Cycle Computing provisioned a 50,000-core
utility supercomputer in the Amazon Web Services (AWS) cloud for Schrödinger and Nimbus Discovery to
accelerate lead identification via virtual screening. This milestone –
the largest of its kind – is Cycle Computing’s fifth massive cluster in
less than two years on the heels of a 30,000-core cluster in October
2011, illustrating Cycle’s continued leadership in delivering
full-featured and scalable cluster deployments. Cycle Computing revealed
the cluster creation during today’s opening keynote at the
AWS Summit in New York City.
Schrödinger’s widely used computational docking application, Glide,
performs high-throughput virtual screening of compound libraries for
identification of drug discovery leads. Computing resource and time
constraints traditionally limit the extent with which ligand
conformations can be explored, potentially leading to false negative
while the same constraints may require a less accurate level of scoring,
which can lead to false positives. Tapping into Cycle’s utility
supercomputing, Schrödinger ran a virtual screen in collaboration with
Nimbus Discovery of 21 million compounds against a protein target. The
run required 12.5 processor years and completed in less than three
hours.
“Typically, we have to weigh tradeoffs between time and accuracy in a
project,” said Ramy Farid, President, Schrödinger. “With Cycle’s
utility supercomputing, we didn’t have to compromise the accuracy in
favor of faster throughput, and we were able to run the virtual screen
using the appropriate levels of scoring and sampling.”
The global 50,000-core cluster was run with
CycleCloud,
Cycle’s flagship HPC in the cloud service that runs on AWS. Replicating
data across seven AWS regions while automating provisioned resources,
CycleCloud run time per job averaged 11 minutes and the total work
completed topping 100,000 hours. Schrödinger’s researchers completed
over 4,480 days of work, nearing 12.5 years of computations in a few
hours, with cost under $4,900 per hour at peak requiring no upfront
capital.
“By leveraging AWS, Cycle Computing is able to perform highly
sophisticated computations in minutes at a fraction of what it would
cost for businesses to purchase the high performance computing
infrastructure themselves,” said Terry Wise, Director of Business
Development, Amazon Web Services. “Cycle Computing brings an incredible
amount of innovation to our partner ecosystem and we’re excited to
continue working with them to enable businesses to take advantage of
AWS’s highly scalable, elastic and low cost technology infrastructure.”
Cluster and performance analytics software CycleServer tracked
utilization, diagnosed performance and managed scientific
workflow. Replicating the success of employing next generation
developments, Cycle engineers continued open source strategies,
including Condor, Linux, and
Opscode’s
Chef cloud infrastructure automation system. Cycle’s Chef monitoring
and analytics plug-in, called Grill, provided visualization into scaling
the infrastructure environment and eliminated the need for additional
Chef servers with alert technology supporting data around installations,
driving down preparation and operational overhead.
Leveraging CycleCloud software and Cycle’s HPC proficiency delivered these stats:
- Infrastructure: 6,742 Amazon EC2 instances /58.79 TB RAM
- Global-scale: Multi-datacenter clusters with simple user interfaces
- Cluster Size: 51,132 cores, 58.78TB RAM
- Security: Engineered with HTTPS, SSH & 256-bit AES encryption
- AWS Regions:7 (us-east, us-west1, us-west2, eu-west, sa-east, ap-northeast,
ap-southeast )
The end-user experience for using CycleCloud is:
- User Effort: One-click global cluster at massive scale
- Start-up Time: Thousands of cores in minutes, full cluster in 2 hours
- Up-front Capital Investment: $0
- Total Infrastructure Cost: $4,828.85/hour
“Researchers can now meet their aspirations and bottom line through
secure, mega-elastic and fully-supported utility supercomputers,” said
Jason Stowe, founder and CEO, Cycle Computing. “By harvesting the raw
infrastructure from AWS, we empower Schrödinger’s scientific accuracy
while allowing them to push the boundaries of computation research.
Creating robust, reliable and importantly repeatable supercomputers
means any industry from life sciences, risk management, quantitative
finance to product design can reap the benefits as we tip the scales
towards the next generation of massive clusters.”
