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]

I didn't mean physically burned up,

Good.

I was talking to hubby about that ATI X1900 card. Maybe with a little finessing and using my feminine wiles, ya never know. lol

[tax]

WooooooHooooo made the top 10. Afraid it's going to be all downhill from here...
aka Linda Geiger

[processing please hold]

WooooooHooooo made the top 10.

Congratulations!

I'm shooting for the 150 mark. :-)

[GOPBiker]

Thanks for your replies and the links. I reboot every couple of days or sooner if I am doing maintenance or something on the machine.

It is still not communicating. I notice the two servers I am trying to reach have a status of 'full'. If it means the obvious then I understand the problem.

My folding app (5.03 windows, running on XP pro) has taken to shutting itself down. It will not stay running until I reinstall it. I don't delete the old one, just install over it and I notice I don't lose the wu in process.

I noticed in the posts that you can set a cap on processing power so I set it at 80 since it was running at 98 most of the time. Still 'low' priority so it wasn't in the way most of the time. It does not pay any attention to the setting though and continues to use all available cycles.

I do have the intel MB monitor so I get alerts if overtemp and so far no problem. It would be good to have a little headroom though because sometimes it is slower when FAH is being greedy.

[dfwddr]

I notice the two servers I am trying to reach have a status of 'full'

Actually, "full" means fully operational, the server is accepting.You can add the flag "-send all" to your command line, and see if that works, but delete the flag after, or it will keep shutting down the client.

My folding app (5.03 windows, running on XP pro) has taken to shutting itself down. It will not stay running until I reinstall it.

See above ?

I don't delete the old one, just install over it and I notice I don't lose the wu in process.

Installing a new client over an old one does no good. If you have a problem with the client, you must remove all traces of the first one. If you really want to reinstall, I suggest using the search function, and deleting all files. Be assured, you will lose the WU that is stalled, but in the long run, your better off doing it sooner than later. We've all lost WU along the way, so don't hesitate to do this to keep your computer crunching for the long run.

I noticed in the posts that you can set a cap on processing power so I set it at 80 since it was running at 98 most of the time. Still 'low' priority so it wasn't in the way most of the time. It does not pay any attention to the setting though and continues to use all available cycles.

This makes me ever more convinced you need to dump all instances of FAH, and do a clean install. I don't know how your changing the proc %, but the easiest way to do it is to edit the client.cfg file in your FAH folder.

Let's see, TB or someone else may have some better ideas, but this will give you something to think about for a while.

[dfwddr]

I was talking to hubby about that ATI X1900 card. Maybe with a little finessing and using my feminine wiles, ya never know. lol

You gotta sit on Santa's lap real nicely now !!!! LOL

[dfwddr]

I just noticed....

My folding app (5.03 windows, running on XP pro)

You should be running 5.04, or maybe 5.91 it you have a duel core(beta). I'm running 5.04 on a duel core with no problems, but I guess I'll have to try the 5.91, just because I can LOL

[texas booster]

Lets review the F@H cores available:

5.03 is the F@H GUI program. Thats the one with the pretty molecules getting drawn on the screen. I will post later on ways to make it run better.

5.04 is the F@H console. This is a DOS windowed product that should be run as a service in the background. Most of us use it.

5.91 is a *special* version of F@H designed for the ATI X1600, X1800 and X1900 series video cards, and also for Symmetric MultiProcessor systems (dual chip). We should not run that one unless you have the exact hardware needed. Which I would love to have under the Christmas tree.

If you are running 5.03 GUI, then you should close out F@H if you are running most games. Games that like OpenGL, which is a lame MS clone of some video standard.

When I return tonight, lets look at your F@H logs to see what has been happening.

Merry Christmas Ya'll!

[dfwddr]

LOL. your right about the 5.91.

That's what I get for having my eyes move faster than my brain.

As a side note to all, and especially Klutz, did anyone notice the SISD team is pretty much shut down. They're sinking very fast. Looks like the ringleader has a home 'puter running, but not much else. Now if TSCRussia would do the same, we could claim the glory we rightfully deserve !(no one passed us and survived).

[dfwddr]

Also, the dummies STILL haven't caught the TITS ----> ( . Y . ) <---- TITS

Why am I not suprised.

[texas booster]

Lets look at the easiest file to post, the unitinfo.txt. My current GUI looks like this:

Current Work Unit

---

Name: p1814_Collagen_POG10more
Download time: December 13 00:12:42
Due time: January 26 00:12:42
Progress: 3% [__________]

The GUI is working on the work unit p1814_Collagen_POG10more. It was downloaded today at 00:12:42 GMT (6:12:42 pm CST), The last date my system can return the unit for credit is Jan 26. And it is 3% finished.

