Overview

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

• New User Orientation ←  For new users logging in for the first time

• Basic guide to O2 and the Slurm job scheduler    ←  Otherwise, new users, start here!
  
  

• Understanding O2 Slurm Accounts/Associations and Unix Accounts/Groups

• How to request an O2 account

• How to login to O2

• Frequently Asked Questions about O2

• Security on O2

O2 Portal

• Access to O2 via a web browser; powered by Open OnDemand

• Simplify transfer to/from O2 and the interaction of popular tools/applications

• Using the O2 Portal on O2

O2 Jobs and the Slurm scheduler

• How to choose a job partition

• 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

• Connect to a running sbatch job

• Get information about current and past jobs

• See your O2 resource utilization

• Optimizing O2 Jobs

• Improving O2 Efficiency by Changing User Priority

Software and Programming on O2

• Using research applications on O2

• Using Software Provided by BioGrids

• Using MATLAB on O2

• Using Mathematica on O2

• Using Conda on O2

• Using Globus on O2

• Using Java on O2

• Using Jupyter on O2

• Using RStudio on O2 

• Maintain your own library of software for different languages

  • Personal Python packages

  • Personal R packages

  • Personal Perl packages

• Installing custom software

• Available Software on O2

General UNIX Information

• Using X11 applications remotely

• UNIX permissions tutorial

• O2 cron service

Data Storage

• There are a number of storage options available for research data, such as Active and Standby

• Copying files to and from O2 (including downloading from websites)

• Home directory and shared network storage on O2

• Quotas on home directory and shared network storage on O2
  
  

Cluster Status

OPERATIONAL

Our O2 Cluster Status has details of service outages and planned maintenance.

Community Events

User Training

• 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

Office Hours

• RC's Office Hours are held every Wednesday, 1 - 3 PM.

  • As part of the HMS response to COVID-19, office hours are being held online, using Zoom.

  • During these hours only, you can join the Zoom meeting room for a consultation. 

• We encourage you to contact us first with a support request before joining Office Hours, please make sure to describe in detail your problems or questions so we can better help you!  Note: the RC team does not schedule meetings during Office Hours, however we are available to schedule meetings at any other time.

Intermediate Slurm

• Batch small jobs together as a big Slurm job

• Get more informative slurm email notification and logs through rcbio/1.3.3

• Get more informative slurm email notification

• Report CPU/Mem usage in slurm job standard output

• VS Code Server on O2

• screen: go back to the same terminal window from anywhere, anytime

• tmux: go back to the same terminal window from anywhere, anytime

• CheckPointing with DMTCP

Bioinformatics

• Research Computing Group custom NGS workflows

• Install and run HiC-Pro-2.10.0

• Install and run salmon-0.10.0 and Trinity-2.6.6

• Using Aspera to Download Data

• sratoolkit/2.10.7 to download NCBI SRA data

• sratoolkit/2.10.7 to download dbGAP data

• Using Genome Browsers (IGV, UCSC Genome Browser)

• Protein Structure Prediction

Grants and Citation Information

• Text about Research Computing and O2 for grant applications

• Published papers that cite HMS Research Computing resources