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FR Folding@Home Project- ATI Stream Computing Drive Bio-Medical Research at Stanford University
ATI Website and Stanford University ^ | Nov 13 2006 | Vijay Pande

Posted on 11/21/2006 8:07:23 PM PST by 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


TOPICS: Health/Medicine
KEYWORDS: ati; fh
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To: HKMk23

... then plug in wifey's favorite movie...who knows what could happen next?




I get banned from most chick flicks fairly fast. Either I try to help correct the screenwriters missing dialog, tell them the plot of the movie or fall asleep and snore.

But if the Cowgirls make it into the playoffs, maybe a good custom built DVR system would come in handy.


61 posted on 11/29/2006 8:12:07 PM PST by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120))
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To: texas booster
But if the Cowgirls make it into the playoffs,

Cheap talk. All hat no cattle. My Seahawks challenge your Cowthings to a game.

.
.

(Dang it Drango, stfu, it's too early for smack talk)

62 posted on 11/29/2006 11:34:23 PM PST by Drango (A liberal's compassion is limited only by the size of someone else's wallet.)
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To: Drango

I think that for all NFC teams, it all depends which yeam shows up to play. This season is pure Jeckel and Hyde for us.

Beat Indy, lose to Wahington.

I think that the Seamolds will be better now that Alexander is back, but ...


63 posted on 11/30/2006 5:52:40 AM PST by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120))
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To: texas booster
Can I ask you a question?

My puter has dual processors, that means 2 right? If it does, how come it only shows 1 active processor?

thanks

64 posted on 11/30/2006 10:10:20 AM PST by processing please hold
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To: processing please hold

You may be running one instance of F@H and not taking advantage of the second processor. But ...

Exactly what processor does your Dell have?

Intel HT? Intel Dual Core? Or just tell me the model number and I'll get the specs.

Intel has released chips that have two cores in one chip. If it is an HT, then you really only have one core with two pipelnes into it.

If you have an Intel Duo Core 2 chip, you have two CPUs in one chip and you will be able to run two instances of F@H, and get almost twice as many points.


65 posted on 11/30/2006 1:50:39 PM PST by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120))
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To: texas booster
I looked around and can't find my paperwork. I put it somewhere where I wouldn't lose it. It's not lost, it's just where I put it.

Is there somewhere on my machine where I can find out what it is?

66 posted on 11/30/2006 1:58:31 PM PST by processing please hold
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To: processing please hold

Look for a model number on the front of the computer or on the side (not the WIndows number though).

Or, right-click on "My Computer", scroll down to Properties, and copy the information from there. The first screen should give info on the CPU, memory etc.


67 posted on 11/30/2006 2:13:45 PM PST by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120))
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To: texas booster
Ok, it says...

Pentium(R) D CPU 2.80 GHZ
2.79 GHZ 1.00 GB of RAM?

Is that helpful?

68 posted on 11/30/2006 2:19:58 PM PST by processing please hold
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To: processing please hold

The Intel Pentium D had two versions that run at 2.80 GHz. Both are double core CPUs.

If you press CTRL-ALT-DELETE the task manager pops up. The second tab is "Processes". Look for the process called "F@HCore_xx.exe". (xx=78 or 82 in most cases).

If you have one F@H running on a single core you will see CPU Utilization = 100% (or close)

If you have one F@H running on a dual core you will see CPU Utilization = 50% ( or close)

Follow these instructions from another thread and you will have two instances of F@H running, maximizing your points potential.




Download the FAH No-Nonsense Text Only Console 5.04 from Stanford downloads here:

http://folding.stanford.edu/download.html

Save it to a download directory or your desktop. DO NOT RUN IT FROM THIS LOCATION.

Make a new folder somewhere safe, such as Program Files. Call it F@H1.

Make a second folder somewhere safe, such as Program Files again. Call it F@H2.

COPY F@H504-Console.exe into the F@H1 directory.

CUT and paste the F@H504-Console.exe into the F@H2 directory.

Enter the F@H1 directory. Run F@H5.04-Console.exe. Enter all the normal stuff (Team 36120, Private_Sector_Does_It_Better, etc). When it asks to "Set Advanced Methods" enter "y".

The Advanced Settings need to have "Run as a Service" = y, and the machine ID needs to be '1' and '2' respectively so the Stanford servers can tell the work units apart.

