Leveraging HPC Hardware to Run Next-generation Molecular Imaging Analysis

By Louis Vistola

October 6, 2016

Deriving the three-dimensional (3D) structure of biological macromolecules is critical to fighting cancer and other diseases. A deeper understanding of the structure can help researchers design inhibitors and develop new drugs to treat or cure patients.

While molecular imaging technology has improved over the years, the computational challenges have grown. Currently, cryo-electron microscopy (cryo-EM) is  rapidly replacing the traditional X-ray crystallography method for elucidating the 3D structures of single biomolecules in a state that is much closer to their native form. A better computational method is needed to extract the 3D structure from microscope’s two-dimensional (2D) images.

This is an area where Dr. Youdong (Jack) Mao has focused his energy. He is using Dell PowerEdge servers with new Intel® Xeon Phi™ processor (a.k.a. Knights Landing) technology to develop a high-performance computing (HPC) molecular imaging analysis platform. The work aims to take advantage of higher performance capabilities of today’s multicore, parallel processor architectures.

Why HPC is required

Like many aspects of modern life sciences research, the analysis of molecular imaging involves large volumes of data. Using cryo-EM, a sample under inspection might have 50,000 to 100,000 single particles in random orientations, generating a massive amount of molecular images. Analyzing these images to determine the 3D molecular structure can take one million CPU hours.

That’s for one molecule and one experimental run. A research facility with three to five microscopes can produce 25 terabytes of raw data per microscope per day, which after processing  results in a approximately 2 to 3 terabytes of data a day and somewhere in the petabyte range per  year.

A second factor that impacts HPC requirements is the noisy data. Because biomolecules are highly sensitive to radiation damage by the microscope’s electron beam, the molecular images have to be taken at a low dose. This gives rise to an extremely high degree of noise in the formation of the image. In fact, the signal to noise ratio is 10 to 100 times lower than normal imaging data. As a result, researchers must use sophisticated averaging and machine learning techniques to classify the image and analyze the 3D structure of a sample.

These issues have limited research in the field. The place to start to improve the situation was to update the analysis software. “The software has evolved from code developed decades ago,” said Dr. Mao. Most of the software was designed to run on a single core and does not take the hardware capabilities of the Intel® Xeon Phi processor into account.

Dr. Mao has had a multi-year collaboration with Dell and Intel at both the Intel® Parallel Computing Center (IPCC) at Dana-Farber Cancer Institute (DFCI) and at Peking University.  “We are trying to modernize the code,” said Dr. Mao. There are cases where the new code, leveraging multiple cores and hardware acceleration technology of the Intel chips, speeds up averaging by a factor of 1,000. “With the speed up, we can think about using more sophisticated software,” said Dr. Mao. For example, artificial intelligence and machine learning methods can be used.

“This opens up new frontiers,” said Dr. Mao. He notes that by harnessing the additional compute capacity, researchers can increase their image analysis throughput by an order of magnitude. Or they can choose to do a deeper analysis of their data. To that latter point, researchers can refine the classification of their images.

Looking to the future

The work in this area goes beyond simply updating old code. The ultimate goal is to develop a cutting-edge solution for the next-generation HPC platform for structural biology, based on Intel®Many Integrated Core Architecture and Intel® Scalable System Framework

Specifically, the research at IPCC at DFCI seeks to capitalize on the tremendous potential of Intel’s processor architecture in system design based on the Scalable System Framework, as well as heterogeneous parallel computing, to process a rapidly increasing volume of electron microscopy data.

One development from this work is the ROME (Refinement and Optimization via Machine lEarning for cryo-EM) software package. The open source ROME package is a parallel computing software system dedicated for high-resolution cryo-EM structure determination and data analysis, which implements advanced machine learning approaches in modern computer sciences and runs natively in an HPC environment. The ROME 1.0 introduces SML (statistical manifold learning)-based deep classification following MAP-based image alignment. It also implemented traditional unsupervised MAP-based classification and includes several useful tools, such as 2D class averaging with CTF (contrast transfer function) correction and a convenient GUI for curation, inspection, and verification of single-particle classes. The ROME system has been optimized on both Intel® Xeon multi-core CPUs and Intel® Xeon Phi many-core coprocessors.

Making use of Dell PowerEdge servers with the new generation of Intel® Xeon Phi processors, researchers have a powerful tool to expand their work in the life sciences. The platform can be used as a general resource for parallel computing applications in structural biology and molecular medicine. Specifically, the combination of Dell and Intel hardware with the optimized analysis software offers a system for the ultra-high-resolution reconstruction of single biomolecules in their native states.

For more information about accelerating life sciences research with new HPC platforms, visit www.dell.com/hpc

For more information on Code Modernization with the Life Sciences Community, visit www.intel.com/healthcare/optimizecode

For more information on Intel® Parallel Computer Center for Structural Biology at Dana Farber Cancer Institute and Harvard Medical School, visit http://ipccsb.dfci.harvard.edu/index.html

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!

