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This project will relocate existing services, consolidate servers, reduce power consumption, and decommission outdated hardware to improve efficiency, enhance resiliency, and lower costs.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

Build Folder Structures From Sample Sheet for rcbio NGS Workflows

Owned by Lingsheng Dong
Last updated: Dec 11, 2023
3 min read

 


Note: You can copy and paste all the text to your Linux command line to run. Anything with "#" is comment, and will be IGNORED by Linux.

Login to O2

# replace user123 with your eCommons ID ssh user123@o2.hms.harvard.edu



Start an interactive session

# this command requests a job in the interactive partition, with one processor for 2 hours srun --pty -p interactive -t 0-02:0:0 --mem 2000MB -n 1 /bin/bash



Make a folder to work in

# Make a directory in scratch file system and work there. We recommend creating separate folders for each project. mkdir -p /n/scratch/users/${USER:0:1}/$USER/test && cd /n/scratch/users/${USER:0:1}/$USER/test



Note: Each user has 25 TiB /n/scratch space. There is no backup for data saved in/n/scratch, and files will be deleted if they are not accessed for a month. You can read more about /n/scratch on the Filesystems page.

Copy testing sample sheet to work directory

Examine sample sheet on local computer

The sample sheet is in Microsoft Excel format. You can look at this file by transferring it to your local computer, and opening in Excel. Programs that can be used to transfer the sample sheet include Filezilla or WinSCP. For help on transferring files to or from the O2 cluster, please read the File Transfer wiki page. 

You can also use our new O2Portal to do file transfer: https://o2portal.rc.hms.harvard.edu/pun/sys/dashboard



Load related modules

Build folder structure from the sample sheet





Look at the folder structure



Now you are ready to run an rcbio workflow

To instead run workflow on your own data, transfer the sample sheet to your local machine following this wiki page and modify the sample sheet. Then you can transfer it back to O2 under your account, then go to the build folder structure step.

 

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