Democratization of HPC Part 2: HPC in Personalized Non-invasive Clinical Treatment of Schizophrenia and Parkinson’s

By Wolfgang Gentzsch

October 4, 2018

This is the second in a series of articles demonstrating the growing acceptance of high-performance computing (HPC) in new user communities and application areas. In this article we present UberCloud use case #200 on how India’s National Institute of Health was able for schizophrenia – and potentially Parkinson’s disease, depression, and other brain disorders – to replace the current highly risky procedure of brain-invasive operations with an innovative technique of non-invasive low-risk treatment based on HPC that is also significantly more affordable.

This UberCloud Experiment #200 is based on computer simulations of non-invasive transcranial electro-stimulation of the human brain in schizophrenia, a serious mental illness characterized by illogical thoughts, bizarre behavior and speech, and delusions or hallucinations. This work represents an initial effort to demonstrate the high value of computational modeling and simulation in improving the clinical application of non-invasive electro-stimulation of the human brain in schizophrenia and other neuropsychiatric disorders. With the addition of HPC, clinicians can now precisely and non-invasively target regions of the brain without affecting major parts of the healthy brain. The HPC simulations have been collaboratively performed by NIMHANS National Institute of Mental Health & Neuro Sciences in India, Dassault SIMULIA, Advania Data Centers, and UberCloud, with sponsorship from Hewlett Packard Enterprise and Intel.

Figure 1: Schematic of electrical stimulation modalities.

The Problem

Neuromodulation refers to neural activity via an artificial stimulus such as an electrical current or a chemical agent. It may involve (highly risky) invasive approaches such as spinal cord stimulation or deep brain stimulation wherein electrodes are implanted directly on the nerves to be stimulated. It may also be performed non-invasively using methods such as electrical stimulation wherein external electrodes induce the required neural activity changes without the need for surgical implantation, but in which low intensity (mA) electrical currents are applied to the head via scalp-mounted electrodes, as shown in Figure 1 [Yavari 2017]. Stimulation with the negative pole (cathode) placed over a selected cortical region will decrease neuronal activity under the electrode, whereas stimulation with the positive pole (anode) will increase neuronal activity under the electrode. Therefore, this method may be used to increase cortical brain activity in specific brain areas that are under aroused, or alternatively decrease activity in areas that are overexcited. This procedure is simple, affordable, and portable, and the human is fully conscious and experiences minimal discomfort.

HPC Brain Simulation in the Advania Cloud

The power of multi-physics technology on the Advania Data Centers Cloud Platform allowed us to simulate deep brain stimulation by placing two sets of electrodes on the scalp to generate temporal interference deep inside the grey matter of the brain. However, a basic level of customization in post processing was required in making this methodology available to the clinician in real time and also reduce overall computational effort, where doctors can choose two pre-computed electrical fields of an electrode pair to generate temporal interference at specific regions of the grey matter of the brain.

After a satisfactory 3D head/brain model was developed, electrode placement was performed with Synopsys Simpleware ScanIP and CAD modules using the 10/10 international convention with the anode at AF3 and the cathode at CP5 (Figure 2). Finally, a high-resolution tetrahedral FE mesh (element size = 1mm3) was generated using the ScanIP and ScanFE modules.

Figure 2: International 10/10 convention (left) showing anode AF3 (red) and cathode CP5 (blue); subject-specific model (right).

A high-fidelity finite element human head model was considered including skin, skull, CSF, sinus grey & white matter, which demanded high computing resources to try various electrode configurations. Access to the HPE cluster at Advania and SIMULIA’s Abaqus 2017 code in an UberCloud HPC container empowered us to simulate numerous configurations of electrode placements and sizes. This also allowed us to study the sensitivity of electrode placements and sizes which was not possible before on our inhouse workstations and HPC systems.

During the final production phase, we have run 26 different SIMULIA Abaqus jobs – each representing a different electrode configuration – on the Advania/UberCloud HPC cluster of HPE ProLiant servers XL230 Gen9 with 2x Intel Broadwell E5-2683 v4 and Intel OmniPath interconnect. Each job contained 1.8M finite elements. On our own cluster with 16 cores, a single run took about 75 minutes, whereas on the UberCloud cluster a single run took about 28 minutes on 24 cores. Thus, we got a significant speedup running on UberCloud/Advania.

Figure 3 results are for two sets of electrical fields superimposed to produce temporal interference. Left: Electrical fields generated from electrodes placed on the left and right side of pre-temporal region of the scalp. Right: Electrical fields generated from electrodes placed on the left of the pre-temporal and rear region of the scalp.

Figure 3: The results show the sensitivity of the temporal interference region deep inside the brain based on two different electrode placements on the scalp.

