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dark_15

Drunken Master JNCIE Senior
Joined
Mar 16, 2004
The Official [email protected] FAQ

Welcome to the Official [email protected] FAQ for Team 32!
Here you will find a great deal of information about the [email protected] Project, how to install, tweak, and maintain FAH on your machines, how to track your stats, and answer other random questions. This FAQ was originally on our Folding Website which can be found here.

Here are some quick links to help you:

  1. Intro to [email protected]
  2. General Hardware Information
  3. Getting Started (Setup)
  4. General Questions
  5. Stats and User information
  6. Additional Software
  7. Monitoring [email protected] with Samba
  8. Troubleshooting [email protected]
 
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OP
dark_15

dark_15

Drunken Master JNCIE Senior
Joined
Mar 16, 2004
Intro to [email protected]

Intro to [email protected]


  • What is [email protected]?

    [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 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 [email protected] website.

    We are team 32 and if you would like help setting up the client you only need to ask and there will be several people ready to help.

    For some great summaries of the [email protected] project, try here and here


  • Where can I find out more about this project?

    You can find out lots more about the FAH project at Stanford's scientific background here.


  • What is the difference between [email protected] and [email protected]?

    The goal of [email protected] is to design new genes that can form working proteins in the cell. [email protected] uses a computer algorithm (SPA), based on the physical and biochemical rules by which genes and proteins behave, to design new proteins (and hence new genes) that have not been found in nature. By comparing these "virtual genomes" to those found in nature, we can gain a much better understanding of how natural genomes have evolved and how natural genes and proteins work. Some important applications of the [email protected] virtual genome protein design database:

    • engineering new proteins for medical therapy


      [*]designing new pharmaceuticals


      [*]assigning functions to the dozens of new genes being sequenced every day


      [*]understanding protein evolution

    If you wish to find out more about [email protected] go here


  • What is a gromac?

    Gromacs is a folding core (FAHcore_78.exe) GROMACS provides extremely high performance compared to all other programs. For some calculations, gromacs affords benefits over the current code in [email protected] (the current code is based on Jay Ponder's Tinker), especially a great speed increase (perhaps up to 10x-20x). This will substantially increase the power of [email protected] for many calculations. You can find a lot more info on the gromacs here and here

    A good thread on how to set the flags for gromacs


  • Is there a list of current projects?

    Yes there is. It can be found here. This list will change from time to time as new projects are added and some are discontiued for a while.


  • Where can I find more information on the proteins?

    More detailed information for each project can be found here. That page is very comprehensive and should give you any info that you need.


  • [email protected] in detail


    • 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 muscle, 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 interations.


    • 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.

      Thanks to BBigJ for writting this.


  • Who "owns" the results? What will happen to them?

    Unlike other distributed computing projects, [email protected] is run by an academic institution (specifically the Pande Group, at Stanford University's Chemistry Department), which is a non-profit institution dedicated to science research and education. We will not sell the data or make any money off of it.

    Moreover, we will make the data available for others to use. In particular, the results from [email protected] will be made available on several levels. Most importantly, analysis of the simulations will be submitted to scientific journals for publication, and these journal articles will be posted on the web page after publication. Next, after publication of these scientific articles which analyze the data, the raw data of the folding runs will be available for everyone, including other researchers, here on this web site.


  • Why don't you post the source code?

    We are working on a version of our code which is appropriate for release. More information will follow. Unlike many computer projects, the paramount concern is not functionality, but the scientific integrity, and posting the source code in a way that would allow people to reverse engineer the code to produce bogus scientific results would make the whole project pointless.


  • 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 [email protected] 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 cycles than we do with the [email protected] cluster! This is possible since PC processors are now very fast and there are hundreds of millions of PCs sitting idle in the world.


  • Can I run [email protected] on a machine I don't own?

    Please only run [email protected] on machines you either own or on which you have the permission of the owner to run our software. Any other use of [email protected] violates our license agreement (and just isn't a good idea in general).
 
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OP
dark_15

dark_15

Drunken Master JNCIE Senior
Joined
Mar 16, 2004
General Hardware Information

General Hardware Information


  • 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.


  • 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)


  • 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)


  • 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!!.


  • 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 has changed though; newer, larger, and more complex proteins (especially the QMD cores) are now more dependant on your memory bandwith.
 
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OP
dark_15

dark_15

Drunken Master JNCIE Senior
Joined
Mar 16, 2004
Getting Started (Setup)

Getting Started (Setup)


  • How Do I Setup [email protected] on Windows 98/2000/XP machine?

    Wedo's Ultimate FAH Install Guide will help you setup [email protected] with just one-click. ;)


  • How Do I Setup [email protected] on a Linux Machine?

    Download the Linux client here and follow the instructions here.


  • How Do I Setup [email protected] on a Free-BSD Machine?

    Taken from Stanford's FAQ:

    1. Install emulators/Linux_base from FreeBSD CD.


      [*]Edit /compat/Linux/etc/yp.conf and put the correct server in there.


      [*]Download the Linux folding console (FAHxConsole, where x is the version number) here and cd to the directory.

      -----------------------

      % brandelf -t Linux FAHxConsole

      -----------------------



      [*]As of Version 3.24, all you have to do from here is specify the "-freeBSD" flag when you run the client:

      -----------------------

      % ./FAHxConsole -freeBSD

      -----------------------


      It will automatically brand the scientific cores it downloads.


  • How Do I Setup [email protected] on an Open-BSD Machine?