If in doubt, edit the "client.cfg" file. Make sure that your name and team number are correct, and that each client.cfg has either a '1' or a '2'.

Thank you very much for working through the setup issues.


69 posted on 11/30/2006 2:42:37 PM PST by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120))
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To: texas booster

Thank you. I printed out your post and will go step by step.


70 posted on 11/30/2006 2:48:06 PM PST by processing please hold
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To: texas booster
fahcore_78.exe says CPU Utilization = 100%

You said, 'follow these instructions from another thread and you will have two....'

1)What thread? 2)Should I uninstall my old F@H first?

71 posted on 11/30/2006 3:01:34 PM PST by processing please hold
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To: processing please hold
fahcore_78.exe says CPU Utilization = 100%

At the bottom of the screen it says..

processes:49 CPU usage:100%

72 posted on 11/30/2006 3:08:37 PM PST by processing please hold
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To: processing please hold

Hmmm ...

Those instructions were from a FR thread we posted a few weeks ago.

I do not remember a true dual core CPU that did NOT come in at 50%. Let me check out one of my systems.

Go to the directory where you have your F@H. Open a file called unitinfo.txt. It will look like this ...

Current Work Unit



Name: p2124_lambda_5way_melt_4_10011
Download time: November 21 17:13:22
Due time: March 11 17:13:22
Progress: 80% [||||||||__]

(Don't worry about the dates at this time).

You normally do not need to uninstall the older F@H first. Just make sure that the new F@H is entered as "machine=2".

It will be a while before I get back. Gotta make a kiddie run and see if the natives left any bread in the stores because of our icy weather.


73 posted on 11/30/2006 3:11:47 PM PST by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120))
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To: processing please hold
I'll be here when you get back.

On the Task Manager page it says.

fahcore_78.exe....the numbers jump around 48-50

At bottom of same page it says...processes:49 CPU Usage 100%

Does that mean anything different.

Also, when I typed in the address you gave me my chioces were.download them all OR save to disk. No save it to download directory or desktop.

74 posted on 11/30/2006 3:25:09 PM PST by processing please hold
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To: texas booster

I did something wrong. I lost my wu I was working on. It had 28000/5000 frames finished. It was a p2126_villian_sigd3.


75 posted on 11/30/2006 4:03:49 PM PST by processing please hold
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To: processing please hold

Firt, having F@Hcore_78 jump between 48 and 50 means that you can add another instance of F@H to the second core.

If F@H is at 50% and CPU is at 100% I am curious what else you are running to take up the extra CPU cycles. What other numbers in Task Manager are above 0?

First create a directory called F@H1 and a directory called F@H2. I would put the new directories in the root directory or under Program Files. When you download, download twice, and save the file first into F@H1 and then into F@H2.

Do not save to the desktop. If you run it from there it will create headaches eventually.

Then enter into each directory, run the F@H5.04. Directions are as before. Accept the default if you are not sure of what to do, EXCEPT one must be machine=1 and the other must be machine=2.


76 posted on 11/30/2006 5:05:29 PM PST by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120))
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To: processing please hold

We may need to take this to FReepmail to keep from boring everyone.

The only was to lose a WU is to delete the files. Therefore, do not empty your trash can.

Is the original directory still where is used to be? Is there anything in it? If so, a reboot will cure most ills.

If the directory is empty or if it has been moved, then we get to ask and answer a lot of questions to save the WU. It can be saved if you want.

Or just forget the old WU like an old boyfriend, install the two new instances and commence to folding anew. (I've been dealing with a teenage daughter)


77 posted on 11/30/2006 5:10:51 PM PST by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120))
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To: texas booster
The only other thing with numbers is...winf@h.exe. It bounces 49-50, that's all with numbers, the rest are zeros.

I have my f@h folders 1&2. When I enter the F@H1 directory, it immediately tries to load me another wu before I can type in the information "SET ADVANCED METHOD'S" enter "y".

Do not save to the desktop. If you run it from there it will create headaches eventually.

I'll have to get rid of that then. oops.

78 posted on 11/30/2006 5:13:40 PM PST by processing please hold
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To: texas booster
do not empty your trash can.

Too late.

79 posted on 11/30/2006 5:14:36 PM PST by processing please hold
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To: texas booster
Or just forget the old WU like an old boyfriend,

Consider him forgotten.

80 posted on 11/30/2006 5:21:13 PM PST by processing please hold
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