Cycle Computing and the HPC Experiment

By Ian Armas Foster

July 15, 2013

With hardware advancing at a relatively stable (if still exponential) rate and datasets increasing at a much higher rate, parallelism is a main tenet of high performance computing today. That parallelism is difficult to attain in a cloud environment, as latencies there are typically higher, thus slowing performance.

Three weeks ago, Jason Stowe, CEO of Cycle Computing, spoke with HPC in the Cloud about their work in renting large clusters of Amazon HPC instances for companies looking for a short but powerful burst of that parallelized computing power. The focus was on how they aided Schrodinger in winning a Bio-IT Best Practices award with their intensive yet relatively inexpensive protein calculations.

That conversation took place on the heels of a presentation done with Wolfgang Gentzsch and Burak Yenier in association with the HPC Experiment, where Stowe went more into detail about the additional use cases in which Cycle Computing has facilitated HPC experimentation in the cloud. Gentzsch and Yenier also went on to provide an update on the HPC experiment, the fourth round of which kicks off this week.

The problem with in-house HPC equipment, according to Stowe, lies in a lack of stability in resource requirement. Oftentimes the HPC cluster goes under-utilized, meaning relatively expensive machinery is idling on valuable floor space. On the other end of the spectrum, the servers may not fulfill the peak needs of the institution.

“The clusters are too small when you need them most…you generally wish it was several times larger than it actually is,” Stowe said of companies with in-house resources when they face the peak of their intermittent computing needs schedule.

The challenge was based on the knowledge that, according to Stowe, that some top ten pharmaceutical companies can run approximately 341,700 hours of computing against a cancer target every year.

“We essentially were able to run very large sets of compounds an order of magnitude over what they normally would have been able to provision against different cancer affiliated proteins,” he said.

As Stowe noted, their work was in drug design and running simulations on how to either stimulate or halt protein activity. “What you’re trying to do,” he said, “is knock small molecules that lock so that they either inhibit or enhance, depending on the nature of the protein and the disease pathway, its function as a protein.”

As mentioned in last month’s article, through their Utility HPC platform, Cycle Computing aims to reduce computing time, resulting in lower costs for the clients.

Of course, while these tests are intriguing and the protein simulations are useful, what really showcases their worth is if such simulations result in the development of cancer drugs that otherwise would not have been possible. According to Stowe, Novartis proved that usefulness.

Two years ago, Novartis ran a 30,000-core Intel Xeon system setup on AWS via Cycle. They announced earlier this year that as a result of those computations, they found three compounds of interest from a drug target perspective.

These things often take time to verify as the drug trial process, which often involves clinical trials with cancerous patients, cannot yet be simulated via a supercomputing cluster. “Part of the enemy is time,” Stowe said. “We’ve run these workloads for significant clients in the past like Novartis and Schrodinger, but oftentimes you don’t know the impact of them until many years have passed.”

One of the advantages here is the ability to access a relatively large cluster for a short amount of time, thus accruing significantly less computing expense. For companies who look to run those 11 hour bursts, it would seem that they may need to prepare their applications ahead of time.

However, as evidenced by the other use cases Stowe referenced, namely CAD/CAM from an engineering perspective and genomics, there exist companies who make consistent use of a Cycle-AWS cluster over the course of three months.

“They had about 1200 of these 576-core jobs that they needed to run, each of which had its own 100-GB dataset,” Stowe said of a company who operated ten clusters concurrently to accomplish those 576-core jobs. Stowe estimated that such a physical system would take nine months to build, whereas that Cycle-facilitated process only ran three months. In another example, Cycle assisted in completing a million compute hours in one week for under $20,000 for a genomics company whose problem was shown below.

As evidenced by Stowe’s use cases and as noted by Gentzsch in the presentation, high performance applications run in the cloud serve a greater use to mid-sized institutions with neither the time nor the funds to purchase and implement an HPC cluster on their own. Those mid-sized institutions constitute a good portion of the 475 participants and 85 ‘teams’ that have participated in the HPC Experiment over its first three rounds.

Round four begins this month, and a more in-depth update will be provided within the next month in an article from Gentzsch. The full presentation from Stowe, Gentzsch, and Yenier can be found below.

 

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!

