Folding@Home and the new Vista Magazine team

If you've spent any time browsing computing forums you'll no doubt be vaguely aware of the phenomenon that is Folding@home .  Practically every computing magazine or forum has a team where readers combine their efforts to further medical research and earn bragging rights in the process.  Since the launch of the Playstation 3, even gamers have been getting in on the act.

What is "Folding"?

Folding@Home is a distributed computing project run by Stanford University, whereby your wasted computing time is put to good use by a program that examines the behaviour of various proteins found in the body.  As Stanford themselves put it:

"  Proteins are biology's workhorses -- its " nanomachines ." Before proteins can carry out these important functions, they assemble themselves, or " fold ." The process of protein folding, while critical and fundamental to virtually all of biology, in many ways remains a mystery.

Moreover, when proteins do not fold correctly (i.e. "misfold"), there can be serious consequences, including many well known diseases , such as Alzheimer's , Mad Cow (BSE), CJD, ALS, Huntington's , Parkinson's disease, and many Cancers and cancer-related syndromes."

Distributed what??

Distributed computing is basically the joining of domestic computers like yours and mine together to form a giant supercomputer to perform complex calculations or process large amounts of data.  Other distributed computing projects you may recognise are SETI@home and the BBC Climate Change Experiment.

As far as Folding@home is concerned, a protein will fold incredibly quickly, some as fast as a millionth of a second.  Unfortunately whilst this may sound quick to you and I, for a computer to simulate it takes a considerable amount of time.  It would take a day to simulate a nanosecond, but even that is a long time for your average protein molecule.  You'll need about 30 CPU years to simulate folding.  A full explaination can be found here: http://folding.stanford.edu/science.html

When you install one of the folding clients, your PC will download its first work unit which will represent a small portion of the job in hand.  You're PC will then work on it while you're not using your PC and then send the results back when its finished.

Getting started

There are a wide variety of folding clients to choose from, depending on what OS you are using, but as this is a Vista magazine, you're probably using Vista or XP, but luckily the file is the same.  You can choose either the screensaver version, which will show you how your PC is getting on with the work unit and display moving images of the protein it is working on, or you can go for a more discrete "no nonsense" client that you can set to start when your computer starts.  This is the most effective client but its probably the more daunting of the two to set up.

You can download the client's here: http://folding.stanford.edu/download.html

Open up "Computer", create a folder on your hard drive called "Folding".  If you're going to run more than one client (dual-core or quad core machines) create a sub-folder for each called CPU1, CPU2 etc.  Download a copy of the client into each folder.  Now, if you're running the no-nonsense client, right click on the file you've just downloaded and select "send to desktop".  Do this for each client if there is more than one.  Go back to your desktop to view the new shortcuts and right click on one of them.  What you need to do now is edit the "target" and add "-local" and "-configonly" (without the quotes) to the end of the line and press OK.  Do this for each of the clients.  The -local command will force it to work within its own folder and -configonly means that it'll open up so you can configure it then close.  If its the graphical client you've chosen you just need to double click on it to install and run it.

Whichever client you choose, you're going to need to pick a name for yourself.  The download page will let you type in your name of choice (such as your forum name) and see if anyone else is using it.  If its free, you can type that in when either client prompts you.

You'll also need to enter a team name.  If you want to fold for the Official Windows Vista Magazine team, type in 66425 when prompted.  Once you complete a work unit, you're name will appear in the team's roster with the number of points you've earned.

For the no-nonsense client there are a few options to configure, so I'll run through the main ones;
Username: the name you've picked such as your forum name
Team number: 66425
Run at startup? Yes
Allow highly optimised cores: Yes
Use internet explorer settings: NO!  it doesn't work well with IE7's settings so just say no.
Core priority: Idle
The rest should be straightforward enough.

Points you say?

Yes, every work unit you process has a points value, depending on how long it takes a reference computer (A 2.8ghz P4) to complete such a unit.  If you have a dual-core CPU, you can run two no-nonsense clients at the same time or one screensaver and one no-nonsense client for more points.  The client is single threaded you see.  There is a multi-threaded version but that's currently going through beta testing and isn't recommended.  The more points you earn, the higher up the rankings you and your team climb.

Our team page on the Stanford website:

http://fah-web.stanford.edu/cgi-bin/main.py?qtype=teampage&teamnum=66425

Are you sure it won't interfere with my work?

Very sure.  With the no-nonsense client you can set it to run in the "idle base priority".  If you press Ctrl-Alt & Delete to bring up the task manager, you'll probably see an entry in the processes tab called "system idle process" and chances are it is using quite a high percentage of your CPU.  It isn't really using your CPU at all, its spare capacity, almost like when your car engine is running but you're not going anywhere.  The folding client will use this spare capacity, but then let go of it when you start doing things like load applications or start playing games etc.  As the screensaver uses your graphics card, it can clash with some applications, so overall I'd recommend using the no-nonsense client.

Are there any side effects?

Your CPU is being properly utilised now, so chances are it is going to get a bit warmer than normal, but it is nothing that your CPU isn't prepared for.  Some people run their machines 24 hours a day, 7 days a week without any ill effects other than a sky-high electricity bill.

What's in it for me?

Well, you'll be safe in the knowledge that your CPU cycles are going towards medical research that could lead to important scientific breakthroughs or even cures or treatments for awful diseases such as cancer and alzheimers.  Failing that, there's a bit of competition to be had and the bragging rights that come with it.

Other clients worth mentioning

Since the PS3 came out in the UK, the PS3 has been able to fold as well.  I'll make no bones about it but the PS3 is making waves on the folding scene and PS3 owners are rising up the ranks fast.  If you have one with firmware 1.6 you can also use that to fold for the WVM folding team, just use the same username and team number and you're away.

If you have an ATI X1900 series graphics card, there is a client available for that on the same download page mentioned above, but it'll put a lot of wear on your graphics card so isn't recommended for extended periods, although it is the most productive client in terms of points and speed.

Theres a thread on the forums in case anyone needs any help getting it started. http://forums.windowsvistamagazine.com/forums/thread/2872.aspx