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This project will relocate existing services, consolidate servers, reduce power consumption, and decommission outdated hardware to improve efficiency, enhance resiliency, and lower costs.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
Protein Structure Prediction on O2
- Alex Truong
Research Computing now supports the use of several cutting-edge protein structure prediction options:
For more details about the individual software, please refer to their respective documentation pages above.
As it may be difficult to determine which is the correct choice of program to leverage, we offer the following usage/troubleshooting flowchart helpfully generated by collaborators at the Center for Computational Medicine (CCB), with whom we held a town hall regarding Alphafold and ColabFold. More information about the town hall can be found at the CCB website.
For users interested in running large volumes of predictions with LocalColabFold, we strongly recommend getting familiar with the local mmseqs2 alignment procedure (Using (Local)ColabFold on O2 | Generating MSAs Using Local MMseqs2 ). This is crucial to avoid getting bottlenecked or blacklisted by the remote server.
A direct link to the AlphaFold database mentioned at the top of the flowchart below can be found here.
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Please contact rchelp@hms.harvard.edu for any questions or clarification.