O2 is a new platform for Linux-based high performance computing at Harvard Medical School. The name is derived from being the next generation of the HMS "Orchestra" cluster, hence "O"2.
- O2 is managed by the Research Computing Group, part of HMS IT.
O2 is an HPC cluster built on Linux and the Slurm open source job scheduler.
- Please submit a request for O2 help or feedback.
- Follow us on Twitter for updates and alerts about service outages.
Getting Started with O2 and Slurm
- Basic guide to O2 and the Slurm job scheduler ← New users, start here!
- Switching workflows from Orchestra to O2 ← Orchestra users, start here!
- How to login to O2
- Frequently Asked Questions about O2
O2 Jobs and the Slurm scheduler
- How to choose a partition (the Slurm equivalent to job queues in LSF)
- Troubleshooting your O2 jobs
- Parallel Jobs in O2
- Using O2 GPU resources
- O2 HPC Cluster and Computing Nodes Hardware Information
- Job Priority
- Examples of O2 commands
- Get information about current and past jobs
Software and Programming on O2
- Using research applications on O2
- Using Matlab on O2
- Using Mathematica on O2
- Using Conda on O2
- Using Java on O2
- Using Jupyter on O2
- Maintain your own library of software for different languages
- Installing custom software
- Using Genome Browsers (IGV, UCSC Genome Browser)
- Available Software on O2
General UNIX Information
- There are a number of storage options available for research data.
- Copying files to and from O2 (including downloading from websites)
- If you had an Orchestra account, you will get access to the same home directory and shared network storage from O2.
Our cluster status page has details of service outages and planned maintenance.
Two Factor Authentication: Since December 2018, all O2 cluster logins from outside of the HMS network require two-factor authentication. Please see:
Two Factor Authentication:
Since December 2018, all O2 cluster logins from outside of the HMS network require two-factor authentication. Please see:
- Classes are offered each semester to the HMS community to help you ramp up your research skills!
- Please check the User Training page for courses, dates, and registration
- RC's Office Hours are held every Wednesday, 1 - 3 PM in Gordon Hall Suite 500
- Please contact us first with a support request before dropping in at office hours so we can better help you!
Grants and Citation Information
- Text about Research Computing and O2 for grant applications
- Published papers that cite HMS Research Computing resources