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 the analysis. If you are curious, take a look at the HCSPH & 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 a Research Computing account is a semi-automated process, requiring a selection of a PI (your PI must have an existing FASRC account) as your sponsor and whose lab you will belong to. The sponsor PI will then approve or deny the request. Once the PI has approved the request, turnaround is generally within the hour (Outline of Process). If the request is for an EXTERNAL user, this may take slightly longer as external users must be vetted manually. After receiving your credentials, you must attend one of our monthly New User Trainings or watch our Introduction to the Cluster videos if you selected cluster access (e.g. – the ability to run jobs). 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 will not have a home directory or be able to run jobs. As such, 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. Additionally, you may have only one account. Please do not sign up for multiple accounts. 

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 40 PB of storage, over 82,000 processing cores, as well as numerous software modules and applications. For further details on accessing the cluster, please see the FAQ or our helpful Access and Login guide.

Billing and Usage

The previous annual per-user charge for FAS Research Computing accounts is no longer used as of the fiscal year 2019. Standard services, including accounts and access to the FAS RC high-performance computing cluster, will be effectively free to all Harvard Chan School community members via the account of an eligible PI (See: HCSPH PI Eligibility Policy). These FASRC computing costs are now covered by the school’s overhead rate. Supplemental resources such as increased storage and VMs still involve additional charges, please see our Billing FAQ.

Authentication and Security

FAS Research Computing uses a two-factor authentication system. 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. 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 The Cluster

Taking advantage of the cluster’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. Additional support for using the FASRC is available via training and weekly HCSPH office hours. Additional computational training related to research computing is available from the Harvard Chan School Bioinformatics Core.

HCSPH has their own partitions of purchased hardware on the cluster. These partitions are open to HSPH users and their allocation is governed by the relative fairshare of each group. These partitions are:

• hsph: This block of 5824 Intel Sapphire Rapids cores. Each node is water-cooled and contains 112 cores, and 1TB of RAM. The nodes are interconnected with NDR Infiniband. This partition has a 3 day time limit.
• hsph_gpu: This block of GPU’s contains 192 AMD Genoa cores and 8 Nvidia H100 GPUs. Each node is water-cooled and contains 96 cores, 1.5TB of RAM, and 4 GPU’s. The nodes are interconnected with NDR Infiniband. This partition has a 3 day time limit.

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

The cluster 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 and Virtual Desktop documentation. If you would like to use a graphical client you need to enable X11 forwarding. A better solution is to use our VDI System.

Data storage and security

Data can be transferred to and from the cluster using multiple file transfer methods. Please see our Transferring Data Internally or Transferring data externally documentation. Certain HCSPH researchers have access to the FAS Research Computing computing file systems, in particular each existing PI with an account and lab group with cluster access RC is eligible for 4TB of base lab share to facilitate basic research workflow. Additional storage can be purchased: See our Data Storage services page.

See also:

• Office of Regulatory Affairs and Research Compliance – Investigator Manual: https://www.hsph.harvard.edu/regulatory-affairs-and-research-compliance/investigator-manual/

Special Security Requirements

The general FAS RC cluster storage environment is not suitable for storing 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

FAS RC has a number of methods for supporting researchers in need of help. Please see our FASRC Support page for details. You may also contact the HCSPH Bioinformatics Core for local help. Additionally, FAS RC hosts Office Hours regularly.