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Jmtyra

Member
Joined
Aug 18, 2010
Location
Dallas/Fort-Worth
Table of Contents:

Getting Started

Folding Statistics and Tools

Further Information and Links

3 Steps To Become An Overclockers.com Folding Team Member

  1. Select a user name for yourself and obtain your passkey.
    • Check the user stats database to see if the name you want to use is already in use.
    • Read the Passkey FAQ for instructions on obtaining your passkey.
  2. Install the [email protected] client. During setup enter your chosen name, team number 32, and the passkey assigned to you by Stanford.
  3. You are on the team! Post in the New Members Thread to say hello to everyone!
Once setup is complete, [email protected] will utilize idle computer time to perform work which will earn points for you and the team!

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What Client Should I Run?

What operating system ("OS") are you running? Windows, Linux, OS X, or do you have a Playstation 3?
  • Windows
    • You've got a few choices here. First, are you running a multiple core/multiple thread processor? (How to find out)
    • If you have a newer machine, you probably have two or more cores/threads. In which case, the SMP client is for you! However, if you only have one core/thread OR you have a slower/older machine then you'll want the classic client.
    • In addition to these two choices, there is also a client for video cards. You can run this in addition to your CPU client. An NVIDIA CUDA-enabled GPU listed on this page or an ATI 26xx series or better GPU is required.
  • Linux
    • There are two native CPU clients available, depending on how many cores/threads your machine has. (How to find out)
    • If you're running a multiple core/multiple thread CPU and running a 64-bit distro, then the SMP client is for you! Otherwise, you'll want the classic client.
    • While there is no native GPU client for Linux, as of this writing, there is an option to use wine for nVidia GPU card owners.
  • OS X (Intel only)
    • Easy choice here, only the SMP client is available for Intel-based OS X machines.
      Note: As of this writing, there is neither a native GPU client nor a classic v6 client for OS X.
  • Playstation 3
    • Ah, your choice is simple. The PS3 only has a single client.
Now that you know the client type you're going to Fold with. Check below for links to the installation instructions. Don't forget to follow the 3 Steps To Become An Overclockers.com Folding Team Member.

Do you have an older machine, an OS not listed here or something else that you're itching to fold on? Check out our Will it fold? guide for info!

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Installation Instructions

Team 32 recommends the official install guides provided by Stanford and maintained by the Folding community at large.

We also have a specific Windows SMP2 install guide written by our resident guru, ChasR, that goes into further details about the settings necessary to get the most from your SMP client installation.
ChasR also has an excellent VMware 3.x.x Folding Guide (including -bigadv) for running Ubuntu within a Virtual Machine on your Windows machine. Thanks ChasR!

For those wanting to go the Linux route, there is an excellent install script written by our forum moderator splat. This will download and install the latest SMP2 client and setup a startup daemon (like a windows service).
Additionally, there is an option for nVidia GPU owners to run the Windows GPU client using wine. There is a wiki available with helpful installation instructions, as well as an unofficial client section at the folding forums.

You may also want to look into notfred's [email protected] Diskless Programs. This guy has done some amazing work putting together packages for [email protected] users, including everything one needs to run Diskless, by Live-CD, by USB Stick, and even by VMWare Virtual Appliance.

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Will it fold? (PPD/Watt discussion)

Running [email protected] clients, aka "Folding", can become rather addictive. You may try to start folding on any hardware you can get your hands on. However, you’ll want to keep in mind of each folder’s PPD/Watt. (You usually don't have to worry about it for newer or higher-end hardware.)

This can be best explained by using an example:
  • Let’s say you find a $10 computer at a yard sale. Score, right? And this smoking machine puts out 100/PPD for you. But, said computer also consumes 500 watts (0.5 kWh) while folding. That’s 360 kWh every 30 days; @ 10?/kWh you’ll pay $36 per month and @ 20?/kWh you’ll pay $72 per month to run that $10 computer. Over a six-month haul, you could pay as much as $432 to run that $10 yard sale computer for 100/PPD.
  • Or, you could save that $432 and get a machine that generates 5,000/PPD but only consumes half the amount of power (watts). While just an example, do you see how the numbers stack up? We are all folding for a cure, and many of us have loved ones affected by cancer, myself included. Any and all hardware would help.
However, we want to be folding as efficiently as possible. True, it’s not about “the points”, but they are a good indicator of how much effort we’re putting forth. If you can save money and help out more, then what do you have to lose?

