Do you Fold (@ Home)?

I'm looking to get a new lappy with one of nvidia's 4**M or ATI 58** series and I was wondering if they are able to run the GPU2/3 client (no reason why they couldn't, but I can't find a mention of it anywhere) and was wondering if anyone does.

If you do fold, could you post your PPD and what hardware your folding on.

 

I wouldn't do it on a laptop. Their cooling isn't nearly as good as a desktop, so running the CPU/GPU/both flat out for long periods of time could cause premature heat-related damage.

 

Hardly.
They were designed to operate at their maximum frequencies for long periods of time.
I've been using mine in a similar manner by playing games that were pretty hard on both cpu and gpu for hours.
No adverse effects apart from heating up (but also no crossing over the safe zone temps)

 

Can you tell me what the point is of folding (what do you get for doing it)?

 

If I can recall correctly from my desktop days, Folding@Home is a client installed on your computer which essentially allows a science lab or something similar to utilize the power of your computer by getting it to remotely perform tasks and applications in the quest for the cure of cancer (I think).

It uses mainly your CPU and GPU. Used to be quite popular, seems to have lost a little bit of that though.

Doesn't make much sense that people would do it though. Science labs have their own Intel Itanium processors and NVIDIA Tesla platforms to mess with, and they are MUCH more powerful than what the consumer has.

 

Folding@Home and other similar projects like Einstein@Home use the computers of the client users to process small amount of data related to scientific calculations. Sure, a home PC isn't very powerful compared to some computers universities and research centers have access to, but thousands of home computers can make for quite some computing power and cheap computing power at that.

The use of clients like that also removes the need to wait if you need to share the use of high performance computers or the added cost if you need to use another university/lab's computers.

Einstein@Home is currently at around 325 TFLOPS as an example.

F@H is studying protein folding which is related to many diseases while E@H is all about physics.

For those that are interested in F@H, you can also run it on your PS3 if you have one.

 

This really depends on the laptop. A ton of the 15" i7 laptops don't cool themselves properly. I can only single-core fold on mine. If I use the multi-core client and let it run wild, the laptop throttles down hard after roughly 20 minutes because of the heat.

 

I leave both my laptops folding sometimes for days on end and one never goes above 64C

Plus if it went above the safe threshold it would auto shutdown.

Folding@home FAQ

You use you're PC to help find cures for diseases (huntingtons, Alzheimers, are some of the more popular ones) What do YOU get? Nothing... Except the possibility of a cure in a few decades.

Yes but... A few hundred thousand CPU's and GPU's are wayyy more powerful than a lab

Folding@Home Stats

 

I would've if electricity was free

 

I'm an undergrad working in a structural biology lab and while we do have some fairly powerful servers, space is still limited and just this morning one of the grad students was spazzing out about some neighboring lab going over their allotted node limit. The issue is that for things like folding, you have to simulate a process that in nature is guided by thousands of tiny physical interactions. If you had a computer lab for your general physics course, think of a program where you had to calculate the position of an object. Generically (and very very simplistically):

Object.pos = <0,0,0>
Object.q = 3 // C
Object.m = 5 // kg
dT = .1 //seconds
Efield = <4,5,6> // N/C
F = Efield * Object.q
while (the program isn't finished)
{
dP = F * dt
Object.pos = Object.pos + (dP/Object.m)*dT
}

Now scale that up by thousands as the program must calculate Van-der-Waals interactions, ionic interactions, and potential energies of each atom, see how these factors would affect a chain of such atoms, and repeat until the atoms don't move (much). You can see how this would eat up a processor pretty quickly. When I make a structure calculation, I let the program run overnight as it can take hours even on a double Xeon server.

I work in a research lab in a public university so while we may not have the latest and greatest toys, we're not exactly poor. I believe F@H is run by a lab in Stanford but I'm not sure who can submit data to the F@H program; if they're allowing other labs from less well-funded schools have access, it would really diminish the load on their own servers.

Thought I'd try to explain

 

I would if I got credit for the work my notebook did (if it finds something useful my name should be on the news ).

 

and once they found, they are gonna charge it at a real Expensive Price rather to have it goes cheap to everyone in need right?

 

Nah, all credit will go straight to MSI... you didn't do any of the work for it after all

 

folding@home has been going on for over a decade and has yet to accomplish anything apart from damaging well meaning, but delusional, people's machines

see also: seti@home

 

AFAIK, the only DC project to produce any result is Prime95.

 

yep, that's the plot of Deus Ex

 

What was the result?

 

Really?

P.S. The 1 decade anniversary is coming up on 10-1-10.

 

Are you a computer science major or a bio major?

Edit: @Danja

 

I fall into the category of not counting it as a result until it's applied. Folding@home has certainly helped advanced distributed computing and protein folding theory, but I'm waiting for an applied science result from it.

