Free Republic
Browse · Search
General/Chat
Topics · Post Article

Skip to comments.

Folding@home - The PS3 and Post-PetaFLOP
Folding@home: The Science ^ | 09/18/2007 | PandeGroup

Posted on 10/04/2007 9:20:01 AM PDT by texas booster

The PandeGroup has all been very excited about the great turnout of FAH donors over the last few weeks, allowing FAH to go over a petaflop. The PS3's have been cranking out some very useful scientific results due to the new scientific software present in v1.2. The PS3's are so fast, we've been looking at the results sometimes 2x to 3x a day (instead of a couple times a month). If all goes well, we're hoping to write up these results soon (maybe a few weeks) for peer reviewed publication.

It's also interesting to think about what we want to do post-petaflop. One idea we have is to make the calculation even more accurate. With the methods we have in mind, this normally would slow us down quite a bit (say 10x slowdown), but on the PS3, it's likely that we may get a lot of that for free, as the memory access is the challenging part and in many ways with that now addressed, we may get more flops for free.

This really changes how we think of the economy of doing these calculations and is pushing us to more and more accurate models. One upshot for FAH is that this would drive the PS3's GFLOP rate (now typically 35 GFLOPS on a new GB WU) even higher, closer to the peak. Since the peak is something like 200 for the Cell, we still have a lot of room to possibly grow (although it's unclear how close one can get to the theoretical peak -- my guess is that 70 to 90 per PS3 may be the max for us). Nevertheless, even 70-90 would mean FAH would start getting close to 2 Petaflops!

-- Vijay Pande


TOPICS: Health/Medicine; Miscellaneous
KEYWORDS: alzheimers; fah; fh; folding; proteins
Navigation: use the links below to view more comments.
first 1-2021-4041-6061-79 next last
Folding@home hit a true petaFLOP on Sept 16. Then the PS3 folders hit a petaFLOP by themselves on Sept 23!


1 posted on 10/04/2007 9:20:04 AM PDT by texas booster
[ Post Reply | Private Reply | View Replies]

To: 1066AD; 11Bush; A.Hun; abner; AbsoluteGrace; Advil; aft_lizard; ahayes; aliquando; ambrose; AMD; ...
Why does this matter? Because every computer and PS3 that has joined the fight to research Alzheimer’s Disease and Parkinson’s Disease puts us that much closer to a CURE for these brain wasting diseases.

Imagine if Ronald Reagan was strong for another 10 years in retirement and had been fully able to participate after his Presidency.

Imagine if YOUR loved one could think and remember and participate in the fullness of their life even into their 80s and 90s.

Imagine if YOU could have full use of a lifetime of learning to be fully cognizant of life, no matter how old.

Our Folding@home team is dedicated to this goal of research, and volunteers our computers and PS3s to collectively join over 240,000 other systems to make a difference!

2 posted on 10/04/2007 9:21:39 AM PDT by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120) Cure Alzheimer's!)
[ Post Reply | Private Reply | To 1 | View Replies]

To: krb; Ladypixel; LandJ; LanPB01; LearnsFromMistakes; Leofl; leow; LFOD777; LibWhacker; ...

Why does this matter? Because every computer and PS3 that has joined the fight to research Alzheimer’s Disease and Parkinson’s Disease puts us that much closer to a CURE for these brain wasting diseases.

Imagine if Ronald Reagan was strong for another 10 years in retirement and had been fully able to participate after his Presidency.

Imagine if YOUR loved one could think and remember and participate in the fullness of their life even into their 80s and 90s.

Imagine if YOU could have full use of a lifetime of learning to be fully cognizant of life, no matter how old.

Our Folding@home team is dedicated to this goal of research, and volunteers our computers and PS3s to collectively join over 240,000 other systems to make a difference!


3 posted on 10/04/2007 9:23:18 AM PDT by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120) Cure Alzheimer's!)
[ Post Reply | Private Reply | To 1 | View Replies]

To: krb; Ladypixel; LandJ; LanPB01; LearnsFromMistakes; Leofl; leow; LFOD777; LibWhacker; ...

