Biotech HPC in the Cloud

By Michael Feldman

June 4, 2009

Hardly a week goes by now where some big IT company isn’t announcing a new cloud computing platform. Jumping into clouds seems metaphorically questionable, but a lot of IT firms see large-scale utility computing as the next big thing in computing, and they don’t want to be left out. Most recently hopping onto the bandwagon are Verizon, Computer Sciences Corp., and Sun Microsystems — its second foray into on-demand computing.

Those three companies add to a growing list of cloud providers, including Google, Microsoft, IBM, HP, AT&T, and dozens of smaller players. But HPC users seem to be gravitating toward the 800-pound gorilla in the room — Amazon and its Elastic Compute Cloud (EC2) offering. Even though EC2 has only been around for three years, it represents the oldest and most established general-purpose cloud computing platform.

In particular, EC2 looks like it’s becoming the platform of choice for biotech companies. Our February report on startup Pathwork Diagnostics is an example of a small company using EC2 to offload a cancer tissue analytics application. They cited Amazon’s $0.10/CPU-hour cost as the main attraction for outsourcing some of their work. Larger biotech companies are using EC2 as well. An article last week in Chemical & Engineering News by Rick Mullin described how a handful of big pharmaceutical firms are tapping into clouds. Pfizer, Eli Lilly & Co., Johnson & Johnson and Genentech are all looking to offload some of their bioinformatics work onto the cloud. From Mullin’s article:

Although Lilly has a sizable installed base of computers, the company’s IT infrastructure is operating at full capacity, says Andrew Kaczorek, senior systems analyst for discovery IT. “Because we have hundreds of different users, what we see is spiky utilization,” Kaczorek says. “The result is that for days at a time our clusters are at 100% of capacity. This means there are actually scientists who have work to be done that is literally sitting in a queue.” Although exact cost savings are difficult to calculate, they are clearly significant, according to Powers and Kaczorek, as are the time savings.

For example, the company was able to rent CPU cycles on EC2 to run a bioinformatics sequencing code on a 64-node EC2 cluster. For a 20 minute run, the cost to Eli Lilly was $6.40. That’s hard to beat when compared to the price of maintaining those additional 64 compute nodes on a permanent basis.

For bioscience businesses, the cloud story is especially compelling. Unlike other traditional HPC users like government labs, financial services firms, and oil & gas companies, life sciences came relatively late to the information technology game, so computing know-how and infrastructure at these companies tend to be spread rather thinly (at least relative to, say, a DOE lab). But today biotech companies are fully immersed in and dependent upon information technology, especially high performance computing. Mullin continues:

[T]he rapid creation of life sciences data keeps pointing to the use of cloud computing, and this is especially true in the area of genomics research. Advances in nanoscale and microfluidic chemistry now allow DNA to be monitored on tiny beads by photographic sensors that, according to Chris Dagdigian, principal consultant for the BioTeam, generate TIFF images in collections of up to 800 gigabytes. “This creates a massive data-capture and handling problem,” he says. “We are now in an era where instruments that are showing up in very small wet laboratories are capable of producing a terabyte or more of data in a day.”

It’s conceivable that the drug companies will bypass the large-scale datacenter build-out that occurred in other HPC verticals and move directly to an on-demand computing model. As such, it may serve as a model for how other HPC users, especially smaller organizations and new users with little high-end computing expertise, can get cloud-enabled.

The early experiences by these drug firms also point to how security concerns are holding back more widespread use of cloud computing. In this case, their main concern is protecting their intellectual property and patents, but almost all HPC users (not to mention just everyday enterprise users) have security issues of one sort or another. It’s worth noting here that Verizon’s new cloud platform offers added security, primary because their cloud runs over their own private network. But they also offer additional security in the form of identity and access management, host intrusion detection, application vulnerability assessment, network application assessment and professional security services. It’s not too hard to imagine that computing in the cloud can be made at least as secure as it is behind a local firewall.

For the HPC crowd, the longer term concern is performance. For a good synopsis of this topic take a look at Douglas Eadline’s recent article in Linux Magazine and the EC2 benchmarking paper (PDF) he references. The main argument put forth is that running applications directly on top of purpose-built HPC machines is always going to be more efficient than running applications through a bunch of cloud layers on general-purpose platforms. My take on this is that focusing on performance and computing efficiency ignores the more useful (but more slippery) concept of productivity. I’ve yet to see a research paper look at HPC in the cloud from this perspective.

There are some early attempts to marry cloud computing services with traditional HPC infrastructure. Darkstrand, Nimbus Services, R Systems, Univa UD, and a handful of other companies are on the leading edge of HPC-as-a-service that bring real supercomputers into the mix. Wolfram Research is also developing its own HPC Cloud Service in partnership with Nimbus and R Systems. Whether HPC will be able to carve out its own niche in cloud computing is an open question, but a deeper discussion of this will have to wait until another day.

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!

SC Bids Farewell to Denver, Heads to Dallas for 30th

November 17, 2017

After a jam-packed four-day expo and intensive six-day technical program, SC17 has wrapped up another successful event that brought together nearly 13,000 visitors to the Colorado Convention Center in Denver for the larg Read more…

By Tiffany Trader

SC17 Keynote – HPC Powers SKA Efforts to Peer Deep into the Cosmos

November 17, 2017

This week’s SC17 keynote – Life, the Universe and Computing: The Story of the SKA Telescope – was a powerful pitch for the potential of Big Science projects that also showcased the foundational role of high performance computing in modern science. It was also visually stunning. Read more…

By John Russell

How Cities Use HPC at the Edge to Get Smarter

November 17, 2017

Cities are sensoring up, collecting vast troves of data that they’re running through predictive models and using the insights to solve problems that, in some cases, city managers didn’t even know existed. Speaking Read more…