To learn more about the development of the 50,000 core-cluster and
Cycle’s projects leading up to this accomplishment, please visit the
Cycle Computing blog: Compute Cycles (
http://blog.cyclecomputing.com/).
About Schrödinger
Schrödinger is committed to innovation and scientific advancement in
computational chemistry. Schrödinger’s complete software solutions
deliver advanced simulation technologies that accelerate R&D
activities, make possible novel discoveries, and provide infrastructural
support for research organizations, streamlining workflows and
facilitating enterprise data sharing, management, and visualization
among modelers, medicinal chemists, biologists, structural biologists,
and other members of a multi-disciplinary team. The predictive power of
Schrödinger's software has been demonstrated in a series of successful
drug discovery collaborations with pharmaceutical and biotech companies,
resulting in numerous patents.
Schrödinger employs approximately 100 full-time Ph.D. scientists, and
operates from locations in New York, Oregon, California, Massachusetts,
Maryland, Germany, France, the UK, and Japan in order to provide the
best possible service and support for its more than 2,000 commercial,
government, and academic customers worldwide. For more information,
visit
www.schrodinger.com.
About Nimbus
Nimbus Discovery is applying advances in computer-based drug
discovery to develop new medicines against important drug targets and
thereby unlock fundamental biological pathways. Nimbus has established a
first-of-its-kind partnership with Schrödinger, the leader in
computational drug discovery, to gain privileged access to cutting-edge
technology and exclusive rights to key targets. Nimbus has already
delivered selective, potent, and differentiated compounds within the
first year for two disease targets that are pivotal in the progression
of an aggressive form of Non-Hodgkin’s lymphoma and obesity,
respectively. Nimbus has built a virtually integrated, globally
distributed R&D organization that leverages an experienced internal
drug discovery team across an external network of R&D partners. The
resulting organization is scalable, capital efficient and has attracted
world-class talent. Nimbus seeks to partner its programs with larger
pharmaceutical companies early in the development process allowing
Nimbus to focus on its competitive advantage in novel drug discovery.
Nimbus programs are held in target-specific subsidiaries under an LLC
umbrella. Nimbus Discovery was founded in 2009 by Atlas Venture and
Schrödinger, Inc. In 2010, Nimbus received three Qualifying Therapeutic
Discovery Project Tax Credit (QTDP) grants for its programs. For more
information please visit
www.nimbusdiscovery.com.
About Cycle Computing
Cycle Computing is the leader in
Utility Supercomputing software.
As a bootstrapped, profitable software company, Cycle delivers proven,
secure and flexible high performance computing (HPC) and data solutions
since 2005. Cycle helps clients maximize existing infrastructure and
speed computations on servers, VMs, and on-demand in the cloud. Our
products help clients maximize internal infrastructure and increase
power as research demands, like the 10000-core cluster for Genentech and
the 30000+ core cluster for a Top 5 Pharma that were covered in Wired,
TheRegister, BusinessWeek, Bio-IT World, and Forbes. Starting with three
initial Fortune 100 clients, Cycle has grown to deploy proven
implementations at Fortune 500s, SMBs and government and academic
institutions including JP Morgan Chase, Purdue University, Pfizer and
Lockheed Martin.
About Amazon Web Services
Launched in 2006, Amazon Web Services (AWS) began exposing key
infrastructure services to businesses in the form of web services -- now
widely known as cloud computing. The ultimate benefit of cloud
computing, and AWS, is the ability to leverage a new business model and
turn capital infrastructure expenses into variable costs. Businesses no
longer need to plan and procure servers and other IT resources weeks or
months in advance. Using AWS, businesses can take advantage of Amazon's
expertise and economies of scale to access resources when their business
needs them, delivering results faster and at a lower cost. Today,
Amazon Web Services provides a highly reliable, scalable, low-cost
infrastructure platform in the cloud that powers hundreds of thousands
of enterprise, government and startup customers businesses in 190
countries around the world. AWS offers over 28 different services,
including Amazon Elastic Compute Cloud (Amazon EC2), Amazon Simple
Storage Service (Amazon S3) and Amazon Relational Database Service
(Amazon RDS). AWS services are available to customers from data center
locations in the U.S., Brazil, Europe, Japan and Singapore.
Update:
- 2012.04.19 - original news release posted