Why does this matter? Because every computer and PS3 that has joined the fight to research Alzheimer’s Disease and Parkinson’s Disease puts us that much closer to a CURE for these brain wasting diseases.

Imagine if Ronald Reagan was strong for another 10 years in retirement and had been fully able to participate after his Presidency.

Imagine if YOUR loved one could think and remember and participate in the fullness of their life even into their 80s and 90s.

Imagine if YOU could have full use of a lifetime of learning to be fully cognizant of life, no matter how old.

Our Folding@home team is dedicated to this goal of research, and volunteers our computers and PS3s to collectively join over 240,000 other systems to make a difference!


4 posted on 10/04/2007 9:23:51 AM PDT by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120) Cure Alzheimer's!)
[ Post Reply | Private Reply | To 1 | View Replies]

To: texas booster
Folding@Home FAQ for new users:

What is Folding@Home?
A Stanford University project to find out how proteins fold.

Why it's important: Proteins folding wrong causes all kinds of diseases, like Alzheimer's, Parkinson's, and forms of cancer. Folding@Home uses novel computational methods and large scale distributed computing, to simulate timescales thousands to millions of times longer than previously achieved. Through Folding@home, scientists now have the horsepower to study the mechanics of protein folding. With its ability to share the workload among hundred of thousands of computers economically, Folding@home can help scientists understand how proteins snap, or don't, into their predestined shapes - and may help to explain the origins of diseases such as Alzheimer's and apparently unrelated diseases. We're fueling research that could end all that.


How does it work?: You download a safe, tested program (see link below) that is certified by Stanford University. It gets work from Stanford, runs calculations using your spare computer power, and sends the results back to the University.

Is it safe? Yes! Folding@Home rarely effects computer performance in any way and won't compromise your privacy in any way. It only uses the computing power you aren't using so it doesn't slow down other programs.


How do I get started folding for Team FreeRepublic?:
1.) Download the folding program from Stanford University's folding download page (Folding@home Client Download). Type in your desired user-name.
2.) Type in 36120 for the team number. THIS IS VERY IMPORTANT - if you get the number wrong, you won't be folding for team FreeRepublic!
3.) The third question asks, "Launch automatically at machine startup, installing this as a service?" - We recommend you answer YES. Otherwise you will have to manually start the program after every reboot.


How can my computer help? Even if they were given exclusive access to all of the world's supercomputers, Stanford still wouldn't have as much processing power as they get from the supercluster of people's desktop systems Folding@home relies on. Modern supercomputers are essentially a cluster of hundreds of processors linked by fast networking. But Stanford needed the power of hundreds of thousands of processors, not just hundreds.


There's no reason to not get involved! It's free, easy, and you can know you're helping every minute without lifting a finger.

*******************************************

List of Relevant Folding Links
Why Fold - Watch This !!


Another Folding Clip


The Inner Life of a Cell


Folding@home Client Download


FreeRepublic.com Folder Stats


Extreme Overclockers Stats for FreeRepublic


Another Stats Page


*******************************************
Competition (Not!!) Dummies ..Daily Kos


Dummie Folding Threads #7 #8 #9#10#11 #12
Hey DUmmies, can't ya'll post a new thread at least once a year?


**************************************************
Other Useful Stuff - Links


How much are those work units worth? And what are they?
All Projects Listed
Point Summary for Workunits


Stat Image Generator


Fahmon Third Party Monitoring Software

**************************************
Past FreeRepublic Folding threads


#1 #2 #3 #4 #5 #6 #7 #8 #9 #10 #11 #12 #13 #14 #15 #16 #17 #18 #19 #20 #21 #22 #23 #24 #25 #26 #27 #28 #29 #30 #31 #32 #33 #34 #35 #36 #37 #38 #39 #40 #41 #42 #43

5 posted on 10/04/2007 9:27:56 AM PDT by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120) Cure Alzheimer's!)
[ Post Reply | Private Reply | To 1 | View Replies]

To: texas booster
My F@H is running under VMware in Windows XP
on a one engine of a 4 engine Mac Pro running OS X

6 posted on 10/04/2007 9:35:59 AM PDT by Uri’el-2012 (you shall know that I, YHvH, your Savior, and your Redeemer, am the Elohim of Ya'aqob. Isaiah 60:16)
[ Post Reply | Private Reply | To 2 | View Replies]

To: texas booster
Notice to all:

F@H considers the kernals that we download a beta programs. They have arbitrarily set a limit on the newer cores as a two month beta. That means we need to reinstall F@H every few months on some systems.