Looking at this file will tell us the basics of what is working on your system. Since the 3 hours it has been running (9:30 - 6:12) has accomplished 3% it should take about 100 hours to complete.

I know from this page:

http://fah-web.stanford.edu/psummary.html

that I will receive 153 points for this WU.

You can also look inside FAHlog.txt for a detailed description of the work unit as it folds merrily along.

What does your unitinfo.txt say? Next we will look at the FAHlog.txt for more info.

[GOPBiker]

dfwddr; I had coded the switch in the startup so that probably explains why it was shutting down. Reinstalling replaces the shortcut without the switch.

Since 'full' does not mean what I thought I am wondering why I cannot seem to communicate. I do have ZoneAlarm pro suite but FAH has permission to access the internet.

I still have three complete WU to send and one mostly done so I would hate to lose all that work (days of 24hr electricity usage, etc.). I hope a wipe and re-install isn't necessary at this point. maybe the queue can be copied and restored after the re-install??

TB; here is my unitinfo.txt;

Current Work Unit ----------------- Name: p2414_Ribo_tryptophan280 Download time: December 7 11:06:33 Due time: February 27 11:06:33 Progress: 64% [||||||____]

here are the last few lines of the log. I just show these because it is pretty long and repetitive. I suspended while doing this because my system was pretty slow for some reason;

[12:07:10] + Attempting to send results

[12:07:19] - Unknown packet returned from server, expected ACK for results

[12:07:19] - Error: Could not transmit unit 04 (completed December 7) to work server.

[12:07:19] + Attempting to send results

[12:07:28] - Unknown packet returned from server, expected ACK for results

[12:07:28] Could not transmit unit 04 to Collection server; keeping in queue.

[12:40:10] Writing local files

[12:40:11] Completed 157500 out of 250000 steps (63)

[15:57:39] Writing local files [15:57:40] Completed 160000 out of 250000 steps (64)

[16:08:28] + Screensaver: no longer idle, ending

[16:24:35] Printing Queue Information

CURRENT QUEUE:

00 EMPTY

01 DONE "Folding@Home" (78) 171.65.103.162:8080 November 19 17:16->November 25 19:26:30

02 EMPTY

03 DONE "Folding@Home" (78) 171.64.122.142:8080 November 27 13:04->December 2 10:30:42

04 DONE "Folding@Home" (78) 171.64.122.142:8080 December 2 10:31->December 7 11:05:16

05 *READY "Folding@Home" (78) 171.65.103.162:8080 December 7 11:06 | February 27 11:06

06 EMPTY

07 EMPTY

08 EMPTY

09 EMPTY

[16:24:53] Opening d:\Program Files\Folding@Home\MyFolding.html...

[16:28:58] + Paused

[16:28:59] Suspending work thread...

Thanks for the help with this.

[processing please hold]

I wish I could play halo while my wu's are folding. I'm just griping and complaining. It's one of those days. :(

Ignore this post. I was not here. Have a good evening.

[texas booster]

First, you haven't lost anything but do not have any credit for the WUs that you have finished.

Second, turn off the screensaver, it will slow F@H down a lot.

Third, you can download new packets but can't upload. My first guess is to stop both Zone Alarm and the Windows firewall. When you start F@H you should be able to upload the results. I am betting on a firewall issue for now.

Let me search some F@H forums and see if I can get some better help.

TB

[texas booster]

Probably not a firewall issue but an IE problem (imagine that!).

http://forum.folding-community.org/fpost157044.html

Check out this thread on IE and F@H uploads.

You may have to reconfigure F@H so that it does NOT use IE settings.

IE7 also has known problems.

If you are setup to use a proxy change it. You can see if you use a proxy here:

http://www.proxyinfo.co.uk/check.php

Its a nice little tool.

[texas booster]

Also, click on these server addresses and see if they come back OK.

http://171.65.103.162:8080

http://171.64.122.142:8080

If it comes back OK then the issue is probably the use of IE Settings = Yes.

[Hawkeye's Girl]

Can anyone help me? My graphic version stopped being able to connect with the server, so I tried the console one only to have the same problem after a few days. I'm stuck on what to do now.

[texas booster]

Look at the above posts, and we will follow the same process with you.

Find your folding folder, usually c:\Program Files\F@H. Look for a file called FAHlog.txt. Please post the last several lines so we can make sure you are still folding or so we can see the error message.

So far, a lot of folks that accepted the IE 7 upgrade in the last few weeks have had problems uploading to the servers.

[processing please hold]

My wu finished and it tried about 7 times to send it in but couldn't. Now it says, 'keeping in queue', how long will it hold it before it tries again, do you know?

[texas booster]

I think that the final date on most WUs is twice the time it takes to complete. Probably two to four weeks.