Researchers Redesigned Cardiod’s Heartbeat Simulation Code

June 12, 2019

June 12, 2019 — A team of Lawrence Livermore National Laboratory (LLNL) researchers has successfully optimized a code that models the human heartbeat for next-generation, graphics processing unit (GPU)-based supercomputers, with an eye on developing it for virtual drug screening and modeling heart activity in clinical settings.

A still from a Cardioid simulation shows the electrical activation of the heart. The colors correspond to the voltage difference across the cardiac cell membrane. Nearby cells signal each other in a propagating electrical wave much like a nerve cell, allowing the heart to coordinate its contraction. Image courtesy of Lawrence Livermore National Laboratory. 

Cardioid, a suite merging mathematical solvers for electrophysiology, fiber-generation, cardiac mechanics, torso-electrocardiograms (ECGs) and cardiac meshing tools, simulates the electrical current running through the heart tissue, triggering cells to contract like cascading dominoes and causing the heart to beat. It was originally developed by LLNL and IBM for Sequoia, at one time the world’s fastest supercomputer, and was a finalist for the 2012 Gordon Bell Prize, supercomputing’s top honor.

LLNL computational scientist David Richards, one of the original Cardioid developers, recalled that “competing for the Gordon Bell Prize meant customizing the code to take advantage of every bit of performance Sequoia could offer. The resulting code was very fast, but it also was specific to Sequoia and wasn’t portable to other computers.”

When LLNL computer scientist Rob Blake came to the Lab in 2016, he was tasked with porting the code over to the heterogenous CPU/GPU systems that would displace Sequoia: Sierra and its unclassified counterpart, Lassen. Blake was one of the founders of a company called Cardiosolv, which used magnetic resonance imaging (MRI) data to model the heart. Cardioid was a good test case for a GPU-based system, Blake said, because the ordinary differential equations (ODEs) required to model the simulation’s 400 million cells — roughly one-fifth of the entire number of cells in the human heart — already were “embarrassingly parallel.”

With help from IBM through the institutional Center of Excellence, Blake and his team set out to release Cardioid as open source and to generalize the code for the new supercomputing systems, redesigning the code to be portable as well as fast. He wrote a language called Melody to describe the differential equations used by the solvers to model the heart’s ion pumps and the team ran the code on Sierra and Lassen in 2018, with promising results.

“It was an amazing feat,” Blake said. “We were able to test a bunch of new ways to port codes to Sierra and form the other code bases. The code is running quickly on Lassen and we’re getting scientific results out of it that would’ve been impossible if the code was still locked to Sequoia.”

Now, with Cardioid working well on GPUs, Blake is heading an internal Laboratory Directed Research and Development (LDRD) project to use Cardioid with machine learning and data from electrocardiograms to determine how the heart is functioning. Using a simple ECG voltage reader, he said, doctors could plug the heart’s electrical activity data into a cellphone to generate a “3D electrical stethoscope.” Preliminary results show the approach is working well, he said. “If this technique works, it could be deployed in every operating room in the country,” Blake said. “With simulations, I can generate as much virtual data as I want, so I can take that virtual data and use that to train a machine learning algorithm. Once that algorithm has been trained, I could take that over to actual clinical results, and then you develop a machine learning system as a software process that can go through [the Food and Drug Administration].”

The work has other national security implications, as LLNL researchers need the ability to prove pharmaceutical countermeasures to biological agents are safe and won’t negatively affect the heart’s functions, Blake said.

“We want to quickly be able to deliver instantaneous results about whether drugs are going to cause problems from a national security standpoint,” Blake said. “The whole idea behind simulation as a science is that we want to simulate things that are too expensive to test. Testing cardiac stuff is really costly in terms of lives of what it takes to get these things working well. If we could simulate that, we could actually bring HPC into medical science.”

