FR Folding@Home Project- ATI Stream Computing Drive Bio-Medical Research at Stanford University

ATI Website and Stanford University ^ | Nov 13 2006 | Vijay Pande

[texas booster]

Today ATI's graphics processors help accelerate complex computations in stream computing applications used in scientific research. ATI is supporting bio-medical research to help scientists understand disease at the genetic level. With a strong understanding of how diseases form, it will become possible to develop diagnostic methods, and preventative treatment and medicine for many acute diseases in humans.

Stanford University is using ATI’s GPUs (Graphics Processor Units) to run Folding@Home, a distributed computing project designed by its chemistry department. This application performs computationally intensive simulations of protein folding, using the stream computing capabilities of ATI’s Radeon® 1900 and 1950 Series processors, which provide incremental power over CPU processing. ATI’s Radeon® X1900 and Radeon® X1950 Series process the complex calculations of the simulation and render advanced 3D visualization of the protein folding process in real time.

Folding@Home will help researchers uncover how certain diseases develop, including:

Cancer

Alzheimer's Disease

Parkinson's Disease

Huntington's Disease

Osteogenesis Imperfecta

Stanford University’s research team discovered that ATI’s Radeon X1900 and Radeon X1950 Series of products provide 20 to 40 times faster processing over CPUs in many of the calculations needed to simulate the folding of proteins.

What is Protein Folding Proteins are necklaces of amino acids – long chain molecules that drive all biochemical reactions in the human body, helping to build bones, muscles and blood vessels, and helping the body fight infections. To accomplish these tasks, proteins must take on a particular shape, or, to “fold”. Proteins that fold incorrectly can cause complications and can lead to critical diseases. Folding@Home simulates the folding process to understand why proteins don’t fold correctly. The findings will help researchers prevent and cure these diseases.

You Can Help Find the Cure Folding@home uses distributed computing to simulate protein folding – instead of using super computers, the workload is broken up into small work units and distributed across 100,000’s of PC systems over the internet. When users throughout the world download and run the application they directly contribute to a good cause through the power of their ATI graphics processor. The GPU version of the application will use the processing power of end users’ GPUs to accelerate the simulation and provide data to Stanford’s researchers faster.

Every new PC that runs the application gets us closer to the cure.

You can help by simply downloading and running the Folding@Home application developed by Stanford University. The application is free and secure. It will run in the background, making use of spare GPU capacity in your PC, without impacting the performance of your other applications.

You can increase your contribution by forming and joining teams and competing against others. 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.

Please note that, currently, only the following products in ATI’s Radeon X1900 Series and Radeon X1950 Series can run the application. We will post information about upcoming products that will support this application in the near future.

Radeon X1900 Series: Radeon X1900 GT, Radeon X1900 XT, Radeon X1900 XTX, Radeon X1900 CrossFire Edition

Radeon X1950 Series: Radeon X1950 XTX, Radeon X1950 CrossFire Edition

[processing please hold]

Is there a way for me to change mine to 30 or is it too late?

I went to the f@h forum, but, didn't see anything about changing it.

I apologize for bugging you so much.

[texas booster]

Open the directory that F@H is in.

Edit the file client.cfg. It may show up as a single line. That's Ok.

Scroll across to Checkpoint=3 and insert a '0' after the 3. Save the file.

Do the same thing to the other F@H folder.

Reboot and you should be fine.

My F@H client.cfg file:

[settings]
username=Texas_Booster
team=36120
asknet=no
machineid=1
local=7

[http]
active=no
host=localhost
port=8080
usereg=no

[core]
priority=96
cpuusage=75
checkpoint=30

[clienttype]
type=3

CPU usage is set at 75% since this is from a low cost laptop. I don't want to chance overheating the system.

[processing please hold]

Thank you very much.

[JosephW]

There is another problem. The username should be set to josephw instead of pbrown. I've noticed a lot of freepers have made this kind of mistake. Do not enter your username instead enter josephw.

And some of you wondered how I climbed up the list so quickly :)

[processing please hold]

Ohhhh, so that's the problem???? And all this time I thought there was a problem with F@H. I'll get right on it./sarc lol

[Drango]

The username should be set to josephw drango1 instead of pbrown.

