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!

What’s New in HPC Research: September (Part 1)

September 18, 2018

In this new bimonthly feature, HPCwire will highlight newly published research in the high-performance computing community and related domains. From exascale to quantum computing, the details are here. Check back every Read more…

By Oliver Peckham

House Passes $1.275B National Quantum Initiative

September 17, 2018

Last Thursday the U.S. House of Representatives passed the National Quantum Initiative Act (NQIA) intended to accelerate quantum computing research and development. Among other things it would establish a National Quantu Read more…

By John Russell

Nvidia Accelerates AI Inference in the Datacenter with T4 GPU

September 14, 2018

Nvidia is upping its game for AI inference in the datacenter with a new platform consisting of an inference accelerator chip--the new Turing-based Tesla T4 GPU--and a refresh of its inference server software packaged as Read more…

By George Leopold

HPE Extreme Performance Solutions

Introducing the First Integrated System Management Software for HPC Clusters from HPE

How do you manage your complex, growing cluster environments? Answer that big challenge with the new HPC cluster management solution: HPE Performance Cluster Manager. Read more…

IBM Accelerated Insights

A Crystal Ball for HPC

People are notoriously bad at predicting the future.  This very much includes experts. In the Forbes article “Why Most Predictions Are So Bad” Philip Tetlock discusses the largest and best-known test of the accuracy of expert predictions which show that any experts would do better if they make random guesses. Read more…

NSF Highlights Expanded Efforts for Broadening Participation in Computing

September 13, 2018

Today, the Directorate of Computer and Information Science and Engineering (CISE) of the NSF released a letter highlighting the expansion of its broadening participation in computing efforts. The letter was penned by Jam Read more…

By Staff

House Passes $1.275B National Quantum Initiative

September 17, 2018

Last Thursday the U.S. House of Representatives passed the National Quantum Initiative Act (NQIA) intended to accelerate quantum computing research and developm Read more…

By John Russell

Nvidia Accelerates AI Inference in the Datacenter with T4 GPU

September 14, 2018

Nvidia is upping its game for AI inference in the datacenter with a new platform consisting of an inference accelerator chip--the new Turing-based Tesla T4 GPU- Read more…

By George Leopold

DeepSense Combines HPC and AI to Bolster Canada’s Ocean Economy

September 13, 2018

We often hear scientists say that we know less than 10 percent of the life of the oceans. This week, IBM and a group of Canadian industry and government partner Read more…

By Tiffany Trader

Rigetti (and Others) Pursuit of Quantum Advantage

September 11, 2018

Remember ‘quantum supremacy’, the much-touted but little-loved idea that the age of quantum computing would be signaled when quantum computers could tackle Read more…

By John Russell

How FPGAs Accelerate Financial Services Workloads

September 11, 2018

While FSI companies are unlikely, for competitive reasons, to disclose their FPGA strategies, James Reinders offers insights into the case for FPGAs as accelerators for FSI by discussing performance, power, size, latency, jitter and inline processing. Read more…

By James Reinders

Update from Gregory Kurtzer on Singularity’s Push into FS and the Enterprise

September 11, 2018

Container technology is hardly new but it has undergone rapid evolution in the HPC space in recent years to accommodate traditional science workloads and HPC systems requirements. While Docker containers continue to dominate in the enterprise, other variants are becoming important and one alternative with distinctly HPC roots – Singularity – is making an enterprise push targeting advanced scale workload inclusive of HPC. Read more…

By John Russell

At HPC on Wall Street: AI-as-a-Service Accelerates AI Journeys

September 10, 2018

AIaaS – artificial intelligence-as-a-service – is the technology discipline that eases enterprise entry into the mysteries of the AI journey while lowering Read more…

By Doug Black

No Go for GloFo at 7nm; and the Fujitsu A64FX post-K CPU

September 5, 2018

It’s been a news worthy couple of weeks in the semiconductor and HPC industry. There were several HPC relevant disclosures at Hot Chips 2018 to whet appetites Read more…

