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

Introduction

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 Odyssey and runs the same OS as the HSPH HPCC environment. If you are curious, take a look at the HSPH & FAS Research Computing Q&A page. A list of the currently installed software on the cluster is available online, though we are transitioning to a new software management system. Please see our Software on Odyssey document for the changes and for installing software yourself.

Requesting an account

Research Computing accounts for both FAS and HSPH users can be requested here. Account turnaround is usually one to two business days once approval from the relevant PI is received (Outline of Process). After receiving your credentials, you must complete the Introduction to Odyssey class within 45 days or your account will be disabled. Training is essential for the proper use of our complex systems.

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

Cluster Access

Computing costs are requested to provide researchers with access to the Harvard University Faculty of Arts & Sciences Research Computing shared use facility (FAS RC). A $3,000 fee per FTE per year is charged for access to the FAS RC. This fee applies to each non-student account and provides users with access to resources hosted in the FAS RC environment, including expert consulting help coupled with extensive resources, such as over 10 PB of storage, over 54,000 processing cores, and numerous software modules and applications.

Student accounts are not charged for cluster access. A student is defined as anyone enrolled in a Harvard University undergraduate or graduate course of study, such as a Master's or doctoral program. This does not include postdocs, researchers, faculty at other academic institutions or anyone else who is not specifically a Harvard University student unless prior arrangements have been made with Research Computing management.

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-key authentication system similar to what many banks and Google offer. The OpenAuth client applications exist for Windows, OSX and Linux as well as iPhone, Blackberry and Android devices.

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

One accesses the RC Odyssey environment 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 and other services at FAS Research Computing you will require an active VPN connection which also allows you off-campus access to your data.

Again, consult our Access and Login guide.

Using Odyssey

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

In addition, please take a look at the documentation section of the website to find information on the following topics: high performance computing, bioinformatics, scientific computing, storage, VPN, OpenAuth, Odyssey software list, instrument sign-up, and application hosting. There is also a How-To page for quick reference and a new user guide.

Resource planning

Dedicated setups exists for high-memory jobs, I/O-intensive tasks or shared memory algorithms, and you can monitor the current status of the system at all times.

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 bundle your jobs in 5 to 10 minute lots.

If in doubt, contact RCHelp.

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 4TB of space per lab (/n/hsphsS10/hsphfs1/scratch). All data stored in this hsphS10 environment is redundantly stored and backed up at a second site. These and other labs can purchase additional storage: 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 by request only.

 Snapshots are like a freeze frame picture of data at a point in time. 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: 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 monthly. If you run into any problems, need grant support or are not sure whom to talk to email Oliver Hofmann.

Last updated: December 15, 2016 at 14:27 pm

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