Conclusion

The HPC application discussed in this case study demonstrates a breakthrough for deep brain stimulation in a non-invasive way which has the potential to replace the more painful/high risk brain surgeries such as in schizophrenia and Parkinson’s. The huge benefits of these HPC simulations are that (i) they predict the electrical current distribution with high resolution; (ii) allow for personalized and quantifiable treatment; (iii) facilitate electrode montage variations; and (iv) clinicians can devise the most effective treatment for a specific patient. HPCwire readers can download UberCloud Case Study #200 by Ganesh Venkatasubramanian from NIMHANS, Umashankar Gunasheker and Karl D’Souza from Dassault Systemes, and Wolfgang Gentzsch from UberCloud.

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!

U.S. CTO Michael Kratsios Adds DoD Research & Engineering Title

July 13, 2020

Michael Kratsios, the U.S. Chief Technology Officer, has been appointed acting Undersecretary of Defense for research and engineering. He replaces Mike Griffin, who along with his deputy Lis Porter, stepped down last wee Read more…

By John Russell

Supercomputer Research Reveals Star Cluster Born Outside Our Galaxy

July 11, 2020

The Milky Way is our galactic home, containing our solar system and continuing into a giant band of densely packed stars that stretches across clear night skies around the world – but, it turns out, not all of those st Read more…

By Oliver Peckham

Max Planck Society Begins Installation of Liquid-Cooled Supercomputer from Lenovo

July 9, 2020

Lenovo announced today that it is supplying a new high performance computer to the Max Planck Society, one of Germany's premier research organizations. Comprised of Intel Xeon processors and Nvidia A100 GPUs, and featuri Read more…

By Tiffany Trader

Xilinx Announces First Adaptive Computing Challenge

July 9, 2020

A new contest is challenging the computing world. Xilinx has announced the first Xilinx Adaptive Computing Challenge, a competition that will task developers and startups with finding creative workload acceleration solutions. Xilinx is running the Adaptive Computing Challenge in partnership with Hackster.io, a developing community... Read more…

By Staff report

Reviving Moore’s Law? LBNL Researchers See Promise in Heterostructure Oxides

July 9, 2020

The reality of Moore’s law’s decline is no longer doubted for good empirical reasons. That said, never say never. Recent work by Lawrence Berkeley National Laboratory researchers suggests heterostructure oxides may b Read more…

By John Russell

AWS Solution Channel

Best Practices for Running Computational Fluid Dynamics (CFD) Workloads on AWS

The scalable nature and variable demand of CFD workloads makes them well-suited for a cloud computing environment. Many of the AWS instance types, such as the compute family instance types, are designed to include support for this type of workload.  Read more…

Intel® HPC + AI Pavilion

Supercomputing the Pandemic: Scientific Community Tackles COVID-19 from Multiple Perspectives

Since their inception, supercomputers have taken on the biggest, most complex, and most data-intensive computing challenges—from confirming Einstein’s theories about gravitational waves to predicting the impacts of climate change. Read more…

President’s Council Targets AI, Quantum, STEM; Recommends Spending Growth

July 9, 2020

Last week the President Council of Advisors on Science and Technology (PCAST) met (webinar) to review policy recommendations around three sub-committee reports: 1) Industries of the Future (IotF), chaired be Dario Gil (d Read more…

By John Russell

Max Planck Society Begins Installation of Liquid-Cooled Supercomputer from Lenovo

July 9, 2020

Lenovo announced today that it is supplying a new high performance computer to the Max Planck Society, one of Germany's premier research organizations. Comprise Read more…

By Tiffany Trader

President’s Council Targets AI, Quantum, STEM; Recommends Spending Growth

July 9, 2020

Last week the President Council of Advisors on Science and Technology (PCAST) met (webinar) to review policy recommendations around three sub-committee reports: Read more…

By John Russell

Google Cloud Debuts 16-GPU Ampere A100 Instances

July 7, 2020

On the heels of the Nvidia’s Ampere A100 GPU launch in May, Google Cloud is announcing alpha availability of the A100 “Accelerator Optimized” VM A2 instance family on Google Compute Engine. The instances are powered by the HGX A100 16-GPU platform, which combines two HGX A100 8-GPU baseboards using... Read more…

By Tiffany Trader

Q&A: HLRS’s Bastian Koller Tackles HPC and Industry in Germany and Europe

July 6, 2020

In this exclusive interview for HPCwire – sadly not face to face – Steve Conway, senior advisor for Hyperion Research, talks with Dr.-Ing Bastian Koller about the state of HPC and its collaboration with Industry in Europe. Koller is a familiar figure in HPC. He is the managing director at High Performance Computing Center Stuttgart (HLRS) and also serves... Read more…

By Steve Conway, Hyperion

OpenPOWER Reboot – New Director, New Silicon Partners, Leveraging Linux Foundation Connections

July 2, 2020

Earlier this week the OpenPOWER Foundation announced the contribution of IBM’s A21 Power processor core design to the open source community. Roughly this time Read more…

By John Russell

Hyperion Forecast – Headwinds in 2020 Won’t Stifle Cloud HPC Adoption or Arm’s Rise