    Taken from Stanford's FAQ:

    It works almost as easily as FreeBSD. Just follow these steps:

    1. Install /usr/ports/emulators/redhat/base from ports on 3.4 or later. If you're on an earlier version, or just prefer packages, install redhat_base-8.0p2.


      [*]Set up a script that redirects the brandelf call to elf2olf, so that core binaries can be marked properly. This script can be downloaded from here, or simply set up on your own:

      -----------------------

      #!/bin/sh
      elf2olf -v -o linux $3

      -----------------------


      In either case, make sure the brandelf script is executable and in the path of the user running FAH.


      [*]When running the client, use the -freeBSD switch, so that it will automatically mark core binaries properly.


      Thanks to Alex Kirk for the OpenBSD info!


  • How Do I Setup [email protected] on a Network?

    Wedo's Ultimate FAH Install Guide will help you setup [email protected] on networks with a few fancy scripts created by our own OCForums Members. ;)


  • How Do I Setup [email protected] on a Cluster Borg?

    [email protected] does not have a cluster client available. However, you can use each node to fold a seperate work unit and then use a central computer to store the node's progress. More information can be found in Wedo's Ultimate FAH Install Guide.


  • How Do I Customize the Google toolbar for Team 32?

    1. Get the google toolbar from here: here (I chose without advance features) and install it.


      [*]Install Google Compute from here


      [*]Open up My Computer and navigate to "C:\Program Files\GoogleDCC\GoogleFah\client.cfg" (minus quotes).


      [*]Open client.cfg in Notepad.


      [*]Replace the Google<randomnumber> with whatever username you are going to use.

      (IMPORTANT: Make sure not to add any spaces or to change the format at all!)


      [*]Replace 446 with 32

      (IMPORTANT: Set it to 32 so that our team will receive credit for the work units!)

      This is what it should look like:

      -----------------------

      [settings]
      username=<Your Username>
      team=32
      asknet=no
      userid=14BEEDFA74270ECE
      machineid=1

      [http]
      active=no
      host=localhost
      port=8080
      usereg=yes

      -----------------------



      [*]Click File -> Save. Now create a new file by going to File -> New.


      [*]Now copy and paste this code:


      <Copy below this line>
      -----------------------

      Windows Registry Editor Version 5.00

      [HKEY_CURRENT_USER\Software\Google\DcClient]
      "UserName"="<Your Username>"
      "TeamNum"="32"

      -----------------------

      <Copy above this line>



      [*]Click File -> Save -> OCREG.reg -> Filetype - All Files


      [*]Navigate to where you saved OCREG.reg and double-click it to merge its settings to the registry.


      [*]Now all the hard work is done. :)
      Click on the google compute icon on the Google Toolbar and select Start Computing.
      Now you are Folding for your username and team 32!


      [*]You can right click on the Google Toolbar and un check it and it will hide.


      Thanks to Kendan for this information!
 
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OP
dark_15

dark_15

Drunken Master JNCIE Senior
Joined
Mar 16, 2004
General Questions

General Questions


  • Which version should I run?

    It is highly recommended that you run the text-only, no non-sense client. As it is this client seems to be a tad bit more efficient, causes less problems, has more options and advantages, and is easier to maintain that the other clients. Some choose to use the graphical client so they can see what they are folding- but this can also be down with EMIII and the console version.


  • How can I choose [email protected] or [email protected], just give a preference, or allow the client to be flexible?

    We've (Stanford) built a lot of flexibility into the client. In particular:

    1. Some want to run only 1 project


      [*]Some want to have a preference for 1 and fall back to the other


      [*]Some just want to help and want to contribute WUs to the most needed project at the moment.


    So, the client will have choices. If you give a [email protected] team, you'll run [email protected] If you give a [email protected] team, you'll run [email protected] If you have only a preference, not a "demand", then you can choose so in the client. If you don't care, then leave the defaults. If you wanted only one type (eg only [email protected]) by setting your team and got another, that's a bug (not a feature) and we'll look into fixing that. We understand how important this is. We are working to try to merge our infrastructure to long term simpify things server side as well as to give us flexibility to do the best science. We understand stats are important and are trying to work out as described above.


  • Why merge the two clients?

    Our goal is to use distributed computing to do science which would not be possible without distributed computing. I'd prefer to put my group's time into doing science, rather than administering a distributed computing system. It's much simpler for us to run 1 infrastructure for the two projects, rather than 2 different infrastructures, hence the union. This will allow my team to concentrate on the results and the science.


  • What about security issues?

    Straight from stanford: We have worked very hard to maintain the best security possible with modern computer science methodology. Our software will upload and download data only from our data server here at Stanford. The data server doesn't download any executable code to your computer. Actually, our software is considerably safer than the browser you're using to read this!
    How is this possible? We take extensive measures to check all of the data entering your computer and the results we send back to Stanford with 2048 bit digital signatures. If the signatures don't match (on either the input out the output) the client will throw away the data and start again. This ensures, using the best software security measures developed to date (digital signatures and PKI in version 3.0), that we are keeping the tightest possible security.

    Finally, the client/screensaver are available for download only from this web site, so that we can guarantee the integrity of the software. We do not support FAH software obtained elsewhere and prohibit others to distribute the software.

    Also, take a look at this thread for more insight on [email protected] and security.


  • Will FAH run in standby mode?

