SDSC’s ‘Trestles’ Supercomputer Still Going Strong Three+ Years Later

By Jan Zverina

December 21, 2018

Supercomputers typically have a useful life of about five years, as these high-performance systems, many running 24/7, slowly succumb to burn-out – of their nodes, that is – as well as steady advances in processing technologies.

Not so with Trestles, which was acquired more than three years ago by the Arkansas High Performance Computing Center (AHPCC) at the University of Arkansas after entering service at the San Diego Supercomputer Center (SDSC) at UC San Diego in mid-2011 under a $2.8 million National Science Foundation (NSF) grant.

(L to R) AHPCC Director David Chaffin; Director of Strategic Initiatives & User Services Jeff Pummill; and Senior Administrator/Program Director Pawel Wolinski, with the Trestles supercomputer. Image courtesy of AHPCC

Billed as a “high-productivity workhorse,” Trestles was based on the concept that by tailoring a system for the majority of modest-scale jobs rather than a handful of researchers who run jobs at thousands of core counts, users could achieve higher throughput and increased scientific productivity.

While at SDSC, Trestles users spanned a wide range of domain applications, including astronomy, biophysics, climate science, computational chemistry, materials science, and more. It was also recognized as a leading platform for science gateway applications; for example, the system served more than 650 users per month via the popular CIPRES phylogenetics portal alone.

“It’s terrific that University of Arkansas researchers have been able to use Trestles for several years beyond its decommissioning as a national NSF resource and to extend the scientific impact of NSF’s HPC investments,” said Richard Moore, the principal investigator for the Trestles award and SDSC’s now-retired deputy director.

Trestles continues to deliver on that strategy today, more than three years into its “next life” as a valuable research resource at the U of A. AHPCC’s latest estimates are that during that time, Trestles has provided more than 136 million CPU hours of service, with over 804,000 jobs run among almost 200 active users.

Trestles came to us at a time where computational needs were peaking in the form of explosive growth and demand in the faculty researcher community,” said AHPCC Director of Strategic Initiatives & User Services Jeff Pummill, who is also a Trestles user in the area of multi-omics, primarily with the U of A’s Biological Sciences and Agricultural departments. “Queue wait times were getting unacceptably long and jobs were stacking up. So the arrival of 8000+ compute cores was a welcome sight for all of us.”

Pummill noted that architecturally, Trestles has been ideal for work in the areas of bioinformatics and genomics, as its software is typically Shared Memory Parallel (SMP), which uses multiple processors on the same computer, as opposed to Distributed Memory Parallel (DMP), which uses multiple processors on either the same or multiple computers. “Trestles’ nodes are configured with 32 compute cores and 64 gigs of memory, which is ideal for smaller bacterial genome work, but useful for many aspects of larger eukaryotic genome work,” he added.


What’s in a name? Some Trestles Trivia

After being transferred to the Arkansas High Performance Computing Center, it was decided to keep the Trestles name. But why Trestles in the first place?

“I was taking up surfing at the time we proposed this system to the NSF, and thought that the Trestles Bridge in San Diego would be a nice way to acknowledge both the local aspect of the system, as well as the idea that it was a bridge to using high-performance computing,” according to Shawn Strande, SDSC’s deputy director.


Research Highlights

Some examples of research projects using Trestles at the U of A include:

  • Materials Engineering: A research team including Salvador Barraza-Lopez, associate professor of physics at the U of A, and Taneshwor Kaloni, a former post-doctoral researcher in Barraza-Lopez’s lab, shed light on the behavior of one of ultrathin materials known as tin telluride (SnTe). The study detailing their findings was published in the journal Advanced Materials.
  • Neurosciences: Vidit Agrawal, a graduate student in the U of A’s Physics Department has been using Trestles to perform simulations of large neural networks and conduct a statistical analysis on experimental results.
  • Supply chain analysis: Agrawal has also used Trestles to investigate the structural fragility of supply networks and explore its relationship with a firm’s equity risk. “AHPCC has been of great help to me as it has cut down my overall computation time from months to days.”
  • Microbiome research: Jiangchao Zhao, an assistant professor with the U of A’s Department of Animal Science, used Trestles to identify gut microbiome signatures that when associated with longevity provides a promising modulation target for healthy aging.