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How To Ask For Help

Our resident guru ChasR has written an excellent guide, found here, which outlines what information is required when requesting assistance as well as how to obtain it.

Once you have the requested diagnostic information in hand, please start a new thread in this forum and one of our friendly and helpful community members will come along and be happy to help.

The Connectivity Test - Check your Internet connection to Stanford with this quick test suite.

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[email protected] Stats Websites and Threads


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[email protected] Stats In Your Signature

You can display your [email protected] stats in your signature using the following syntax:
[FSTATS]<EOC user number>[/FSTATS]

Here is an example signature with the EOC user number shown:
[FSTATS]525307[/FSTATS]

This will display your [email protected] stats, like this:
Folding User Stats

To obtain your EOC user number, go to to http://folding.extremeoverclocking.com/
Use the name search on the left-side of the page; type in your name, choose 'User', and click on 'Search'.

1642798231268.png

Note: Verify the spelling of your user name if no results are found.

You will be presented with one or more matches. If you have been on other teams, these will also be listed here.
Click on your user name that is located next to the www.overclockers.com team in the results.

1642798236647.png

You will then be presented with a page showing your [email protected] stats. The URL will look something like:
http://folding.extremeoverclocking.com/user_summary.php?s=&u=525307

The numbers located at the end of the URL is your EOC user number. In this case, it's 525307.
This is the number you'll use between the [FSTATS][/FSTATS] tags in your signature.

Note: The limit of 12 lines in your signature still applies. The [email protected] stats in your signature counts as 5 lines. Ergo, you can only add 7 additional lines in total.

Note: See this thread for more information pertaining to signature rules, limits, content and such.

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Monitoring and Client Tools

  • How can I keep track of my client(s)?
    • HFM.NET is home-baked right here on Team 32. Written by harlam357. It is the recommended monitoring solution for Team 32 Folders. Program highlights: Ability to track Completed and Failed WUs, Work Unit Benchmarking, Robust HTML Generation (with multiple color schemes and FTP upload capability), Multiple Configurations, Encrypted Password Fields (so you're secure), Monitor Clients Locally, via HTTP, or via FTP, Checks for Duplicate Client Configurations and Duplicate Work Units, Color Codes the FAH Log File in the Viewer for better readability.
      Requirements: .NET Framework 3.5 or Mono 2.4+
    • FahMon is another excellent program for tracking the progress of local and/or networked clients.
    • However, a monitoring program is not required to check the progress of work units. The unitinfo.txt file, located in the folder where FAH is installed, has the current WU Project Number (Run, Clone, Gen), and the current percentage of completion. You can also check the FAHlog.txt file, which is the full [email protected] client log, located in the same folder.
  • Landshark's Stats Gadgets
    Our good friend Landshark has developed several neat little stats toys for inclusion on your Desktop and/or Browser.
  • qd-tools Homepage (includes qfix binary download)
    • qd-tools is a collection of programs for use by FAH donors and FAH utility developers. The most used program (by donors) in this collection is qfix.
      The qfix utility is used to repair a broken queue.dat file. The queue.dat file is what sequences the work units as they are downloaded from Stanford.
      Linux Minded Software - the home of qd-tools
  • How can I hide the console client command window in Windows?
    • A nice little utility called TrayIt will allow you to minimize your console windows to the system tray.
    • Landshark (once again) has put together some batch files for use with cmdow, a command-line utility that also allows command prompts to be hidden.
      You can find the homepage for cmdow here. You can download Landshark's cmdow package here
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General Folding Links

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Team 32 Links

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Advanced Topics:

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Frequently Asked Questions:

Q: I have feedback, questions, complaints, comments, etc regarding this sticky. Where do I send it?
A: Reply in the T32 Super Sticky discussion thread, or send me a PM.

