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!

UCSD, AIST Forge Tighter Alliance with AI-Focused MOU

January 18, 2018

The rich history of collaboration between UC San Diego and AIST in Japan is getting richer. The organizations entered into a five-year memorandum of understanding on January 10. The MOU represents the continuation of a 1 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 Tennessee), Satoshi Matsuoka (Tokyo Institute of Technology), Read more…

By John Russell

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 and Spectre security updates on the performance of popular H Read more…

By Tiffany Trader

HPE Extreme Performance Solutions

HPE and NREL Take Steps to Create a Sustainable, Energy-Efficient Data Center with an H2 Fuel Cell

As enterprises attempt to manage rising volumes of data, unplanned data center outages are becoming more common and more expensive. As the cost of downtime rises, enterprises lose out on productivity and valuable competitive advantage without access to their critical data. Read more…

Fostering Lustre Advancement Through Development and Contributions

January 17, 2018

Six months after organizational changes at Intel's High Performance Data (HPDD) division, most in the Lustre community have shed any initial apprehension around the potential changes that could affect or disrupt Lustre Read more…

By Carlos Aoki Thomaz

UCSD, AIST Forge Tighter Alliance with AI-Focused MOU

January 18, 2018

The rich history of collaboration between UC San Diego and AIST in Japan is getting richer. The organizations entered into a five-year memorandum of understandi 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

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

Fostering Lustre Advancement Through Development and Contributions

January 17, 2018

Six months after organizational changes at Intel's High Performance Data (HPDD) division, most in the Lustre community have shed any initial apprehension aroun Read more…

By Carlos Aoki Thomaz

When the Chips Are Down

January 11, 2018

In the last article, "The High Stakes Semiconductor Game that Drives HPC Diversity," I alluded to the challenges facing the semiconductor industry and how that may impact the evolution of HPC systems over the next few years. I thought I’d lift the covers a little and look at some of the commercial challenges that impact the component technology we use in HPC. Read more…

By Dairsie Latimer

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

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

ANL’s Rick Stevens on CANDLE, ARM, Quantum, and More

January 8, 2018

Late last year HPCwire caught up with Rick Stevens, associate laboratory director for computing, environment and life Sciences at Argonne National Laboratory, f Read more…

By John Russell

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

US Coalesces Plans for First Exascale Supercomputer: Aurora in 2021

September 27, 2017

At the Advanced Scientific Computing Advisory Committee (ASCAC) meeting, in Arlington, Va., yesterday (Sept. 26), it was revealed that the "Aurora" supercompute Read more…

By Tiffany Trader

Japan Unveils Quantum Neural Network

November 22, 2017

The U.S. and China are leading the race toward productive quantum computing, but it's early enough that ultimate leadership is still something of an open questi Read more…

By Tiffany Trader

AMD Showcases Growing Portfolio of EPYC and Radeon-based Systems at SC17

November 13, 2017

AMD’s charge back into HPC and the datacenter is on full display at SC17. Having launched the EPYC processor line in June along with its MI25 GPU the focus he Read more…

By John Russell

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

IBM Begins Power9 Rollout with Backing from DOE, Google

December 6, 2017

After over a year of buildup, IBM is unveiling its first Power9 system based on the same architecture as the Department of Energy CORAL supercomputers, Summit a 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

GlobalFoundries Puts Wind in AMD’s Sails with 12nm FinFET

September 24, 2017

From its annual tech conference last week (Sept. 20), where GlobalFoundries welcomed more than 600 semiconductor professionals (reaching the Santa Clara venue Read more…

By Tiffany Trader

Leading Solution Providers

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

Perspective: What Really Happened at SC17?

November 22, 2017

SC is over. Now comes the myriad of follow-ups. Inboxes are filled with templated emails from vendors and other exhibitors hoping to win a place in the post-SC thinking of booth visitors. Attendees of tutorials, workshops and other technical sessions will be inundated with requests for feedback. Read more…

By Andrew Jones

Tensors Come of Age: Why the AI Revolution Will Help HPC

November 13, 2017

Thirty years ago, parallel computing was coming of age. A bitter battle began between stalwart vector computing supporters and advocates of various approaches to parallel computing. IBM skeptic Alan Karp, reacting to announcements of nCUBE’s 1024-microprocessor system and Thinking Machines’ 65,536-element array, made a public $100 wager that no one could get a parallel speedup of over 200 on real HPC workloads. Read more…

By John Gustafson & Lenore Mullin

Delays, Smoke, Records & Markets – A Candid Conversation with Cray CEO Peter Ungaro

October 5, 2017

Earlier this month, Tom Tabor, publisher of HPCwire and I had a very personal conversation with Cray CEO Peter Ungaro. Cray has been on something of a Cinderell Read more…

By Tiffany Trader & Tom Tabor

Flipping the Flops and Reading the Top500 Tea Leaves

November 13, 2017

The 50th edition of the Top500 list, the biannual publication of the world’s fastest supercomputers based on public Linpack benchmarking results, was released Read more…

By Tiffany Trader

GlobalFoundries, Ayar Labs Team Up to Commercialize Optical I/O

December 4, 2017

GlobalFoundries (GF) and Ayar Labs, a startup focused on using light, instead of electricity, to transfer data between chips, today announced they've entered in 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

HPC Chips – A Veritable Smorgasbord?

October 10, 2017

For the first time since AMD's ill-fated launch of Bulldozer the answer to the question, 'Which CPU will be in my next HPC system?' doesn't have to be 'Whichever variety of Intel Xeon E5 they are selling when we procure'. Read more…

By Dairsie Latimer

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