Blake said he wants to work with the FDA to develop Cardioid for use in a clinical setting and someday virtually screen potential new prescription drugs for their effect on the heart without having to test the drugs on animals. The FDA, for example, is a partner in the Comprehensive in Vitro Proarrhythmia Assay (CiPA) initiative, an attempt to reconstruct electrophysiologic activity within a heart cell to help predict negative reactions to a given drug, perhaps replacing animal testing with simulations.

Blake said the “next big thing” in medical research is using simulation the way it’s been used in engineering for years. He believes the next software-only medical device will be released in the next five years, and that Cardioid is “definitely a candidate to run on that track.”

“In engineering, we started by building tiny models of bridges and trying to break it, and that’s pretty much all moved over to simulation now,” he said. “There’s a real revolution going on in engineering design because of that. Medical is largely missing all of that. To take hard medical problems, simulate them first and study what will happen, and then apply the therapy, that’s going to be the future of medicine.”

Other collaborators included project co-developer and LLNL bioscience researcher Xiaohua Zhang, Changhoan Kim of IBM, code developer Jamie Bramwell and HPC systems engineer Phil Regier of LLNL and former LLNL scientist Jean Luc Fattebert, who is now at Oak Ridge National Laboratory.


Source: Lawrence Livermore National Laboratory

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 Unveils Latest Achievements in AI Hardware

December 13, 2019

“The increased capabilities of contemporary AI models provide unprecedented recognition accuracy, but often at the expense of larger computational and energetic effort,” IBM Research wrote in a blog post. “Therefor Read more…

By Oliver Peckham

Focused on ‘Silicon TAM,’ Intel Puts Gary Patton, Former GlobalFoundries CTO, in Charge of Design Enablement

December 12, 2019

Change within Intel’s upper management – and to its company mission – has continued as a published report has disclosed that chip technology heavyweight Gary Patton, GlobalFoundries’ CTO and R&D SVP as well a Read more…

By Doug Black

Quantum Bits: Rigetti Debuts New Gates, D-Wave Cuts NEC Deal, AWS Jumps into the Quantum Pool

December 12, 2019

There’s been flurry of significant news in the quantum computing world. Yesterday, Rigetti introduced a new family of gates that reduces circuit depth required on some problems and D-Wave struck a deal with NEC to coll Read more…

By John Russell

How Formula 1 Used Cloud HPC to Build the Next Generation of Racing

December 12, 2019

Formula 1, Rob Smedley explained, is maybe the biggest racing spectacle in the world, with five hundred million fans tuning in for every race. Smedley, a chief engineer with Formula 1’s performance engineering and anal Read more…

By Oliver Peckham

RPI Powers Up ‘AiMOS’ AI Supercomputer

December 11, 2019

Designed to push the frontiers of computing chip and systems performance optimized for AI workloads, an 8 petaflops (Linpack) IBM Power9-based supercomputer has been unveiled in upstate New York that will be used by IBM Read more…

By Doug Black

AWS Solution Channel

Making High Performance Computing Affordable and Accessible for Small and Medium Businesses with HPC on AWS

High performance computing (HPC) brings a powerful set of tools to a broad range of industries, helping to drive innovation and boost revenue in finance, genomics, oil and gas extraction, and other fields. Read more…

IBM Accelerated Insights

GPU Scheduling and Resource Accounting: The Key to an Efficient AI Data Center

[Connect with LSF users and learn new skills in the IBM Spectrum LSF User Community!]

