Scientists Using Intel-Cray ‘Theta’ Supercomputer to Map Brain Function

September 14, 2017

Sept. 14, 2017 — A neuroscientist and a computational scientist walk into a synchrotron facility to study a mouse brain… Sounds like a great set-up for a comedy bit, but there is no punchline. The result is cutting-edge science that can only be accomplished in a facility as scientifically integrated as the U.S. Department of Energy’s (DOE) Argonne National Laboratory.

At a casual, or even a more attentive glance, Doga Gursoy and Bobby Kasthuri would seem at opposite ends of the research spectrum. Gursoy is an assistant computational scientist at Argonne’s Advanced Photon Source (APS), a DOE Office of Science User Facility; Kasthuri, an Argonne neuroscientist.

But together, they are using Argonne’s vast arsenal of innovative technologies to map the intricacies of brain function at the deepest levels, and describing them in greater detail than ever before through advanced data analysis techniques.

Gursoy and Kasthuri are among the first group of researchers to access Theta, the new 9.65 petaflops Intel-Cray supercomputer housed at the Argonne Leadership Computing Facility (ALCF), also a DOE Office of Science User Facility. Theta’s advanced and flexible software platform supports the ALCF Data Science Program (ADSP), a new initiative targeted at big data problems, like Gursoy and Kasthuri’s brain connectome project.

ADSP projects explore and improve a variety of computational methods that will enable data-driven discoveries across all scientific disciplines.

“By developing and demonstrating rapid analysis techniques, such as data mining, graph analytics and machine learning, together with workflows that will facilitate productive usage on our systems for applications, we will pave the way for more and more science communities to use supercomputers for their big data challenges in the future,” said Venkat Vishwanath, ALCF Data Sciences Group Lead.

All about the connections

This new ADSP study of connectomes maps the connections of every neuron in the brain, whether human or mouse. Determining the location of every cell in the brain and how they communicate with each other is a daunting task, as each cell makes thousands of connections. The human brain, for example, has some 100 billion neurons, creating 100 trillion connections. Even the average mouse brain has 75 million neurons.

This ALCF award targets big data problems and our application of brain imaging does just that,” said Gursoy, assistant computational scientist in the X-Ray Science Division of Argonne’s Advanced Photon Source. “The basic goal is simple — we would like to be able to image all of the neurons in the brain — but the datasets from X-rays and electron microscopes are extremely large. They are at the tera- and petabyte scales. So we would like to use Theta to build the software and codebase infrastructure in order to analyze that data.”

This research was supported by the U.S. Department of Energy’s Office of Science. A portion of the work was also supported by Argonne’s Laboratory-Directed Research and Development (LDRD) program.

The process begins with two imaging techniques that will provide the massive sets of data for analysis by Theta. One is at the APS, where full brains can be analyzed at submicron resolution — in this case, the brain of a petite shrewmouse — through X-ray microtomography, a high-resolution 3-D imaging technique. Argonne’s X-ray Sciences Division of the APS provides the expertise for the microtomography research. Much like a CT scanner, it produces images as micro-thin slices of a material whose structure can be meticulously scrutinized. While this resolution provides a detailed picture of blood vessels and cell bodies, the researchers aim to go still deeper.

That depth of detail requires the use of an electron microscope, which transmits a short-wavelength electron beam to deliver resolution at the nanometer scale. This will allow for the capture of all the synaptic connections between individual neurons at small targeted regions guided by the X-ray microtomography.

For years, scientists at the APS have used these techniques to deepen our understanding of a wide variety of materials, from soil samples to new materials to biological matter,” said Kamel Fezzaa from sector 32-ID at the APS. “By coordinating our efforts with Argonne high-speed computing capabilities for this project, we are able to provide some truly revolutionary images that could provide details about brain functions that we have never before been able to observe.”

Both techniques can produce petabytes of information a day and, according to the researchers, the next generations of both microscopes will increase that amount dramatically.