That's not to say the knowledge gained thus far is not useful. It's just that many of the papers are highly theoretical models of microsecond processes rather than anything resembling a functional protein or drug that affects said protein. The bulk of the advances that come out of distributed computing have to do with networking, multi-processing systems, and workload distribution, and not with (as yet) functional biological knowledge.

 

I think asking for an applied biomedical result at this point is a bit much given the state of the technology.

 

Prime95 is a way to actually win some $$$$ if you find a prime of certain constraints. And get your name on the news. It's also pretty pointless and has very little real-world application.

Granted I haven't really looked into it, but I'm not really sure what the purpose of fold@home is... the idea behind it, I think, is to find an optimal way of folding a sequence of amino acids via energy minimization. In essence, given a sequence of amino acids (or DNA), we will be able to predict the tertiary structure of a given protein. This has immense value. However, my understanding is that our able to predict tertiary structures is pretty damn poor.

Basically, whatever they predict at fold@home, I'd think they'd have to reverify in the wetlab. A good way for this is to magically crystalize the protein in question, then use the predicted tertiary structure as a reference to solve the phase problem.

tl;dr someone explain to me what fold@home does exactly and what it's use is please!

 

True, it probably takes 10-15 years of applied lab work to take any of the theory out of F@H and turn it into a medically applicable product. I just laid out my personal line in the sand for what counts as a result. For all the computing power thrown at SETI, nothing really came out of it. Prime95 came up with a big prime, but the usefulness of massive prime numbers outside of maybe cryptography is negligible. F@H is useful and helps understand what's going on at the microscopic level, but really can't help us make better proteins for at least another decade (I have no support for this estimation)

Is that a question or a response? It's not a bad summary of the problem F@H addresses. I'd just add that part of the idea behind F@H is that many illnesses (you can find a list on the F@H website) are hypothesized to be caused by improper protein folding (usually as a result of some mutation).

 

It was a question. I've wondered for awhile what fold@home accomplishes, or what it hopes to accomplish.

I know more about protein folding than your average joe (so most faq's explanation of 'it'll help cure diseases!' does not satisfy me) but at the same time, maybe I don't know enough to really understand the importance (if any) of it?

prime95/seti@home on the other hand, I feel like I know exactly what I'm accomplishing.

 

It seems to me that they think the diseases listed on their wiki page may be partially caused by protein aggregation. If you're familiar with prions (Mad cow, scrapie, kuru, etc.), you'll remember that the disease is caused by a misfolded protein which has both the activity required to misfold other proteins and high affinity for these misfolded proteins themselves. This causes them to come together and form ever-growing plaques, which disrupt surrounding tissue. I had never heard of misfolded proteins acting in this way outside of prions but it's not too much of a stretch to suggest that a protein that's misfolded due to mutation can behave in a similar way and aggregate into a cluster.

I found this site while doing a quick bit of research for the above post. It gives pretty good information about what they're hoping to gain from all of this, and suggests that their research is being incorporated into drug design.

@Woofer00, you're correct in your time frame. I believe the average time between when a drug is conceptualized and when it's approved for distribution by the FDA is ~ 10 years. That means that even if F@H were to have instantly found promising data the moment it debuted (highly unlikely), the market version of that research would just now be coming out.

@Crazysoccerman14, I'm a bio & chem double major but I learned some CS on the fly for my lab work, which makes me probably the worst programmer on campus .

Sorry if I seem a little overzealous on this topic; I finally found a discussion where I do have at least a little bit of practical experience so I wanted to weigh in my side and show some evidence that it's not a complete waste of time developed by satan to burn out your gpu as quickly as possible

 

10 years is after it's been beakered, purified, identified, and remotely conceived of as achieving {x} result. Folding isn't meant for that, but it'll hopefully produce results that will improve the design process from the not-so-old "throw some amino acids together in {yzx} order and maybe maybe we'll end up with more than goop" approach (I'm very cynical about the efficiency of the pharma approach to making new drugs/enzymes). We're only barely beginning to designer enzymes reach the market, and I have no idea whether efficacy numbers are in yet.

As far as what the program is actually doing, well, my orgo classes didn't go so well, but here's my grasp - f@h simulates the behavior of proteins on a distributed computing scale. On an average consumer desktop, you might be able to crunch enough numbers to simulate a nanosecond (give or take) of protein folding. Proteins fold on a roughly a tens of microseconds scale, so given ten thousand years on that one computer, you might simulate one very specific instances of folding. F@H distributes the workload amongst all its users so that the time is severely reduced. Protein folding is inherently serial - you can't achieve one conformation without reaching the one before it - so distributing the workload is ridiculously tricky. This is where I think F@H has been more successful - figuring out how to distribute a serial workload amongst numerous parallel processes. The practical effect of advances in distributed computing are beginning to come out now that results are getting published, but we're still far from a "useful" result.