Oct 1st introduced a new SMP beta. Please reload if you are using SMP. You know who you are!

The PS3 beta changes in early September. If you have not reloaded the F@H core yet, DO SO NOW! You will see nearly 25% more folding due to a reworked core. It is this the speed boost that shot F@H over a petaFLOP, and it can be yours for a quick download.

The GPU kernals were reinstalled in August. By now most folks have already switched to the new core. We will keep an eye out for you since the new beta in November may be a significant boost in performance. beta 6 is current.

For those running Windows console or GUI (you can right click on the red flower in your system tray and see the molecule being folded) stay tuned. The first beta for F@H v6 has just been posted and should be tested by the end of October.

If you want to be a F@H v6 beta 1 guinea pig then follow this link to get the appropriate folding client:

http://www.stanford.edu/group/pandegroup/folding/download.html

7 posted on 10/04/2007 9:40:13 AM PDT by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120) Cure Alzheimer's!)
[ Post Reply | Private Reply | To 1 | View Replies]

To: XeniaSt; JosephW
I love it when you talk to me that way! GRRRRrrr!

When you finish this work unit consider trying out the Mac SMP client. Double points on a really fast system like yours.

With the intro of SMP v6 betas, look into it. I think that josephw is running such a creature, and he is consistently in the Top 5 of FReeper folders.

Here are a couple of notes on the SMP client under OSX:

OSX Install Notes

8 posted on 10/04/2007 9:48:32 AM PDT by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120) Cure Alzheimer's!)
[ Post Reply | Private Reply | To 6 | View Replies]

To: Ernest_at_the_Beach
Don't know if you're on this list, and I figured this would be of interest:
The PS3's are so fast, we've been looking at the results sometimes 2x to 3x a day (instead of a couple times a month). If all goes well, we're hoping to write up these results soon (maybe a few weeks) for peer reviewed publication. It's also interesting to think about what we want to do post-petaflop. One idea we have is to make the calculation even more accurate. With the methods we have in mind, this normally would slow us down quite a bit (say 10x slowdown), but on the PS3, it's likely that we may get a lot of that for free, as the memory access is the challenging part and in many ways with that now addressed, we may get more flops for free. This really changes how we think of the economy of doing these calculations and is pushing us to more and more accurate models. One upshot for FAH is that this would drive the PS3's GFLOP rate (now typically 35 GFLOPS on a new GB WU) even higher, closer to the peak. Since the peak is something like 200 for the Cell, we still have a lot of room to possibly grow (although it's unclear how close one can get to the theoretical peak -- my guess is that 70 to 90 per PS3 may be the max for us). Nevertheless, even 70-90 would mean FAH would start getting close to 2 Petaflops!

9 posted on 10/04/2007 9:53:17 AM PDT by SunkenCiv (Profile updated Wednesday, September 27, 2007. https://secure.freerepublic.com/donate/)
[ Post Reply | Private Reply | To 1 | View Replies]

To: texas booster

BTTT


10 posted on 10/04/2007 9:57:55 AM PDT by E.G.C.
[ Post Reply | Private Reply | To 2 | View Replies]

9.4922239E-4
8.507923E-4
3.1400966E-3
1.6774614E-3
.05947441217
.02480551886

5.1247504E-3


11 posted on 10/04/2007 9:59:22 AM PDT by SunkenCiv (Profile updated Wednesday, September 27, 2007. https://secure.freerepublic.com/donate/)
[ Post Reply | Private Reply | To 1 | View Replies]

To: texas booster
I love it when you talk to me that way! GRRRRrrr!