GDPR’s Impact on Scientific Research Uncertain

May 24, 2018

Amid the angst over preparations—or lack thereof—for new European Union data protections entering into force at week’s end is the equally worrisome issue of the rules’ impact on scientific research. Among the Read more…

By George Leopold

Intel Pledges First Commercial Nervana Product ‘Spring Crest’ in 2019

May 24, 2018

At its AI developer conference in San Francisco yesterday, Intel embraced a holistic approach to AI and showed off a broad AI portfolio that includes Xeon processors, Movidius technologies, FPGAs and Intel’s Nervana Neural Network Processors (NNPs), based on the technology it acquired in 2016. Read more…

By Tiffany Trader

Pattern Computer – Startup Claims Breakthrough in ‘Pattern Discovery’ Technology

May 23, 2018

If it weren’t for the heavy-hitter technology team behind start-up Pattern Computer, which emerged from stealth today in a live-streamed event from San Francisco, one would be tempted to dismiss its claims of inventing Read more…

By John Russell

HPE Extreme Performance Solutions

HPC and AI Convergence is Accelerating New Levels of Intelligence

Data analytics is the most valuable tool in the digital marketplace – so much so that organizations are employing high performance computing (HPC) capabilities to rapidly collect, share, and analyze endless streams of data. Read more…

IBM Accelerated Insights

Mastering the Big Data Challenge in Cognitive Healthcare

Patrick Chain, genomics researcher at Los Alamos National Laboratory, posed a question in a recent blog: What if a nurse could swipe a patient’s saliva and run a quick genetic test to determine if the patient’s sore throat was caused by a cold virus or a bacterial infection? Read more…

Silicon Startup Raises ‘Prodigy’ for Hyperscale/AI Workloads

May 23, 2018

There's another silicon startup coming onto the HPC/hyperscale scene with some intriguing and bold claims. Silicon Valley-based Tachyum Inc., which has been emerging from stealth over the last year and a half, is unveili Read more…

By Tiffany Trader

Intel Pledges First Commercial Nervana Product ‘Spring Crest’ in 2019

May 24, 2018

At its AI developer conference in San Francisco yesterday, Intel embraced a holistic approach to AI and showed off a broad AI portfolio that includes Xeon processors, Movidius technologies, FPGAs and Intel’s Nervana Neural Network Processors (NNPs), based on the technology it acquired in 2016. Read more…

By Tiffany Trader

Pattern Computer – Startup Claims Breakthrough in ‘Pattern Discovery’ Technology

May 23, 2018

If it weren’t for the heavy-hitter technology team behind start-up Pattern Computer, which emerged from stealth today in a live-streamed event from San Franci Read more…

By John Russell

Silicon Startup Raises ‘Prodigy’ for Hyperscale/AI Workloads

May 23, 2018

There's another silicon startup coming onto the HPC/hyperscale scene with some intriguing and bold claims. Silicon Valley-based Tachyum Inc., which has been eme Read more…

By Tiffany Trader

Japan Meteorological Agency Takes Delivery of Pair of Crays

May 21, 2018

Cray has supplied two identical Cray XC50 supercomputers to the Japan Meteorological Agency (JMA) in northwestern Tokyo. Boasting more than 18 petaflops combine Read more…

By Tiffany Trader

ASC18: Final Results Revealed & Wrapped Up

May 17, 2018

It was an exciting week at ASC18 in Nanyang, China. The student teams braved extreme heat, extremely difficult applications, and extreme competition in order to cross the cluster competition finish line. The gala awards ceremony took place on Wednesday. The auditorium was packed with student teams, various dignitaries, the media, and other interested parties. So what happened? Read more…

By Dan Olds

Spring Meetings Underscore Quantum Computing’s Rise

May 17, 2018

The month of April 2018 saw four very important and interesting meetings to discuss the state of quantum computing technologies, their potential impacts, and th Read more…

By Alex R. Larzelere

Quantum Network Hub Opens in Japan

May 17, 2018

Following on the launch of its Q Commercial quantum network last December with 12 industrial and academic partners, the official Japanese hub at Keio University is now open to facilitate the exploration of quantum applications important to science and business. The news comes a week after IBM announced that North Carolina State University was the first U.S. university to join its Q Network. Read more…

By Tiffany Trader

Democratizing HPC: OSC Releases Version 1.3 of OnDemand

May 16, 2018

Making HPC resources readily available and easier to use for scientists who may have less HPC expertise is an ongoing challenge. Open OnDemand is a project by t Read more…

By John Russell

MLPerf – Will New Machine Learning Benchmark Help Propel AI Forward?

