High Performance Computing

Stony Brook University offers researchers several different options depending on needs.

High Performance Computing Clusters

Stony Brook University researchers may access the services provided by the following two HPC clusters: 

LI-red

LI-red is a computational cluster using top-of-the-line components from Cray, IBM, Intel, Mellanox and other technology partners. It is intended for members of the campus community, as well as industrial partners, and is located in the Institute for Advanced Computational Science's (IACS) server room.  

 

Learn more about LI-red

SeaWulf

SeaWulf is a computational cluster using top of the line components from Penguin, DDN, Intel, Nvidia, Mellanox and numerous other technology partners.  It is intended for members of the campus community, as well as industrial partners, and is located in the Computing Center.

 

Learn more about SeaWulf

 

New User Warnings

  • If you have never used a high performance computing cluster, or are not familiar with SeaWulf, YOU WILL WANT to read and follow the instructions in the FAQ below (start with the Getting Started Guide!).  It is a common practice by new users to ignore this FAQ and simply try to run jobs without understanding what they are doing. Such carelessness can and WILL easily impact the many users who are currently running critical jobs on the cluster. If your actions compromise the health of SeaWulf, your account will be LOCKED so please make sure you thoroughly read the guides below before you embark on running jobs.
  • Do NOT use the login nodes for computationally intensive work of any kind.  This includes compiling software.  If everyone runs CPU- or RAM-intensive processes on either login node, it will crash and prevent all other SeaWulf users from being able to login to the cluster.  If you need to test or compile your code, please request an interactive job instead of testing it on the login nodes!
  • Do NOT use your home directory (/gpfs/home/NETID) to store large files as you may quickly exceed the directory’s storage limit (20 GB).  It is best to place large or temporary files in your scratch directory (/gpfs/scratch/NETID), though please keep in mind that files and directories in scratch are automatically removed after 30 days.   If your research group needs a persistent directory with a larger storage limit, consider requesting a shared project space.
  • Never submit a large number of jobs (greater than 5) without first running a small test case to make sure your code works as expected. Start slow and then ramp up with jobs once you are familiar with how things work.
  • SeaWulf is managed by a small number of System Administrators and students.   If you encounter an issue or have problems running your job, please make sure you read through the FAQ items below before submitting a ticket to HPC Support.

Announcements

August 24, 2020

Intel Parallel studio 2020 version 20.0.2 has been installed on SeaWulf.  In order to ensure stability and improve the user experience, 20.0.2 has  been set as the default version of the Intel compilers, MKL,  and MPI when the intel-stack module is loaded.  Older versions of the Intel modules are still available and may be loaded individually.

July 20, 2020

Emergency electrical maintenance will be performed on the circuits feeding the 24-core queues on Thursday 7/23/2020. This outage is not expected to impact the 28-core or 40-core queues, nor the login nodes. In anticipation of this maintenance, the 24-core queues will be disabled starting at 5:00 PM on Wednesday 7/22/2020. We currently anticipate the 24-core queues will be back up by the end of business on 7/23/2020, pending timely completion of the emergency electrical maintenance.

July 02, 2020

Due to preventive maintenance on the Campus Data Center’s generator and scheduled maintenance on SeaWulf’s Compute Nodes, the SeaWulf cluster’s job queues will be disabled starting at 5:00 PM on Monday July 13th. During this maintenance window, all SeaWulf Nodes will be unavailable and login nodes will be off-line. We will be updating the operating system and security packages in order to provide a more robust computational environment.  The work is expected to be completed by the end of business on Tuesday July 14th.  

May 21, 2020

SeaWulf users may now receive email updates about their Slurm jobs using the "--mail-type" and "--mail-user" SBATCH directives.  For more information regarding this new functionality, please see the following FAQ page:

https://it.stonybrook.edu/help/kb/example-slurm-job-script

March 30, 2020

Our HPC Support Team will now be offering online office hours via a recurring Zoom meeting. Support staff will be available from 2pm - 4pm every Wednesday starting this Wednesday, April 1st, until the end of the semester. You can also try joining the meeting at anytime and, if available, one of support staff may be able to join the meeting to assist you. Click here to join office hours.

March 30, 2020

We will be performing scheduled maintenance Wednesday, April 15th starting at 9:00 AM on the SeaWulf cluster. During this maintenance window, all SeaWulf queues will be down and login nodes will be off-line. We will be setting up Duo as a two-factor authentication method and updating the operating system and security packages in order to provide a more robust computational environment. The maintenance is expected to be completed by the end of business on Wednesday.

