HPC Bolsters Life Sciences

By Tiffany Trader

March 14, 2013

Last month, the Massachusetts Life Sciences Center (MLSC) announced more than $9 million in funding for life science-related projects in Western Massachusetts. Approximately half of that award, or $4.54 million, will allow the Massachusetts Green High Performance Computing Center (MGHPCC) in Holyoke, Mass., to create a cloud-based resource for computational biology. The remaining funds were split between several local community colleges and technical schools.

MLSC President and CEO Susan Windham-Bannister described the impetus and framing for the grants. The MLSC is administering a 10-year, billion-dollar initiative enacted by the Massachusetts legislature in 2008. The investment will go toward strengthening life sciences – a cluster of sectors that includes biotech, pharmaceuticals, medical devices, medical devices and bioinformatics.

As a funding and investment organization, one of MLSC’s main goals is to invest dollars in capital projects that play to the different strengths of the regions within the state. Another goal is to invest in unique resources that support innovation in the life sciences. And the final piece of their mission is to strategically leverage funds to encourage collaboration.

The $4.5 million grant to the MGHPCC meets all of those objectives, according to Windham-Bannister.

The Massachusetts Green High Performance Computing Center

The MGHPCC is a brand-new, state-of-the-art datacenter dedicated to research computing. It was put together by five area universities: Boston University, Harvard University, the Massachusetts Institute of Technology, Northeastern University and the University of Massachusetts.

The Center serves as a nucleus for collaborative work across the partner institutions, says John T. Goodhue, executive director of the Massachusetts Green High Performance Computing Center Inc. “When everyone’s data is in the same place, it’s easier to exchange it, and when they’re all working on and around the same facility, it’s easier to get conversations started,” he adds.

The MLSC award will support the creation of the Commonwealth Computational Cloud for Data Driven Biology. According to Goodhue, it is the first MGHPCC-based system that will be jointly owned by all five universities. The proposal focused on the advantages of creating a resource that was larger than any of the individual schools could feasibly stand up on their own. The project also includes industry partners Astra-Zeneca, Pfizer, Merck, Merrimack Pharmaceuticals, EMC and IBM, among others.

MLSC proposal team leader Chris Hill envisions the facility as a virtual meeting place. He says it’s too soon to commit to hardware and design specifications, but he reports the system will support both genetics sequencing and systems biology work. The hardware decisions will be driven by those areas, says Hill, who is also the principal research engineer at MIT’s Department of Earth, Atmospheric and Planetary Sciences. He adds that his colleagues are “interested in exploring the innovative spaces that will allow researchers to do things that they cannot easily do at the moment.”

Asked whether it will be more of an HPC machine or a big data machine, Hill is quick to respond that they want to bring the compute and the data together, so it will need to satisfy big-compute and big-data demands. “On the genetics side, there’s a lot of data processing that goes on, but on the systems biology side, there’s a lot of modeling work. These two models can drive architectures in somewhat different directions,” says Hill, “So it may be we end up with a hybrid or it may be that there’s a nice solution out there that addresses both under one umbrella.”

Next >>

As the architectural details have yet to be worked out, the cloudiness of the system is still unclear. Hill sees the virtue in “giving the machine a personality that meets researchers’ needs” and says virtualization may be a part of making this happen. He describes a resource that is more on-demand, more directly tied-in to lab analysis, experiments, measurements in hospitals and so on. “Rather than the traditional HPC batch environment, there will be a more responsive and interactive way of operating with this system,” he says.

Hill adds that the design team is keeping a close eye on advancements in server architectures, especially in the microserver space. “It’s too early to do anything with them this year,” he says, “but they are on an interesting trajectory in terms of performance per joule of energy.”

The partners are rolling out the new system in three stages, which will allow them to evolve the technology both in response to user needs and in regards to the latest technology developments. They are aiming to have an initial system up by the end of the year.