When you finish this work unit consider trying out the Mac SMP client. Double points on a really fast system like yours.

It seems like there are four FAH running; one in each core.

Do they run as "NICE" ?

Thanks


12 posted on 10/04/2007 10:19:09 AM PDT by Uri’el-2012 (you shall know that I, YHvH, your Savior, and your Redeemer, am the Elohim of Ya'aqob. Isaiah 60:16)
[ Post Reply | Private Reply | To 8 | View Replies]

To: texas booster

One click, Tex :)


13 posted on 10/04/2007 10:19:51 AM PDT by wastedyears (George Orwell was a clairvoyant.)
[ Post Reply | Private Reply | To 4 | View Replies]

To: SunkenCiv

For our next lesson on the TI 83, SunkenCiv presents ...


14 posted on 10/04/2007 10:27:52 AM PDT by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120) Cure Alzheimer's!)
[ Post Reply | Private Reply | To 11 | View Replies]

To: XeniaSt
If you set up four single cores then you would be accomplishing a lot of folding.

Your points show that a work unit is completed about every 48 hours, and occasionally multiple units in the same day.

I would want the opinion of a Mac guru before I gave additional advice. It does seem to me that running OSX code natively on a dual chip system would be more efficient.

15 posted on 10/04/2007 10:34:29 AM PDT by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120) Cure Alzheimer's!)
[ Post Reply | Private Reply | To 12 | View Replies]

To: texas booster
I started only one FAH.

My machine has two dual cores i.e. a 4 core machine each at 2.66 Ghz

One core is running at about 80 %

the other three are running at 55 - 60 % each


16 posted on 10/04/2007 10:43:25 AM PDT by Uri’el-2012 (you shall know that I, YHvH, your Savior, and your Redeemer, am the Elohim of Ya'aqob. Isaiah 60:16)
[ Post Reply | Private Reply | To 15 | View Replies]

To: texas booster

And while we’re on that subject, why isn’t my F@H TI-83 contribution on the scoreboard? ;’)


17 posted on 10/04/2007 10:43:40 AM PDT by SunkenCiv (Profile updated Wednesday, September 27, 2007. https://secure.freerepublic.com/donate/)
[ Post Reply | Private Reply | To 14 | View Replies]

To: SunkenCiv
Cause its' still trying to finish the calculations on this ribosome?

Tough to do with only one color on the calculator ...

18 posted on 10/04/2007 10:48:36 AM PDT by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120) Cure Alzheimer's!)
[ Post Reply | Private Reply | To 17 | View Replies]

To: texas booster

Oh, sure, play the color card. ;’)


19 posted on 10/04/2007 10:54:44 AM PDT by SunkenCiv (Profile updated Wednesday, September 27, 2007. https://secure.freerepublic.com/donate/)
[ Post Reply | Private Reply | To 18 | View Replies]

To: XeniaSt
Now that is playing nice. It looks like you were able to load up four separate cores on your quad core with no effort.

You are not running SMP, but still getting a lot of life out of the Mac.

One of the last work units you submitted was for project p3711. here is a bit of detail on what the system was working on.

"The p3600 and p3700 series projects aim to study the folding free energy landscapes of RNA hairpin-loop motifs in explicit solvent via the Simulated Tempering and Serial Replica Exchange Sampling Methods. They are part of a large scale effort to understand the folding of RNA hairpin-loops with systematic sequence variations."

20 posted on 10/04/2007 10:55:07 AM PDT by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120) Cure Alzheimer's!)
[ Post Reply | Private Reply | To 16 | View Replies]


Navigation: use the links below to view more comments.
first 1-2021-4041-6061-79 next last

Disclaimer: Opinions posted on Free Republic are those of the individual posters and do not necessarily represent the opinion of Free Republic or its management. All materials posted herein are protected by copyright law and the exemption for fair use of copyrighted works.

Free Republic
Browse · Search
General/Chat
Topics · Post Article

FreeRepublic, LLC, PO BOX 9771, FRESNO, CA 93794
FreeRepublic.com is powered by software copyright 2000-2008 John Robinson