Sequoia Supercomputer Pumps Up Heart Research

By Tiffany Trader

October 24, 2012

Cardioid code image

The Cardioid code developed by a team of Livermore and IBM scientists divides the heart into a large number of manageable pieces, or subdomains. The development team used two approaches, called Voronoi (left) and grid (right), to break the enormous computing challenge into much smaller individual tasks. Source: LLNL

The world’s fastest computer has created the fastest computer simulation of the human heart.

The Lawrence Livermore National Laboratory’s Sequoia supercomputer, a TOP500 chart topper, was built to handle top secret nuclear weapons simulations, but before it goes behind the classified curtain, it is pumping out sophisticated cardiac simulations.

Earlier this month, Sequoia, which currently ranks number one on the TOP500 list of the world’s fastest computer systems, received a 2012 Breakthrough Award from Popular Mechanics magazine. Now the magazine is reporting on Sequoia’s ground-breaking heart simulations.

Clocking in at 16.32 sustained petaflops (20 PF peak), Sequoia is taking modeling and simulation to new heights, enabling researchers to capture greater complexity in a shorter time frame. With this advanced capability, LLNL scientists have been able to simulate the human heart down to the cellular level and use the resulting model to predict how the organ will respond to different drug compounds.

Principal investigator Dave Richards couldn’t resist a little showboating: “Other labs are working on similar models for many body systems, including the heart,” he told Popular Mechanics. “But Lawrence Livermore’s model has one major advantage: It runs on Sequoia, the most powerful supercomputer in the world and a recent PM Breakthrough Award winner.”

The simulations were made possible by an advanced modeling program, called Cardioid, that was developed by a team of scientists from LLNL and the IBM T. J. Watson Research Center. The highly scalable code simulates the electrophysiology of the heart. It works by breaking down the heart into units; the smaller the unit, the more accurate the model.

Until now the best modeling programs could achieve 0.2 mm in each direction. Cardioid can get down to 0.1 mm. Where previously researchers could run the simulations for tens of heartbeats, Cardioid executing on Sequoia captures thousands of heartbeats.

Scientists are seeing 300-fold speedups. It used to take 45 minutes to simulate just one beat, but now researchers can simulate an hour of heart activity – several thousand heartbeats – in seven hours.

With the less sophisticated codes, it was impossible to model the heart’s response to a drug or perform an electrocardiogram trace for a particular heart disorder. That kind of testing requires longer run times, which just wasn’t possible before Cardioid.

The model could potentially test a range of drugs and devices like pacemakers to examine their affect on the heart, paving the way for safer and more effective human testing. But it is especially suited to studying arrhythmia, a disorder of the heart in which the organ does not pump blood efficiently. Arrhythmias can lead to congestive heart failure, an inability of the heart to supply sufficient blood flow to meet the needs of the body.

There are various types of medications that disrupt cardiac rhythms. Even those designed to prevent arrhythmias can be harmful to some patients, and researchers do not yet fully understand exactly what causes these negative side effects. Cardioid will enable LLNL scientists to examine heart function as an anti-arrhythmia drug enters the bloodstream. They’ll be able to identify when drug levels are highest and when they drop off.

“Observing the full range of effects produced by a particular drug takes many hours,” noted computational scientist Art Mirin of LLNL. “With Cardioid, heart simulations over this timeframe are now possible for the first time.”

The Livermore–IBM team is also working on a mechanical model that simulates the contraction of the heart and pumping of blood. The electrical and mechanical simulations will be allowed to interact with each other, adding more realism to the heart model.

It’s not entirely clear why a national defense lab took on this heart simulation work. Fred Streitz, director of the Institute for Scientific Computing Research at LLNL, would say only that “there are legitimate national security implications for understanding how drugs affect human organs,” adding that the project stretched the limits of supercomputing in a manner that is relatable to the American people.

The cardiac modeling work was performed during the system’s “shakedown period” – the set-up and testing phase – and the team had to hurry to finish in the allotted time span. Once Sequoia becomes classified, it’s unclear if it will still be available to run Cardioid and other unclassified programs, although access will certainly be more difficult since the machine’s principle mission is running nuclear weapons codes.

Sequoia is an integral part of the NNSA’s Advanced Simulation and Computing (ASC) program, which is run by partner organizations LLNL, Los Alamos National Laboratory and Sandia National Laboratories. With 96 racks, 98,304 compute nodes, 1.6 million cores, and 1.6 petabytes of memory, Sequoia will help the NNSA fulfill its mission to “maintain and enhance the safety, security, reliability and performance of the U.S. nuclear weapons stockpile without nuclear testing.”

