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This project will relocate existing services, consolidate servers, reduce power consumption, and decommission outdated hardware to improve efficiency, enhance resiliency, and lower costs.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

User Training

Current Training Schedule: Fall 2024

Please note that we are transitioning to offering classes on Thursdays, when we have held classes on Wednesdays for many years.

Please note the location for your selected class. We are offering both in-person and virtual classes this year.

Important note: for virtual classes, you should receive an confirmation email from the Harvard Training Portal with a Zoom link. If you do not have your email address on file in the Training Portal, such messages cannot be sent to you. Please contact us for the Zoom meeting details if you do not get a confirmation email.

Class

Date

Time

Location

Training Materials

Registration

Class

Date

Time

Location

Training Materials

Registration

Intro to MATLAB

Thursday, September 19, 2024

10am to 12pm

online

User Training github

Register here!

Intro to Parallel Computing

Thursday, September 26, 2024

10am to 12pm

online

User Training github

Register here!

Optimizing O2 Jobs

Thursday, October 3, 2024

10am to 12pm

in person

User Training github

Register here!

Intro to Python

Thursday, October 10, 2024

10am to 12pm

online

User Training github

Register here!

Parallel Computing with MATLAB

Thursday, October 17, 2024

10am to 12pm

in person

User Training github

Register here!

Data Management: Computing Strategies and Resources

(in collaboration with Countway Library and FAS Research Computing)

Thursday, October 24, 2024

10am to 11am

online

 

Register here!

O2 Portal - Simplifying the Interaction and Experience of Using an HPC Environment

Thursday, October 31, 2024

10am to 12pm

online

User Training github

Register here!

Intro to Python

Thursday, November 14, 2024

10am to 12pm

online

User Training github

Register here!

Intro to O2

Thursday, November 21, 2024

10am to 12pm

in person

User Training github

Register here!

RCBio: easy and quick HPC pipeline builder & runner

Thursday, December 5, 2024

10am to 12pm

online

User Training github

Register here!

Shell Tips and Tricks on O2: HBC Current Topics in Bioinformatics

Wednesday, December 11, 2024

1pm to 4pm

online

 

Register here!

Additional classes will be added for the Spring semester.

Class Registration Process

Registrations are managed through the Harvard Training Portal, which requires a Harvard ID (HUID). Those members of the extensive HMS community who do not currently have HUIDs - such as employees at affiliate hospitals, or collaborators from other institutions - may self-register for one as a "Harvard Sponsored Role” with their faculty member's sponsorship. This form may take several days to process, please visit this page for details: Harvard Sponsored Role (HSR)

Class Descriptions

Classes taught by HMS Research Computing Staff:

Intermediate O2 is for current O2 users who would like to brush up on their bash skills, learn more advanced file transfer techniques, and unleash some of the powerful features of the SLURM scheduler.

This course introduces Git and GitHub and covers topics including: Getting Started with Git for version control, Using GitHub Desktop effectively, Collaborating with others on GitHub, and Utilizing GitHub Flow for better workflow. No previous exposure is assumed. We hope attendees will leave the class with the knowledge and tools necessary to start integrating Git into their workflows and excited to begin collaborating on GitHub.

Matlab has become the “language of science” in the past few decades. It is simple to use, yet powerful enough to be productive on large computing infrastructures. If you need: 1) Fast prototyping of research ideas; or 2) avoid spending too much time in coding instead of doing real science by taking advantage of Matlab’s built-in functions; 3) User friendly graphical interface and educational documentation; 4) Simplicity of code; 5) Easy access to GPU computing power; 6) Easy plotting and presentation of data; you will find this introduction course useful. This course will introduce the basics of the MATLAB coding language with O2-scalability and data presentation.

Intro to O2 addresses the needs of users who have very little linux experience, and are just getting started with the O2 high performance compute cluster. We will cover linux basics, and the concept of the Slurm scheduler and jobs, as well as data management best practices.

This is a short introduction to Parallel Computing that will include an overview of the basic concepts of parallel programming: from running your job in an embarrassingly parallel way to writing simple shared and distributed memory parallelization codes in different languages. The seminar will cover several examples of actual parallel codes however it will not have any "hands on" components. A basic programming experience (of any language, no parallelization) is preferred in order to better follow the topics presented during the seminar.

Classes sponsored by HMS Research Computing but taught by our partner organizations:

Additional computational trainings available through other groups

Please reach out directly to the above groups if you are interested in attending their trainings.

Contact us

Please reach out to HMS Research Computing at rchelp@hms.harvard.edu with any questions about training. We are here to assist if you are having difficulty registering for a class, or if you are wondering when a topic will be offered next!