Images produced by these datasets have to be processed, reconstructed and analyzed. Through the ADSP, Gursoy and Kasthuri are developing a series of large-scale data and computational steps — a pipeline — that integrates exascale computational approaches into an entirely new set of tools for brain research.

Taming of the shrew

The first case study for this pipeline is the reconstruction of an entire adult shrewmouse brain, which, they estimate, will produce one exabyte of data, or one billion gigabytes. And the studies only get bigger from there.

Machine learning will go through these datasets and help come up with predictive models. For this project, it can help with segmentation or reconstruction of the brain and help classify or identify features of interest,” said Vishwanath.

Lessons learned from the smaller shrewmouse brain will be applied to a large mouse brain, which constitutes a 10-fold increase in volume. Comparisons between the two will reveal how organizational structures form during development, from embryo to adult, and how they evolve. The reconstruction of a non-human primate brain, with a volume 100 times larger than a mouse brain, is being considered for a later study.

A neuroscientist and a computational scientist leave a synchrotron facility with studies from a mouse brain . . .  armed with new techniques to analyze this data. The images produced by their work will provide a clearer understanding of how even the smallest changes to the brain play a role in the onset and evolution of neurological diseases, such as Alzheimer’s and autism, and perhaps lead to improved treatments or even a cure.

Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation’s first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America’s scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science.

The U.S. Department of Energy’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, visit the Office of Science website.


Source: John Spizzirri, Argonne 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!

With New Owner and New Roadmap, an Independent Omni-Path Is Staging a Comeback

July 23, 2021

Put on a shelf by Intel in 2019, Omni-Path faced a uncertain future, but under new custodian Cornelis Networks, OmniPath is looking to make a comeback as an independent high-performance interconnect solution. A "significant refresh" – called Omni-Path Express – is coming later this year according to the company. Cornelis Networks formed last September as a spinout of Intel's Omni-Path division. Read more…

PEARC21 Panel Reviews Eight New NSF-Funded HPC Systems Debuting in 2021

July 23, 2021

Over the past few years, the NSF has funded a number of HPC systems to further supply the open research community with computational resources to meet that community’s changing and expanding needs. A review of these systems at the PEARC21 conference (July 19-22) highlighted... Read more…

Chameleon’s HPC Testbed Sharpens Its Edge, Presses ‘Replay’

July 22, 2021

“One way of saying what I do for a living is to say that I develop scientific instruments,” said Kate Keahey, a senior fellow at the University of Chicago and a computer scientist at Argonne National Laboratory, as s Read more…

PEARC21 Plenary Session: AI for Innovative Social Work

July 21, 2021

AI analysis of social media poses a double-edged sword for social work and addressing the needs of at-risk youths, said Desmond Upton Patton, senior associate dean, Innovation and Academic Affairs, Columbia University. S Read more…

Summer Reading: “High-Performance Computing Is at an Inflection Point”

July 21, 2021

At last month’s 11th International Symposium on Highly Efficient Accelerators and Reconfigurable Technologies (HEART), a group of researchers led by Martin Schulz of the Leibniz Supercomputing Center (Munich) presented a “position paper” in which they argue HPC architectural landscape... Read more…

AWS Solution Channel

Accelerate innovation in healthcare and life sciences with AWS HPC

With Amazon Web Services, researchers can access purpose-built HPC tools and services along with scientific and technical expertise to accelerate the pace of discovery. Whether you are sequencing the human genome, using AI/ML for disease detection or running molecular dynamics simulations to develop lifesaving drugs, AWS has the infrastructure you need to run your HPC workloads. Read more…

PEARC21 Panel: Wafer-Scale-Engine Technology Accelerates Machine Learning, HPC

July 21, 2021

Early use of Cerebras’ CS-1 server and wafer-scale engine (WSE) has demonstrated promising acceleration of machine-learning algorithms, according to participants in the Scientific Research Enabled by CS-1 Systems panel Read more…

