New Dell Cluster Refreshes Rocky Mountain HPC

By Tiffany Trader

February 26, 2016

Researchers from the University of Colorado Boulder (CU-Boulder), Colorado State University (CSU) and the Rocky Mountain Advanced Computing Consortium will soon have access to a half-petaflop heterogeneous Dell PowerEdge C-series supercomputer. Funding for the $3.5 million project was secured through a $2.7 million grant from the National Science Foundation with the remaining amount being provided by the universities as “matching funds.”

CU-Boulder is ready for this refresh. The new 450-teraflops supercomputer, named Summit after the local topology, will replace Janus, another Dell cluster that at five-years-old is ready for retirement. The new Haswell- and GPU-based machine will be three times faster and use half as much energy as its Westmere-based predecessor.

Summit is being rolled out in two phases: the initial 450-teraflops Dell cluster, comprising high-end Xeon nodes, high-memory nodes and GPGPU nodes, is expected to arrive in late May; and a 20-node Intel Xeon Knights Landing partition is expected for late Q3. The main system will employ 22 Intel Omni-Path 48-port switches (8 core/spines) arranged into nonblocking islands of 32 compute nodes with 2:1 oversubscription between islands.

For storage, CU-Boulder and its partners will leverage IBM’s GPFS on DDN’s SFA14KE hyper-converged storage appliance. Packed with 350 4TB drives, there is a total of 1PB usable storage with room for another 1PB of growth capacity.

CU-Boulder opted for the SFA 14KE, DDN’s hyper-converged solution, because of its price/performance relative to the specs needed for the expected workloads.  They have a relatively modest number of GPFS client nodes, so didn’t require a ton of huge fleet of NSD server systems. As we reported in November, the SFA 14K series natively supports Intel’s Omni-Path Architecture (OPA).

While the KNL component is relatively small, Pete Ruprecht, CU-Boulder senior HPC analyst and co-PI of the project, said he is looking forward to using the hardware for proof-of-concept work in tandem with local partners, including the Intel Parallel Computing Center and NCAR, the atmospheric research facility that has massive weather and climate applications. “This will be a great opportunity to begin porting codes onto the KNL manycore architecture,” said Ruprecht.

Although the KNL partition is not expected until the fall, there is already talk about offering access to that portion of the cluster to XSEDE, so that those researchers can begin preparing their codes for the coming generation of larger KNL-systems, such as Cori (at NERSC) and Aurora (at ALCF).

Enthusiastic as to the potential of the socketed Knights Landing, Ruprecht, who led the technical aspect of the NSF grant and the RFP process by which they designed and procured the machine, characterized his experience with the original Phi coprocessor as “only modestly successful.”

“With GPGPU, we’ve had quite good results with people running applications that were designed for the GPU environment allowing them to just download and compile with CUDA. Not too many of our users develop their own GPU software,” he shared. “There’s not the same kind of support in terms of existing software base for Phi right now, so it’s been confined to our more sophisticated users to be able to even try using the Phi coprocessors. From an administrative point of view, having an operating system within an operating system is pretty hard to deal with. I think the advantages of having the Phi directly in the motherboard in the main processor socket make a lot of those concerns go away.”

“Our niche is to be an entry point into really large scale computing and if it’s too difficult for people they just won’t make that step,” added Ruprecht.

This concern over ease-of-use is shared by many in the research computing space. When San Diego Supercomputer Center (SDSC) got their Dell C-Series cluster “Comet” last year, the stakeholders referred to the project as “supercomputing for the 99 percent” highlighting the necessity of serving a large number of researchers who don’t have the resources to build their own cluster. TACC’s Wrangler machine was hatched with a similar mandate.

Like other HPC-capable institutions, CU-Boulder is moving to support more of a mixed workload model. Ruprecht reports that their existing cluster was designed for Linpack-like applications.

“Going forward, we need to expand the breadth of applications beyond that,” he said, “so we are doubling the amount of RAM per core, putting an SSD in each node to help support file-intensive applications that we see in the life sciences, and we are going to use GPFS for the scratch file system because we’ve had pretty clear indications that it will be better for file operation-intensive workloads, which we see with these data-type applications, in comparison with Lustre, which is a more traditional large-file parallel I/O.”

The system will serve more than 1,000 users at CU-Boulder in addition to the CSU and the Rocky Mountain Advanced Computing Consortium contingent. The CU user base is drawn from every college on the campus. The heaviest users are the usual suspects in engineering, astrophysics, material science, although demand is ramping up from fields such as economics, geography and life sciences with many genomics researchers anticipated from the CSU campus.

The system will follow a standard allocated, scheduled model with 10 percent of cycles going to RMACC, and of the remaining portion, two-thirds will go to CU-Boulder and the remaining one-third to CSU. “We will continue with our existing SLURM setup to be able to support wide jobs as well as single-core jobs,” said Ruprecht. “One thing that is different is that we will allow jobs to share nodes so we’ll have a more high-throughput workflow so many little jobs can run through a single core.”

