Dassault, NIMHANS, and UberCloud Foster Innovative Schizophrenia Treatment

By Wolfgang Gentzsch and Burak Yenier, UberCloud

March 29, 2018

In a series of challenging high performance computing applications in the life sciences, UberCloud’s HPC containers have been packaged recently with several scientific workflows and application data to simulate complex phenomena in human’s heart and brain. As the core software for these HPC cloud experiments we are using the (containerized) Abaqus solver running in a fully automated multi-node HPE environment in the Advania HPC Cloud.

Treatment of Schizophrenia is complex, lengthy, and often risky

Schizophrenia is a chronic brain disorder that affects about one percent of the world’s population. When schizophrenia is active, symptoms can include delusions, hallucinations, trouble with thinking and concentration, and lack of motivation. Symptoms include hearing internal voices, having false beliefs, disorganized thoughts and behavior, and being emotionally flat. These symptoms may leave a person feeling fearful and withdrawn.

Often, schizophrenia cannot be treated successfully by using just one type of medicine. Therefore, a range of treatments including drugs are available and the key to a successful outcome is to find the right combination of the right drugs for the individual patient. Different people will respond differently to different treatments. Finding the right treatment regime can be a very lengthy process and finding the right medication at the right dose can take a lot of time.

As an alternative to drugs, Deep Brain Stimulation (DBS) is being applied to treat schizophrenia, involving implanting electrodes within certain areas of the brain to produce electrical impulses that regulate abnormal impulses in a patient’s brain. But this treatment is intrusive and comes with a certain risk for potential complications such as stroke, cerebrospinal fluid (CSF) leakage, bleeding, etc. And not every patient can afford DBS surgery considering their individual health conditions and high-cost medical procedures.

A New Method: Non-Invasive Direct Current Stimulation

In recent years, so-called transcranial Direct Current Stimulation (tDCS) has been introduced which is a new form of non-invasive neurostimulation that is used to safely treat a variety of clinical conditions including depression, obsessive-compulsive disorder, migraine, and central and neuropathic chronic pain. tDCS involves the injection of a weak (very low amperage) electrical current to the head through surface electrodes to generate an electric field that selectively modulates the activity of neurons in the cerebral cortex of the brain. Extensive neurophysiological research has shown that direct current electricity modifies neuronal cross-membrane resting potentials and thereby influences neuronal excitability and firing rates. And, tDCS is inexpensive, lightweight, and can be conducted anywhere.

Figure 1: Illustration of transcranial Direct Current stimulation device. Courtesy Bipolar Network News.

The UberCloud Experiment #200

In the last six years, UberCloud has performed 200 cloud experiments with engineers and scientists and their complex applications. This latest HPC cloud experiment is based on computer simulations of a novel non-invasive transcranial electro-stimulation of the human brain to treat schizophrenia. The experiment has been collaboratively performed by the National Institute of Mental Health & Neuro Sciences in India (NIMHANS), Dassault SIMULIA, Advania, and UberCloud, and generously sponsored by Hewlett Packard Enterprise and Intel. The current work demonstrates the high value of computational modeling and simulation in improving the clinical application of non-invasive transcranial electro-stimulation of the human brain in schizophrenia.

NIMHANS is India’s premier neuroscience organization involved in clinical research and patient care in the area of neurological and psychiatric disorders. Since 2016, Dassault Systemes has been collaborating with NIMHANS on a project to demonstrate that computational modeling and simulation can improve the efficacy of Transcranial Direct Current Stimulation (tDCS), a noninvasive clinical treatment for schizophrenia. Successful completion of the first stage of this project has already raised awareness and interest in simulation-based personalized neuromodulation in the clinical community in India.

Our project demonstrates an innovative method that can stimulate deep inside the brain noninvasively/non-surgically, using multiple electric fields applied from scalp. This procedure is able to precisely activate selective regions of the brain, leaving minimal risk and also making it affordable to all. With this method clinicians can precisely target regions of the brain without affecting major parts of the healthy brain!

A high fidelity finite element human head model was considered including skin, skull, cerebro-spinal fluid, sinus grey & white matter, demanding HPC resources to try various electrode configurations. Access to HPE’s HPC infrastructure in the Advania Cloud and SIMULIA’s Abaqus 2017 code packaged in an UberCloud HPC container empowered the researcher to run numerous configurations of electrode placements and sizes to explore best possible electrode placement which was not possible before on the user’s in-house workstations and HPC systems.