Scalable Informatics Ceases Operations

March 23, 2017

On the same day we reported on the uncertain future for HPC compiler company PathScale, we are sad to learn that another HPC vendor, Scalable Informatics, is closing its doors. Read more…

By Tiffany Trader

‘Strategies in Biomedical Data Science’ Advances IT-Research Synergies

March 23, 2017

“Strategies in Biomedical Data Science: Driving Force for Innovation” by Jay A. Etchings is both an introductory text and a field guide for anyone working with biomedical data. Read more…

By Tiffany Trader

HPC Compiler Company PathScale Seeks Life Raft

March 23, 2017

HPCwire has learned that HPC compiler company PathScale has fallen on difficult times and is asking the community for help or actively seeking a buyer for its assets. Read more…

By Tiffany Trader

Google Launches New Machine Learning Journal

March 22, 2017

On Monday, Google announced plans to launch a new peer review journal and “ecosystem” Read more…

By John Russell

HPE Extreme Performance Solutions

HFT Firms Turn to Co-Location to Gain Competitive Advantage

High-frequency trading (HFT) is a high-speed, high-stakes world where every millisecond matters. Finding ways to execute trades faster than the competition translates directly to greater revenue for firms, brokerages, and exchanges. Read more…

Swiss Researchers Peer Inside Chips with Improved X-Ray Imaging

March 22, 2017

Peering inside semiconductor chips using x-ray imaging isn’t new, but the technique hasn’t been especially good or easy to accomplish. Read more…

By John Russell

LANL Simulation Shows Massive Black Holes Break ‘Speed Limit’

March 21, 2017

A new computer simulation based on codes developed at Los Alamos National Laboratory (LANL) is shedding light on how supermassive black holes could have formed in the early universe contrary to most prior models which impose a limit on how fast these massive ‘objects’ can form. Read more…

Quantum Bits: D-Wave and VW; Google Quantum Lab; IBM Expands Access

March 21, 2017

For a technology that’s usually characterized as far off and in a distant galaxy, quantum computing has been steadily picking up steam. Read more…

By John Russell

Intel Ships Drives Based on 3D XPoint Non-volatile Memory

March 20, 2017

Intel Corp. has begun shipping new storage drives based on its 3D XPoint non-volatile memory technology as it targets data-driven workloads. Intel’s new Optane solid-state drives, designated P4800X, seek to combine the attributes of memory and storage in the same device. Read more…

By George Leopold

HPC Compiler Company PathScale Seeks Life Raft

March 23, 2017

HPCwire has learned that HPC compiler company PathScale has fallen on difficult times and is asking the community for help or actively seeking a buyer for its assets. Read more…

By Tiffany Trader

Quantum Bits: D-Wave and VW; Google Quantum Lab; IBM Expands Access

March 21, 2017

For a technology that’s usually characterized as far off and in a distant galaxy, quantum computing has been steadily picking up steam. Read more…

By John Russell

Trump Budget Targets NIH, DOE, and EPA; No Mention of NSF

March 16, 2017

President Trump’s proposed U.S. fiscal 2018 budget issued today sharply cuts science spending while bolstering military spending as he promised during the campaign. Read more…

By John Russell

CPU-based Visualization Positions for Exascale Supercomputing

March 16, 2017

In this contributed perspective piece, Intel’s Jim Jeffers makes the case that CPU-based visualization is now widely adopted and as such is no longer a contrarian view, but is rather an exascale requirement. Read more…

By Jim Jeffers, Principal Engineer and Engineering Leader, Intel

US Supercomputing Leaders Tackle the China Question

March 15, 2017

Joint DOE-NSA report responds to the increased global pressures impacting the competitiveness of U.S. supercomputing. Read more…

By Tiffany Trader

New Japanese Supercomputing Project Targets Exascale

March 14, 2017

Another Japanese supercomputing project was revealed this week, this one from emerging supercomputer maker, ExaScaler Inc., and Keio University. The partners are working on an original supercomputer design with exascale aspirations. Read more…

By Tiffany Trader

Nvidia Debuts HGX-1 for Cloud; Announces Fujitsu AI Deal

March 9, 2017

On Monday Nvidia announced a major deal with Fujitsu to help build an AI supercomputer for RIKEN using 24 DGX-1 servers. Read more…

By John Russell

HPC4Mfg Advances State-of-the-Art for American Manufacturing

March 9, 2017

Last Friday (March 3, 2017), the High Performance Computing for Manufacturing (HPC4Mfg) program held an industry engagement day workshop in San Diego, bringing together members of the US manufacturing community, national laboratories and universities to discuss the role of high-performance computing as an innovation engine for American manufacturing. Read more…

By Tiffany Trader

For IBM/OpenPOWER: Success in 2017 = (Volume) Sales

January 11, 2017

To a large degree IBM and the OpenPOWER Foundation have done what they said they would – assembling a substantial and growing ecosystem and bringing Power-based products to market, all in about three years. Read more…

By John Russell

TSUBAME3.0 Points to Future HPE Pascal-NVLink-OPA Server

February 17, 2017

Since our initial coverage of the TSUBAME3.0 supercomputer yesterday, more details have come to light on this innovative project. Of particular interest is a new board design for NVLink-equipped Pascal P100 GPUs that will create another entrant to the space currently occupied by Nvidia's DGX-1 system, IBM's "Minsky" platform and the Supermicro SuperServer (1028GQ-TXR). Read more…