Q: What is [email protected]?
A: [email protected] ([email protected]) 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 develop better treatments/cures for many of today's serious diseases.

Another important part of the [email protected] Project is putting together an effective model of how to fold and unfold proteins. This is an extremely complicated process that requires awesome amounts of computing power, which 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, then return 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 pieced back together at Stanford University. There are results and more information posted on the [email protected] website.

Q: How can I determine how many cores/threads my processor has?
A: Look up your processor on Intel's Ark site, or AMD's CPU site. Each will reference how many cores/threads your CPU has.
A: Download and install CPU-Z. It will show how many cores/threads you have at the lower-right. Below is an example:

1642798248838.png

A: On a Windows machine, hold down Ctrl+Shift, then press Esc one time. This will run Task Manager. Click on the Performance tab, and count the number of threads shown. The example below has a total of two threads.

1642798251954.png

Q: What is the difference between a GPU/SMP/Classic client?
A: Each client type leverages a different hardware type. GPU for graphics cards, SMP for multi-threaded processors, and classic for single processor or older machines.

Q: Where can I find out more about this project?
A: You can find out lots more about the FAH project and Stanford's scientific background here.

Q: Why are some WUs worth more points than others?
A: Generally speaking, the point value of a WU is determined by Stanford and Vijay Pande. The value is a representation of how much computational power is required to process the WU in question.

Q: What is the Quick Return Bonus (QRB) and what are the requirements?
A: The QRB can be explained via Stanford's [email protected] FAQ, with additional information available on the FaHWiki site.

Q: Can I fold on machines that I do not own?
A: No, unless you have been granted explicit, written permission by the party responsible for the machine in question.

Q: What is GROMACS?
A: GROMACS is the current software behind the [email protected] Core. GROMACS provides extremely high performance compared to all other programs of its type. You can find a lot more info on GROMACS here and here

Q: Where can I find more information on the proteins?
A: More detailed information for each project can be found here (very comprehensive and should give you any info that you need) or here (search for a specific project).

Q: Can you explain the whys and hows of [email protected] to me in more detail?
A: Our thanks goes to BBigJ for writing the following response:

WHY?

This project tries to understand how proteins fold. Proteins are the machines that do all of the work in your body from digesting food, to flexing muscles, to firing neurons. Proteins are made of long chains of similar molecules. The building blocks of proteins have identical backbones, but each have a unique chemical group that hangs off the side of the chain. After the protein is assembled, the chain will "fold" into a unique structure that puts the chemical groups in the proper position to do their job. Now that the human genome project has been completed, we know the sequence of building blocks for every protein in the human body. However, due to the complexity of the folding process, we are far from knowing what each protein actually does and how it does it. A better understanding of the folding process will allow researchers to use the wealth of information from the genome project quickly and easily for curing diseases. Diseases like Alzheimer's and Mad Cow actually involve proteins that fold incorrectly (Mad Cow is caused by misfolded proteins, but in Alzheimer's it is unclear if the misfolding is the cause or just an effect), although all diseases from the common cold, to cancer, to the black plague ultimately depend on protein interactions.

HOW?

We think we understand the physics that controls atoms and small molecules. However, proteins are huge molecules consisting of thousands of atoms. In order to understand the motion of the entire protein we have to track the motion of each atom in the protein as well as any other atom that may come in contact with that protein (like water.) This is extremely difficult to do. To make matters worse, due to the randomness of all the atoms bumping around, the protein can take many different paths to get from the unfolded chain to the folded state. This means that simulating the folding process just once will not give you an accurate description of how the "average" protein folds. This project tackles the problem by getting thousands of computers to run the simulation at the same time. Your computer will download the starting coordinates for each atom in the protein, then solve Newton's equations of motion (it is a little more complicated than this) for a few picoseconds worth of protein time (this will take hours to days of computer time.) Then it will send the final coordinates back to the server. The server will decide what the new "average" position is (from all the results it gets) then send these coordinates back out for simulation.

Q: My question is not listed here.
A: Check the official FAQ on Stanford's website for additional questions, or start a new thread in our Team 32 Folding forum.
 
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