    The answer is no or hardly at all. For best the results and the best chance of avoiding problems with the client use these settings: ideally you want to disable any screensavers and set power management to:

    • monitor = shuts off after XX minutes


      [*]harddrive = always on


      [*]standby= never


    (note if you want to you can use a screensaver, not using one will just save you a little power and free a little more resources) Do yourself a favor and DONT use the FAH screensaver.


  • What Time Zone does FAH use and can I change it?

    The client user GMT(Greenwich Mean Time; The mean solar time for the meridian at Greenwich, England, used as a basis for calculating time throughout most of the world. Also called Greenwich time, Greenwich Mean Time, Zulu time.) According to Vijay, the reason they use GMT is so that all clients and servers logs will show the same time. Makes it easier for them to compare logs between a misbehaving client and the server it's contacting.

    And no it is not possible to change this.


  • I am behind a firewall, can I still use FAH?

    Yes. Please configure your Firewall or Proxy server in the config panel or config settings.
    FAH uses outbound connections with ports 80 and 8080.


  • Why should I try to keep my client up to date?

    This can be very important because many times new clients are released to fix bugs that are found in the previous client. Also, if you are not using the newest client, you could be shorting yourself from being able to take advantage of new options and features.


  • Can I run FAH and SETI at the same time?

    If you want to get the most out of folding this is not recommended because it takes twice as long to finish work. It also takes more ram for SETI and FAH to run at the same time. If you still want to run both, you will have to change the priority to LOW (rather than the default of IDLE) and limit the CPU usage to 50% for FAH.

    Assuming [email protected] is already installed, Here is how to do it:

    For the Graphical Client:

    1. Go to preferences and you will find an option for a more aggressive priority, put a check for this option.


      [*]Move the slider for CPU usage to 50



    For the text-based client (the one-click uses it):

    1. Stop the FAH client if it is currently on. If you see a black box hit Control-C to stop it. If it's installed as a service (which is what the “one-click install” does) then right click My Computer and click Manage. On the left click the plus next to Services and Applications, then click Services. Find FAH in the list, right click on it and click stop.


      [*]Navigate to the directory FAH is installed to (C:/Program Files/FAH is where the one-click installs it). Right click FAHx-Console and click create shortcut. Rename the shortcut that you just made to "FAH config". Right click it and click Properties. On the shortcut tab add -configonly (including the dash [-]) to the end of what's already in the target field.


      [*]Double click the shortcut.


      [*]Keep hitting enter to keep everything at default until you come to "change advanced settings". Type yes for that and hit enter. Then type Low and hit enter. Type 50 and hit enter. Keep hitting enter until the box closes.

      Set SETI to limit CPU usage to 50% also. Afterwards, when both SETI and FAH are started, task manager should show each of them running at 50% (or close to that).


  • Will FAH keep me from doing the things I normally do?

    NO. The client only uses idle cycles so it is not possible for it to take them from other programs you have runnning. Personally, i play games all the time while folding and am yet to see any side effects from it or notice any slow downs.


  • How do I send back a protein when I am done with it?

    You don't! The client will automatically do this for you if a connection is present. Another exception to this comes from whether you told it to prompt before sending or not. (again the recommended is not to prompt)


  • How long do I have to finish a work unit?

    Taken from Stanford's FAQ:

    Each work unit is benchmarked on a dedicated 2.8 GHz Pentium 4 machine with SSE2 disabled. Next, we apply this equation:

    • timeout = 20 * (daysPerWU) + 2


      [*]deadline = max(30* (daysPerWU) + 2,10)


    Where daysPerWU is the number of days it took to complete the unit. The "+2" days is there to give an additional buffer for fast WUs (to allow for servers down, etc). If 30*daysPerWU is less than 10 days, we set the deadline to 10 days, as a minimum time for all projects. The timeout is the time at which the WU is resent to another client and the deadline is the last time which we will give stats credit for the WU.

    Occasionally, deadlines may be set shorter or longer than the above calculation indicates, but the reason for having deadlines at all is that the sooner we get back work units, the sooner we can put the results to good use. The assignment server does take machine performance into account in making assignments, thereby allowing slower machines to receive more appropriate work units.


  • Can I download more than one unit at a time, is caching available with this client?

    Yes, but caching for the FAH client is different than you may think. You cannot download several WU's at one time to work on for days or weeks, but there is a form of caching that will hold on to work that could not be sent back to Stanford while allowing the client to download more work. It will send back the completed work when it can. The reason that you cannot get more work than you need is because this project is progressive. The old work is necessary to help create new work.


  • I keep getting the same work units over and over is this a problem?

    If you just just sent a unit and got the same one again don't worry, you can and will get many protein over and over again. This is not a problem at all, epecially if it is the nice 600-pointers!


  • I am running more than one client and they are both working on the same work unit, is this a problem?

    This will not be a problem if you followed our guide to setting up more than one client and each console is in a different folder and has a uniquie machine ID( you can find out how to do this in the guides section). However, if you did not setup the machine ID's then this is a problem, both clients will have the same ID number so your work from one of the clients won't count towards the folding project or to the stats.


  • Why does adjusting the core process priority via the task manager not affect its performance? How do I manually adjust the priority of the [email protected] core?

    Currently when users try to change the priority of the core via the Windows NT/2000/XP task manager this does not affect how much CPU the core gets. The reason for this is that the work is done by the core thread, which is fixed to run at idle priority and is not affected by the task manager priority for the process (which displays as 'normal' by default). In order to change the priority manually users must use a program that allows thread-level priority adjustments.
 
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OP
dark_15

dark_15

Drunken Master JNCIE Senior
Joined
Mar 16, 2004
Stats, Tracking, and User Information

Tracking, Stats, and User Information


  • How can I keep track of my client?