The Cardioid simulation has been named as a finalist in the 2012 Gordon Bell Prize competition, awarded each year to recognize supercomputing’s crowning achievements. Research partners, Streitz, Richards, and Mirin, will reveal their results at the Supercomputing Conference in Salt Lake City, Utah, on November 13.

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!

Hedge Funds (with Supercomputing help) Rank First Among Investors

May 22, 2017

In case you didn’t know, The Quants Run Wall Street Now, or so says a headline in today’s Wall Street Journal. Quant-run hedge funds now control the largest Read more…

By John Russell

IBM, D-Wave Report Quantum Computing Advances

May 18, 2017

IBM said this week it has built and tested a pair of quantum computing processors, including a prototype of a commercial version. That progress follows an an Read more…

By George Leopold

PRACEdays 2017 Wraps Up in Barcelona

May 18, 2017

Barcelona has been absolutely lovely; the weather, the food, the people. I am, sadly, finishing my last day at PRACEdays 2017 with two sessions: an in-depth loo Read more…

By Kim McMahon

US, Europe, Japan Deepen Research Computing Partnership

May 18, 2017

On May 17, 2017, a ceremony was held during the PRACEdays 2017 conference in Barcelona to announce the memorandum of understanding (MOU) between PRACE in Europe Read more…

By Tiffany Trader

HPE Extreme Performance Solutions

Exploring the Three Models of Remote Visualization

The explosion of data and advancement of digital technologies are dramatically changing the way many companies do business. With the help of high performance computing (HPC) solutions and data analytics platforms, manufacturers are developing products faster, healthcare providers are improving patient care, and energy companies are improving planning, exploration, and production. Read more…

NSF, IARPA, and SRC Push into “Semiconductor Synthetic Biology” Computing

May 18, 2017

Research into how biological systems might be fashioned into computational technology has a long history with various DNA-based computing approaches explored. N Read more…

By John Russell

DOE’s HPC4Mfg Leads to Paper Manufacturing Improvement

May 17, 2017

Papermaking ranks third behind only petroleum refining and chemical production in terms of energy consumption. Recently, simulations made possible by the U.S. D Read more…

By John Russell

PRACEdays 2017: The start of a beautiful week in Barcelona

May 17, 2017

Touching down in Barcelona on Saturday afternoon, it was warm, sunny, and oh so Spanish. I was greeted at my hotel with a glass of Cava to sip and treated to a Read more…

By Kim McMahon

NSF Issues $60M RFP for “Towards a Leadership-Class” System

May 16, 2017

In case you missed it, the National Science Foundation issued the request for proposals (RFP) for the next ‘Towards a Leadership-Class Computing Facility – Read more…

By John Russell

Cray Offers Supercomputing as a Service, Targets Biotechs First

May 16, 2017

Leading supercomputer vendor Cray and datacenter/cloud provider the Markley Group today announced plans to jointly deliver supercomputing as a service. The init Read more…

By John Russell

HPE’s Memory-centric The Machine Coming into View, Opens ARMs to 3rd-party Developers

May 16, 2017

Announced three years ago, HPE’s The Machine is said to be the largest R&D program in the venerable company’s history, one that could be progressing tow Read more…

By Doug Black

What’s Up with Hyperion as It Transitions From IDC?

May 15, 2017

If you’re wondering what’s happening with Hyperion Research – formerly the IDC HPC group – apparently you are not alone, says Steve Conway, now senior V Read more…

By John Russell

Nvidia’s Mammoth Volta GPU Aims High for AI, HPC

May 10, 2017

At Nvidia's GPU Technology Conference (GTC17) in San Jose, Calif., this morning, CEO Jensen Huang announced the company's much-anticipated Volta architecture a Read more…

By Tiffany Trader

HPE Launches Servers, Services, and Collaboration at GTC

May 10, 2017

Hewlett Packard Enterprise (HPE) today launched a new liquid cooled GPU-driven Apollo platform based on SGI ICE architecture, a new collaboration with NVIDIA, a Read more…

By John Russell

IBM PowerAI Tools Aim to Ease Deep Learning Data Prep, Shorten Training 

May 10, 2017

A new set of GPU-powered AI software announced by IBM today brings automation to many of the tedious, time consuming and complex aspects of AI project on-rampin Read more…

By Doug Black

Bright Computing 8.0 Adds Azure, Expands Machine Learning Support

May 9, 2017

Bright Computing, long a prominent provider of cluster management tools for HPC, today released version 8.0 of Bright Cluster Manager and Bright OpenStack. The Read more…