By Tiffany Trader

Tokyo Tech’s TSUBAME3.0 Will Be First HPE-SGI Super

February 16, 2017

In a press event Friday afternoon local time in Japan, Tokyo Institute of Technology (Tokyo Tech) announced its plans for the TSUBAME3.0 supercomputer, which will be Japan’s “fastest AI supercomputer,” Read more…

By Tiffany Trader

IBM Wants to be “Red Hat” of Deep Learning

January 26, 2017

IBM today announced the addition of TensorFlow and Chainer deep learning frameworks to its PowerAI suite of deep learning tools, which already includes popular offerings such as Caffe, Theano, and Torch. Read more…

By John Russell

Lighting up Aurora: Behind the Scenes at the Creation of the DOE’s Upcoming 200 Petaflops Supercomputer

December 1, 2016

In April 2015, U.S. Department of Energy Undersecretary Franklin Orr announced that Intel would be the prime contractor for Aurora: Read more…

By Jan Rowell

Is Liquid Cooling Ready to Go Mainstream?

February 13, 2017

Lost in the frenzy of SC16 was a substantial rise in the number of vendors showing server oriented liquid cooling technologies. Three decades ago liquid cooling was pretty much the exclusive realm of the Cray-2 and IBM mainframe class products. That’s changing. We are now seeing an emergence of x86 class server products with exotic plumbing technology ranging from Direct-to-Chip to servers and storage completely immersed in a dielectric fluid. Read more…

By Steve Campbell

Enlisting Deep Learning in the War on Cancer

December 7, 2016

Sometime in Q2 2017 the first ‘results’ of the Joint Design of Advanced Computing Solutions for Cancer (JDACS4C) will become publicly available according to Rick Stevens. He leads one of three JDACS4C pilot projects pressing deep learning (DL) into service in the War on Cancer. Read more…

By John Russell

BioTeam’s Berman Charts 2017 HPC Trends in Life Sciences

January 4, 2017

Twenty years ago high performance computing was nearly absent from life sciences. Today it’s used throughout life sciences and biomedical research. Genomics and the data deluge from modern lab instruments are the main drivers, but so is the longer-term desire to perform predictive simulation in support of Precision Medicine (PM). There’s even a specialized life sciences supercomputer, ‘Anton’ from D.E. Shaw Research, and the Pittsburgh Supercomputing Center is standing up its second Anton 2 and actively soliciting project proposals. There’s a lot going on. Read more…

By John Russell

Leading Solution Providers

HPC Startup Advances Auto-Parallelization’s Promise

January 23, 2017

The shift from single core to multicore hardware has made finding parallelism in codes more important than ever, but that hasn’t made the task of parallel programming any easier. Read more…

By Tiffany Trader

HPC Technique Propels Deep Learning at Scale

February 21, 2017

Researchers from Baidu’s Silicon Valley AI Lab (SVAIL) have adapted a well-known HPC communication technique to boost the speed and scale of their neural network training and now they are sharing their implementation with the larger deep learning community. Read more…

By Tiffany Trader

CPU Benchmarking: Haswell Versus POWER8

June 2, 2015

With OpenPOWER activity ramping up and IBM’s prominent role in the upcoming DOE machines Summit and Sierra, it’s a good time to look at how the IBM POWER CPU stacks up against the x86 Xeon Haswell CPU from Intel. Read more…

By Tiffany Trader

IDG to Be Bought by Chinese Investors; IDC to Spin Out HPC Group

January 19, 2017

US-based publishing and investment firm International Data Group, Inc. (IDG) will be acquired by a pair of Chinese investors, China Oceanwide Holdings Group Co., Ltd. Read more…

By Tiffany Trader

Trump Budget Targets NIH, DOE, and EPA; No Mention of NSF

March 16, 2017

President Trump’s proposed U.S. fiscal 2018 budget issued today sharply cuts science spending while bolstering military spending as he promised during the campaign. Read more…

By John Russell

US Supercomputing Leaders Tackle the China Question

March 15, 2017

Joint DOE-NSA report responds to the increased global pressures impacting the competitiveness of U.S. supercomputing. Read more…

By Tiffany Trader

Intel and Trump Announce $7B for Fab 42 Targeting 7nm

February 8, 2017

In what may be an attempt by President Trump to reset his turbulent relationship with the high tech industry, he and Intel CEO Brian Krzanich today announced plans to invest more than $7 billion to complete Fab 42. Read more…

By John Russell

Nvidia Sees Bright Future for AI Supercomputing

November 23, 2016

Graphics chipmaker Nvidia made a strong showing at SC16 in Salt Lake City last week. Read more…

By Tiffany Trader

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