May 2, 2018

Let the AI benchmarking wars begin. Today, a diverse group from academia and industry – Google, Baidu, Intel, AMD, Harvard, and Stanford among them – releas Read more…

By John Russell

How the Cloud Is Falling Short for HPC

March 15, 2018

The last couple of years have seen cloud computing gradually build some legitimacy within the HPC world, but still the HPC industry lies far behind enterprise I Read more…

By Chris Downing

Russian Nuclear Engineers Caught Cryptomining on Lab Supercomputer

February 12, 2018

Nuclear scientists working at the All-Russian Research Institute of Experimental Physics (RFNC-VNIIEF) have been arrested for using lab supercomputing resources to mine crypto-currency, according to a report in Russia’s Interfax News Agency. Read more…

By Tiffany Trader

Nvidia Responds to Google TPU Benchmarking

April 10, 2017

Nvidia highlights strengths of its newest GPU silicon in response to Google's report on the performance and energy advantages of its custom tensor processor. Read more…

By Tiffany Trader

Deep Learning at 15 PFlops Enables Training for Extreme Weather Identification at Scale

March 19, 2018

Petaflop per second deep learning training performance on the NERSC (National Energy Research Scientific Computing Center) Cori supercomputer has given climate Read more…

By Rob Farber

AI Cloud Competition Heats Up: Google’s TPUs, Amazon Building AI Chip

February 12, 2018

Competition in the white hot AI (and public cloud) market pits Google against Amazon this week, with Google offering AI hardware on its cloud platform intended Read more…

By Doug Black

US Plans $1.8 Billion Spend on DOE Exascale Supercomputing

April 11, 2018

On Monday, the United States Department of Energy announced its intention to procure up to three exascale supercomputers at a cost of up to $1.8 billion with th Read more…

By Tiffany Trader

Lenovo Unveils Warm Water Cooled ThinkSystem SD650 in Rampup to LRZ Install

February 22, 2018

This week Lenovo took the wraps off the ThinkSystem SD650 high-density server with third-generation direct water cooling technology developed in tandem with par Read more…

By Tiffany Trader

Leading Solution Providers

SC17 Booth Video Tours Playlist

Altair @ SC17

Altair

AMD @ SC17

AMD

ASRock Rack @ SC17

ASRock Rack

CEJN @ SC17

CEJN

DDN Storage @ SC17

DDN Storage

Huawei @ SC17

Huawei

IBM @ SC17

IBM

IBM Power Systems @ SC17

IBM Power Systems

Intel @ SC17

Intel

Lenovo @ SC17

Lenovo

Mellanox Technologies @ SC17

Mellanox Technologies

Microsoft @ SC17

Microsoft

Penguin Computing @ SC17

Penguin Computing

Pure Storage @ SC17

Pure Storage

Supericro @ SC17

Supericro

Tyan @ SC17

Tyan

Univa @ SC17

Univa

HPC and AI – Two Communities Same Future

January 25, 2018

According to Al Gara (Intel Fellow, Data Center Group), high performance computing and artificial intelligence will increasingly intertwine as we transition to Read more…

By Rob Farber

Google Chases Quantum Supremacy with 72-Qubit Processor

March 7, 2018

Google pulled ahead of the pack this week in the race toward "quantum supremacy," with the introduction of a new 72-qubit quantum processor called Bristlecone. Read more…

By Tiffany Trader

HPE Wins $57 Million DoD Supercomputing Contract

February 20, 2018

Hewlett Packard Enterprise (HPE) today revealed details of its massive $57 million HPC contract with the U.S. Department of Defense (DoD). The deal calls for HP Read more…

By Tiffany Trader

CFO Steps down in Executive Shuffle at Supermicro

January 31, 2018

Supermicro yesterday announced senior management shuffling including prominent departures, the completion of an audit linked to its delayed Nasdaq filings, and Read more…

By John Russell

Deep Learning Portends ‘Sea Change’ for Oil and Gas Sector

February 1, 2018

The billowing compute and data demands that spurred the oil and gas industry to be the largest commercial users of high-performance computing are now propelling Read more…

By Tiffany Trader

Nvidia Ups Hardware Game with 16-GPU DGX-2 Server and 18-Port NVSwitch

March 27, 2018

Nvidia unveiled a raft of new products from its annual technology conference in San Jose today, and despite not offering up a new chip architecture, there were still a few surprises in store for HPC hardware aficionados. Read more…

By Tiffany Trader

Hennessy & Patterson: A New Golden Age for Computer Architecture

April 17, 2018

On Monday June 4, 2018, 2017 A.M. Turing Award Winners John L. Hennessy and David A. Patterson will deliver the Turing Lecture at the 45th International Sympo Read more…

By Staff

Part One: Deep Dive into 2018 Trends in Life Sciences HPC

March 1, 2018

Life sciences is an interesting lens through which to see HPC. It is perhaps not an obvious choice, given life sciences’ relative newness as a heavy user of H Read more…

By John Russell

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