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Thread: Ultimate Guide To Folding@home

  1. #1
    Spicker's Avatar AKA jaigandhi5 BT Rep: +7BT Rep +7
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    1. What is FAH?
    FAH is a distributed computing project, the purpose of which is to learn how proteins fold and misfold. By breaking down the process by which proteins are created we can find out what causes them to miscreate or misfold. The hope is that this will lead to future research that can help scientists come up with better treatments/cures for many of todays common ailments. But the most important part of the project is putting together an effective model of how to fold and unfold proteins with supercomputer power.

    This is an extremely complicated process that requires awesome amounts of computing power that was virtually unattainable prior to the start of this project. This project harnesses the power of thousands of individual PC's connected to the internet by breaking down the necessary work and allowing those individual computers to work on small pieces of information and then returning the calculated results to stanford university. Once the work is done and returned your computer will automatically get fresh data to calculate. The work is then piece back together at Stanford university. There are results and more information posted on the Folding@Home website at http://folding.stanford.edu/.

    We are team 34905 and if you would like help setting up the client you only need to ask and there will be several people ready to help.

    2. What is Protein Folding?

    Most of you are at least vaguely aware of the Human Genome Project. That was an attempt to map out human genetic structure so geneticists could figure out just what all those chromosomes and genes do to earn their pay.

    What scientists found out while doing this, though, is that knowing genetic structure is only the first piece of the puzzle.

    A map of the human genetic structure is a lot like an organizational chart of a company. It certainly tells you something about a company, and who's in charge of what, but it doesn't really tell you how the company does things.

    The reason for that is that genes don't really do the work. What they do is provide instructions for the kinds of workers it needs to get the various jobs done, sort of like a genetic recruitment staff.

    There's two big differences between this hiring staff and a corporation's though. For this staff, the "workers" aren't people, they're proteins. And to the envy of human hiring staffs everywhere, genes can clone its workers.

    So proteins are the real workers in the human body; millions of proteins doing millions of jobs, sometimes alone, sometimes in conjunctions with other worker proteins.

    3. How do proteins work?

    To do their work, proteins often have to get into the right position to do a certain job. Think of it like the difference between walking and swimming, you get into different positions to do either.

    Part of the reason why proteins need to get into the right position is that they often act as keys to lock or unlock other proteins. The "key" has to be put into just the right position to get into the "lock."

    We call all this manuevering around "protein folding." It's just a fancy way of saying, "how proteins do their job."
    _JOHN_LENNON_:
    1. Doing ANYTHING stresses the life of your processor, but this F@H (Folding @ Home) uses spare CPU cycles, so you dont notice it while your playing BF 1942, or while im playing Halo. But if say you leave your computer for a bit, it will notice the free processor, and pick up the slack.

    2. It really doesnt hurt your computer like I said above, I konw people that have this running on no less than 20 machines and have been doing for awhile.

    3. Yes, I said 20 MACHINES. People take this very seriously, as over at AMDMB.com.

    4. I have been folding for over a year now for the AMDMB.com team, and I think were maybe 5th or 6th world wide. I know from our forums that we have several people like I said with the 20+ Computers running 24/7 just to fold for cancer. (yes the electric bill gets raised a few ticks) I know that also we have taken donation on 4 complete machines, and then given them to people to they can be Folding for the team in the privacy of their own homes. I think were currently taking donations for the 5th one.

    5. You guys should all get into this, haha Bigdawg, being about my age I know your parents have asked you around the house at times (whats your computer doing on right now, when your not even infront of it.) Well, atleast now you could say Fighting Cancer Mom! Heh, no but serious guys, every computer can help, even if its just a few work units a month. And we all have Spare CPU Cycles to spare because none of us are maxing out our PC all day. Half the time I have my PC on im just tinkering with some and I have WMP on and Folding @ Home.

    6. Now everyone go download the folding at home command Client
    OC TEAM:
    What are the system requirements for folding?
    You will need to have the equivalent of a 200MHz Pentium to be able to process the work in time. The time limits for turning in completed work vary depending on the size and complexity of the protein that you are given to work on. NOTE: in some cases users have gotten even slower computers than this to fold and get units on time. The slowest i have seen get units in on time is a P166 mhz. If you think it is too slow to fold, give it a chance, what's that worse that can happen.




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      Can I be a dial up user and still use FAH?

    Can I be a dial up user and still use FAH?
    Certainly. A 24/7 connection is not required to fold. The client only needs a conncetion to send and recieve work units. So, as a dial up user you can either connect whenever there is a work unit to send manually, or you can configure it to dial automatically (this was covered in part 8 of setup and guides)




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      Is there support for dual processors?

    Is there support for dual processors?
    The answer is still no to smp support, but it is possible to run more than one instance of the client. Yes, with the console (text-only) version. The best way to do this now is to install FAH twice in two different directories, and run them with the flag "-local". If two copies of FAH run in the same directory, they will interfere with each other, and will only lead to bad things. IMPORTANT- Make sure that each client has it's own machine ID (covered it part 7 of setup and guides)




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      Will running my computer at 100% 24/7 shorten the life of my computer?

    Will running my computer at 100% 24/7 shorten the life of my computer?
    No. Actually processors were/are made to run a 100% load all the time. Computers generally a better left on, with very little temparature fluctuation because as the chip heats up it expands and when you switch it off it contracts, this constant expansion and contraction of the cpu over a long period of time causes it to crack, meaning dead cpu! So if your cpu is well cooled with a good hsf(heatsink and fan) and it is at a constant temp at full load it is actually healthier for the chip!! Besides, you will get more done if you are folding 24/7!!.



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      Is there anyway to speed up my folding times?

    Is there anyway to speed up my folding times?
    You can, of course, overclock your computer to make it run faster, but then that's why you're at overclockers.com right? Some motherboards however don't support overclocking but don't worry if you have one of these board there is a shareware program called cpufsb 2.2.6 that makes it possible for you to raise your fsb.

    If you have the Text Only version you can set the idle sensitivity for the client by right clicking on the client in the task bar and going to properties. When the window comes up click on the Misc tab. Go to idle sensitivity and slide it all the way over to "Low". This will make the client a little more aggressive with idle cycles.

    NOTE: It has always been the rule that raw mhz is what makes you fold faster (whether 1800 is 180x10 or 150x12.) This might soon change though; with the coming of newer and larger and more complex protein that are more dependant on your memory. This is speculation at this point.
    LINKS:
    Download the GUI version here
    Original thread here
    OC TEAM here (got some of my info from here

    REMEMBER OUR TEAM IS 34905

    i will be adding an installation guide, and info on GROMACS
    and ofcourse my fav "BORGING" that means spreading it around to other computers with simple programs tht run witht the services and HIDE but i highly recommend that you get PERMISSION from the person who owns the computer first...

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  2. Lounge   -   #2
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    why dont you just update the first page of the old topic?

    {I}{K}{E}

    btw. wasnt this spammed before on all the worlds?

    I move this to the lounge because I think it fits there better.

  3. Lounge   -   #3
    Spicker's Avatar AKA jaigandhi5 BT Rep: +7BT Rep +7
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    INSTALLATION GUIDE
    Step One: Installing the Client
    The first step is to download the Folding@Home GUI client from the Folding@Home client download page. Log in as Administrator (if necessary), and double-click on the downloaded file to start the installation. You will see a welcome screen as shown below. Click next at that screen, and then proceed to click through the license and readme screens.

    Next, you must enter the username you wish to use to be identified in the Folding@Home statistics. If this is the first system you are setting up for Folding@Home, you should check to see whether or not the username that you want to use is already used by someone else (it is ok, however, to use the same username on multiple computers that you own). Go to the Folding@Home User Rankings page and use the box next to the search button to see if the name you want is already taken. If it isn't, you're ready to proceed on to the next screen.

    Now, you can choose what folder to install Folding@Home to (the default is fine), and what you want the Start menu group to be called. The next screen asks you to confirm your settings before the installation begins. Finally, after the installation is complete, uncheck "View Readme" and press "Finish."


    Step Two: Client Configuration
    After the installation has been completed successfully, a configuration panel window will appear. You may adjust your settings in this window. If at any time you wish to change these settings in the future, you may access the dialog again from the menu obtained by right clicking on the Folding@Home system tray icon.

    Your username should already be filled in properly if you entered it correctly while installing the Folding@Home client. If it is not, here is your chance to change it. For the team number, enter "34905"

    On the Connection tab you will find the network settings. These will probably not need to be changed, however it is a good idea for you to check them out anyway to make sure.

    Finally, on the Advanced tab, you will find more in-depth settings. Most of them do not need to be changed, but you should set the Client Type to Folding@Home.


    Step Three: The Client in Action
    After Ok-ing the Configuration dialog, the client will begin running as an icon in the system tray. You can right click on it and choose display to observe it as it sets up files and prepares to work on a unit.

    Immediately after configuration, the client will attempt to download the scientific core and begin to process a work unit. If you display it soon enough after configuration, you will see it downloading the core as shown in the screenshot below.

    Once the core has downloaded, the Folding@Home client will download its first work unit and begin to process it. When this happens, you will see a screen similar to the one shown below. You can safely minimize the client to the system tray by clicking on its "X" button. To restore it, right click on its icon, and choose Display.


    and thts it...i will be adding GROMACS and other stuff soon..
    Last edited by Spicker; 11-26-2006 at 03:46 AM.

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  4. Lounge   -   #4
    Spicker's Avatar AKA jaigandhi5 BT Rep: +7BT Rep +7
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    Originally posted by {I}{K}{E}@22 January 2004 - 00:31
    why dont you just update the first page of the old topic?

    {I}{K}{E}

    btw. wasnt this spammed before on all the worlds?

    I move this to the lounge because I think it fits there better.
    i did not know if it was spammed in the worlds....sorry...



    i guess thts it...
    if anybody wants to know more and would like to know about GROMACS...just ask and ill post tht too

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  5. Lounge   -   #5
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    I also thought that if I moved it to here more people would read it.

    I hope you can find people here that would do this

    {I}{K}{E}

  6. Lounge   -   #6
    Spicker's Avatar AKA jaigandhi5 BT Rep: +7BT Rep +7
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    Originally posted by {I}{K}{E}@22 January 2004 - 00:43
    I also thought that if I moved it to here more people would read it.

    I hope you can find people here that would do this

    {I}{K}{E}
    k thanx

    and btw here is our team statistics..
    http://folding.stanford.edu/cgi-bin/teampage?q=34905

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  7. Lounge   -   #7
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    I'm installing it
    but it seems that the setuppages are not the same as you posted maybe you have an older build?

    {I}{K}{E}

    How long does it take to do 1 part/section?

  8. Lounge   -   #8
    Spicker's Avatar AKA jaigandhi5 BT Rep: +7BT Rep +7
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    Originally posted by {I}{K}{E}@22 January 2004 - 00:51
    I'm installing it
    but it seems that the setuppages are not the same as you posted maybe you have an older build?

    {I}{K}{E}

    How long does it take to do 1 part/section?
    it all depends on the protein u are doing..if you are doing a simple protein then it doesnt take long time....usually a one WU takes 12hrz some times even TRIPLE THAT it also depends on your CPU the faster the better
    (EVERY MHz COUNTS )

    currently i hav P41.9GHZ OCED @ 2.10GHZ the WU im working on now is out of 600 and its going pretty fast itll get done in 12hrz...the one b4 was 400 and it took like a day or 2..

    and one more thing if u turn off ur computer it continues WHERE YOU LEFT OFF...
    so you dont hav to start all over again...

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  9. Lounge   -   #9
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    Thnx. I understand it now...

    I try to let it run 24/7

    {I}{K}{E}

  10. Lounge   -   #10
    Spicker's Avatar AKA jaigandhi5 BT Rep: +7BT Rep +7
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    Originally posted by {I}{K}{E}@22 January 2004 - 01:05
    Thnx. I understand it now...

    Hope I can contribute

    {I}{K}{E}
    thanx

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