By Doug Black

HPE Extreme Performance Solutions

Harness Scalable Petabyte Storage with HPE Apollo 4510 and HPE StoreEver

As a growing number of connected devices challenges IT departments to rapidly collect, manage, and store troves of data, organizations must adopt a new generation of IT to help them operate quickly and intelligently. Read more…

SC17 Student Cluster Competition Configurations: Fewer Nodes, Way More Accelerators

November 16, 2017

The final configurations for each of the SC17 “Donnybrook in Denver” Student Cluster Competition have been released. Fortunately, each team received their equipment shipments on time and undamaged, so the teams are r Read more…

By Dan Olds

SC Bids Farewell to Denver, Heads to Dallas for 30th

November 17, 2017

After a jam-packed four-day expo and intensive six-day technical program, SC17 has wrapped up another successful event that brought together nearly 13,000 visit Read more…

By Tiffany Trader

SC17 Keynote – HPC Powers SKA Efforts to Peer Deep into the Cosmos

November 17, 2017

This week’s SC17 keynote – Life, the Universe and Computing: The Story of the SKA Telescope – was a powerful pitch for the potential of Big Science projects that also showcased the foundational role of high performance computing in modern science. It was also visually stunning. Read more…

By John Russell

How Cities Use HPC at the Edge to Get Smarter

November 17, 2017

Cities are sensoring up, collecting vast troves of data that they’re running through predictive models and using the insights to solve problems that, in some Read more…

By Doug Black

Student Cluster LINPACK Record Shattered! More LINs Packed Than Ever before!

November 16, 2017

Nanyang Technological University, the pride of Singapore, utterly destroyed the Student Cluster Competition LINPACK record by posting a score of 51.77 TFlop/s a Read more…

By Dan Olds

Hyperion Market Update: ‘Decent’ Growth Led by HPE; AI Transparency a Risk Issue

November 15, 2017

The HPC market update from Hyperion Research (formerly IDC) at the annual SC conference is a business and social “must,” and this year’s presentation at S Read more…

By Doug Black

Nvidia Focuses Its Cloud Containers on HPC Applications

November 14, 2017

Having migrated its top-of-the-line datacenter GPU to the largest cloud vendors, Nvidia is touting its Volta architecture for a range of scientific computing ta Read more…

By George Leopold

HPE Launches ARM-based Apollo System for HPC, AI

November 14, 2017

HPE doubled down on its memory-driven computing vision while expanding its processor portfolio with the announcement yesterday of the company’s first ARM-base Read more…

By Doug Black

OpenACC Shines in Global Climate/Weather Codes

November 14, 2017

OpenACC, the directive-based parallel programming model used mostly for porting codes to GPUs for use on heterogeneous systems, came to SC17 touting impressive Read more…

By John Russell

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

NERSC Scales Scientific Deep Learning to 15 Petaflops

August 28, 2017

A collaborative effort between Intel, NERSC and Stanford has delivered the first 15-petaflops deep learning software running on HPC platforms and is, according Read more…

By Rob Farber

Oracle Layoffs Reportedly Hit SPARC and Solaris Hard

September 7, 2017

Oracle’s latest layoffs have many wondering if this is the end of the line for the SPARC processor and Solaris OS development. As reported by multiple sources 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

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

Google Releases Deeplearn.js to Further Democratize Machine Learning

August 17, 2017

Spreading the use of machine learning tools is one of the goals of Google’s PAIR (People + AI Research) initiative, which was introduced in early July. Last w 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

Amazon Debuts New AMD-based GPU Instances for Graphics Acceleration

September 12, 2017

Last week Amazon Web Services (AWS) streaming service, AppStream 2.0, introduced a new GPU instance called Graphics Design intended to accelerate graphics. The Read more…

By John Russell

Leading Solution Providers

EU Funds 20 Million Euro ARM+FPGA Exascale Project

September 7, 2017

At the Barcelona Supercomputer Centre on Wednesday (Sept. 6), 16 partners gathered to launch the EuroEXA project, which invests €20 million over three-and-a-half years into exascale-focused research and development. Led by the Horizon 2020 program, EuroEXA picks up the banner of a triad of partner projects — ExaNeSt, EcoScale and ExaNoDe — building on their work... Read more…

By Tiffany Trader

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

Reinders: “AVX-512 May Be a Hidden Gem” in Intel Xeon Scalable Processors

June 29, 2017

Imagine if we could use vector processing on something other than just floating point problems.  Today, GPUs and CPUs work tirelessly to accelerate algorithms Read more…

By James Reinders

Cray Moves to Acquire the Seagate ClusterStor Line

July 28, 2017

This week Cray announced that it is picking up Seagate's ClusterStor HPC storage array business for an undisclosed sum. "In short we're effectively transitioning the bulk of the ClusterStor product line to Cray," said CEO Peter Ungaro. Read more…

By Tiffany Trader

Intel Launches Software Tools to Ease FPGA Programming

September 5, 2017

Field Programmable Gate Arrays (FPGAs) have a reputation for being difficult to program, requiring expertise in specialty languages, like Verilog or VHDL. Easin Read more…

By Tiffany Trader

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

IBM Advances Web-based Quantum Programming

September 5, 2017

IBM Research is pairing its Jupyter-based Data Science Experience notebook environment with its cloud-based quantum computer, IBM Q, in hopes of encouraging a new class of entrepreneurial user to solve intractable problems that even exceed the capabilities of the best AI systems. Read more…

By Alex Woodie

How ‘Knights Mill’ Gets Its Deep Learning Flops

June 22, 2017

Intel, the subject of much speculation regarding the delayed, rewritten or potentially canceled “Aurora” contract (the Argonne Lab part of the CORAL “ Read more…

By Tiffany Trader

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