Additional research projects can be found here.

Re-use, Not Recycling

While many supercomputers still end up on the scrap heap, the continued operation of Trestles beyond its expected lifespan is just one example of lasting computational power and productivity.

In early 2017, SDSC and the Simons Foundation’s Flatiron Institute in New York reached an agreement under which the majority of SDSC’s data-intensive Gordon supercomputer would be used by Simons for ongoing research following completion of the system’s tenure as a NSF resource on March 31 of that year, following five years of service. While Gordon is now primarily used by the Simons Foundation, the system remains housed in SDSC’s data center.

“It’s very gratifying to see SDSC’s HPC systems continue to serve a wide range of researchers following their NSF tenures,” said SDSC Director Michael Norman. “For us, it’s testimony to designing a robust architecture from the start, which contributes to their useful lives well beyond what’s typical for such systems.”

In early 2018, the NSF extended the use of SDSC’s current petascale system, Comet, for a sixth year of service, into March of 2021. Comet is now one of the most widely used supercomputers in the NSF’s XSEDE program. Under a separate NSF award valued at about $900,000 SDSC recently doubled the number of graphic processing units (GPUs) on Comet in direct response to growing demand for GPU computing among a wide range of research domains.

About AHPCC

The Arkansas High Performance Computing Center, a core research facility under the Office of Research and Innovation at the University of Arkansas and founded in 2008, supports research for about 260 users in about 30 academic areas across the University of Arkansas campus, including bioinformatics, condensed matter physics, integrated nanoscience, computational chemistry, computational biomagnetics, materials science, spatial science, and economics among others.

About SDSC

As an Organized Research Unit of UC San Diego, SDSC is considered a leader in data-intensive computing and cyberinfrastructure, providing resources, services, and expertise to the national research community, including industry and academia. Cyberinfrastructure refers to an accessible, integrated network of computer-based resources and expertise, focused on accelerating scientific inquiry and discovery. SDSC supports hundreds of multidisciplinary programs spanning a wide variety of domains, from earth sciences and biology to astrophysics, bioinformatics, and health IT. SDSC’s petascale Comet supercomputer is a key resource within the National Science Foundation’s XSEDE (eXtreme Science and Engineering Discovery Environment) program.

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!

GigaIO Gets $14.7M in Series B Funding to Expand Its Composable Fabric Technology to Customers

September 16, 2021

Just before the COVID-19 pandemic began in March 2020, GigaIO introduced its Universal Composable Fabric technology, which allows enterprises to bring together any HPC and AI resources and integrate them with networking, Read more…

What’s New in HPC Research: Solar Power, ExaWorks, Optane & More

September 16, 2021

In this regular feature, HPCwire highlights newly published research in the high-performance computing community and related domains. From parallel programming to exascale to quantum computing, the details are here. Read more…

Cerebras Brings Its Wafer-Scale Engine AI System to the Cloud

September 16, 2021

Five months ago, when Cerebras Systems debuted its second-generation wafer-scale silicon system (CS-2), co-founder and CEO Andrew Feldman hinted of the company’s coming cloud plans, and now those plans have come to fruition. Today, Cerebras and Cirrascale Cloud Services are launching... Read more…

AI Hardware Summit: Panel on Memory Looks Forward

September 15, 2021

What will system memory look like in five years? Good question. While Monday's panel, Designing AI Super-Chips at the Speed of Memory, at the AI Hardware Summit, tackled several topics, the panelists also took a brief glimpse into the future. Unlike compute, storage and networking, which... Read more…

ECMWF Opens Bologna Datacenter in Preparation for Atos Supercomputer

September 14, 2021

In January 2020, the European Centre for Medium-Range Weather Forecasts (ECMWF) – a juggernaut in the weather forecasting scene – signed a four-year, $89-million contract with European tech firm Atos to quintuple its supercomputing capacity. With the deal approaching the two-year mark, ECMWF... Read more…

AWS Solution Channel

Supporting Climate Model Simulations to Accelerate Climate Science

The Amazon Sustainability Data Initiative (ASDI), AWS is donating cloud resources, technical support, and access to scalable infrastructure and fast networking providing high performance computing (HPC) solutions to support simulations of near-term climate using the National Center for Atmospheric Research (NCAR) Community Earth System Model Version 2 (CESM2) and its Whole Atmosphere Community Climate Model (WACCM). Read more…