“Our goal is to support both the larger and smaller workflows and we’ll have to do some reconfiguration of the scheduling system but it’s nothing that SLURM can’t handle,” he continued. “We have right now in our current system everything from multi-hundred node jobs down to single node jobs and they all just fit together.”

CU-Boulder is hoping to take delivery of Summit in late May, pending availability of the Omni-Path switches, which have seen a several month delay. Deployment will necessarily be accelerated and compressed on account of that pushing out of general availability. From delivery to acceptance to production, the CU staff is looking at a narrow window of about two months, yet there is a pressing need to rise to the occasion as their current cluster is going off support and will not be able to meet their needs for much longer.

In their favor, CU-Boulder is an early access customer for Omni-Path and Summit is expected to be one of the first large clusters to go into production with the interconnect.

Here’s a further breakdown of the architecture involved:

Phase 1:

  • 370 PowerEdge C6320 server nodes with two-socket Haswell E5-2680v3 processors (12-core, 2.5Ghz)
  • 5 PowerEdge R930 high-memory nodes with four-socket E7-4830v3 processors with 2 TB RAM
  • 10 PowerEdge C4130 GPU nodes with 2x K80
  • 22 OPA 48-port switches
  • GPFS scratch storage – DDN SFA 14KE – 350 4TB drives

Phase 2:

  • 20 Phi nodes with socketed Knights Landing, dual on-die Omni-Path per node
Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

IBM Touts OpenPOWER Ecosystem, Announces New Customers, Products for AI and Hyperscale

March 20, 2018

At SC17 in Denver four months ago, Ken King, GM, OpenPOWER, IBM Systems Group, told a somewhat jaundiced trio of journalists that 2018 would, finally, after several years of expectations, be the year OpenPOWER and IBM’ Read more…

By Doug Black

Deep Learning at 15 PFlops Enables Training for Extreme Weather Identification at Scale

March 19, 2018

Petaflop per second deep learning training performance on the NERSC (National Energy Research Scientific Computing Center) Cori supercomputer has given climate scientists the ability to use machine learning to identify e Read more…

By Rob Farber

Mellanox Reacts to Activist Investor Pressures in Letter to Shareholders

March 16, 2018

Activist investor Starboard Value has been exerting pressure on Mellanox Technologies to increase its returns. In response, the high-performance networking company on Monday, March 12, published a letter to shareholders outlining its proposal for a May 2018 extraordinary general meeting (EGM) of shareholders and highlighting its long-term growth strategy and focus on operating margin improvement. Read more…

By Staff

HPE Extreme Performance Solutions

Harness the Full Power of HPC Servers with an Effective Cooling Approach

High performance computing (HPC) innovation is rapidly transforming the way we operate – with an onslaught of cutting-edge technologies designed to optimize applications and workloads, increase productivity, and enable better business outcomes. Read more…

Quantum Computing vs. Our ‘Caveman Newtonian Brain’: Why Quantum Is So Hard

March 15, 2018

Quantum is coming. Maybe not today, maybe not tomorrow, but soon enough. Within 10 to 12 years, we’re told, special-purpose quantum systems will enter the commercial realm. Assuming this happens, we can also assume that quantum will, over extended time, become increasingly general purpose as it delivers mind-blowing power. Read more…

By Doug Black

IBM Touts OpenPOWER Ecosystem, Announces New Customers, Products for AI and Hyperscale

March 20, 2018

At SC17 in Denver four months ago, Ken King, GM, OpenPOWER, IBM Systems Group, told a somewhat jaundiced trio of journalists that 2018 would, finally, after sev Read more…

By Doug Black

Deep Learning at 15 PFlops Enables Training for Extreme Weather Identification at Scale

March 19, 2018

Petaflop per second deep learning training performance on the NERSC (National Energy Research Scientific Computing Center) Cori supercomputer has given climate Read more…

By Rob Farber

How the Cloud Is Falling Short for HPC

March 15, 2018

The last couple of years have seen cloud computing gradually build some legitimacy within the HPC world, but still the HPC industry lies far behind enterprise I Read more…

By Chris Downing

Stephen Hawking, Legendary Scientist, Dies at 76

March 14, 2018

Stephen Hawking passed away at his home in Cambridge, England, in the early morning of March 14; he was 76. Born on January 8, 1942, Hawking was an English theo Read more…

By Tiffany Trader

Hyperion Tackles Elusive Quantum Computing Landscape

March 13, 2018

Quantum computing - exciting and off-putting all at once - is a kaleidoscope of technology and market questions whose shapes and positions are far from settled. Read more…

By John Russell

Part Two: Navigating Life Sciences Choppy HPC Waters in 2018

March 8, 2018

2017 was not necessarily the best year to build a large HPC system for life sciences say Ari Berman, VP and GM of consulting services, and Aaron Gardner, direct Read more…