Once online, the Commonwealth Computational Cloud will be part of a high-speed academic network. The MGHPCC partners have been investing time and money toward creating a network infrastructure that enables fast remote access. End-to-end fiber supports 10 Gigabit speeds between the partner institutions and the datacenter, which is also hooked into high-speed research networks like Northern Crossroads and Internet2.

Changing Lives

The MGHPCC is located in Holyoke, Mass., a successful paper mill town in its heyday. The site is not far from some of the best colleges in the country, but it has suffered from high rates of unemployment in recent decades. Winning the bid for this state-of-the-art computing center is a real boon for the community.

Awarding the funds for a life science-based computational project was a strategic move by the MLSC.

“Some of the biggest breakthroughs in life science are being enabled by breakthroughs in computing. Personalized medicine, for example, is enabled by genomics. Genomics and genome-mapping has been enabled by high-performance computing,” remarks MLSC CEO Windham-Bannister.

“It’s important for us to make investments that impact the pace and success of innovation in the life sciences and we believe that high-performance computing is crucial,” she adds.

Investment in life sciences has not only enabled significant quality-of-life benefits, but it has been a proven model for driving economic development – a point that Windham-Bannister emphasizes:

“There are so many strong life sciences communities around the US – Massachusetts, California, Ohio, North Carolina, New York, Texas, and others – all of us are in search of ways to continue to make innovation in the life sciences the hallmark of the US, the hallmark of our state, and a way in which we can reinvent the economy here in the US. I think all of our states have seen the erosion of economic sectors that were historically very strong, and we need to find a way to replace those, and the 21st century economy appears to be the innovation economy.”

The MLSC CEO expects that the way we identify new drugs and new biologics is going to be fundamentally altered by high-performance, high-throughput computing. She suggests that in addition to supporting the research of hospitals and academic institutions, the new cloud-based system will attract the interest of life sciences outfits, companies like Pfizer, Novartis, Biogen, Amgen, Synovis, all of which have grown their presence in Massachusetts. “Our hope,” says Windham-Bannister, “is they will take advantage of this resource to support their drug discovery and drug development activities.”

Asked what she is most excited about in the field of life sciences, Windham-Bannister points to the important advances coming from the fields of personalized medicine and precision medicine, especially as it relates to treating pediatric cancer. “More and more, we’re seeing this notion of exactly the right drug and a companion diagnostic that goes with it so that we understand the genetic makeup of the individual and the molecular makeup of the tumor, and the very best way to treat that,” she says.

This new era brings the intelligence of a supercomputer and the ability to run massive amounts of data together, obviating the need to search one by one – which is the way diagnostics and treatments were done in the past. The ability to start with a more precise treatment to begin with is game-changing, says Windham-Bannister: “It’s computing changing our lives.”

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!

AI-Focused ‘Genius’ Supercomputer Installed at KU Leuven

April 24, 2018

Hewlett Packard Enterprise has deployed a new approximately half-petaflops supercomputer, named Genius, at Flemish research university KU Leuven. The system is built to run artificial intelligence (AI) workloads and, as Read more…

By Tiffany Trader

New Exascale System for Earth Simulation Introduced

April 23, 2018

After four years of development, the Energy Exascale Earth System Model (E3SM) will be unveiled today and released to the broader scientific community this month. The E3SM project is supported by the Department of Energy Read more…

By Staff

RSC Reports 500Tflops, Hot Water Cooled System Deployed at JINR

April 18, 2018

RSC, developer of supercomputers and advanced HPC systems based in Russia, today reported deployment of “the world's first 100% ‘hot water’ liquid cooled supercomputer” at Joint Institute for Nuclear Research (JI Read more…

By Staff

HPE Extreme Performance Solutions

Hybrid HPC is Speeding Time to Insight and Revolutionizing Medicine

High performance computing (HPC) is a key driver of success in many verticals today, and health and life science industries are extensively leveraging these capabilities. Read more…

New Device Spots Quantum Particle ‘Fingerprint’

April 18, 2018

Majorana particles have been observed by university researchers employing a device consisting of layers of magnetic insulators on a superconducting material. The advance opens the door to controlling the elusive particle Read more…

By George Leopold

AI-Focused ‘Genius’ Supercomputer Installed at KU Leuven

April 24, 2018

Hewlett Packard Enterprise has deployed a new approximately half-petaflops supercomputer, named Genius, at Flemish research university KU Leuven. The system is Read more…

By Tiffany Trader

Cray Rolls Out AMD-Based CS500; More to Follow?