HPC Cloud Hardware and Results

We ran 26 different Abaqus jobs on the Advania HPC cluster – each representing a different montage (electrode configuration). Each job contained 1.8 million finite elements. For comparison purposes, on the user’s own server 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 of about 2x for each job running in the cloud. In the future, it will be possible to run many electrode placement simulations in parallel, thus dramatically speeding up the search for the optimal electrode placement for an individual patient, with the final goal to perform such a search in (almost) real time. In addition, during this cloud experiment, the Abaqus 2017 software container has always been accessible through the user’s browser, from anywhere, on demand, for any kind of interactive and batch work, and for remote visualization of the simulation results.

Figure 2: Localization of the peak electrical potential gradient value in Abaqus 2017 for different combinations of electrodes.

Conclusion

The application discussed here demonstrates a novel method for “Deep Brain Stimulation” in a non-invasive way which has the potential to replace some of the painful/high risk brain surgeries such as in schizophrenia and Parkinson’s disorders. The huge benefits of these simulations are that they (i) predict the current distribution with high resolution; (ii) allow for patient-specific treatment and outcome evaluation; (iii) facilitate parameter sensitivity analyses and montage variations; and (iv) can be used by clinicians in an interactive real-time manner. However, there is still a lot of work to be done in collaboration with the Doctors/Clinicians at NIMHANS and other Neurological Research Centers on how this method can be appraised and fine-tuned for real time clinical use.

A longer more detailed version of this article can be downloaded from here:
https://community.theubercloud.com/category/UberCloud-Voice-march2018/

Acknowledgement: The author is deeply grateful for the support from Hewlett Packard Enterprise and Intel (the Sponsors), Dassault Systemes SIMULIA (for Abaqus 2017), Advania (providing HPC Cloud resources), and our UberCloud technical team for containerizing Abaqus and integrating all software and hardware components into one seamless and fully automated cloud solution stack. The UberCloud Case Study 200 has been co-authored by G. Umashankar, Karl D’Souza, J Jofeetha from Dassault SIMULIA and Dr. G. Venkatasubramanian from NIMHANS. Big Thank You.

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!

HPC Career Notes: April 2020 Edition

April 2, 2020

In this monthly feature, we’ll keep you up-to-date on the latest career developments for individuals in the high-performance computing community. Whether it’s a promotion, new company hire, or even an accolade, we’ Read more…

By Mariana Iriarte

AMD Epyc CPUs Now on Bare Metal IBM Cloud Servers

April 1, 2020

AMD’s expanding presence in the datacenter and cloud computing markets took a step forward with today’s announcement that its 7nm 2nd Gen Epyc 7642 CPUs are now available on IBM Cloud bare metal servers. AMD, whose Read more…

By Doug Black

Supercomputer Testing Probes Viral Transmission in Airplanes

April 1, 2020

It might be a long time before the general public is flying again, but the question remains: how high-risk is air travel in terms of viral infection? In an article for the Texas Advanced Computing Center (TACC), Faith Si Read more…

By Staff report

ECP Milestone Report Details Progress and Directions

April 1, 2020

The Exascale Computing Project (ECP) milestone report issued last week presents a good snapshot of progress in preparing applications for exascale computing. There are roughly 30 ECP application development (AD) subproj Read more…

By John Russell

Russian Supercomputer Employed to Develop COVID-19 Treatment

March 31, 2020

From Summit to [email protected], global supercomputing is continuing to mobilize against the coronavirus pandemic by crunching massive problems like epidemiology, therapeutic development and vaccine development. The latest a Read more…

By Staff report

AWS Solution Channel

Amazon FSx for Lustre Update: Persistent Storage for Long-Term, High-Performance Workloads

Last year I wrote about Amazon FSx for Lustre and told you how our customers can use it to create pebibyte-scale, highly parallel POSIX-compliant file systems that serve thousands of simultaneous clients driving millions of IOPS (Input/Output Operations per Second) with sub-millisecond latency. Read more…

What’s New in HPC Research: Supersonic Jets, Skin Modeling, Astrophysics & More

March 31, 2020

In this bimonthly 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…

By Oliver Peckham

Pandemic ‘Wipes Out’ 2020 HPC Market Growth, Flat to 12% Drop Expected

March 31, 2020

As the world battles the still accelerating novel coronavirus, the HPC community has mounted a forceful response to the pandemic on many fronts. But these efforts won't inoculate the HPC industry from the economic effects of COVID-19. Market watcher Intersect360 Research has revised its 2020 forecast for HPC products and services, projecting... Read more…

By Tiffany Trader

Weather at Exascale: Load Balancing for Heterogeneous Systems

March 30, 2020

The first months of 2020 were dominated by weather and climate supercomputing news, with major announcements coming from the UK, the European Centre for Medium- Read more…

By Oliver Peckham

Q&A Part Two: ORNL’s Pooser on Progress in Quantum Communication

March 30, 2020

Quantum computing seems to get more than its fair share of attention compared to quantum communication. That’s despite the fact that quantum networking may be Read more…