By John Russell

Google Chases Quantum Supremacy with 72-Qubit Processor

March 7, 2018

Google pulled ahead of the pack this week in the race toward "quantum supremacy," with the introduction of a new 72-qubit quantum processor called Bristlecone. Read more…

By Tiffany Trader

SciNet Launches Niagara, Canada’s Fastest Supercomputer

March 5, 2018

SciNet and the University of Toronto today unveiled "Niagara," Canada's most-powerful supercomputer, comprising 1,500 dense Lenovo ThinkSystem SD530 high-perfor Read more…

By Tiffany Trader

Inventor Claims to Have Solved Floating Point Error Problem

January 17, 2018

"The decades-old floating point error problem has been solved," proclaims a press release from inventor Alan Jorgensen. The computer scientist has filed for and Read more…

By Tiffany Trader

Japan Unveils Quantum Neural Network

November 22, 2017

The U.S. and China are leading the race toward productive quantum computing, but it's early enough that ultimate leadership is still something of an open questi Read more…

By Tiffany Trader

Researchers Measure Impact of ‘Meltdown’ and ‘Spectre’ Patches on HPC Workloads

January 17, 2018

Computer scientists from the Center for Computational Research, State University of New York (SUNY), University at Buffalo have examined the effect of Meltdown Read more…

By Tiffany Trader

IBM Begins Power9 Rollout with Backing from DOE, Google

December 6, 2017

After over a year of buildup, IBM is unveiling its first Power9 system based on the same architecture as the Department of Energy CORAL supercomputers, Summit a Read more…

By Tiffany Trader

Fast Forward: Five HPC Predictions for 2018

December 21, 2017

What’s on your list of high (and low) lights for 2017? Volta 100’s arrival on the heels of the P100? Appearance, albeit late in the year, of IBM’s Power9? Read more…

By John Russell

Russian Nuclear Engineers Caught Cryptomining on Lab Supercomputer

February 12, 2018

Nuclear scientists working at the All-Russian Research Institute of Experimental Physics (RFNC-VNIIEF) have been arrested for using lab supercomputing resources to mine crypto-currency, according to a report in Russia’s Interfax News Agency. Read more…

By Tiffany Trader

Nvidia Responds to Google TPU Benchmarking

April 10, 2017

Nvidia highlights strengths of its newest GPU silicon in response to Google's report on the performance and energy advantages of its custom tensor processor. Read more…

By Tiffany Trader

Chip Flaws ‘Meltdown’ and ‘Spectre’ Loom Large

January 4, 2018

The HPC and wider tech community have been abuzz this week over the discovery of critical design flaws that impact virtually all contemporary microprocessors. T Read more…

By Tiffany Trader

Leading Solution Providers

GlobalFoundries, Ayar Labs Team Up to Commercialize Optical I/O

December 4, 2017

GlobalFoundries (GF) and Ayar Labs, a startup focused on using light, instead of electricity, to transfer data between chips, today announced they've entered in Read more…

By Tiffany Trader

How Meltdown and Spectre Patches Will Affect HPC Workloads

January 10, 2018

There have been claims that the fixes for the Meltdown and Spectre security vulnerabilities, named the KPTI (aka KAISER) patches, are going to affect applicatio Read more…

By Rosemary Francis

Perspective: What Really Happened at SC17?

November 22, 2017

SC is over. Now comes the myriad of follow-ups. Inboxes are filled with templated emails from vendors and other exhibitors hoping to win a place in the post-SC thinking of booth visitors. Attendees of tutorials, workshops and other technical sessions will be inundated with requests for feedback. Read more…

By Andrew Jones

V100 Good but not Great on Select Deep Learning Aps, Says Xcelerit

November 27, 2017

Wringing optimum performance from hardware to accelerate deep learning applications is a challenge that often depends on the specific application in use. A benc Read more…

By John Russell

Lenovo Unveils Warm Water Cooled ThinkSystem SD650 in Rampup to LRZ Install

February 22, 2018

This week Lenovo took the wraps off the ThinkSystem SD650 high-density server with third-generation direct water cooling technology developed in tandem with par Read more…

By Tiffany Trader

AMD Wins Another: Baidu to Deploy EPYC on Single Socket Servers

December 13, 2017

When AMD introduced its EPYC chip line in June, the company said a portion of the line was specifically designed to re-invigorate a single socket segment in wha Read more…

By John Russell

World Record: Quantum Computer with 46 Qubits Simulated

December 18, 2017

Scientists from the Jülich Supercomputing Centre have set a new world record. Together with researchers from Wuhan University and the University of Groningen, Read more…

New Blueprint for Converging HPC, Big Data

January 18, 2018

After five annual workshops on Big Data and Extreme-Scale Computing (BDEC), a group of international HPC heavyweights including Jack Dongarra (University of Te Read more…

By John Russell

  • arrow
  • Click Here for More Headlines
  • arrow
Share This