    There are currently 2 popular programs that will do this- EMIII and FAHstats.
    Check out HERE for more information on how to use these monitoring programs.

    A monitoring program is not required, however. There's a file called unitinfo.txt located in the folder where FAH is installed (the one-click installs it to C:\Program Files\FAH) that shows the status. Also you can check FAHlog.txt.


  • I have machines on a network, is there a way to monitor them all from one place?

    Both of the aforementioned programs have the ability to do this in one way or another.


  • How can I get a more detailed logfile?

    Start FAH with the -verbosity 9 flag. NOTE: If you used Wedo's awesome one-click installer, this is already enabled. To do this, first atop FAH by right clicking on My Computer. Click Manage, and in the left pane click the plus next to Services and Applications, then click Services. From there:

    If you have it installed as a service:

    • Click start -> run, type regedit and hit enter.


      [*]Navigate to HKLM\SYSTEM\CurrentControlSet\Services\[email protected](path).
      (HKLM = HKEY_LOCAL_MACHINE)


      [*]On the right, double click Image Path and put a space after what is there and add -verbosity 9. While you're there, add -forceasm too by putting another space after -verbosity 9 and add -forceasm


      [*]Start FAH again.


    If you're using the GUI version or the text based version not installed as a service:

    1. Go to start -> all programs -> startup and right click the shortcut to FAH and click properties.


      [*]On the shortcut tab add a space and add -verbosity 9. While you're at it add -forceasm too by putting another space after -verbosity 9 and add -forceasm


      [*]Click OK.


      [*]Start FAH again by clicking the shortcut.


  • Where can I find my personal stats and the team stats and server stats?

    You have several options:

    • Stanford

      The official stats at Stanford can be found HERE.
      Our team stats page at the can be found HERE.

      Click on your name to see your individual stats.



      [*]Extreme Overclocking (EOC):

      EOC News - HERE
      Teams Overall Rank - HERE
      Individual Overall Rank - HERE
      Our Team - HERE



      [*][email protected] Stats:

      Teams Overall Rank - HERE
      Individual Overall Rank - HERE
      Our Team - HERE



      [*]Statsman

      Team Comparison Charts


      The Java based pages are here:

      Top 1000 teams - HERE
      Top 1000 Users - HERE
      Our Team - HERE


      The HTML only pages are here:

      Top 1000 teams - HERE
      Top 1000 users - HERE
      Our Team - HERE


  • How do I change my user name?

    With the text client you can switch names by starting it with the -config flag on the end. If you use the graphical client then go to the configuration panel (right click in the graphical display or click on the sys tray icon )

    Also, unlike SETI folding stats do not travel with you- if you switch teams, the team you were with keeps those stats; you will just have a note in your stats saying "yournamehere has contributed work units with more than one different team number. The contributions are listed below."


  • I just joined but I don't I see myself in the stats?

    No worries! It usually takes at least SIX hours and sometimes it can take up to a DAY AND A HALF for Stanford to work you into the stats.
    Back to top


  • On Stanfords stat's page I am higher in the stats than on Statsman's page; I have the same number of points on both pages, as do all the people around me? What's wrong??

    Statsman will combine virtually identical names. It ignores changes of case and may ignore differences between names with (www.overclockers.com) and names without that addition. This will bring someone lower than you past you if their combined stats are better. Stanfords stats are slightly goofed up and statsman has made an effort to reduce that. I only wish that our name combinations went that well.

    Anyway. that's probably why it shows you at a spot lower on statsman than you would be on stanfords stats. Kendan also brings up a good point in that stanford updates more frequently than statsman.
 
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OP
dark_15

dark_15

Drunken Master JNCIE Senior
Joined
Mar 16, 2004
Additional Software

Additional Software


  • Is there any way to display my [email protected] stats in my OCForums Signature?

    Yes! Our very own Cristoph and JerMe have created ways to add a signature displaying your [email protected] stats and current work units. It uses some nifty perl scripts, and it works for Windows and Linux machines.

    [email protected] Stats in Your Sig How-To
    FAH Stats Sig Generator (Windows Only)


  • What is Electron Microscope III and how do I set it up?

    "Electron Microscope, EMIII for short, is a program used to track Stanford’s distributed computing program client called Folding at Home, FAH. It will monitor up to 50 clients and give you the details about each client’s progress as the FAH client runs. EM will also show you what each change in the protein looks like as the process continues. Normally there are 100 Frames per work unit, but sometimes you will see work units with anywhere from 10 frames to 200. To date I have not seen a work unit smaller than 10 or larger than 200 frames. Frame rates vary according to CPU speed. In the FAH world the AMD processor is King of the Hill. I’ve seen an AMD Duron out perform a P4 so if you want the most bang for the money, get AMD processors for the FAH project. Frame rates are variable. They can take from less than a minute each to over an hour per frame." - L. Perry

    EMIII Links:

    Home Page
    EMIII Feature List
    EMIII FAQ


  • How do I get EMIII out of stealth mode?


    This way works sometimes:

    2000/XP:

    1. Bring up the task manager by pressing Ctrl+Alt+Del.


      [*]Click applications -> click EMIII -> click Switch To.


      [*]Then press and hold the scroll lock for 30 seconds or longer.



    98/ME:

    1. Minimize all other programs.


      [*]Press and hold the scroll lock for 30+ seconds.


      [*]That doesn't always seem to work. At the worst you'll have to remove emIII and reinstall it. :(



    This way works every time:

    1. Make a copy of any file and put it in the EM folder.


      [*]Rename the file to "show.me" (minus quotes).


      [*]Within 30 seconds EM will pop into view!


  • Is there an O/C skin for EMIII?

    There sure is! There are two really but for a purpose! One is for people who only monitor a cpu and the other is for those who monitor more than one cpu with EMIII.

    There is a 'single' skin version, for monitoring one client and there is a 'multi' version for monitoring multiple clients.

    They were made by NASsoccer and you can get them right here:

    --Click Links to Download--

    Single Skin
    Multi Skin


  • What is FoldMonitor and how do I set it up?

    FoldMonitor Yahoo Group Site

    Please note that you must have a Yahoo account to download their software.


  • Is there an O/C skin for Fold monitor?

    Not presently, maybe you can be the first to make one!


  • What is KDfold and how do I set it up?

    KDfold Home Page

    While discontinued, KDFold was another utility to manage [email protected] on multiple machines.


  • Is there an O/C skin for KDfold?

    Not presently, maybe you can be the first to make one of these too!


  • Is there a IRC stats script available for FAH?

    Yes there is! The script is made by legolas (OCAU), but the link is broken. If anyone has a link to the script, please let me know.


  • If I have any problems with these programs where can I get more help?

    If you have a problem that you need extra help with then please stop by our forum here. We will be more than happy to assist you in any way possible and try to help you solve any problems you may have.
 
Last edited:
OP
dark_15

dark_15

Drunken Master JNCIE Senior
Joined
Mar 16, 2004
Monitoring [email protected] with Samba

Monitoring [email protected] with Samba


Our more ambitious Folders here at Overclockers.com often build Folding 'farms,' that is, a collection of computers, all dedicated 100% to Folding, and designed to be controlled via network, therefore eliminating the need for a monitor. However, in operations such as these, it can get quite expensive to buy a Windows license for each machine. Fortunately, this is completely unnecessary. An operating system known as Linux, which is open source software, hence, completely free, can allow for the creation of Folding farms without the cost of the OS. You don't need to waste those precious CPU cycles generating the Windows graphical interface that will never be used. Plus, Linux is much more stable than Windows. Less reboots = more Folding.

In this article, I'm going to discuss the monitoring of Linux farms using a program called Electron Microscope 3. It can be downloaded here.

EM3 will be run on a computer running Windows, which will collect information from Linux systems running the Folding client. The entire farm will be monitored from this computer. This is made possible by a Linux program called Samba. Once Samba is set up, the Folding farm should be able to virtually 'run itself,' with little or no user intervention. For those who don't know, Samba is a program designed to allow Linux to serve Windows file and printer shares.

Electron Microscope 3 interacts with machines running [email protected] by reading the files in the [email protected] working directory. This is where Samba comes in. We will use Samba to share these directories over a LAN. I'm not going to cover installation of Samba, mainly because most Linux systems install it by default. I'm going to assume a very basic knowledge of Linux console commands, that typical of your average newbie (we will not be using the X Window graphical user interface at all). If you would like to learn more about Linux and how to use it, I highly suggest you check out LinuxNewbie.

Samba, like many Unix programs, its configured via a text file, in this case, smb.conf. To change the way the Samba server behaves, you change this file.

Assuming you have Samba correctly installed:

  1. Locate your smb.conf file. Generally, this is located in /etc/samba/. If you can't find it there, this is how you can locate it:

    As root, run:

    -----------------------

    slocate -u

    -----------------------


    this will build a database of the files on your system, and will take a while. After it is done, run:

    -----------------------

    slocate smb.conf

    -----------------------


    and it will tell you where to find it.



    [*]Before we actually get started configuring Samba, we must do some preparation for the system. First, let's create a user that Samba can run under. First, make the user with the useradd command, like so: (as root of course)

    -----------------------

    /usr/sbin/useradd -m username

    -----------------------


    The m argument tells the system to build a home directory for our new user, at /home/username. This is generally a good idea, but it is up to you.

    We will set a Samba password for our new user, but that requires the samba server to be running, so we'll wait on that for a little while. Note, that this is different from a regular user password.

    IMPORTANT: The user name should be the same as the user name of the Windows computer with which you want to share. It is a good idea to make sure you know the user name and password of the Windows system that will be accessing the Folding boxes. This information will be required several times throughout the process.



    [*]Finally, it's a good idea to change your hostname from something other than the default, 'localhost', before we go any further. Localhost refers to the loopback interface. This is how a computer talks to itself. Therefore, if a computer tries to connect to another machine named localhost, the request will be sent to itself, and not to the intended destination. There are several ways to change your hostname, I will cover the way thats most likely to work. Please consult your distribution's documentation for more information. If your on a Local Area Network(LAN), which most Folding setups are, you can use any name you want. However, it is a good idea not to have any two computers with the same hostname.



    [*]We will edit three files, /etc/sysconfig/network, /etc/hostname, and /etc/hosts. This must be done as root. For the purpose of this how to, we will use pico as the text editor. Type: pico /etc/sysconfig/network and change the HOSTNAME= line to reflect your new hostname. For example, if you wanted your machine to be 'foldingbox,' you would do this:

    -----------------------

    HOSTNAME=foldingbox.localdomain

    -----------------------




    [*]When you are done, hit ctrl x, y and enter a few times to confirm and save the file. Now we will edit /etc/hostname:

    -----------------------

    pico /etc/hostname

    -----------------------




    [*]Sometimes this file does not exist, if so you probably don't need it, but it can't hurt to have it. Replace (or add if the file is new) the hostname in the following format:

    -----------------------

    foldingbox.localdomain

    -----------------------




    [*]Save and exit. Some distributions use /etc/HOSTNAME instead (Linux filenames are case sensitive, so this does matter).



