Folding@home
From Wikipedia, the free encyclopedia
 |
|
|---|---|
 The recently announced PlayStation 3 Folding@Home client displays a 3D model of the protein being simulated. |
|
| Maintainer: | Stanford University \ Pande Group |
| Stable release: | 5.03 (Windows), 5.02 (Linux), 5.02 (Mac OS X), () [+/-] |
| Preview release: | 5.04 (Windows), 5.04 (Linux), 5.91beta2 (GPU), 5.91 (Mac OS X-SMP), 5.91 (Linux-SMP) (December 1, 2006) [+/-] |
| OS: | Cross-platform |
| Use: | Distributed computing |
| License: | Proprietary [1] |
| Website: | folding.stanford.edu |
Folding@home (also known as FAH) is a distributed computing project designed to perform computationally intensive simulations of protein folding and other molecular dynamics simulations. It was launched on October 1, 2000, and is currently managed by the Pande Group, within Stanford University's Chemistry department, under the supervision of Professor Vijay S. Pande. Folding@home is one of the largest distributed computing projects.[1]
The goal of the project is "to understand protein folding, misfolding, and related diseases."[2]
Accurate simulations of protein folding and misfolding enable the scientific community to better understand the development of many diseases, including Alzheimer's disease, BSE (mad cow disease), Cancer, Huntington's Disease, Cystic Fibrosis and other aggregation related diseases. More fundamentally, understanding the process of protein folding -- how biological molecules assemble themselves into a functional state -- is one of the outstanding problems of molecular biology. So far, the Folding@home project has successfully simulated folding in the 5-10 microsecond range—a time scale thousands of times longer than was previously thought possible.[3]
As of November 9, 2006 45 scientific research papers have been published using the project's work.[4]
A University of Illinois at Urbana-Champaign report dated October 22, 2002 states that FAH distributed simulations of protein folding are demonstrably accurate.[5]
Contents |
[edit] How it works
Folding@home does not rely on powerful supercomputers for its data processing; instead, the primary contributors to the Folding@home project are many thousands of personal computer users who have installed a small client program. The client will, at the user's choice, run in the background utilizing otherwise unused CPU power, or run as a screensaver only while the user is away. In most modern personal computers, the CPU is rarely used to its full capacity at all times; the Folding@home client takes advantage of this unused processing power.
The Folding@home client periodically connects to a server to retrieve "work units," which are packets of data upon which to perform calculations. Each completed work unit is then sent back to the server. As data integrity is a major concern for all distributed computing projects, all work units are validated through the use of a 2048 bit digital signature.
The Folding@home client utilizes modified versions of four molecular simulation programs for calculation: TINKER, GROMACS, AMBER, and CPMD.[6]
Contributors to Folding@home may have user names used to keep track of their contributions. Each user may be running the client on one or more CPUs; for example, a user with two computers could run the client on both of them. Users may also contribute under one or more team names; many different users may join together to form a team. Contributors are assigned a score indicating the number and difficulty of completed work units. Rankings and other statistics are posted to the Folding@home website.
[edit] Participation
As of November 2006, more than 188,000 CPUs were actively participating in Folding@Home (active CPUs are defined as those returning work units within the last 50 days), with over 1,800,000 CPUs registered.[1] This level of participation makes the Folding@home distributed supercomputer one of the most powerful supercomputers in the world, capable of a sustained computational level of over 190 teraFLOPS. Shortly after breaking the 200,000 active CPU count on September 20, 2005, the Folding@Home project celebrated its fifth anniversary on October 1, 2005.
[edit] Google & Folding@home
There used to be cooperation between Folding@home and Google Labs. This came in the form of Google Compute. However, with the new Google Toolbar, this platform is no longer supported and even the old Google Toolbar client will not work.[7]
Google Compute supported FAH when it was at an early stage -- when FAH had ~10,000 active CPUs. At that time, a boost of 20,000 machines was very significant. Now, the FAH client is considerably more mature than it was 5 years ago, and the project has a large number of active CPUs. The number of new clients joining Google Compute was very low (most people opted for the FAH client instead) and so it didn't make sense to continue it. Indeed, the fraction of FAH clients through Google Compute is relatively small. Also, the Google Compute clients have certain hard limits (eg can only run the Tinker core and limited naming and team options). Due to all of these reasons, Google support has been minimal over the last few years and this is the natural conclusion of this.