June 30, 2020

The semiannual taking of HPC’s pulse by Hyperion Research – late fall at SC and early summer at ISC – is a much-watched indicator of things come. This yea Read more…

By John Russell

Racism and HPC: a Special Podcast

June 29, 2020

Promoting greater diversity in HPC is a much-discussed goal and ostensibly a long-sought goal in HPC. Yet it seems clear HPC is far from achieving this goal. Re Read more…

Top500 Trends: Movement on Top, but Record Low Turnover

June 25, 2020

The 55th installment of the Top500 list saw strong activity in the leadership segment with four new systems in the top ten and a crowning achievement from the f Read more…

By Tiffany Trader

Supercomputer Modeling Tests How COVID-19 Spreads in Grocery Stores

April 8, 2020

In the COVID-19 era, many people are treating simple activities like getting gas or groceries with caution as they try to heed social distancing mandates and protect their own health. Still, significant uncertainty surrounds the relative risk of different activities, and conflicting information is prevalent. A team of Finnish researchers set out to address some of these uncertainties by... Read more…

By Oliver Peckham

[email protected] Turns Its Massive Crowdsourced Computer Network Against COVID-19

March 16, 2020

For gamers, fighting against a global crisis is usually pure fantasy – but now, it’s looking more like a reality. As supercomputers around the world spin up Read more…

By Oliver Peckham

Rosetta[email protected] Rallies a Legion of Computers Against the Coronavirus

March 24, 2020

Last week, we highlighted [email protected], a massive, crowdsourced computer network that has turned its resources against the coronavirus pandemic sweeping the globe – but [email protected] isn’t the only game in town. The internet is buzzing with crowdsourced computing... Read more…

By Oliver Peckham

Supercomputer Simulations Reveal the Fate of the Neanderthals

May 25, 2020

For hundreds of thousands of years, neanderthals roamed the planet, eventually (almost 50,000 years ago) giving way to homo sapiens, which quickly became the do Read more…

By Oliver Peckham

DoE Expands on Role of COVID-19 Supercomputing Consortium

March 25, 2020

After announcing the launch of the COVID-19 High Performance Computing Consortium on Sunday, the Department of Energy yesterday provided more details on its sco Read more…

By John Russell

Neocortex Will Be First-of-Its-Kind 800,000-Core AI Supercomputer

June 9, 2020

Pittsburgh Supercomputing Center (PSC - a joint research organization of Carnegie Mellon University and the University of Pittsburgh) has won a $5 million award Read more…

By Tiffany Trader

Honeywell’s Big Bet on Trapped Ion Quantum Computing

April 7, 2020

Honeywell doesn’t spring to mind when thinking of quantum computing pioneers, but a decade ago the high-tech conglomerate better known for its control systems waded deliberately into the then calmer quantum computing (QC) waters. Fast forward to March when Honeywell announced plans to introduce an ion trap-based quantum computer whose ‘performance’ would... Read more…

By John Russell

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…

By Doug Black

Leading Solution Providers

Contributors

Nvidia’s Ampere A100 GPU: Up to 2.5X the HPC, 20X the AI

May 14, 2020

Nvidia's first Ampere-based graphics card, the A100 GPU, packs a whopping 54 billion transistors on 826mm2 of silicon, making it the world's largest seven-nanom Read more…

By Tiffany Trader

‘Billion Molecules Against COVID-19’ Challenge to Launch with Massive Supercomputing Support

April 22, 2020

Around the world, supercomputing centers have spun up and opened their doors for COVID-19 research in what may be the most unified supercomputing effort in hist Read more…

By Oliver Peckham

Australian Researchers Break All-Time Internet Speed Record

May 26, 2020

If you’ve been stuck at home for the last few months, you’ve probably become more attuned to the quality (or lack thereof) of your internet connection. Even Read more…

By Oliver Peckham

15 Slides on Programming Aurora and Exascale Systems

May 7, 2020

Sometime in 2021, Aurora, the first planned U.S. exascale system, is scheduled to be fired up at Argonne National Laboratory. Cray (now HPE) and Intel are the k Read more…

By John Russell

Summit Supercomputer is Already Making its Mark on Science

September 20, 2018

Summit, now the fastest supercomputer in the world, is quickly making its mark in science – five of the six finalists just announced for the prestigious 2018 Read more…

By John Russell

TACC Supercomputers Run Simulations Illuminating COVID-19, DNA Replication

March 19, 2020

As supercomputers around the world spin up to combat the coronavirus, the Texas Advanced Computing Center (TACC) is announcing results that may help to illumina Read more…

By Staff report

$100B Plan Submitted for Massive Remake and Expansion of NSF

May 27, 2020

Legislation to reshape, expand - and rename - the National Science Foundation has been submitted in both the U.S. House and Senate. The proposal, which seems to Read more…

By John Russell

John Martinis Reportedly Leaves Google Quantum Effort

April 21, 2020

John Martinis, who led Google’s quantum computing effort since establishing its quantum hardware group in 2014, has left Google after being moved into an advi 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