February 17, 2020

We will be performing scheduled maintenance this Friday, February 21st starting at 9:00 AM on the SeaWulf cluster. During this maintenance window, all SeaWulf queues will be down and login nodes will be off-line. We will be updating the operating system and security packages in order to provide a more robust computational environment. The maintenance is expected to be completed by the end of business on Friday.

 

We apologize for the inconvenience and thank you for your patience while we complete these updates.

February 06, 2020

The IACS is sponsoring a SeaWulf HPC training workshop on Monday, March 2 and Tuesday, March 3 from 1 -4pm in the IACS Seminar Room.  This workshop is aimed at researchers (grad students, professors, postdocs, and undergrads are all welcome!) who are interested in using High Performance Computing resources for their research but have limited experience in this area.  

The workshop is free but requires registration.  Please see the IACS events calendar for more information.  You may also register for the workshop here.

December 06, 2019

The shared module is now deprecated on Seawulf. All modules can now be loaded directly after logging in to Seawulf. It does no harm to load or unload the shared module; it will just no longer have an effect on the search path for modulefiles. This means there is no need to remove it from any scripts you have, but it's no longer necessary to use going forward.

November 21, 2019

The SeaWulf cluster will be going down for upgrades on Monday November 25th at the close of business. During this upgrade window, the remainder of the SeaWulf nodes on Torque will be switched over to the Slurm scheduler. The upgrades are expected to be completed by the close of business on Tuesday November 26th.

 

The below section in our FAQ may be useful in assisting with switching workflows from the Torque scheduler to Slurm:

https://it.stonybrook.edu/help/kb/using-the-slurm-workload-manager

October 16, 2019

The SeaWulf cluster will be going down for upgrades on Monday October 28th at the close of business. During this upgrade window, the former LI-red nodes (-24core) will be switched over to the Slurm scheduler. The upgrades are expected to be completed by the close of business on Tuesday October 29th.

This section of our FAQ may be useful in assisting with switching workflows from the Torque scheduler to Slurm.

The remainder of the SeaWulf cluster is expected to be migrated to Slurm in November.

Partners

Institute for Advanced Computational Science (IACS)

The mission of the IACS is to make sustained advances in the fundamental techniques of computation and in high-impact applications with a vision that by 2017, it will be an internationally-recognized institute having vibrant multidisciplinary research and education programs with demonstrated economic benefit to New York State. Including students and staff. the IACS aims to grow close to 100 people by 2018. There are presently 10 faculty spanning chemistry, materials by design, condensed matter, astrophysics, atmospheric science, nano-science, sociology, applied mathematics, and computer science. Another approximate 20 faculty are affiliated with the institute from diverse departments.

Office of the Vice President for Research (OVPR)

The Office of the Vice President for Research helps strategically position the University to be successful in attracting external support for research from federal and other government sources, industry, private foundations, philanthropy, and through partnerships with allied organizations such as Brookhaven National Lab, Cold Spring Harbor, and others. It facilitates the process of applying for grants and contracts and manages awards to assure that research is carried out successfully and that the requirements of sponsoring agencies are fulfilled. It also provides technology tools to disseminate information, facilitate collaboration, and streamline research administration. 

University Libraries

Stony Brook Libraries are known for a wide-range of print and digital resources and world-renowned special collections. The Stony Brook Libraries belong to the Association of Research Libraries (ARL), with a Health Sciences Center Library that is a member of the Association of Academic Health Sciences Libraries. The Libraries’ collection exceed 2 million volumes, including eBooks, print and electronic holdings of scholarly journal subscriptions, microforms, music recordings, and a sizable map collection.The University’s Libraries stand as the largest academic research library on Long Island, serving as a resource in the local community, state-wide, and nationally through the National Network of the National Libraries of Medicine.​

Service Providers

Internet2 (NYSERNet)

Stony Brook offers researchers high-capacity, high-speed connections to the Internet as a member of NYSERNet and Internet2.

XSEDE

XSEDE is a single virtual system that scientists can use to interactively share computing resources, data and expertise. People around the world use these resources and services — things like supercomputers, collections of data and new tools — to improve our planet.

Brookhaven National Lab

Brookhaven National Lab acts as an extension of Stony Brook University for faculty as another service provider. 

Additional Information


There are no additional resources available for this service.

Please Contact


IACS Support System