Project details, big picture
What is Folding@home? What is protein folding?
Originally Posted by Narong30
What is folding?
What is the benefit?
And how to do that?
Folding@home is a distributed computing project, that very simply stated, studies protein folding and misfolding. Protein folding is explained in more detail in the scientific background section.
What is distributed computing?
Distributed Computing is a method of computer processing in which different parts of a program, or different portions of data, are processing simultaneously on two or more computers that are communicating with each other over a network or through the Internet.
Who "owns" the results? What will happen to them?
Unlike other distributed computing projects, Folding@home is run by an academic institution (specifically the Pande Group, at Stanford University's - Chemistry Department), which is a nonprofit institution dedicated to science research and education. We will not sell the data or make any money off of it.
Moreover, we will make the data available for others to use. In particular, the results from Folding@home will be made available on several levels. Most importantly, analysis of the simulations will be submitted to scientific journals for publication, and these journal articles will be posted on the web page after publication. Next, after publication of these scientific articles that analyze the data, the raw data of the folding runs will be available for everyone, including other researchers, here on this web site.
What has been "folded" so far, and how much have I folded?
We keep many types of statistics of users and work accomplished in our Stats section. You can check your Individual stats, Team stats, and overall Project stats. Please also review the Results and Awards sections.
What has the project completed so far?
We have been able to fold several proteins in the 5-10 microsecond time range with experimental validation of our folding kinetics. This is a fundamental advance over previous work. Scientific papers detailing our results can be found in the Results section. We are now moving to other important proteins used in structural biology studies of folding as well as proteins involved in disease. There are many peer-reviewed and published in top journals (Science, Nature, Nature Structural Biology, PNAS, JMB, etc) that have resulted from FAH. Currently, the FAH project has published more papers than all of the other major distributed computing projects combined!
Why not just use a supercomputer?
Modern supercomputers are essentially clusters of hundreds of processors linked by fast networking. The speed of these processors is comparable to (and often slower than) those found in PCs! Thus, if an algorithm (like ours) does not need the fast networking, it will run just as fast on a supercluster as a supercomputer. However, our application needs not the hundreds of processors found in modern supercomputers, but hundreds of thousands of processors. Hence, the calculations performed on Folding@home would not be possible by any other means! Moreover, even if we were given exclusive access to all of the supercomputers in the world, we would still have fewer computing cycles than we do with the Folding@home cluster! This is possible since PC processors are now very fast and there are hundreds of millions of PCs sitting idle in the world.
What are the minimum system requirements?
All computers can contribute to Folding@home. However, if the computer is too slow (e.g. wasn't bought in the last 3-4 years or so), the computer might not be fast enough to make the deadlines of typical work units. A Pentium 3 450 MHz or newer equivalent computer (with SSE) is able to complete work units before they expire.
Why should I update my Folding@home software to the current version?
We are continuously improving the Folding@home software and adding new features. We release new versions to fix bugs reported by the users to help make the project run as smoothly as possible.
How do the results get back to you?
Your computer will automatically upload the results to our server each time it finishes a work unit, and download a new work at that time.
How long does it take to finish a work unit? How do you measure a work unit?
This varies, of course, on the speed of the computer and the size of the protein under study. Depending on the protein and the properties studied, different size work units may be used. The Project Summary page has information on particular proteins' sizes and the deadlines allotted for completion.
How can I make sure my results are being sent back and used? How can I tell how much work I've processed?
To find out data that has been reported back you can check the Stats page for Individual stats, Team stats, and overall Project stats. If your computer is returning data, you should see your username there along with the number of work units completed. If your name isn't there, and your screen saver or console version seems to be working fine, then either it hasn't finished a unit yet (this can take a few days, or even longer with an older computer), the list hasn't been updated yet. Check back in a day or two, and it should be there . . . as long as you remember correctly what you typed in for your donor user name.
Can I run Folding@home when SETI@home is running?
