Harvard T.H. Chan School of Public Health + FAS Research Computing Overview


The Harvard T.H. Chan School of Public Health (HSPH) is using the FAS Research Computing environment to host data and run analysis. The compute cluster is Odyssey3, based on CentOS 7. If you are curious, take a look at the HSPH & FAS Research Computing Q&A page for additional information. A list of the currently installed software on the cluster is available online. Please see our document on installing software yourself.

Requesting an account

Requesting and Research Computing account is a semi-automated process, requiring a selection of a PI as your sponsor and whose lab you will belong to. The sponsor PI will then approve or deny the request. Account turnaround is generally within the hour once approval from the relevant PI is received (Outline of Process).

After receiving your credentials, you must complete the Introduction to Odyssey video and quiz within 45 days or your account risks being disabled. Training is essential for the proper use of our complex systems. The email stating your account has been created will have links to the necessary getting started and running jobs documentation necessary to get started on the cluster

NOTE: If you did not request cluster access, you are not required to take the cluster quiz but will still need to set your password and acquire your OpenAuth token as shown in the getting started docs.

Important: Regarding Account Sharing - The sharing of accounts is a violation of Harvard and RC information security policies. You cannot share your account with another individual, nor should anyone else know your login credentials.

Cluster Access

An account with cluster access provides users with access to resources hosted in the FAS RC environment, including expert consulting help coupled with extensive resources, such as over 35 PB of storage, over 70,000 processing cores, as well as numerous software modules and applications. 

Computing costs are no longer tied to individual accounts (as of FY19), but are instead based on the cluster usage of each PI lab group. Each quarter the relevant school, unit, or lab group will receive a detailed listing of charges which can be paid via 33-digit billing code or at the school level. Each HCSPH PI lab group will be billed directly for their quarterly cluster usage using a 33-digit code.

For further details on accessing the cluster, please see the FAQ or our helpful Access and Login guide.

Authentication and Security

FAS Research Computing uses a two-factor authentication system similar to what many banks and Google offer. The OpenAuth client application exists for Windows, OSX and Linux, or you can import your RC token into Google Authenticator or Duo to display the necessary auth code there.

Each account and token is unique to the individual account holder. Please note that the sharing of accounts/credentials is a violation of Harvard and RC security policies.

Cluster users will access the RC Odyssey cluster via SSH. Typing your password and verification code (OpenAuth) for every data transfer and shell can quickly become tedious, but OpenSSH supports aggregating of authentication sessions.

Finally, in order to access some of the web servers, storage, and other services at FAS Research Computing, whether on wired or wireless, you will likely need to use a VPN connection. Again, consult our Access and Login guide for more details.

Using Odyssey

Taking advantage of Odyssey's massive compute capabilities is easy if you've read through our Quick Start Guide and Running Jobs document.

You'll find many more helpful documents in our online documentation. Your local Bioinformatics group is also well-versed in the use of the cluster and joins us for local Office Hours.

Resource planning

Note that it is relatively easy to overload the file storage system. Please use our high-performance scratch storage filesystems for high I/O jobs. Also, if you are submitting a large number of tasks, please see our Submitting Large Numbers of Jobs document, and please try to keep your jobs efficient and bundle them in 6 to 10 minute lots.

If in doubt, contact us.

Interactive sessions

Odyssey allows interactive use which is great for exploring new tools or running shell-based sessions (SAS, MATLAB, R) without having to submit jobs. Please see our Interactive Sessions information.

If you would like to use a graphical client you need to enable X11 forwarding. A better solution is to use our NoMachineX lightweight GUI. Please see our NX Remote Desktop information.

Data storage and security

Data can be transferred to and from Odyssey using multiple file transfer methods. Please see our Copying Files and FileZilla file transfer client information.

Certain HSPH researchers have access to the FAS Research Computing computing file systems, in particular each PI with a lab group on Odyssey is eligible for 4TB of lab storage . All data stored in this space is backed up in case of critical failure. Additional storage can be purchase: Please contact RCHelp to discuss needs and billing options.

 Backups are a a second copy of data. Though all FAS storage hardware has built-in redundancy so that a limited number of disk drive failures and other hardware faults can be tolerated, a backup is required in order for the data to survive a catastrophic failure of the entire system or facility. The Odyssey cluster consists of several data centers and offers off-site (inter-datacenter) backup. Backups are not accessible from the cluster or campus network. Recovery from backups is for disaster recovery and by request only. Backups should not be relied on as a solution for day-to-day single file or directory deletions as restoration is often very labor=intensive.

 Snapshots are like a freeze frame picture of data at a point in time. Only home directories have snapshots. You can use home directory Snapshots to undo recent changes to files, recover deleted files, etc. Though Snapshots function much like a backups, they’re not backups, since the data still only exist as one copy in one place (Snapshots are reconstructed algorithmically, not stored as separate copies). See our Snapshot FAQ for more information.

Special Security Requirements

The RC/Odyssey environment does not have a default process for handling data with special security requirements. If access to your data needs to be limited in any way, contact RCHelp prior to transferring data.

Important: Do not store data which is covered under a data use agreement or is otherwise considered high risk without consulting FAS RC first.

Important: The sharing of accounts is a violation of Harvard and RC information security policies. Please contact us if you have a special need.

Contact and support

RC has a number of methods for supporting researchers in need of help. Please see our RC Support page for details. Also, RC hosts Office Hours at HSPH regularly during term.

Last updated: July 3, 2018 at 15:10 pm

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