[processing please hold]

With this version of F@H, is there a way to find out the estimated time of when my WU's will finish? They've given me two p2124 proteins.

[JosephW]

There you go confusing users. The username should only be drango1 on a Mac. All PC based system should use josephw.

[Drango]

Remember when we hacked into DU and changed some of their user names to our own and ran up massive points for FR? Good times.

Let's do it again. Use your decoder ring to see how below.

If you are from DU, slink away. We have no decoder rings and there is no conspiracy to hack your site. Or is there? 

Great idea huh?

[Egon]

With this version of F@H, is there a way to find out the estimated time of when my WU's will finish? They've given me two p2124 proteins.

Not with the console version, no.

FAHMonitor is able to do this, as well as some other available monitoring applications.

According to FAHMonitor's compiled stats, our group of users has completed p2124 350 times, with an average completion time of 164 hours 41 minutes.

[processing please hold]

Thank you. Then I'll just sit back and let it do it's thing.

[processing please hold]

it's - its?

[texas booster]

For the console version you either need to do some math or you need Egon's monitor.

It happens that I am working on one of the p2124's myself. If you open up the "unitinfo.txt" file you will see something like this:

Current Work Unit

---

Name: p2124_lambda_5way_melt_4_10011
Download time: November 30 02:21:18
Due time: March 20 02:21:18
Progress: 42% [||||______]

Keep in mind that there are lots of variations of the p2124 data set.

I started on Nov 30 at 2:21 am. It is now Dec 3 at 10:00 am. It is 42% finished. That gives me 3.333 days of work / 42% = 7.936 days to complete problem. Call it 8 days on this particular system. (Rounding off is my friend).

I searched the web and found numerous discussions on the Excel function DATEDIF. A real mathematician that knew Excel could create a spreadsheet to find th result.

Its probabaly already been done for F@H, I just haven't found it yet.

Calling for expert help!

[processing please hold]

This is 1)Current Work Unit ----------------- Name: p2124_lambda_5way_melt_4_10011 Download time: December 2 00:45:59 Due time: March 22 00:45:59 Progress: 38% [|||_______]

2)Current Work Unit ----------------- Name: p2124_lambda_5way_melt_4_10011 Download time: December 2 00:45:59 Due time: March 22 00:45:59 Progress: 35% [|||_______]

Please tell me I'm seeing things. They won't be finished till March! eeeek.

[processing please hold]

Sorry, very ugly.

1) Current Work Unit -----------------
Name: p2124_lambda_5way_melt_4_10011
Download time: December 2 00:45:59
Due time: March 22 00:45:59 Progress: 38%
[|||_______]

)2 Current Work Unit -----------------
Name: p2124_lambda_5way_melt_4_10011
Download time: December 2 00:45:59
Due time: March 22 00:45:59 Progress: 35%
[|||_______]

[texas booster]

No, that is the last date that this work unit can be received for credit, when downloaded on your start date.

Stanford needs to keep the results fairly current, so they have established that you have 120 days for completion. A lot of work units are run on systems that do not have regular Internet access, do not run every day or are old and slow.

[texas booster]

Thanks for joining the team. It looks like you got a pretty big work unit your first time out.

Please ping us if you have any questions!

[processing please hold]

Ok. Thanks. Sceered me for a minute there. :-)

[Egon]

Just noticed something interesting:

I run FAH on my desktop workstation, which runs Ubuntu Linux. If I have Mozilla Thunderbird open (not minimized-- haven't checked minimized), it's taking 96% of the CPU cycles, leaving F@H with only 1- 2%.

So, regardless of the OS you're running, you might want to check periodically against "top", or Windows Task Manager and see if any of the applications you leave running on a regular basis are hogging the CPU.

[papasmurf]

Egon:

I've been playin' around with Ubuntu for about a year now. I finally loaded it (dual boot) on my Tablet PC so I can start to actually learn something.

What I really need to know, most of all-first of all, are commands (with example usage) and syntax. I have some instructions on how to get the Tablet portion running, and the pcmcia, but I don't understand them! LOL

Can you point me in the right direction?

Thanks so much...


:O)

P