GPUs are the new CPUs

GPUs have become a staple technology in modern HPC and AI data centers. Read more…

At SC19: Developing a Digital Twin

December 11, 2019

In the not too distant future, we can expect to see our skies filled with unmanned aerial vehicles (UAVs) delivering packages, maybe even people, from location to location. In such a world, there will also be a digital twin for each UAV in the fleet: a virtual model that will follow the UAV through its existence, evolving with time. Read more…

By Aaron Dubrow

Focused on ‘Silicon TAM,’ Intel Puts Gary Patton, Former GlobalFoundries CTO, in Charge of Design Enablement

December 12, 2019

Change within Intel’s upper management – and to its company mission – has continued as a published report has disclosed that chip technology heavyweight G Read more…

By Doug Black

Quantum Bits: Rigetti Debuts New Gates, D-Wave Cuts NEC Deal, AWS Jumps into the Quantum Pool

December 12, 2019

There’s been flurry of significant news in the quantum computing world. Yesterday, Rigetti introduced a new family of gates that reduces circuit depth require Read more…

By John Russell

RPI Powers Up ‘AiMOS’ AI Supercomputer

December 11, 2019

Designed to push the frontiers of computing chip and systems performance optimized for AI workloads, an 8 petaflops (Linpack) IBM Power9-based supercomputer has Read more…

By Doug Black

At SC19: Developing a Digital Twin

December 11, 2019

In the not too distant future, we can expect to see our skies filled with unmanned aerial vehicles (UAVs) delivering packages, maybe even people, from location to location. In such a world, there will also be a digital twin for each UAV in the fleet: a virtual model that will follow the UAV through its existence, evolving with time. Read more…

By Aaron Dubrow

Intel’s Jim Clarke on its New Cryo-controller and why Intel isn’t Late to the Quantum Party

December 9, 2019

Intel today introduced the ‘first-of-its-kind’ cryo-controller chip for quantum computing and previewed a cryo-prober tool for characterizing quantum proces Read more…

By John Russell

On the Spack Track @SC19

December 5, 2019

At the annual supercomputing conference, SC19 in Denver, Colorado, there were Spack events each day of the conference. As a reflection of its grassroots heritage, nine sessions were planned by more than a dozen thought leaders from seven organizations, including three U.S. national Department of Energy (DOE) laboratories and Sylabs... Read more…

By Elizabeth Leake

Intel’s New Hyderabad Design Center Targets Exascale Era Technologies

December 3, 2019

Intel's Raja Koduri was in India this week to help launch a new 300,000 square foot design and engineering center in Hyderabad, which will focus on advanced com Read more…

By Tiffany Trader

AWS Debuts 7nm 2nd-Gen Graviton Arm Processor

December 3, 2019

The “x86 Big Bang,” in which market dominance of the venerable Intel CPU has exploded into fragments of processor options suited to varying workloads, has n Read more…

By Doug Black

Using AI to Solve One of the Most Prevailing Problems in CFD

October 17, 2019

How can artificial intelligence (AI) and high-performance computing (HPC) solve mesh generation, one of the most commonly referenced problems in computational engineering? A new study has set out to answer this question and create an industry-first AI-mesh application... Read more…

By James Sharpe

D-Wave’s Path to 5000 Qubits; Google’s Quantum Supremacy Claim

September 24, 2019

On the heels of IBM’s quantum news last week come two more quantum items. D-Wave Systems today announced the name of its forthcoming 5000-qubit system, Advantage (yes the name choice isn’t serendipity), at its user conference being held this week in Newport, RI. Read more…

By John Russell

DARPA Looks to Propel Parallelism

September 4, 2019

As Moore’s law runs out of steam, new programming approaches are being pursued with the goal of greater hardware performance with less coding. The Defense Advanced Projects Research Agency is launching a new programming effort aimed at leveraging the benefits of massive distributed parallelism with less sweat. Read more…

By George Leopold

Ayar Labs to Demo Photonics Chiplet in FPGA Package at Hot Chips

August 19, 2019

Silicon startup Ayar Labs continues to gain momentum with its DARPA-backed optical chiplet technology that puts advanced electronics and optics on the same chip Read more…

By Tiffany Trader

SC19: IBM Changes Its HPC-AI Game Plan

November 25, 2019

It’s probably fair to say IBM is known for big bets. Summit supercomputer – a big win. Red Hat acquisition – looking like a big win. OpenPOWER and Power processors – jury’s out? At SC19, long-time IBMer Dave Turek sketched out a different kind of bet for Big Blue – a small ball strategy, if you’ll forgive the baseball analogy... Read more…