By John Russell

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

[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

Conversation: ANL’s Rick Stevens on DoE’s AI for Science Project

March 23, 2020

With release of the Department of Energy’s AI for Science report in late February, the effort to build a national AI program, modeled loosely on the U.S. Exascale Initiative, enters a new phase. Project leaders have already had early discussions with Congress... Read more…

By John Russell

Servers Headed to Junkyard Find 2nd Life Fighting Cancer in Clusters

March 20, 2020

Ottawa-based charitable organization Cancer Computer is on a mission to stamp out cancer and other life-threatening diseases, including coronavirus, by putting Read more…

By Tiffany Trader

Kubernetes and HPC Applications in Hybrid Cloud Environments – Part II

March 19, 2020

With the rise of cloud services, CIOs are recognizing that applications, middleware, and infrastructure running in various compute environments need a common management and operating model. Maintaining different application and middleware stacks on-premises and in cloud environments, by possibly using different specialized infrastructure and application... Read more…

By Daniel Gruber,Burak Yenier and Wolfgang Gentzsch, UberCloud

[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

Julia Programming’s Dramatic Rise in HPC and Elsewhere

January 14, 2020

Back in 2012 a paper by four computer scientists including Alan Edelman of MIT introduced Julia, A Fast Dynamic Language for Technical Computing. At the time, t Read more…

By John Russell

Global Supercomputing Is Mobilizing Against COVID-19

March 12, 2020

Tech has been taking some heavy losses from the coronavirus pandemic. Global supply chains have been disrupted, virtually every major tech conference taking place over the next few months has been canceled... Read more…

By Oliver Peckham

[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

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

Steve Scott Lays Out HPE-Cray Blended Product Roadmap

March 11, 2020

Last week, the day before the El Capitan processor disclosures were made at HPE's new headquarters in San Jose, Steve Scott (CTO for HPC & AI at HPE, and former Cray CTO) was on-hand at the Rice Oil & Gas HPC conference in Houston. He was there to discuss the HPE-Cray transition and blended roadmap, as well as his favorite topic, Cray's eighth-gen networking technology, Slingshot. Read more…

By Tiffany Trader

Fujitsu A64FX Supercomputer to Be Deployed at Nagoya University This Summer

February 3, 2020

Japanese tech giant Fujitsu announced today that it will supply Nagoya University Information Technology Center with the first commercial supercomputer powered Read more…

By Tiffany Trader

Tech Conferences Are Being Canceled Due to Coronavirus

March 3, 2020

Several conferences scheduled to take place in the coming weeks, including Nvidia’s GPU Technology Conference (GTC) and the Strata Data + AI conference, have Read more…

By Alex Woodie

Leading Solution Providers

SC 2019 Virtual Booth Video Tour

AMD
AMD
ASROCK RACK
ASROCK RACK
AWS
AWS
CEJN
CJEN
CRAY
CRAY
DDN
DDN
DELL EMC
DELL EMC
IBM
IBM
MELLANOX
MELLANOX
ONE STOP SYSTEMS
ONE STOP SYSTEMS
PANASAS
PANASAS
SIX NINES IT
SIX NINES IT
VERNE GLOBAL
VERNE GLOBAL
WEKAIO
WEKAIO

Cray to Provide NOAA with Two AMD-Powered Supercomputers

February 24, 2020

The United States’ National Oceanic and Atmospheric Administration (NOAA) last week announced plans for a major refresh of its operational weather forecasting supercomputers, part of a 10-year, $505.2 million program, which will secure two HPE-Cray systems for NOAA’s National Weather Service to be fielded later this year and put into production in early 2022. Read more…

By Tiffany Trader

Exascale Watch: El Capitan Will Use AMD CPUs & GPUs to Reach 2 Exaflops

March 4, 2020

HPE and its collaborators reported today that El Capitan, the forthcoming exascale supercomputer to be sited at Lawrence Livermore National Laboratory and serve 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

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 energet Read more…

By Oliver Peckham

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

IBM Debuts IC922 Power Server for AI Inferencing and Data Management

January 28, 2020

IBM today launched a Power9-based inference server – the IC922 – that features up to six Nvidia T4 GPUs, PCIe Gen 4 and OpenCAPI connectivity, and can accom Read more…

By John Russell

Summit Joins the Fight Against the Coronavirus

March 6, 2020

With the coronavirus sweeping the globe, tech conferences and supply chains are being hit hard – but now, tech is hitting back. Oak Ridge National Laboratory Read more…

By Staff report

University of Stuttgart Inaugurates ‘Hawk’ Supercomputer

February 20, 2020

This week, the new “Hawk” supercomputer was inaugurated in a ceremony at the High-Performance Computing Center of the University of Stuttgart (HLRS). Offici Read more…

By Staff report

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