With New Owner and New Roadmap, an Independent Omni-Path Is Staging a Comeback

July 23, 2021

Put on a shelf by Intel in 2019, Omni-Path faced a uncertain future, but under new custodian Cornelis Networks, OmniPath is looking to make a comeback as an independent high-performance interconnect solution. A "significant refresh" – called Omni-Path Express – is coming later this year according to the company. Cornelis Networks formed last September as a spinout of Intel's Omni-Path division. Read more…

Chameleon’s HPC Testbed Sharpens Its Edge, Presses ‘Replay’

July 22, 2021

“One way of saying what I do for a living is to say that I develop scientific instruments,” said Kate Keahey, a senior fellow at the University of Chicago a Read more…

Summer Reading: “High-Performance Computing Is at an Inflection Point”

July 21, 2021

At last month’s 11th International Symposium on Highly Efficient Accelerators and Reconfigurable Technologies (HEART), a group of researchers led by Martin Schulz of the Leibniz Supercomputing Center (Munich) presented a “position paper” in which they argue HPC architectural landscape... Read more…

PEARC21 Panel: Wafer-Scale-Engine Technology Accelerates Machine Learning, HPC

July 21, 2021

Early use of Cerebras’ CS-1 server and wafer-scale engine (WSE) has demonstrated promising acceleration of machine-learning algorithms, according to participa Read more…

15 Years Later, the Green500 Continues Its Push for Energy Efficiency as a First-Order Concern in HPC

July 15, 2021

The Green500 list, which ranks the most energy-efficient supercomputers in the world, has virtually always faced an uphill battle. As Wu Feng – custodian of the Green500 list and an associate professor at Virginia Tech – tells it, “noone" cared about energy efficiency in the early 2000s, when the seeds... 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…

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…

ExaWind Prepares for New Architectures, Bigger Simulations

July 10, 2021

The ExaWind project describes itself in terms of terms like wake formation, turbine-turbine interaction and blade-boundary-layer dynamics, but the pitch to the Read more…

AMD Chipmaker TSMC to Use AMD Chips for Chipmaking

May 8, 2021

TSMC has tapped AMD to support its major manufacturing and R&D workloads. AMD will provide its Epyc Rome 7702P CPUs – with 64 cores operating at a base cl 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…

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…

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…

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…

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…

CERN Is Betting Big on Exascale

April 1, 2021

The European Organization for Nuclear Research (CERN) involves 23 countries, 15,000 researchers, billions of dollars a year, and the biggest machine in the worl 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

HPE Launches Storage Line Loaded with IBM’s Spectrum Scale File System

April 6, 2021

HPE today launched a new family of storage solutions bundled with IBM’s Spectrum Scale Erasure Code Edition parallel file system (description below) and featu 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…

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…

GTC21: Nvidia Launches cuQuantum; Dips a Toe in Quantum Computing

April 13, 2021

Yesterday Nvidia officially dipped a toe into quantum computing with the launch of cuQuantum SDK, a development platform for simulating quantum circuits on GPU-accelerated systems. As Nvidia CEO Jensen Huang emphasized in his keynote, Nvidia doesn’t plan to build... Read more…

Microsoft to Provide World’s Most Powerful Weather & Climate Supercomputer for UK’s Met Office

April 22, 2021

More than 14 months ago, the UK government announced plans to invest £1.2 billion ($1.56 billion) into weather and climate supercomputing, including procuremen Read more…

Q&A with Jim Keller, CTO of Tenstorrent, and an HPCwire Person to Watch in 2021

April 22, 2021

As part of our HPCwire Person to Watch series, we are happy to present our interview with Jim Keller, president and chief technology officer of Tenstorrent. One of the top chip architects of our time, Keller has had an impactful career. 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…

Senate Debate on Bill to Remake NSF – the Endless Frontier Act – Begins

May 18, 2021

The U.S. Senate today opened floor debate on the Endless Frontier Act which seeks to remake and expand the National Science Foundation by creating a technology Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire