rationalskepticism.org

OK some of you may have been folding at home team members at RDFRS and some may just be interested in distributed computing. A new team has been formed by RPizzle, currently based out of Rationalia, but should also be the team for here. A new generalized name should be in the pipeline, no need to split up our efforts more.
Current Team discussion here:
http://rationalia.com/forum/viewtopic.php?f=55&t=9052
Team stats page here:
http://fah-web.stanford.edu/cgi-bin/mai ... num=182116

Team number is: 182116.

What is Folding@Home?
It is a 'distributed computing' project where people donate their unused computer processing power to scientific research.

What is distributed computing?

Distributed Computing is a method of computer processing in which different parts of a program, or different portions of data, are processing simultaneously on two or more computers that are communicating with each other over a network or through the Internet.

What is the goal of this research?

Our goal: to understand protein folding, misfolding, and related diseases

What is protein folding?
Proteins are biology's workhorses -- its "nanomachines." Before proteins can carry out these important functions, they assemble themselves, or "fold." The process of protein folding, while critical and fundamental to virtually all of biology, in many ways remains a mystery.

Protein folding is linked to disease, such as Alzheimer's, ALS, Huntington's, Parkinson's disease, and many Cancers
Moreover, when proteins do not fold correctly (i.e. "misfold"), there can be serious consequences, including many well known diseases, such as Alzheimer's, Mad Cow (BSE), CJD, ALS, Huntington's, Parkinson's disease, and many Cancers and cancer-related syndromes.


You can help scientists studying these diseases by simply running a piece of software.
Folding@home is a distributed computing project -- people from throughout the world download and run software to band together to make one of the largest supercomputers in the world. Every computer takes the project closer to our goals. Folding@home uses novel computational methods coupled to distributed computing, to simulate problems millions of times more challenging than previously achieved.



Why distributed computing?

Why not just use a supercomputer?

Modern supercomputers are essentially clusters of hundreds of processors linked by fast networking. The speed of these processors is comparable to (and often slower than) those found in PCs! Thus, if an algorithm (like ours) does not need the fast networking, it will run just as fast on a supercluster as a supercomputer. However, our application needs not the hundreds of processors found in modern supercomputers, but hundreds of thousands of processors. Hence, the calculations performed on Folding@home would not be possible by any other means! Moreover, even if we were given exclusive access to all of the supercomputers in the world, we would still have fewer computing cycles than we do with the Folding@home cluster! This is possible since PC processors are now very fast and there are hundreds of millions of PCs sitting idle in the world.




Quotes from F@H Home page and FAQ:
http://folding.stanford.edu/English/Main

So now you have an idea what F@H and what distributing computing is why would you want to take part?
People contribute or donate their computer processing power for various reasons, some have people they know suffering from these conditions and want to 'strike back' others are interested in contributing to science or just taking part in this amazing project.

What do you need to contribute?
A computer or PS3 that is connected to the internet and you have permission to run applications on, there are programs (called 'clients')to run this research on the normal processor of your computer, the graphics processor (video card) or your PS3.
You don't need a super powerful computer to run the basic client and team members here are running with every thing from laptops to powerful gaming systems.

Why teams? Teams are a fun part of contributing adding support and a little competition to make things more interesting and effective.
You can join our team, another or just donate anonymously, joining a team has no strings attached. Don't feel the need to join our team, if you are already a member of another one you are still welcome to post here, but if you have no team consider joining us .
When you set up your client all that is required is you put 182116 as your team number and you're in!

What are the 'points' that I read about and see in posters sig lines?
Points are an aproximation of science complete a metric or a currency we are 'paid' in. Every work unit (research packet) that you complete will have a point value attached to it that you are 'paid' with, every point you earn as a team member is awarded to you individually and your team. Points drive the team competition, but are also a measure of how much 'work' was required to complete the work unit.

Foldon!

Please read here for some more frequently asked questions on:
Answers to: Reasons for not using F@H.
Thanks to John Naylor. (F@H Beta Tester and Administrator FAHAddict)
http://foldingforum.org/viewtopic.php?f=16&t=1164#p9750

Will F@H reduce the security of my computer?


The Folding@home client and distributed computing system is no less safe than other programs that you can download from the internet and run on your computer. Because security of the F@H client is very important to the Pande Group, they have designed the F@H system to be as secure as feasible through encrypted downloads/uploads, file checksums, etc. F@H should not reduce the security of your computer. But, to ensure maximum security of your computer, never download a client or purported client update from anywhere other than the official download page.

Can’t they just use a Supercomputer? /They already have 400,000 processors, how is my one processor going to make any difference?


F@H is more than three times as powerful as the world’s current most powerful supercomputer, in terms of operations per second, so using a supercomputer would be a massive step backwards for the project. Even with that in mind, the project is still restricted by the power available to it and needs all the extra silicon it can get.

Won't this stop me using my computer?


F@H is designed to give priority to any process other than itself, so if you use your computer it will back off to allow the programs you run to have all the power they need. This applies to the CPU and SMP clients, but GPUs do not have this functionality so it is recommended that GPU clients are paused if a GPU-heavy program is to be used.

I’m worried about the environment, won’t running this program increase greenhouse gas emissions?/ Won’t running my computer at full or near full usage all the time make my electricity bill skyrocket?


F@H needs only to be run when your computer is running. From the folding@home website here the average computer uses 100W a day if heavily loaded, which works out at about $10/month (using a value of $0.15/kWh) if the computer is run flat out 24/7. If you factor in the time that you would be using that machine anyway, the cost is going to be much lower. As for the PS3, thus uses about 200W (using the original power supply) and about 115W on the newer power supplies in the 40/80gig models. That is between $12 and $20 a month again assuming the machine folds 24/7 and $0.15/kWh.
Cheers to Tarx:There is also the fact that treating all the diseases which this project can and probably will help find cures for, has a significant environmental cost (i.e. to power all the necessary machinery), and also a significant financial cost should you become a victim of the diseases. The comparatively small extra outlay for running F@H is peanuts compared to the cost of treating these diseases.

Won’t running my computer at full usage/100% all the time damage it?


Modern computer chips are precision instruments, they are designed to be able to operate continuously at full speed without degrading. A typical example of this would be the humble web server. These serve thousands, maybe tens of thousands of connections a minute and are fully loaded for long periods at a time, yet hardly ever fail due to hardware faults. For the more technically minded, it is usually a good idea to clean out any heatsinks though (this applies to both desktops and laptops).
Good point by kikimarie:You may wish to install a temperature program and watch the temperatures if you are using a laptop to run F@H. Well designed laptops should stay within their defined operating temperatures but will almost certainly get noisy, and the temperature monitor program should ensure peace of mind about the noise. However if your laptop cannot cope with the extra heat then the monitoring program will alert you to its' overheating and the need to buy a cooling pad or similar device, to enable continued running of F@H.

This is pointless; you can’t solve something like this without lab work!


This is correct, however Folding@Home uses independently tested and proven techniques to advance and work alongside the work done in laboratories across the planet.

F@H is irrelevant now due to [Corporation X]’s research. Why bother?


As long as we lack complete knowledge about how and why proteins misfold, the work of the Folding@Home project will remain relevant. Maybe the project will render itself irrelevant by solving these problems, we don’t know. But for the foreseeable future, the project will not be rendered irrelevant by the research of any one company or group of companies.

How can I be sure that my resources, "loaned" for free, will not be used to generate research that will then be sold for profits, e.g. like United Devices?


Folding@Home is a project run by Stanford University, and they release all of their findings into the world free of charge, in the form of peer reviewed papers. See here for more. Anyone in the world can then use the results to further their own research without the need to redo these computationally intensive simulations.

I have an internet usage cap, using F@H will use more than I am allowed, will it not?


Put simply, no. The uniprocessor clients use up to 10MB each way at their normal settings (assuming use of v6 clients), but most computers if run just during the day will only finish a Work Unit every 2 or 3 days. Over a 30 day period that is an absolute maximum of 300MB (if a WU is completed every 2 days, so 15 WUs at 10MB each way), or well within any usage cap. Most Work Units are far smaller than that limit anyway, and the v5 and v6 clients can be set to limit Work Unit downloads to 5MB each way.
WARNING: Unfortunately the same cannot be said of the GPU clients if run on higher-end GPUs - if run for ten hours a day internet usage can be as high as 30MB... which over a thirty day period is 900MB. Please consider this if you have a high- or top-end GPU and want to run the client, but have a bandwidth cap.