    [*]Just follow the same steps and create(or alter) /etc/HOSTNAME just as you did /etc/hostname. Now, for the final file, /etc/hosts:

    -----------------------

    pico /etc/hosts

    -----------------------


    ADD a line to the file, below any other entries:

    -----------------------

    127.0.0.1 foldingbox.localdomain

    -----------------------




    [*]Reboot the machine, and check that your hostname is what you selected. You should be able to see it after your user name at the bash prompt. If there is any doubt, run 'hostname' and it should return your hostname, as you just set it.
    By far, the easiest way to deal with host names is to set them correctly during installation, although there is no need to reinstall just to change your hostname.



    [*]Now we're ready to jump into smb.conf. The basic format of smb.conf consisted of keys, organized under groups. It looks like this:

    -----------------------

    [group]
    key = value

    -----------------------


    Pretty straightforward. A very basic smb.conf looks like this:

    -----------------------

    [global]
    workgroup = yourworkgroup

    [homes]
    guest ok = no
    read only = no

    -----------------------


    This brings up something very important: workgroup. If your workgroup is not exactly the same for all computers you want to have access to, your Samba servers will not show up in a Windows computer's 'Network Neighborhood,' and you will have to search for them.



    [*]Change into your Samba directory (cd /etc/samba or whatever your directory is) and use pico to create that smb.conf file for now (pico smb.conf). If you have a sample smb.conf file, rename it so you can use it later (do it like so: mv smb.conf smb.sample.conf). Now, lets test our Samba configuration.



    [*]Let's test our smb.conf syntax first. Type testparm and look at what it returns. If there are any errors it will tell you, and you must fix them before continuing.



    [*]Second, start the two Samba daemons (programs that run in the background waiting for connections). As root, run:

    -----------------------

    /usr/sbin/nmbd
    /usr/sbin/smbd

    -----------------------




    [*]It is possible your daemons are somewhere else, if so, just do a slocate on nmbd and smbd and you'll find them. Make sure that the two processes are running by typing the following:

    -----------------------

    ps ax | more

    -----------------------


    Press enter to scroll down the list and look for nmbd and smbd. If they are there, you're on track.



    [*]This is a good time to set up your user's Samba password. This is done with the smbpasswd command, as root. The basic syntax is:

    -----------------------

    smbpasswd -a username password

    -----------------------


    If you want a blank password, use the n (as in null) argument like this:

    -----------------------

    smbpasswd -an username

    -----------------------


    Note that if you use null passwords, your smb.conf should have the following under the [global] section:

    -----------------------

    null passwords = yes

    -----------------------


    Many people have blank Windows passwords, so they don't have to type them when they log on. This tends to cause trouble with Samba, as a Windows 'blank' password is NOT equal to a Samba null password. If you must use a blank password, set the Samba password like this:

    -----------------------

    smbpasswd -a username

    -----------------------


    Samba will ask you for the password twice, just press enter each time.



    [*]Now, let's make sure that your NetBIOS name is working correctly. Type the following command:

    -----------------------

    nmblookup HOSTNAME

    -----------------------


    of course, replace HOSTNAME with your hostname (should be in caps though). You should see something like this:

    -----------------------

    querying HOSTNAME on 192.168.123.255
    192.168.123.176 HOSTNAME<00>

    -----------------------


    The IPs are for my network, yours may differ. As long as there aren't any errors, let's continue.


    [*]To confirm that you can log in, use the following command:

    -----------------------

    smbclient \\\\HOSTNAME\\username

    -----------------------



    Samba should ask you for your password and 'log you in' to your home directory. Note that if you are using null passwords and get an error when you try to log in, it's because you forgot the line: 'null passwords = yes' in the [global] section of your smb.conf.



    [*]Now that we have the basics down, use the sample smb.conf file and read the comments in it; there is a lot of information in there. Try editing the file yourself and experiment with the various features. If you put a # in front of a line, Samba ignores it. After making your changes, save the file and run testparm. If it checks out, you can force the Samba daemons to re-read the config file like this:

    -----------------------

    killall -HUP smbd
    killall -HUP nmbd

    -----------------------




    [*]To add a custom share, you must declare it:

    -----------------------

    [sharename]
    path = path/to/share

    -----------------------


    Technically, this is all you need to create a share, but it may be more functional if you set some more options, such as:

    -----------------------

    public = yes
    writable = yes

    -----------------------



    Here is a smb.conf that should be sufficient to share the working directory of a Linux [email protected] setup:

    -----------------------

    [global]
    workgroup = YOUR_WORKGROUP_HERE
    server string = FAH Server
    security = user
    encrypt passwords = yes
    log file = /var/log/samba.%m
    max log size = 50

    [homes]
    guest ok = yes
    read only = no

    [folding]
    path = /home/folding
    public = yes
    writable = yes

    -----------------------





    [*]If you use this file, be sure to change the workgroup to reflect your network. Also, alter the share definitions to the directories you want to share. Note that this configuration is not terribly secure, as anyone on the network has full access to the shares.