By Dairsie Latimer

TACC Wins Next NSF-funded Major Supercomputer

July 30, 2018

The Texas Advanced Computing Center (TACC) has won the next NSF-funded big supercomputer beating out rivals including the National Center for Supercomputing Ap Read more…

By John Russell

IBM at Hot Chips: What’s Next for Power

August 23, 2018

With processor, memory and networking technologies all racing to fill in for an ailing Moore’s law, the era of the heterogeneous datacenter is well underway, Read more…

By Tiffany Trader

Requiem for a Phi: Knights Landing Discontinued

July 25, 2018

On Monday, Intel made public its end of life strategy for the Knights Landing "KNL" Phi product set. The announcement makes official what has already been wide Read more…

By Tiffany Trader

CERN Project Sees Orders-of-Magnitude Speedup with AI Approach

August 14, 2018

An award-winning effort at CERN has demonstrated potential to significantly change how the physics based modeling and simulation communities view machine learni Read more…

By Rob Farber

ORNL Summit Supercomputer Is Officially Here

June 8, 2018

Oak Ridge National Laboratory (ORNL) together with IBM and Nvidia celebrated the official unveiling of the Department of Energy (DOE) Summit supercomputer toda Read more…

By Tiffany Trader

New Deep Learning Algorithm Solves Rubik’s Cube

July 25, 2018

Solving (and attempting to solve) Rubik’s Cube has delighted millions of puzzle lovers since 1974 when the cube was invented by Hungarian sculptor and archite Read more…

By John Russell

AMD’s EPYC Road to Redemption in Six Slides

June 21, 2018

A year ago AMD returned to the server market with its EPYC processor line. The earth didn’t tremble but folks took notice. People remember the Opteron fondly 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

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

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

Sandia to Take Delivery of World’s Largest Arm System

June 18, 2018

While the enterprise remains circumspect on prospects for Arm servers in the datacenter, the leadership HPC community is taking a bolder, brighter view of the x86 server CPU alternative. Amongst current and planned Arm HPC installations – i.e., the innovative Mont-Blanc project, led by Bull/Atos, the 'Isambard’ Cray XC50 going into the University of Bristol, and commitments from both Japan and France among others -- HPE is announcing that it will be supply the United States National Nuclear Security Administration (NNSA) with a 2.3 petaflops peak Arm-based system, named Astra. Read more…

By Tiffany Trader

D-Wave Breaks New Ground in Quantum Simulation

July 16, 2018

Last Friday D-Wave scientists and colleagues published work in Science which they say represents the first fulfillment of Richard Feynman’s 1982 notion that Read more…

By John Russell

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

Intel Announces Cooper Lake, Advances AI Strategy

August 9, 2018

Intel's chief datacenter exec Navin Shenoy kicked off the company's Data-Centric Innovation Summit Wednesday, the day-long program devoted to Intel's datacenter Read more…

By Tiffany Trader

TACC’s ‘Frontera’ Supercomputer Expands Horizon for Extreme-Scale Science

August 29, 2018

The National Science Foundation and the Texas Advanced Computing Center announced today that a new system, called Frontera, will overtake Stampede 2 as the fast Read more…

By Tiffany Trader

GPUs Power Five of World’s Top Seven Supercomputers

June 25, 2018

The top 10 echelon of the newly minted Top500 list boasts three powerful new systems with one common engine: the Nvidia Volta V100 general-purpose graphics proc Read more…

By Tiffany Trader

The Machine Learning Hype Cycle and HPC

June 14, 2018

Like many other HPC professionals I’m following the hype cycle around machine learning/deep learning with interest. I subscribe to the view that we’re probably approaching the ‘peak of inflated expectation’ but not quite yet starting the descent into the ‘trough of disillusionment. This still raises the probability that... Read more…

By Dairsie Latimer

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