Yes, SETI@home and other distributed applications can be run alongside Folding@home, provided you have enough system memory. Some programs, including SETI@home run at a higher priority than Folding@home, which prevents FAH from progressing if it is run at the same time. If you notice the FAH client is not progressing, you can fix this by enabling the "Slightly Higher Priority" Option in the FAH client. This can be done through the advanced options page for the Windows GUI client, or by running the Console client with the -config switch.
Note: FAH work units are time sensitive, while work units from other projects typically are not time sensitive. Therefore we strongly recommend giving the FAH client a higher priority, or to dedicate a processor core to FAH while allowing other projects to use the remaining computer resources.
Are there any limits to how long my machine can take to finish a work unit (WU)?
Yes. Work Units are serial in nature. When a completed WU is sent back, a new work unit is generated from those results. This must happen many times over within each project (group of work units). A generation 1 work unit must be turned in before a generaton 2 work unit is created and sent out.
To keep these generations moving along, we have to set expiration deadlines in the event a work unit is not uploaded in a timely manner (lost, deleted, whatever). These unfinished work units "expire" and are reassigned to new machines. You will still receive credit for all WUs completed and uploaded prior to the preferred deadline. However, after the preferred deadline, your contribution is not as useful scientifically because another copy of that work unit had to be sent out to another contributor. Even if you eventually complete the work unit, that other contributor still had to process duplicate work to assure the science moves forward. And it would be unfair not to also credit that second contributor.
Even so, full credit is given up until the final deadline. After the final deadline has expired, the client will automaticlly discard the work unit and download new work. If you have trouble completing work units before the preferred deadline, it is recommended to either run the FAH client more hours each day, or to run the client on a faster computer.
As we move to larger and longer WUs, we will extend the expiration time as needed. Deadlines vary on the order of a few days to a several weeks, depending on the nature of the WU. Turn in a work unit just before the deadline is not the goal. It is most helpful to the project to return work units as quickly as possible. And how these deadlines are determined is explained a few answers below.
How much power/money does keeping a FAH running 24/7 on a computer use?
Roughly, a CPU uses about as much power (watts) as a typical light bulb. Here's a report on computer power management from Lawrence Berkeley government labs, and there are other references on the web you can find. Although power supplies on most computers are rated at 400 watts, average usage is lower. On average, a Pentium-type computer uses about 100 watts (if the monitor is off). So, the daily difference between off and running FAH is about 24x100 = 2.4 kWh. At $0.15 per kWh ( from PG&E here in California), this works out to about $0.36 per day. In general, lighting and climate control use a much larger share of household power than computers do. So the best bet for cutting costs and conserving energy would be to turn off lights, turn off your computer monitors (which use more power than a CPU), and turn down the heat.
My monitor is set to turn off after a while.
Can I still run the screen saver? Energy saving features, which turn the monitor off after a specified period of time, does not affect the screen saver. As long as the computer is running, the screen saver will continue to run and accumulate useful data, even if the monitor is off.
Does the screen saver use a lot of CPU time?
The screen saver is designed to use very little CPU time. Even without any OpenGL hardware, the screen saver only uses about 5% of the CPU time for graphics. If you have some sort of OpenGL support on your graphics card, the CPU time becomes virtually zero. Since the space filling ("orb") drawing of the atoms can be seen in the process of drawing, it may look like it is taking a lot of processor space, but that delay is set by a timer, and does not occur because it takes a long time to draw.
Will extra 3D hardware help make the screen saver go faster?
3D acceleration cards will make a small difference for complex proteins. However, the accelerator does not aid in processing the proteins, is simply offloads the graphical workload from the CPU so it can fold faster.
How do I shut down the screen saver?
The screen saver is designed so that it shuts down on mouse click or key press. It will NOT shut down by simply moving the mouse. This is to prevent users from inadvertently closing down Folding@home, since it takes a short while to start processing every time it starts up.