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Beta cluster available for learning Slurm; new scheduler to be part of upcoming cluster updates

By | Flux, General Interest, Happenings, HPC, News

New HPC resources to replace Flux and updates to Armis are coming.  They will run a new scheduling system (Slurm). You will need to learn the commands in this system and update your batch files to successfully run jobs. Read on to learn the details and how to get training and adapt your files.

In anticipation of these changes, ARC-TS has created the test cluster “Beta,” which will provide a testing environment for the transition to Slurm. Slurm will be used on Great Lakes; the Armis HIPAA-aligned cluster; and a new cluster called “Lighthouse” which will succeed the Flux Operating Environment in early 2019.

Currently, Flux and Armis use the Torque (PBS) resource manager and the Moab scheduling system; when completed, Great Lakes and Lighthouse will use the Slurm scheduler and resource manager, which will enhance the performance and reliability of the new resources. Armis will transition from Torque to Slurm in early 2019.

The Beta test cluster is available to all Flux users, who can login via ssh at ‘beta.arc-ts.umich.edu’. Beta has its own /home directory, so users will need to create or transfer any files they need, via scp/sftp or Globus.

Slurm commands will be needed to submit jobs. For a comparison of Slurm and Torque commands, see our Torque to Slurm migration page. For more information, see the Beta home page.

Support staff from ARC-TS and individual academic units will conduct several in-person and online training sessions to help users become familiar with Slurm. We have been testing Slurm for several months, and believe the performance gains, user communications, and increased reliability will significantly improve the efficiency and effectiveness of the HPC environment at U-M.

The tentative time frame for replacing or transitioning current ARC-TS resources is:

  • Flux to Great Lakes, first half of 2019
  • Armis from Torque to Slurm, January 2019
  • Flux Operating Environment to Lighthouse, first half of 2019
  • Open OnDemand on Beta, which replaces ARC Connect for web-based job submissions, Jupyter Notebooks, Matlab, and additional software packages, fall 2018

U-M selects Dell EMC, Mellanox and DDN to Supply New “Great Lakes” Computing Cluster

By | Flux, General Interest, Happenings, HPC, News

The University of Michigan has selected Dell EMC as lead vendor to supply its new $4.8 million Great Lakes computing cluster, which will serve researchers across campus. Mellanox Technologies will provide networking solutions, and DDN will supply storage hardware.

Great Lakes will be available to the campus community in the first half of 2019, and over time will replace the Flux supercomputer, which serves more than 2,500 active users at U-M for research ranging from aerospace engineering simulations and molecular dynamics modeling to genomics and cell biology to machine learning and artificial intelligence.

Great Lakes will be the first cluster in the world to use the Mellanox HDR 200 gigabit per second InfiniBand networking solution, enabling faster data transfer speeds and increased application performance.

“High-performance research computing is a critical component of the rich computing ecosystem that supports the university’s core mission,” said Ravi Pendse, U-M’s vice president for information technology and chief information officer. “With Great Lakes, researchers in emerging fields like machine learning and precision health will have access to a higher level of computational power. We’re thrilled to be working with Dell EMC, Mellanox, and DDN; the end result will be improved performance, flexibility, and reliability for U-M researchers.”

“Dell EMC is thrilled to collaborate with the University of Michigan and our technology partners to bring this innovative and powerful system to such a strong community of researchers,” said Thierry Pellegrino, vice president, Dell EMC High Performance Computing. “This Great Lakes cluster will offer an exceptional boost in performance, throughput and response to reduce the time needed for U-M researches to make the next big discovery in a range of disciplines from artificial intelligence to genomics and bioscience.”

The main components of the new cluster are:

  • Dell EMC PowerEdge C6420 compute nodes, PowerEdge R640 high memory nodes, and PowerEdge R740 GPU nodes
  • Mellanox HDR 200Gb/s InfiniBand ConnectX-6 adapters, Quantum switches and LinkX cables, and InfiniBand gateway platforms
  • DDN GRIDScaler® 14KX® and 100 TB of usable IME® (Infinite Memory Engine) memory

“HDR 200G InfiniBand provides the highest data speed and smart In-Network Computing acceleration engines, delivering HPC and AI applications with the best performance, scalability and efficiency,” said Gilad Shainer, vice president of marketing at Mellanox Technologies. “We are excited to collaborate with the University of Michigan, Dell EMC and DataDirect Networks, in building a leading HDR 200G InfiniBand-based supercomputer, serving the growing demands of U-M researchers.”

“DDN has a long history of working with Dell EMC and Mellanox to deliver optimized solutions for our customers. We are happy to be a part of the new Great Lakes cluster, supporting its mission of advanced research and computing. Partnering with forward-looking thought leaders as these is always enlightening and enriching,” said Dr. James Coomer, SVP Product Marketing and Benchmarks at DDN.

Great Lakes will provide significant improvement in computing performance over Flux. For example, each compute node will have more cores, higher maximum speed capabilities, and increased memory. The cluster will also have improved internet connectivity and file system performance, as well as NVIDIA Tensor GPU cores, which are very powerful for machine learning compared to prior generations of GPUs.