April 18, 2018

Cray was the latest OEM to bring AMD back into the fold with introduction today of a CS500 option based on AMD’s Epyc processor line. The move follows Cray’ Read more…

By John Russell

IBM: Software Ecosystem for OpenPOWER is Ready for Prime Time

April 16, 2018

With key pieces of the IBM/OpenPOWER versus Intel/x86 gambit settling into place – e.g., the arrival of Power9 chips and Power9-based systems, hyperscaler sup Read more…

By John Russell

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

Cloud-Readiness and Looking Beyond Application Scaling

April 11, 2018

There are two aspects to consider when determining if an application is suitable for running in the cloud. The first, which we will discuss here under the title Read more…

By Chris Downing

Transitioning from Big Data to Discovery: Data Management as a Keystone Analytics Strategy

April 9, 2018

The past 10-15 years has seen a stark rise in the density, size, and diversity of scientific data being generated in every scientific discipline in the world. Key among the sciences has been the explosion of laboratory technologies that generate large amounts of data in life-sciences and healthcare research. Large amounts of data are now being stored in very large storage name spaces, with little to no organization and a general unease about how to approach analyzing it. Read more…

By Ari Berman, BioTeam, Inc.

IBM Expands Quantum Computing Network

April 5, 2018

IBM is positioning itself as a first mover in establishing the era of commercial quantum computing. The company believes in order for quantum to work, taming qu Read more…

By Tiffany Trader

FY18 Budget & CORAL-2 – Exascale USA Continues to Move Ahead

April 2, 2018

It was not pretty. However, despite some twists and turns, the federal government’s Fiscal Year 2018 (FY18) budget is complete and ended with some very positi Read more…

By Alex R. Larzelere

Inventor Claims to Have Solved Floating Point Error Problem

January 17, 2018

"The decades-old floating point error problem has been solved," proclaims a press release from inventor Alan Jorgensen. The computer scientist has filed for and Read more…

By Tiffany Trader

Researchers Measure Impact of ‘Meltdown’ and ‘Spectre’ Patches on HPC Workloads

January 17, 2018

Computer scientists from the Center for Computational Research, State University of New York (SUNY), University at Buffalo have examined the effect of Meltdown Read more…

By Tiffany Trader

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

Chip Flaws ‘Meltdown’ and ‘Spectre’ Loom Large

January 4, 2018

The HPC and wider tech community have been abuzz this week over the discovery of critical design flaws that impact virtually all contemporary microprocessors. T Read more…

By Tiffany Trader

How Meltdown and Spectre Patches Will Affect HPC Workloads

January 10, 2018

There have been claims that the fixes for the Meltdown and Spectre security vulnerabilities, named the KPTI (aka KAISER) patches, are going to affect applicatio Read more…

By Rosemary Francis

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

Leading Solution Providers

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

Fast Forward: Five HPC Predictions for 2018

December 21, 2017

What’s on your list of high (and low) lights for 2017? Volta 100’s arrival on the heels of the P100? Appearance, albeit late in the year, of IBM’s Power9? Read more…

By John Russell

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

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

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

New Blueprint for Converging HPC, Big Data

January 18, 2018

After five annual workshops on Big Data and Extreme-Scale Computing (BDEC), a group of international HPC heavyweights including Jack Dongarra (University of Te Read more…

By John Russell

Momentum Builds for US Exascale

January 9, 2018

2018 looks to be a great year for the U.S. exascale program. The last several months of 2017 revealed a number of important developments that help put the U.S. Read more…

By Alex R. Larzelere

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

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