High Performance Computing Core
The High Performance Computing (HPC) Core is NYU Langone’s central resource for performing computational research at scale and for analyzing big data. We provide a range of integrative services using supercomputing to perform basic, translational, and clinical informatics research. As a core facility, we are well-positioned to advise scientists at NYU Langone on best practices for improving the quality and range of their research.
Based in the wider Medical Center Information Technology (MCIT) group and established in 2009, we maintain locally installed HPC infrastructure with substantial computing and data-storage capabilities. We work in partnership with other core facilities, such as the Genome Technology Center, to store locally produced next-generation sequencing data. We also partner with the Applied Bioinformatics Laboratories to provide informatics services on data sets acquired from the Genome Technology Center or external sources.
We provide access to data-storage resources attached to a powerful supercomputer and a software stack capable of executing sophisticated deep learning, predictive analytics, image processing, and mathematical modeling algorithms with a variety of types of data. Our computing environment provides a shared platform for development of new computational workflows, support of clinical trials informed by the latest research in molecular biology, and enabling discoveries that lead to better diagnosis, treatment, and prevention of disease.
NYU School of Medicine currently operates a terascale HPC cluster, called Phoenix, and is in the process of transitioning from Dell EMC Isilon to IBM Elastic Storage Server (ESS) storage technology. In 2018 we will put into production a state-of-the-art 90-node Cray HPC system including a 4 PB ESS-based IBM Spectrum Scale parallel file system complemented by a 500 TB ESS-based IBM Spectrum Scale solid–state drive scratch space.
This new petascale supercomputer will deliver expanded computational capabilities, in particular in its graphics processing unit–based subsystems. The new HPC cluster will be the backbone of our big data strategy; additional growth is planned in two expansion phases, in 2019 and 2021.
Anyone from the NYU Langone community with a valid Kerberos ID and an HPC account can request access to the HPC cluster.
To apply for an account, please email us at email@example.com with the subject line “HPC Account Request.” Include the following information in the body of the email:
- the new user’s full name
- the new user’s Kerberos ID (usually the user’s initials or part of the user’s name followed by a number of digits)
- the new user’s email address (to receive important announcements via our mailing list)
- the new user’s department or center and division or section
- the name of the new user’s principal investigator
- the title of the project for which HPC resources are to be used
- a brief description of the research being conducted by the new user
- a brief description of the HPC needs, such as data storage, computing power, data transfers, remote access (from outside the MCIT network), and so on
- the new user’s Secure Shell (SSH) public key (this can be sent in a separate email; see also the instructions for generating keys on Unix-like systems and on Windows)
Requests for multiple accounts can be sent in a single email. Accounts are usually created within one business day. HPC administrators will notify the new user with account confirmation.
Upon request, a consultation for a prospective user can be arranged. The initial consultation is free and can be done over the phone. Possible topics include:
- overview of the available resources and services
- best practices for accessing and using the resources
- user responsibilities and costs associated with HPC accounts
- any questions the prospective user may have, in particular concerning account creation or how to generate SSH keys
The High Performance Computing Core is located among Medical Center Information Technology teams at the address below. We also hold a weekly face-to-face meeting with the team (no appointment necessary) on the main NYU Langone campus. All HPC account holders receive a weekly email notice with the time and place of the meeting.
We are also able to meet with users individually outside of the weekly meeting to discuss any concerns regarding HPC. Please email us to coordinate.
High Performance Computing Core
Medical Center Information Technology Research
NYU Langone Health
360 Park Avenue South, 12th Floor
New York, NY 10010