HPC PROJECTS: CLOUD COMPUTING
most promising starting point for developing a drug. Our software tests these millions of compounds to see how strongly they will bind against an identified receptor. It narrows the list down from 10 million candidates to something more like 2,000, for example.’ In terms of computing requirements, the software is moderately hungry: ‘Typically, to screen three million compounds takes about a year of CPU time. On the cloud we could do it in 18 hours, using 480 processors, which is a typical, non-maximal size for a virtual cluster. This is why the cloud is such a win for our software and for our industry,’ says Shenkin.
Screening millions of compounds for drug-receptor interactions is a compute intensive process. Customers of software provider Schrödinger are able to use the flexibility of cloud computing to increase their screening capacity as and when they need to. Here, the interaction of a staurosporine molecule and a CDK2 receptor has been simulated by the software. Image courtesy of Schrödinger
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clusters with various pricing structures. ‘The term “cloud computing” is used to mean a few different things,’ says Foster, ‘but I think that the most interesting aspect of it is the emergence of real commercial providers of computing services – the emergence of Amazon [EC2] in particular, although others are also getting into the space. That aspect of cloud is about providing the reliable sources of computing that were perhaps lacking in the early days of grid computing. We ended up building our own supplies of storage, computing and other things, but we could never operate those as efficiently as a company like Amazon could do. It’s a very exciting development.’
Commercialising cloud
Jason Stowe started Cycle Computing in 2005 with a view to helping to manage internal clusters across a wide range of HPC-using organisations. ‘There wasn’t really a cloud at that time,’ he notes. ‘The application environments ranged from small life-science clusters of tens of nodes to a university with 32,000 cores. We noticed that a lot of our customers had a peak vs. median usage problem; essentially, they couldn’t provision enough nodes to make computing power available when they needed it the most.’ In 2007, Cycle’s answer was to develop cluster management software
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that would re-size the cluster, depending on the work that was put into the queue. The software not only makes use of the on- demand processing offered by Amazon and similar cloud service providers, but it also allows the user to harvest and use internal resources efficiently.
Peter Shenkin is vice president of US-based software company Schrödinger, which he describes as the largest supplier of ‘hardcore scientific simulation software and molecular modelling software into the pharmaceutical industry’. Pharmaceutical companies use the company’s software in drug discovery, to evaluate drug-receptor interactions in silico. ‘When a drug company decides to target a particular disease, there are many pathways in the body that lead to that disease, and by enhancing some and knocking out others, you can attack, control, or in some cases cure that disease,’ explains Shenkin. ‘Once a pathway has been chosen, and once the developer has decided which particular receptor (usually a specific protein in the body) to target, that’s when our software comes into play.’ Most pharmaceutical companies already have large in-house compound libraries, often running into millions of compounds acquired through R&D and through IP purchases. ‘[The pharma companies] want to figure out which of these millions of compounds is the
SCIENTIFIC COMPUTING WORLD JUNE/JULY 2010
Currently, Schrödinger’s customers request additional usage of the software from the company, with Cycle supplying the compute power, courtesy of Amazon. Shenkin explains that there were several reasons why the company chose to use Cycle as a supplier, rather than to deal directly with Amazon’s service: ‘Cycle’s infrastructure is cloud- agnostic; on the back end it knows how to talk to Amazon, but it also knows how to talk to several other cloud vendors. If a customer should, for example, have a close relationship with IBM, Cycle just points the back-end towards IBM’s cloud service, and we don’t
‘Cloud computing is partly a business model and partly a usage model’
have to worry about porting our software to a different set of standards.’ Another reason for choosing to access the cloud via Cycle was ease of integration: ‘Cycle takes care of making the Amazon cloud look like a standard cluster, while maintaining its elasticity; compute nodes on the virtual cluster go in and out of existence dependant on the workload,’ explains Shenkin. Shenkin is quick to point out that Schrödinger does not intend to move to a software-as-a-service model, although billing may become automated in the future. ‘We want to maintain a close relationship with our customer base,’ he notes, adding that the company’s software is complicated, and that cloud computing can be expensive if used incorrectly. ‘It’s not a huge expense as these things go, but somehow or other, people’s perceptions change when it’s real money,
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www.scientific-computing.com
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