 

Wrote out this huge thing... and finally figured out what my misunderstanding was! Evidently I had no idea what "misfold" meant. I was under the assumption that these diseases were due to different primary structures... didn't realize they were the same but were folding differently. Ah well, shows how much bio I really know

However, I still think that we understand way too little about molecular dynamics to be throwing all this processing power at it. At least with primes, we pretty much know everything there is to know about it, and any improvement in algorithm will be slight. Thus, consumption of processing power feels less wasted to me (despite the fact that these primes almost have no use whatsoever)

@woofer00 - yeah most of the articles published on fold@home seems to be about advances in distributive computing - not biology related things - which made it seem less biology related than computer science related.

 

Speculating about molecular dynamics without throwing a planet-load of computing power ends up creating more theory. There's (probably) progress being made, it just depends on your idea of how big a step counts as progress.

Frankly, I feel like aside from the individuals who choose to run a DC boxen farm, a good chunk of the processing power comes from computer owners who want to say "mine is bigger than yours." Regardless of their motivation, the processing power is useful.

 

@Danja
Cool im a soph. majoring in mcb

 

you'd be much better off just playing Progress Quest
much less taxing on the system, too

 

Not running that kind of sht on my computers .. go read about how can they use it to create bio weapons.

Do you think aids created itself .. Every virus and sickness that didn't exist 100-s of years ago all was created in laboratories and let lose to the world.

Run seti if you really want to waste power.

 

If folding@home actually led to development of bioweapons I'd enthusiastically support it and run it on every PC I own.

 

I've started looking for a large prime:
Free Software - GIMPS

At least I'll get some credit this way

 

The more I think about it... why would I want to volunteer my (or my pc's) labor to a company that will not only take all the credit for any fruits it bears, but also charge an exorbitant amount of money and who is more than willing to let anyone who can't afford to pay for the treatment die.

 

I really hope you're just being a sarcastic troll. Otherwise, that's one of the most ignorant comments I've read in weeks, maybe months.

Back on topic: Read this article if you want to understand more about folding. The different clients are designed to only use the idle CPU/GPU time of your computer and not significantly hinder normal usage, even when the client is running.

I've been folding for about 10-11 months now and I've built up around 1.1 million points over 4 different computers and 3 different usernames. My desktop's Q6600 at 3.4GHz gets me about 8000-8300 ppd with the SMP (multi-core) client and my laptop's i5-540M at 2.13GHz gets 2500 ppd with the same client.

If any of you are skeptical about whether or not it's worth the time, effort, and relatively small monetary cost, check out these results. If you are too lazy and/or have no interest in what these results mean, then folding is probably not for you. Just don't go around trying to discredit it as if you knew anything about it.

 

TL;DR version: Folding is feel-good simulated biochemistry, not practical biomedicine.

----

I love discrediting folding. Those are some great stats, but what is there to show for the size of the point pile in your pants pocket? I've been running seti, folding, boinc for the better part of the last decade. I've begun to view DC projects as akin to non-profit charities: for all the noise about using our computers to find aliens and cure cancer, the end result is roughly the equivalent of donating $10 to feed kids in Africa - I don't see the result, maybe I helped do some good in the world, but I sure feel better about myself at the end of the day.

Note above I said I love discrediting folding but didn't mention the other projects. I wouldn't mind so much if folding simply said it was a study of protein folding without going into the "study disease" area. It's been 10 years and really only one paper that contemplates the avenue a disease takes has come out of it. There are some papers on Alzheimer's pathways in the works for some time, but they're taking forever to pass peer review. Understanding the method of protein folding is in itself an important goal to accomplish, but F@H pulls on heartstrings without giving anything much back other than to propose new models for study.

 

you don't understand biology, microbiology, disease, or politics, and yet elected to comment anyway.

had you not made any comment, you could have kept your ignorance a secret.

and yet, here we are.

 

Echo that.

 

It's not a company - it is stanford university.

And where's the problem if they take credit? I'm sure they will cite the fact that they used distributed computing to achieve their goal, but after all, they did all of the difficult scientific work to do the research.

 

Are you serious??? Did you even do some fact checking before spouting that nonsense?
Folding@home - Papers

 

A big thing with folding at home is that although they have tons and tons of data being accumulated, they go through it a lot slower.

Also folding is fun for the stats. If it wasn't for that, I wouldn't do it.

 

So... I take not many people fold on here then.

 

It's not super laptop friendly. Laptops are quite underpowered for it anyway.

 

Folding@Home is referenced in papers.
It has not led to anything tangible.

It's a waste of time and resources, and if you disagree you understand neither distributed computing or biochemistry.

 

So? Research can be over a hundred years before "anything tangible." Also like I said, data is being produced at an extraordinary rate, but looking into that data is orders of magnitude slower.

Maybe for you, but saying that anyone who doesn't agree with you is ignorant is a fairly bone-headed statement to make. I fold for the competitive aspect of it, as do many other people, and saying that the data being generated could never be useful is just asinine.

 

I totally agree.

 

That made me lol a bit. But very true! I used to fold like 6-7 years ago, but I didn't bother with it when I built my new computer(s).