By John Russell

Microsoft Azure Will Debut Pascal GPU Instances This Year

May 8, 2017

As Nvidia's GPU Technology Conference gets underway in San Jose, Calif., Microsoft today revealed plans to add Pascal-generation GPU horsepower to its Azure clo Read more…

By Tiffany Trader

Quantum Bits: D-Wave and VW; Google Quantum Lab; IBM Expands Access

March 21, 2017

For a technology that’s usually characterized as far off and in a distant galaxy, quantum computing has been steadily picking up steam. Just how close real-wo Read more…

By John Russell

Google Pulls Back the Covers on Its First Machine Learning Chip

April 6, 2017

This week Google released a report detailing the design and performance characteristics of the Tensor Processing Unit (TPU), its custom ASIC for the inference Read more…

By Tiffany Trader

Trump Budget Targets NIH, DOE, and EPA; No Mention of NSF

March 16, 2017

President Trump’s proposed U.S. fiscal 2018 budget issued today sharply cuts science spending while bolstering military spending as he promised during the cam Read more…

By John Russell

HPC Compiler Company PathScale Seeks Life Raft

March 23, 2017

HPCwire has learned that HPC compiler company PathScale has fallen on difficult times and is asking the community for help or actively seeking a buyer for its a Read more…

By Tiffany Trader

Nvidia Responds to Google TPU Benchmarking

April 10, 2017

Last week, Google reported that its custom ASIC Tensor Processing Unit (TPU) was 15-30x faster for inferencing workloads than Nvidia's K80 GPU (see our coverage Read more…

By Tiffany Trader

CPU-based Visualization Positions for Exascale Supercomputing

March 16, 2017

Since our first formal product releases of OSPRay and OpenSWR libraries in 2016, CPU-based Software Defined Visualization (SDVis) has achieved wide-spread adopt Read more…

By Jim Jeffers, Principal Engineer and Engineering Leader, Intel

TSUBAME3.0 Points to Future HPE Pascal-NVLink-OPA Server

February 17, 2017

Since our initial coverage of the TSUBAME3.0 supercomputer yesterday, more details have come to light on this innovative project. Of particular interest is a ne Read more…

By Tiffany Trader

Facebook Open Sources Caffe2; Nvidia, Intel Rush to Optimize

April 18, 2017

From its F8 developer conference in San Jose, Calif., today, Facebook announced Caffe2, a new open-source, cross-platform framework for deep learning. Caffe2 is Read more…

By Tiffany Trader

Leading Solution Providers

Nvidia’s Mammoth Volta GPU Aims High for AI, HPC

May 10, 2017

At Nvidia's GPU Technology Conference (GTC17) in San Jose, Calif., this morning, CEO Jensen Huang announced the company's much-anticipated Volta architecture a Read more…

By Tiffany Trader

Tokyo Tech’s TSUBAME3.0 Will Be First HPE-SGI Super

February 16, 2017

In a press event Friday afternoon local time in Japan, Tokyo Institute of Technology (Tokyo Tech) announced its plans for the TSUBAME3.0 supercomputer, which w Read more…

By Tiffany Trader

Is Liquid Cooling Ready to Go Mainstream?

February 13, 2017

Lost in the frenzy of SC16 was a substantial rise in the number of vendors showing server oriented liquid cooling technologies. Three decades ago liquid cooling Read more…

By Steve Campbell

MIT Mathematician Spins Up 220,000-Core Google Compute Cluster

April 21, 2017

On Thursday, Google announced that MIT math professor and computational number theorist Andrew V. Sutherland had set a record for the largest Google Compute Eng Read more…

By Tiffany Trader

IBM Wants to be “Red Hat” of Deep Learning

January 26, 2017

IBM today announced the addition of TensorFlow and Chainer deep learning frameworks to its PowerAI suite of deep learning tools, which already includes popular Read more…

By John Russell

HPC Technique Propels Deep Learning at Scale

February 21, 2017

Researchers from Baidu's Silicon Valley AI Lab (SVAIL) have adapted a well-known HPC communication technique to boost the speed and scale of their neural networ Read more…

By Tiffany Trader

US Supercomputing Leaders Tackle the China Question

March 15, 2017

As China continues to prove its supercomputing mettle via the Top500 list and the forward march of its ambitious plans to stand up an exascale machine by 2020, Read more…

By Tiffany Trader

DOE Supercomputer Achieves Record 45-Qubit Quantum Simulation

April 13, 2017

In order to simulate larger and larger quantum systems and usher in an age of "quantum supremacy," researchers are stretching the limits of today's most advance Read more…

By Tiffany Trader

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