By John Russell

Cray, Fujitsu Both Bringing Fujitsu A64FX-based Supercomputers to Market in 2020

November 12, 2019

The number of top-tier HPC systems makers has shrunk due to a steady march of M&A activity, but there is increased diversity and choice of processing compon Read more…

By Tiffany Trader

Crystal Ball Gazing: IBM’s Vision for the Future of Computing

October 14, 2019

Dario Gil, IBM’s relatively new director of research, painted a intriguing portrait of the future of computing along with a rough idea of how IBM thinks we’ Read more…

By John Russell

Kubernetes, Containers and HPC

September 19, 2019

Software containers and Kubernetes are important tools for building, deploying, running and managing modern enterprise applications at scale and delivering enterprise software faster and more reliably to the end user — while using resources more efficiently and reducing costs. Read more…

By Daniel Gruber, Burak Yenier and Wolfgang Gentzsch, UberCloud

Leading Solution Providers

SC 2019 Virtual Booth Video Tour

AMD
AMD
CEJN
CJEN
DDN
DDN
MELLANOX
MELLANOX
ONE STOP SYSTEMS
ONE STOP SYSTEMS
PANASAS
PANASAS
SIX NINES IT
SIX NINES IT
VERNE GLOBAL
VERNE GLOBAL
WEKAIO
WEKAIO

Intel Debuts New GPU – Ponte Vecchio – and Outlines Aspirations for oneAPI

November 17, 2019

Intel today revealed a few more details about its forthcoming Xe line of GPUs – the top SKU is named Ponte Vecchio and will be used in Aurora, the first plann Read more…

By John Russell

Dell Ramps Up HPC Testing of AMD Rome Processors

October 21, 2019

Dell Technologies is wading deeper into the AMD-based systems market with a growing evaluation program for the latest Epyc (Rome) microprocessors from AMD. In a Read more…

By John Russell

SC19: Welcome to Denver

November 17, 2019

A significant swath of the HPC community has come to Denver for SC19, which began today (Sunday) with a rich technical program. As is customary, the ribbon cutt Read more…

By Tiffany Trader

When Dense Matrix Representations Beat Sparse

September 9, 2019

In our world filled with unintended consequences, it turns out that saving memory space to help deal with GPU limitations, knowing it introduces performance pen Read more…

By James Reinders

Cerebras to Supply DOE with Wafer-Scale AI Supercomputing Technology

September 17, 2019

Cerebras Systems, which debuted its wafer-scale AI silicon at Hot Chips last month, has entered into a multi-year partnership with Argonne National Laboratory and Lawrence Livermore National Laboratory as part of a larger collaboration with the U.S. Department of Energy... Read more…

By Tiffany Trader

With the Help of HPC, Astronomers Prepare to Deflect a Real Asteroid

September 26, 2019

For years, NASA has been running simulations of asteroid impacts to understand the risks (and likelihoods) of asteroids colliding with Earth. Now, NASA and the European Space Agency (ESA) are preparing for the next, crucial step in planetary defense against asteroid impacts: physically deflecting a real asteroid. Read more…

By Oliver Peckham

Jensen Huang’s SC19 – Fast Cars, a Strong Arm, and Aiming for the Cloud(s)

November 20, 2019

We’ve come to expect Nvidia CEO Jensen Huang’s annual SC keynote to contain stunning graphics and lively bravado (with plenty of examples) in support of GPU Read more…

By John Russell

IBM Opens Quantum Computing Center; Announces 53-Qubit Machine

September 19, 2019

Gauging progress in quantum computing is a tricky thing. IBM yesterday announced the opening of the IBM Quantum Computing Center in New York, with five 20-qubit Read more…

By John Russell

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This