[edit] Platforms
[edit] Graphical Processing Units
Current research is aimed at accelerating computational power by utilizing a computer's graphics processing unit (GPU) in addition to the Central processing unit (CPU). News about the progress of porting Folding@Home onto GPUs can be found in the "High performance client FAQ" section of the Folding@Home FAQ pages.[8] Recent test data indicate performance gains of up to 40x that of an Intel Pentium 4 CPU are possible. (Note: this performance varies with different GPUs). Stanford has recently cited further advances with the high performance client and stated they will be releasing a public, beta trial at the end of September 2006. However, this trial is specific to ATI Technologies' GPUs due to the performance characteristics of the processors for this application.[9]
As of October 2, 2006, the FAH GPU client has been released into a public beta test. After 9 days of processing from the Beta client the FAH project had received 31 teraFLOPS of computational performance from just 450 X1900 GPUs, averaging at over 70x the performance of current CPU submissions.[1]
[edit] PlayStation 3
Stanford announced in August 2006 that a folding client will be available to run on the PlayStation 3 called Cure@PS3.[10] The intent is that gamers be able to contribute to the project by merely "contributing electricity," leaving their PlayStation 3 consoles running the client while not playing games. It is estimated that with the addition of approximately 10,000 machines the Folding@home project would be able to reach petaflop scale.
[edit] Multi Core Processing Client
As newer CPUs tend to have multi core, the Pande Group is finally adding the Symmetric multiprocessing (SMP) support to the FAH client as well.
On November 13, 2006, the beta SMP FAH clients for x86-64 Linux and x86-64 Mac OS X have been released.[11]
[edit] See also
Human Proteome Folding Project
[edit] Notes and references
- ^ a b c Client Statistics by OS. Folding@home distributed computing. Stanford University (2006-11-12 (updated automatically)). Retrieved on 2006-11-12.
- ^ Vijay Pande (2006). Folding@home distributed computing home page. Stanford University. Retrieved on 2006-11-12.
- ^ Validity of Folding@home (Blog). Folding@home support forum. Stanford University. Retrieved on 2006-11-12.
- ^ Vijay Pande (2006). Recent Pande Group research papers. Folding@home distributed computing. Stanford University. Retrieved on 2006-11-12.
- ^ C. Snow, H. Nguyen, V. S. Pande, and M. Gruebele. (2002). "Absolute comparison of simulated and experimental protein-folding dynamics". Nature 420 (6911): 102–106. PMID 12422224.
- ^ Vijay Pande (2005-10-16). Folding@Home with QMD core FAQ (FAQ). Stanford University. Retrieved on 2006-12-03. The site indicates that Folding@home uses a modification of CPMD allowing it to run on the supercluster environment.
- ^ What is the state of Google Compute client? (Blog). Folding@home support forum. Stanford University. Retrieved on 2006-11-12.
- ^ Folding@Home high performance client FAQ. FAQs on new hardware, Folding@Home. Vijay Pande and Stanford University. Retrieved on 2006-12-01.
- ^ Vijay Pande (2006-11-06). Folding@Home on ATI GPU FAQ. Stanford University. Retrieved on 2006-11-13.
- ^ Vijay Pande (2006-10-22). PS3 FAQ. Stanford University. Retrieved on 2006-11-13.
- ^ Vijay Pande (2006-11-13). Folding@Home SMP Client FAQ. Stanford University. Retrieved on 2006-11-13.
- M. R. Shirts and V. S. Pande. (2000). "Screen Savers of the World, Unite!". Science 290: 1903–1904.
- C. Snow, H. Nguyen, V. S. Pande, and M. Gruebele. (2002). "Folding of a bba protein: simulation and theory.". Nature 420: 102–106.
- C. D. Snow, E. J. Sorin, Y. M. Rhee, and V. S. Pande. (2005). "How well can simulation predict protein folding kinetics and thermodynamics?". Annual Reviews of Biophysics 34: 43–69.
- L. T. Chong, C. D. Snow, Y. M. Rhee, and V. S. Pande. (2004). "Dimerization of the p53 oligomerization domain: Identification of a folding nucleus by molecular dynamics simulations.". Journal of Molecular Biology 345: 869–78.
- I. Suydam, C. D. Snow, V. S. Pande and S. G. Boxer. (2006). "Electric Fields at the Active Site of an Enzyme: Direct Comparison of Experiment with Theory.". Science in press.
