Folding@Home and Distributed Computing

Folding@Home is an open-source distributed computing project launched by Stanford University professor Vijay Pande in October 2000. It aids in disease research by simulating the myriad ways in which proteins “fold” or assemble themselves to perform some basic function. Though protein folding is an essential biological process, mis-folding can lead to diseases such as Parkinson’s, Huntington’s, and Alzheimer’s. Consequently, the examination of folding models can help scientists understand how these diseases develop and assist in designing drugs to combat their effects. As of March 2018, 160 peer-reviewed papers have been published based on results obtained from Folding@Home simulations.

Distributed computing describes the method of a larger task being broken down into portions and shared across multiple computers. In the context of Folding@Home, client PCs download a “work unit” from the project’s work servers, perform the computational work needed to model the protein’s folding, then re-upload the results to a server when complete. The workload behind this folding is significant, and there may be a large number of work units involved in one specific model.

The Folding@Home client software is installed on a user’s PC and is commonly configured to sit idle until the PC is left unattended for a period of several minutes, similar to how one would use a desktop screensaver. The software then consumes idle CPU and GPU resources to perform its task (this is also configurable, as pushing CPU and GPU usage also increases energy consumption and results in excess heat generation). Several computing platforms are supported; beyond the commonly available Windows, OS X, and Linux clients, versions of the software have also been developed for the Sony PlayStation 3 and Android mobile devices.

Though distributed computing models are extremely common in a business/scientific context (weather modelling, graphic rendering, and cryptocurrency mining all share a similar approach), most of these examples rely on a centralized cluster of computers owned by a single company or research organization, often benefitting the financial interests of the singular organization rather than accomplishing a public good.

In contrast, Folding@Home is part of a smaller subset of “volunteer computing” projects intended to reach its goal through harnessing the computational resources of hobbyists. SETI@Home is arguably the most well-known of these projects and is devoted to the search for extraterrestrial life based on the analysis of radio signals. Enigma@Home has assisted in decoding previously-unbroken messages encrypted by the German Enigma machines during the Second World War. The European research organization CERN also threw its own hat in the ring by offloading portions of its research around the Large Hadron Collider to volunteer computing enthusiasts.

Such projects are not always benevolent: distributed and volunteer computing can also be used as a destructive force. Botnets and distributed denial-of-service (DDoS) attacks are two common examples of this phenomenon. The LOIC (Low Orbit Ion Cannon) is a notable DDoS application used by the Anonymous group over the past decade to deny public access to websites they deemed objectionable.

I’ve personally been lending my resources to Folding@Home since the summer of 2010 and recently reached the top 1% of nearly 2 million contributors. Beyond the obvious philanthropic qualities of the project, it’s also taught me a great deal about a variety of computer science concepts. Hardware selection, performance tuning and performance monitoring all play an important part in optimizing a folding cluster, making Folding@Home is a great starter point for aspiring home labbers and sysadmins.

You can find out more about Folding@Home here – http://folding.stanford.edu/

 

 

 

Leave a Reply

Your email address will not be published. Required fields are marked *