O2

Working with the HMS O2 cluster

Introduction to O2

O2 is the high performance computing (HPC) cluster maintained by Harvard Medical School. O2 official documentation is located here:

Setting up your O2 account

Obtain your O2 account

Kwon Lab is an “off-quad” Harvard Medical School affiliated lab that uses O2 computing services. This section was created using the official O2 documentation as reference.

  1. Submit PPMS form and wait for RC Core admin (rccore@hms.harvard.edu) for approval. Approval notifications are sent to email submitted in PPMS form.
  2. Sign the HMS RC Core user agreement that is sent via email (requires PI to co-sign)

Accessing O2

Using your computer’s terminal, use the following command to access O2 and enter your credentials accordingly.

ssh <hms_id>@o2.hms.harvard.edu

Setting up 2-Factor Authentication with Duo

O2 login requires 2-Factor Authentication and it is recommended to execute this through the Duo app, which can be installed on your phone.

  1. Download the app on phone
  2. Email itservicedesk@hms.harvard.edu or call 617-432-2000 to ask HMS IT to register and connect your HMS account with Duo.
  3. Logging into O2 by default asks you to pick a Duo authentication method (push, call or text). Set your Duo app to either send a push or call your phone each time automatically. DO NOT set text as your default.

(On the login node) Run the following on O2 terminal:

For push: (recommended, but only if you already have Duo push!)

echo 'export DUO_PASSCODE=push' >> $HOME/.bashrc

For phone call:

echo 'export DUO_PASSCODE=phone' >> $HOME/.bashrc

Setup passwordless login (SSH keys)

Please refer to SSH keys tutorial here

Getting oriented with O2

Save all your files into one of the two locations:

  1. /n/groups/kwon/<your_name> Your own folder within the Kwon Lab group folder and main storage location.
  2. /n/groups/scratch/<first_letter_of_hms_id>/<hms_id> Scratch directory is for temporary storage and files are deleted in 45 days.

Request access to the /n/groups/kwon/ groups folder

To request access, email rchelp@hms.harvard.edu to ask for access to the group folder /n/groups/kwon on O2. Please copy dkwon@mgh.harvard.edu and jelsherbini@mgh.harvard.edu.

Use the following command in the O2 terminal to access the Kwon Lab folder and make a folder under your own name:

cd /n/groups/kwon/
mkdir <your name>

To access your own folder within the Kwon Lab group folder on the O2 terminal:

cd /n/groups/kwon/<your name>

Making a scratch directory

Note: the scratch directory is for TEMPORARY STORAGE. All files in scratch are automatically deleted 45 days after their last modification date. Everything you want to keep needs to be moved to your folder in /n/groups/kwon/<your name>.

(On the login node) Run the following on O2 terminal:

/n/cluster/bin/scratch_create_directory.sh

To access scratch directory:

cd /n/groups/scratch/users/<first_letter_of_hms_id>/<hms_id>