    [*]At this point, if your smb.conf is set properly, you should be able to see your Linux server on the Windows machine. I recommend creating a user solely for Folding (this can also be your samba user). Run the following command to do so:

    -----------------------

    /usr/sbin/useradd -m folding

    -----------------------




    [*]Now, you have a new user name 'folding' and a home directory for that user, located at /home/folding. We can use this directory as the [email protected] working directory. In order to 'become' this user without setting a password and logging in, you can log in as root and run:

    -----------------------

    su folding

    -----------------------


    And you will become the folding user.



    [*]Before we can begin monitoring the Folding client with EM3, we have to change file permissions. EM3 needs write access to set up the first time, but afterward read-only access only is necessary, provided you don't want to change settings remotely. First, download the Linux [email protected] client to your folding directory. The permissions need to be changed so that the system knows it is a program that can executed. So, as root , run:

    -----------------------

    chmod +x /home/folding/FAHxxx.exe

    -----------------------


    Depending on which client you have and where your working directory is, you will have to alter that command.



    [*]Now, run the folding client (as your folding user)

    -----------------------

    ./FAHxxx.exe

    -----------------------


    Once you answer the questions and it begins running, it will create several files in its working directory, and we must change permissions on all these files. This is done with the following command, as root:

    -----------------------

    chmod 777 -R /home/folding/*

    -----------------------


    Now you should be able to monitor the [email protected] client from EM3. It might complain that the directory does not appear to be a [email protected] directory, but that's OK, it will still work.



    [*]You may want Samba to start automatically on boot. In that case, you should add the following to a rc file, which you can find in /etc/rc.d/ (I tend to use rc.local).

    -----------------------

    /usr/sbin/nmbd
    /usr/sbin/smbd

    -----------------------


    If you want to start from a command promt, use the same commands above, except append a -D to the end of each. The -D option tells the server to run as a daemon, so it won't die if the session is closed. Samba must be started as root.



    [*]Finally, when troubleshooting problems, the most important thing to check is your physical network. Make sure the machines can ping each other, etc. Only then look at software issues, which tend to be more complex and take a longer time to deal with.


    I think I've covered the basics here. If anyone has any suggestions, comments, or anything, feel free email me at [size=3][color=cyan][email protected][/color][/size]


Here are some links to more samba info:

http://www.redhat.com/support/resources/tips/Samba-Tips/Samba-Tips.html
http://www.troubleshooters.com/linux/samba.htm
http://www.linuxfocus.org/English/March2002/article177.shtml
http://k12linux.mesd.k12.or.us/using_samba/
http://www.tldp.org/HOWTO/SMB-HOWTO.html

And my personal favorite for problems you can't seem to find a solution to:

http://www.google.com/linux

Now go Fold for Team 32!


-Matthew Cannizzaro, aka Titan386 on forums
 
Last edited:
OP
dark_15

dark_15

Drunken Master JNCIE Senior
Joined
Mar 16, 2004
Troubleshooting [email protected]

Troubleshooting [email protected]


  • I am using windows and I get a dll error when i try to run the folding client?

    Like always you can find dll's at on their site - www.microsoft.com

    Most of the time this is a Win95 issue because 98/2000/NT/XP have these, but the early 95 releases do not.

    NOTE:The dll's that the client requires are: OpenGL32.dll and winsock2.

    • The OpenGl issue can be fixed by getting the OpenGL 1.1 self-extractor from the Microsoft via ftp - here.


      [*]The winsock2 issue can be solved with the Windows Socket 2 Update, that can be had at the Microsoft site - here.



    FAH looks strange (windows) or segfaults (Linux)

    This is something you are bound to encounter in your quest to feed your addiction and build some dedicated folding rigs. The problem here is that FAH needs at least 32 MB of RAM to operate coreectly.



    My screensaver just looks like a black screen with little dots floating around. What gives?

    We think we have diagnosed this problem. It appears to be caused by a monitor or graphics card that does not support 8-bit color. Also, we have found problems with old graphics drivers. If you are having problems, please make sure that you have the most recent graphics and OpenGL drivers.
    The screensaver has been the source of endless questions about problems with the client freezing. If you don't need to use it, Please don't.



    I get an error like "Format:MyForm not found" when I try to download.

    This appears to be an error with Stanford's server, not our computers, and we are trying to identify the exact cause of the problem. It is fairly rare, however, and for now we suggest trying again at a later time.



    I get an error like "Network Recv Timeout" or in the console version (or in the file scrlog.txt).

    If you get something like:

    -----------------------

    Deleting files IP = 171.64.122.81

    Network Recv Timeout

    GetWork Failed

    -----------------------


    then don't worry. It is having problems connecting to the server, and is waiting to try again. We have a few server problems right now, and many users are having this same problem. Just wait for a while, and it will connect. If it fails to connect for a day or so, it might be best to start it over again or reinstall. For the console version, hit Cntl-C to exit gracefully (note: this feature was recently added in, so it may not work for your version, and you may have to kill it instead), and start it again.



    I get an error like "Running self tests.......test failed, error -1" in the console version (or in the file scrlog.txt), but it seems to be running OK after that.

    Don't worry, if it seems to be working fine, it is. This error message is part of the Cosm distributed computing library upon which FAH is based, and as far as we have been able to tell, does not affect normal functioning of the FAH programs.

    OR:

    Uninstall, make sure the foldingathome folder in the "Program Files" folder has been removed, and reinstall. Most of the time, this should work.



    When I'm running the screensaver, it crashes, and says something about a page fault.

    If you get something like this:

    -----------------------

    The error message reads FOLDINGATHOME caused an invalid page fault in module FOLDINGATHOME.SCR at 015f:00420494.