“Users of Great Lakes will have access to more cores, faster cores, faster memory, faster storage, and a more balanced network,” said Brock Palen, Director of Advanced Research Computing – Technology Services (ARC-TS).

The Flux cluster was created approximately 8 years ago, although many of the individual nodes have been added since then. Great Lakes represents an architectural overhaul that will result in better performance and efficiency. Based on extensive input from faculty and other stakeholders across campus, the new Great Lakes cluster will be designed to deliver similar services and capabilities as Flux, including the ability to accommodate faculty purchases of hardware, access to GPUs and large-memory nodes, and improved support for emerging uses such as machine learning and genomics.

ARC-TS will operate and maintain the cluster once it is built. Allocations of computing resources through ARC-TS include access to hundreds of software titles, as well as support and consulting from professional staff with decades of combined experience in research computing.

Updates on the progress of Great Lakes will be available at https://arc-ts.umich.edu/greatlakes/.

ARC-TS begins work on new “Great Lakes” cluster to replace Flux

By | Flux, Happenings, HPC, News

Advanced Research Computing – Technology Services (ARC-TS) is starting the process of creating a new, campus-wide computing cluster, “Great Lakes,” that will serve the broad needs of researchers across the University. Over time, Great Lakes will replace Flux, the shared research computing cluster that currently serves over 300 research projects and 2,500 active users.

“Researchers will see improved performance, flexibility and reliability associated with newly purchased hardware, as well as changes in policies that will result in greater efficiencies and ease of use,” said Brock Palen, director of ARC-TS.

The Great Lakes cluster will be available to all researchers on campus for simulation, modeling, machine learning, data science, genomics, and more. The platform will provide a balanced combination of computing power, I/O performance, storage capability, and accelerators.

ARC-TS is in the process of procuring the cluster. Only minimal interruption to ongoing research is expected. A “Beta” cluster will be available to help researchers learn the new system before Great Lakes is deployed in the first half of 2019.

The Flux cluster is approximately 8 years old, although many of the individual nodes are newer. One of the benefits of replacing the cluster is to create a more homogeneous platform.

Based on extensive input from faculty and other stakeholders across campus, the new Great Lakes cluster will be designed to deliver similar services and capabilities as Flux, including the ability to accommodate faculty purchases of hardware, access to GPUs and large-memory nodes, and improved support for emerging uses such as machine learning and genomics. The cluster will consist of approximately 20,000 cores.

For more information, contact hpc-support@umich.edu, and see arc-ts.umich.edu/systems-services/greatlakes, where updates to the project will be posted.

CSCAR provides walk-in support for new Flux users

By | Data, Educational, Flux, General Interest, HPC, News

CSCAR now provides walk-in support during business hours for students, faculty, and staff seeking assistance in getting started with the Flux computing environment.  CSCAR consultants can walk a researcher through the steps of applying for a Flux account, installing and configuring a terminal client, connecting to Flux, basic SSH and Unix command line, and obtaining or accessing allocations.  

In addition to walk-in support, CSCAR has several staff consultants with expertise in advanced and high performance computing who can work with clients on a variety of topics such as installing, optimizing, and profiling code.  

Support via email is also provided via hpc-support@umich.edu.  

CSCAR is located in room 3550 of the Rackham Building (915 E. Washington St.). Walk-in hours are from 9 a.m. – 5 p.m., Monday through Friday, except for noon – 1 p.m. on Tuesdays.

See the CSCAR web site (cscar.research.umich.edu) for more information.

ARC-TS seeks input on next generation HPC cluster

By | Events, Flux, General Interest, Happenings, HPC, News

The University of Michigan is beginning the process of building our next generation HPC platform, “Big House.”  Flux, the shared HPC cluster, has reached the end of its useful life. Flux has served us well for more than five years, but as we move forward with replacement, we want to make sure we’re meeting the needs of the research community.

ARC-TS will be holding a series of town halls to take input from faculty and researchers on the next HPC platform to be built by the University.  These town halls are open to anyone and will be held at:

  • College of Engineering, Johnson Room, Tuesday, June 20th, 9:00a – 10:00a
  • NCRC Bldg 300, Room 376, Wednesday, June 21st, 11:00a – 12:00p
  • LSA #2001, Tuesday, June 27th, 10:00a – 11:00a
  • 3114 Med Sci I, Wednesday, June 28th, 2:00p – 3:00p

Your input will help to ensure that U-M is on course for providing HPC, so we hope you will make time to attend one of these sessions. If you cannot attend, please email hpc-support@umich.edu with any input you want to share.

U-M team uses Flux HPC cluster for pre-surgery simulations

By | Flux, General Interest, News

Last summer, Alberto Figueroa’s BME lab at the University of Michigan achieved an important “first” – using computer-generated blood flow simulations to plan a complex cardiovascular procedure.

“I believe this is the first time that virtual surgical planning was done for real and not as a retrospective theoretical exercise ,” says Figueroa.

Using a patient’s medical and imaging data, Figueroa was able to create a model of her unique vasculature and blood flow, then use it to guide U-M pediatric cardiologists Aimee Armstrong, Martin Bocks, and Adam Dorfman in placing a graft in her inferior vena cava to help alleviate complications from pulmonary arteriovenous malformations (PAVMs). The simulations were done using the Flux HPC cluster.

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