID.

For example, the scratch directory for a user with the username "abc123" would be located at:

  • /n/scratch/users/a/abc123

For an HMS ID of “zz999” the scratch directory will be at:

  • /n/scratch/users/z/zz999

Scratch Directories: Groups

On scratch, labs folders can be found under:

  • /n/scratch/groups/<institution>/<department>/<lab>

The scratch groups spaces are intended to facilitate collaboration between users in a lab.

Note that any data placed under /n/scratch/groups/ is still counted against the default user’s quota limits (25TiB and 2.5M files).

/n/scratch/groups spaces are created upon request. If your lab wants a scratch space, please contact us at rchelp@hms.harvard.edu, indicating your existing Active Compute Lab’s storage.

Create a User Scratch Directory

To create your own scratch directory on O2, please run the following command from a login node (not an interactive job):

/n/cluster/bin/scratch_create_directory.sh

Scratch Storage Usage

The storage usage is on a user basis rather than a group. To check your personal and group storage utilization and limits, please run the following command:

quota-v2

More information about the O2 quota-v2 command can be found on this wiki page.

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