O2 is a 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
- Security on 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.
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Our cluster status page has details of service outages and planned maintenance.
- 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.
- Please contact us first with a support request before joining 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