The Project has been running since 2000, but I don't see any cures. Why not?


For this, a note from the director of the project:

VijayPande wrote:In terms of big picture highlights, we spent the first 5-6 years working out how to use distributed computing to efficiently tackle protein folding and then applying it to do the first simulations of protein folding reaching the folded state with experimental validation, etc. This was one of our primary goals laid out in the Science section and we're excited to have accomplished that. Part of our work today involves continuing in that direction with more complex systems, continuing to push the state of the art.

The other part of our work is to apply these methods to study disease, especially Alzheimer's Disease (AD) and Huntington's Disease (HD). We are interested in understanding what's going on in these diseases to facilitate a cure. Indeed, our motto in big letters on our web page is "Our goal: to understand protein folding, misfolding, and related diseases," and we are on track for that. One could ask "how do you know if you understand the disease?" A good answer is new small molecule drugs which appear to prevent or minimize the effects of the disease. This too is in the works, with encouraging results in the lab (but it's not time to talk about this publicly until it passes peer review).

However, it takes a long time (often as much as 2-3 years) from the point where we have something interesting in the lab to where we are talking about the results publicly (it has to be validated by ourselves and go through peer review). Our first results on AD and HD will hopefully be coming out soon, i.e. in the next 6 to 12 months or so.

Finally as for a cure -- a cure takes a while to test and develop. First, one has to understand what's going on and that's where basic science comes in and most of what FAH does. However, we and others are excited to take the published results from FAH and apply them to real world problems such as AD and HD and our expectation is that our work could give some critical insights into these diseases, thereby helping to accelerate a cure.

If you have any other questions re this project please post them here and someone will attempt to answer them.
If you do decide to contribute, drop by for some advice or just to say hello.
Further team discussion can be found on the Rationalia team page:
http://rationalia.com/forum/viewtopic.php?f=55&t=9052
kiore.

Handy Folding Links:


To download Folding@home clients and get started:
http://folding.stanford.edu/English/Download

Our team home page, with up to date stats and a list of all team members:
http://fah-web.stanford.edu/cgi-bin/mai ... num=182116

Another Stats page Kakoastats:
http://kakaostats.com/t.php?t=182116

Project summary points and details:
http://fah-web.stanford.edu/psummary.html

The Support Forum for F@H: Technical help, advice and other peoples stuff:
http://foldingforum.org/index.php

3rd Party tool for monitoring clients and progress:
http://code.google.com/p/hfm-net/
http://fahmon.net/

For Apple Users, a tool to download and monitor your clients: 'Increase'
http://calxalot.net/downloads/

To make a stats signature:
http://folding.extremeoverclocking.com/?nav=IMAGES

A full list of tools:
http://foldingforum.org/viewtopic.php?f=14&t=52

The Folding AT Home, Home Page. Where to start if not currently on board but want to be, and what the hell everyone else is talking about...
When I first saw this thread I thought it was about ironing services..
http://folding.stanford.edu/

Up quick update, new team output is now over 130kppd and seems likely to climb a little higher as those current team members switch over their clients without any new members factored in. At this rate we will be in the top 1000 teams in 4-5 weeks.

This thread is for those interested in F@H, it doesn't matter what team you fold for, please feel free to post questions or comments anyway. New recruits to the project are always welcome and new recruits to the team doubly so.

William.Young wrote:One of my current WU types is Gromacs and the work unit is indicated as 'system'. It is the 'system' work unit name that has me puzzled.

Before (and I have only completed two on this particular processor) there was a longer name for the WU. Does anyone know what is meant by 'system'?

This is on a 2GHz PPC.

Unsure but know that PPC v5 workunits are being phased down as the number of functioning PPC systems has dropped, apparently they will continue to produce them in small quantities.
Are you using Increase? What project number does it say they are?

Hmmm do you see steps being completed on it? Sorry I've stopped folding on my old PPC mac, it is reserved purely for writing now, so have not been keeping up on what's happening there.