Quantum Computer Market Headed to $830M in 2024

September 13, 2021

What is one to make of the quantum computing market? Energized (lots of funding) but still chaotic and advancing in unpredictable ways (e.g. competing qubit technologies), the quantum computing landscape is transforming Read more…

Cerebras Brings Its Wafer-Scale Engine AI System to the Cloud

September 16, 2021

Five months ago, when Cerebras Systems debuted its second-generation wafer-scale silicon system (CS-2), co-founder and CEO Andrew Feldman hinted of the company’s coming cloud plans, and now those plans have come to fruition. Today, Cerebras and Cirrascale Cloud Services are launching... Read more…

AI Hardware Summit: Panel on Memory Looks Forward

September 15, 2021

What will system memory look like in five years? Good question. While Monday's panel, Designing AI Super-Chips at the Speed of Memory, at the AI Hardware Summit, tackled several topics, the panelists also took a brief glimpse into the future. Unlike compute, storage and networking, which... Read more…

ECMWF Opens Bologna Datacenter in Preparation for Atos Supercomputer

September 14, 2021

In January 2020, the European Centre for Medium-Range Weather Forecasts (ECMWF) – a juggernaut in the weather forecasting scene – signed a four-year, $89-million contract with European tech firm Atos to quintuple its supercomputing capacity. With the deal approaching the two-year mark, ECMWF... Read more…

Quantum Computer Market Headed to $830M in 2024

September 13, 2021

What is one to make of the quantum computing market? Energized (lots of funding) but still chaotic and advancing in unpredictable ways (e.g. competing qubit tec Read more…

Amazon, NCAR, SilverLining Team for Unprecedented Cloud Climate Simulations

September 10, 2021

Earth’s climate is, to put it mildly, not in a good place. In the wake of a damning report from the Intergovernmental Panel on Climate Change (IPCC), scientis Read more…

After Roadblocks and Renewals, EuroHPC Targets a Bigger, Quantum Future

September 9, 2021

The EuroHPC Joint Undertaking (JU) was formalized in 2018, beginning a new era of European supercomputing that began to bear fruit this year with the launch of several of the first EuroHPC systems. The undertaking, however, has not been without its speed bumps, and the Union faces an uphill... Read more…

How Argonne Is Preparing for Exascale in 2022

September 8, 2021

Additional details came to light on Argonne National Laboratory’s preparation for the 2022 Aurora exascale-class supercomputer, during the HPC User Forum, held virtually this week on account of pandemic. Exascale Computing Project director Doug Kothe reviewed some of the 'early exascale hardware' at Argonne, Oak Ridge and NERSC (Perlmutter), while Ti Leggett, Deputy Project Director & Deputy Director... Read more…

IBM Introduces its First Power10-based Server, the Power E1080; Targets Hybrid Cloud

September 8, 2021

IBM today introduced the Power E1080 server, its first system powered by a Power10 IBM microprocessor. The new system reinforces IBM’s emphasis on hybrid cloud markets and the new chip beefs up its inference capabilities. IBM – like other CPU makers – is hoping to make inferencing a core capability... Read more…

Ahead of ‘Dojo,’ Tesla Reveals Its Massive Precursor Supercomputer

June 22, 2021

In spring 2019, Tesla made cryptic reference to a project called Dojo, a “super-powerful training computer” for video data processing. Then, in summer 2020, Tesla CEO Elon Musk tweeted: “Tesla is developing a [neural network] training computer called Dojo to process truly vast amounts of video data. It’s a beast! … A truly useful exaflop at de facto FP32.” Read more…

Berkeley Lab Debuts Perlmutter, World’s Fastest AI Supercomputer

May 27, 2021

A ribbon-cutting ceremony held virtually at Berkeley Lab's National Energy Research Scientific Computing Center (NERSC) today marked the official launch of Perlmutter – aka NERSC-9 – the GPU-accelerated supercomputer built by HPE in partnership with Nvidia and AMD. Read more…

