Cycle Computing Orchestrates Cancer Research on Google Cloud

By Tiffany Trader

September 10, 2015

This week HPC cloud software specialist Cycle Computing announced that its full suite of products can now be used to spin up clusters on Google’s cloud platform. As testament to the new partnership, Cycle leveraged Google Compute Engine (GCE) to run a 50,000-core cancer gene analysis workload for the Broad Institute.

As Cycle Computing explains, Broad’s Cancer Group approached them with the need to perform a highly-complex genome analysis. The researchers already had powerful processing systems in-house, but running the analysis would take months and would require extensive coordination.

The decision was made to utilize the newly-launched “preemptible virtual machine” instances on GCE to further their cancer research. Preemptible VMs are Google’s answer to competitor Amazon’s spot instances. The preemptible instances are 60-70 percent cheaper than their on-demand counterparts. The catch is that Compute Engine can terminate (preempt) these instances at any time and there are a finite number available.

For applications that are “interruption friendly” (aka fault-tolerant), preemptible VMs offer a nice discount, and as Cycle explains, its software handles resiliency, enabling the orchestration of “clustered applications at any scale.”

Both classic “big compute” jobs as well as batch processing jobs can run on preemptible instances. If some instances terminate during processing, the job slows but does not completely stop.

Cycle expects the following applications will stand to benefit from preemptible VMs:

  • Computational chemistry
  • Needle-in-a-haystack simulations
  • Financial pricing, back testing, modeling
  • Genomics, bioinformatics, proteomics
  • Insurance risk management
  • Rendering, media encoding
  • Hadoop, Spark, Redis, other IoT processing frameworks

Enabling greater access to utility-scale computing has always been the primary mission of Cycle Computing. The company has until now relied solely on Amazon’s cloud cycles, but by expanding its partner ecosystem it can better match and meet its customer needs. Recall that Broad and Google were already collaborating to develop new tools to facilitate and propel biomedical research. And in June, Broad Institute’s Genome Analysis Toolkit, or GATK, became available on Google Cloud Platform, as part of Google Genomics.

Cycle CEO Jason Stowe said Cycle doesn’t one recommend vendor over another, and that the applications cited are also well suited for AWS spot instances. “We provide tools that allow companies to benchmark their workloads on differing infrastructure and to be able to run them in production quality fashion; we stay out selection decisions. We obviously tell customers the options they have but we follow the customer.”

In general, he said, “Throughput-oriented stateless workloads tend to work well on that type of infrastructure and are definitely able to run on both Google GCE preemptible VMs and AWS spot instances.” The costs benefits can be substantial.

Broad’s Cancer Program has data sets pertaining to hundreds of cancer cell lines with information about genetic mutations, gene expression, and molecular interaction. Each level of data is massive in its own right, but exposing the hidden connections between these layers requires a comprehensive analysis. These relationships act as signposts directing the Cancer Program toward future research endeavors.

The scale of Broad’s scientific workload was not unfamiliar to Cycle, a company that prides itself on inspiring researchers to ask the “big questions” without regard to the limits of computing power. As Cycle describes it, this was a project that was at risk of not going forward if limited to available local resources.

“These types of analyses provide the clues that can lead to breakthroughs in disease research, such as cancer research, and this kind of cloud-based infrastructure helps us remove some of the local computing barriers that can stand in the way,” said Chris Dwan, acting director of information technology at the Broad Institute. “Flexible processing power allows us to think on a much larger scale.”

Revealing this map requires compute-intensive machine learning algorithms, the kind that would take months to execute on Broad’s on-premise system. The researchers already had the workload set up to run on an existing cloud-based StarCluster framework, so the challenge was to get this working on Google.

Cycle connected its CycleCloud to Google Cloud Platform, and ensured that its workload placement, data schedule, and at-scale computing capabilities were available on Google. Cycle says they were able to get this job up and running at moderate scales in 90 minutes using Cycle’s automation and orchestration tools as well as their cluster containers.

“The porting process for CycleCloud was very easy to accomplish. We were even able to simplify some of our existing code, because Google features like per-minute billing mean that we don’t have to worry about optimizing usage for hourly charges,” said Rob Futrick, chief technology officer for Cycle Computing.

Finding that the application hit its scaling sweet spot at about 50,000 cores, the Cycle team set the cluster to autoscale to 51,200 cores, requiring 3,210 16-core instances, using a mix of both n1-highmem and n1-standard types. Provisioned for less than the cost of a single server, this petascale cluster enabled Broad’s Cancer Group to complete their mapping workload in one afternoon. And as it so happens, some of the instances were preempted, but CycleCloud automatically reconfigured the cluster sans nodes, so the jobs continued.

After about six hours of computation, Broad’s map was complete. Analysis and curation will reveal the full extent of the relationships that were uncovered.


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!

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

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

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’s introduction of an ARM-based system (XC-50) last November. Read more…

By John Russell

HPE Extreme Performance Solutions

HPC and AI Convergence is Accelerating New Levels of Intelligence

Data analytics is the most valuable tool in the digital marketplace – so much so that organizations are employing high performance computing (HPC) capabilities to rapidly collect, share, and analyze endless streams of data. Read more…

Hennessy & Patterson: A New Golden Age for Computer Architecture

April 17, 2018

On Monday June 4, 2018, 2017 A.M. Turing Award Winners John L. Hennessy and David A. Patterson will deliver the Turing Lecture at the 45th International Symposium on Computer Architecture (ISCA) in Los Angeles. The Read more…

By Staff

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

Nvidia Ups Hardware Game with 16-GPU DGX-2 Server and 18-Port NVSwitch

March 27, 2018

Nvidia unveiled a raft of new products from its annual technology conference in San Jose today, and despite not offering up a new chip architecture, there were still a few surprises in store for HPC hardware aficionados. Read more…

By Tiffany Trader

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

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

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

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

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

Leading Solution Providers

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

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

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

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

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

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

HPE Wins $57 Million DoD Supercomputing Contract

February 20, 2018

Hewlett Packard Enterprise (HPE) today revealed details of its massive $57 million HPC contract with the U.S. Department of Defense (DoD). The deal calls for HP Read more…

By Tiffany Trader

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