    -----------------------


    followed by a bazillion dialog boxes you have to click away, there is not enough memory for the screensaver to start. Suggestions for solving this are closing other applications when the screensaver is running, and setting the wait time higher (perhaps 5 or 10 minutes), so that the screensaver won't come on while you are working.
    Once again. Please abandon the folding screensaver if you don't need it.



    I get an error like "Running self tests.......test failed, error -1" in the console version (or in the file scrlog.txt), and it dies.

    Uninstall, make sure the foldingathome folder in the "Program Files" folder has been removed, and reinstall. Most of the time, this should work.
 
Last edited:

TollhouseFrank

Senior Headphone Guru
Joined
Nov 29, 2004
Location
T3h [email protected]!
why so many reservations, Dark? What are ya doin? If its anything I can help with, lemme know.

**edit**

i see ya got it well in hand. You could very well be making the uber-sticky we were looking for. Great work man, and keep it up.
 
Last edited:

David

Forums Super Moderator
Joined
Feb 20, 2001
This looks cool :D

Much <3 to dark and Frank for all their work!
 

jcw122

Member
Joined
Jun 25, 2004
wow thats alot of reserves...u havent even used up the entire space of the other ones...have u? is there even a limit on those? Anyway, good job so far
 
OP
dark_15

dark_15

Drunken Master JNCIE Senior
Joined
Mar 16, 2004
Thanks. I could use a little help though. If anyone wants to read through the questions and answers to look for inaccuracies, broken links, and older information that would be a TON of help for me.
 
Last edited:
OP
dark_15

dark_15

Drunken Master JNCIE Senior
Joined
Mar 16, 2004
Random Bump for people to critique the work done so far...

Feel free to post in this thread or send me a PM.

I'M ALL DONE!!!!! YAY!!!!

Tell me what you like, dislike, features to add/remove, or anything else random. Thanks!
 
Last edited:

Adak

Senior Member
Joined
Jan 9, 2006
Troubleshooting [email protected]


  • I am using windows and I get a dll error when i try to run the folding client?

    Like always, you can find dll's at on (either at or on, but not both) their site - www.microsoft.com

    Most of the time this is a Win95 issue because 98/2000/NT/XP have these, but the early 95 releases do not.

    NOTE:The dll's that the client requires are: OpenGL32.dll and winsock2.

    • The OpenGl issue can be fixed by getting the OpenGL 1.1 self-extractor from the Microsoft via ftp - here.


      [*]The winsock2 issue can be solved with the Windows Socket 2 Update, that can be had at the Microsoft site - here.



    FAH looks strange (windows) or segfaults (Linux)

    This is something you are bound to encounter in your quest to feed your addiction and build some dedicated folding rigs. The problem here is that FAH needs at least 32 MB of RAM to operate coreectly.



    My screensaver just looks like a black screen with little dots floating around. What gives?

    We think we have diagnosed this problem. It appears to be caused by a monitor or graphics card that does not support 8-bit color. Also, we have found problems with old graphics drivers. If you are having problems, please make sure that you have the most recent graphics and OpenGL drivers.
    The screensaver has been the source of endless questions about problems with the client freezing. If you don't need to use it, Please don't.



    I get an error like "Format:MyForm not found" when I try to download.

    This appears to be an error with Stanford's server, not our computers, and we are trying to identify the exact cause of the problem. It is fairly rare, however, and for now we suggest trying again at a later time.



    I get an error like "Network Recv Timeout" or in the console version (or in the file scrlog.txt).

    If you get something like:

    -----------------------

    Deleting files IP = 171.64.122.81

    Network Recv Timeout

    GetWork Failed

    -----------------------


    then don't worry. It is having problems connecting to the server, and is waiting to try again. We have a few server problems right now, and many users are having this same problem. Just wait for a while, and it will connect. If it fails to connect for a day or so, it might be best to start it over again or reinstall. For the console version, hit Cntl (Ctrl)-C to exit gracefully (note: this feature was recently added in, so it may not work for your version, and you may have to kill it instead), and start it again.



    I get an error like "Running self tests.......test failed, error -1" in the console version (or in the file scrlog.txt), but it seems to be running OK after that.

    Don't worry, if it seems to be working fine, it is. This error message is part of the Cosm distributed computing library upon which FAH is based, and as far as we have been able to tell, does not affect normal functioning of the FAH programs.

    OR:

    Uninstall, make sure the foldingathome folder in the "Program Files" folder has been removed, and reinstall (add "it"). Most of the time, this should work.



    When I'm running the screensaver, it crashes, and says something about a page fault.

    If you get something like this:

    -----------------------

    The error message reads FOLDINGATHOME caused an invalid page fault in module FOLDINGATHOME.SCR at 015f:00420494.

    -----------------------


    followed by a bazillion dialog boxes you have to click away, there is not enough memory for the screensaver to start. Suggestions for solving this are closing other applications when the screensaver is running, and setting the wait time higher (perhaps 5 or 10 minutes), so that the screensaver won't come on while you are working.
    Once again. Please abandon the folding screensaver if you don't need it. Should be either double spaced as a new paragraph, or started on the same line as the previous paragraph.



    I get an error like "Running self tests.......test failed, error -1" in the console version (or in the file scrlog.txt), and it dies.

    Uninstall, make sure the foldingathome folder in the "Program Files" folder has been removed, and reinstall. Most of the time, this should work.

Magenta = remove
Red = has a problem and needs attention