Google Launches TPU v4 AI Chips

May 20, 2021

Google CEO Sundar Pichai spoke for only one minute and 42 seconds about the company’s latest TPU v4 Tensor Processing Units during his keynote at the Google I Read more…

Esperanto, Silicon in Hand, Champions the Efficiency of Its 1,092-Core RISC-V Chip

August 27, 2021

Esperanto Technologies made waves last December when it announced ET-SoC-1, a new RISC-V-based chip aimed at machine learning that packed nearly 1,100 cores onto a package small enough to fit six times over on a single PCIe card. Now, Esperanto is back, silicon in-hand and taking aim... Read more…

Enter Dojo: Tesla Reveals Design for Modular Supercomputer & D1 Chip

August 20, 2021

Two months ago, Tesla revealed a massive GPU cluster that it said was “roughly the number five supercomputer in the world,” and which was just a precursor to Tesla’s real supercomputing moonshot: the long-rumored, little-detailed Dojo system. “We’ve been scaling our neural network training compute dramatically over the last few years,” said Milan Kovac, Tesla’s director of autopilot engineering. Read more…

CentOS Replacement Rocky Linux Is Now in GA and Under Independent Control

June 21, 2021

The Rocky Enterprise Software Foundation (RESF) is announcing the general availability of Rocky Linux, release 8.4, designed as a drop-in replacement for the soon-to-be discontinued CentOS. The GA release is launching six-and-a-half months after Red Hat deprecated its support for the widely popular, free CentOS server operating system. The Rocky Linux development effort... Read more…

Intel Completes LLVM Adoption; Will End Updates to Classic C/C++ Compilers in Future

August 10, 2021

Intel reported in a blog this week that its adoption of the open source LLVM architecture for Intel’s C/C++ compiler is complete. The transition is part of In Read more…

Iran Gains HPC Capabilities with Launch of ‘Simorgh’ Supercomputer

May 18, 2021

Iran is said to be developing domestic supercomputing technology to advance the processing of scientific, economic, political and military data, and to strengthen the nation’s position in the age of AI and big data. On Sunday, Iran unveiled the Simorgh supercomputer, which will deliver.... Read more…

Leading Solution Providers

Contributors

AMD-Xilinx Deal Gains UK, EU Approvals — China’s Decision Still Pending

July 1, 2021

AMD’s planned acquisition of FPGA maker Xilinx is now in the hands of Chinese regulators after needed antitrust approvals for the $35 billion deal were receiv Read more…

Hot Chips: Here Come the DPUs and IPUs from Arm, Nvidia and Intel

August 25, 2021

The emergence of data processing units (DPU) and infrastructure processing units (IPU) as potentially important pieces in cloud and datacenter architectures was Read more…

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been i Read more…

Julia Update: Adoption Keeps Climbing; Is It a Python Challenger?

January 13, 2021

The rapid adoption of Julia, the open source, high level programing language with roots at MIT, shows no sign of slowing according to data from Julialang.org. I Read more…

HPE Wins $2B GreenLake HPC-as-a-Service Deal with NSA

September 1, 2021

In the heated, oft-contentious, government IT space, HPE has won a massive $2 billion contract to provide HPC and AI services to the United States’ National Security Agency (NSA). Following on the heels of the now-canceled $10 billion JEDI contract (reissued as JWCC) and a $10 billion... Read more…

Intel Launches 10nm ‘Ice Lake’ Datacenter CPU with Up to 40 Cores

April 6, 2021

The wait is over. Today Intel officially launched its 10nm datacenter CPU, the third-generation Intel Xeon Scalable processor, codenamed Ice Lake. With up to 40 Read more…

Quantum Roundup: IBM, Rigetti, Phasecraft, Oxford QC, China, and More

July 13, 2021

IBM yesterday announced a proof for a quantum ML algorithm. A week ago, it unveiled a new topology for its quantum processors. Last Friday, the Technical Univer Read more…

Frontier to Meet 20MW Exascale Power Target Set by DARPA in 2008

July 14, 2021

After more than a decade of planning, the United States’ first exascale computer, Frontier, is set to arrive at Oak Ridge National Laboratory (ORNL) later this year. Crossing this “1,000x” horizon required overcoming four major challenges: power demand, reliability, extreme parallelism and data movement. Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire