Fenix25's Guide to Folding

Distributed Computing Projects Folding @ Home
1

All credit goes to fenix25 for his sterling work in producing this excellent guide/how to for the TPR folding team.

All links checked and working as of 30/05/06

Index

01: Installing Folding@home. Windows Console Edition - Single Client.: Here

02: Installing Folding@home. Windows Console Edition - Multiple Clients: Here

03: Folding@home flags: Here

04: Folding@home Utilities and 3rd party downloads: Here

05: Folding@home Cores: Here

06: Running Folding@home as a Windows Service: Here

07: Switching from the GUI client to the Console client: Here

08: Folding@home and Windows 98: Here

09: Folding@home Sneakernetting Guide: Here

10: Folding@Home error guide: Here

11: Windows GUI (Graphical) Client Setup: Here

12: Operating the Folding@home GUI client: Here

13: Reporting Errors or Problems with Folding@home: Here

14: Folding@home Files (console client): Here

15: The fahlog.txt file: Part 1. Part 2

  1. Folding on a Graphics Card: Here

if you think there is something missing or would like to add to the thread please pm either fenix25 or Curly99.

2

Folding@Team Phoenix Rising

Installing Folding@home. Windows Console Edition - Single Client.

  1. Download the latest version of folding@home from http://folding.stanford.edu/download.html

  2. Create a folder for folding. (ie: FAH)

  3. Copy the client (FAHXXX-Console.exe) to your folding directory that you just created. (Replace X with the version of the console.)

  4. Click START->RUN->“CMD”

  5. Navigate to your folding directory that you created and type “FAH504-Console.exe -configonly”

  6. Configuring the options (see below)

User name? – Your User name. Case sensitive.

Team Number? – Team Phoenix Risings team number is 315, enter 315 only

Launch automatically at machine startup, installing this as a service? – Allows you to run the client as a windows service and be invisible. The configuration of the client as a service is beyond the scope of this how-to. For more information visit http://fahwiki.net/index.php/How_do_I_run_the_console_as_a_Service%3F

Ask before fetching/sending work? – The client will prompt you when it needs to connect to the internet to download new work or upload results. If you have a broadband (always on) connection choose no.

Use Internet Explorer Settings? – This option will use Microsofts Internet Explorer settings to connect to the internet. If you are using a proxy to connect to the internet, you can avoid setting it up in the client if it is already set in IE. Basically, if IE will load a webpage, you can use this option for connection settings.

Allow receipt of work assignments and return of work results greater than 5MB in size (such work units…)? – Otherwise known as Big Work units setting. This option will download some of the larger work units that may take longer and have higher memory demands than normal units. This setting is also important if you wish to download QMD work units (should they return).

Change advanced options? – Continues on to advanced options. Choose yes.

Core Priority (idle/low) – The CPU priority for the core. Choosing IDLE will only activate the core when no other applications are using the cpu, chosing LOW will run the core all the time, but allow other applications to cut into the cores cpu cycles.

CPU Usage requested? – Choose 100%. Lowering this number will make work take much longer and should only be changed if the client is interupting other applications from performing correctly.

Disable highly optimized assembly code? – NO! Choosing yes will disable the SSE/SSE2 etc and drastically increase folding time.

Pause if battery power is being used? – For laptops. You would probably want to use this option because folding@home will eat the battery in around an hour.

Interval, in minutes, between checkpoints? – Use the default of 15. Choosing a more frequent checkpoint frequency can
increase your chances of checksum errors if somthing goes wrong when writing to the hard disk.

Memory, in MB, to indicate? – Choose all your memory as a default. This number is reported to the assignment server and used to help it choose a work unit for your system.

Request work units without deadlines? – For slow computers, or computers that aren’t folding 24/7. If you find yourself missing deadlines, choose this option.

Set -advmethods flag always, requesting new advanced scientific cores and/or work units if available? – Choose no. The flag can be set at any time when starting the folding@home client and is not necessary for your day-to-day activities. There is no real advantage, points or otherwise.

Ignore any deadline information (blah blah blah)? – Choose no. Missing a deadline will give you no points.

Machine ID? – Choose 1 as this is a single client installation.

  1. Now your client is configured. Close the console screen and create a shortcut on your desktop pointing to the FAHXXX-Console.EXE file.

  2. Right-Click the shortcut and choose “Properties”

  3. Under the “Shortcut” tab and in the “Target” section, move to the end of the entry after the quotation marks. Add: -local -verbosity 9

  4. Next, under the “Start in” section make sure the location matches the location of the client. Click ok.

  5. Your client and Shortcut have been created and configured. You can copy the shortcut to your startup folder so the client will start when you logon to windows.

3

Installing Folding@home. Windows Console Edition - Multiple Clients

Running multiple clients on a single computer should only be done on a system with multiple CPU’s, a Intel “HT” processor or a AMD “dual core” processor.

  1. Follow the exact same instructions listed in the single client setup except repeat them twice. Create seperate folders for each client

  2. During the clients configuration, under “Machine ID” one client should use “1” and the other “2” (or more for each client you are running.

  3. It is very important with Multiple client configurations that you use the -local flag in the shortcut.

Folding@home flags

-config – Allows to to change your configuration options as described in the client setup. After completing the configuration with this flag the client will begin folding.

-configonly – Same as above however the client will exit after the configuration is complete

-verbosity x – Where x is the verbosity level. Use 9 to get the most information from the clients log.

-oneunit – Completes one unit (or the current unit) and then quits.

-forceasm – Forces the assembly optimizations such as SSE regardless if the client can use them or they have been disabled. This can be handy because a client that is shutdown incorrectly can have is optimizations disabled.

-advmethods – Downloads work units in the described as “advanced”. Usually between public and beta. There is a chance these units may encounter more errors.

-local – Uses the local folder for work and configuration files. Very important for multiple clients.

-help – Displays all the flags available.

These flags are just the basic ones you should know. There are a few more that aren’t as important but can be found at
http://folding.stanford.edu/console-userguide.html

4

Folding@home Utilities and 3rd party downloads

For a complete list check out : http://forum.folding-community.org/viewtopic.php?t=11700

MONITORS

Folding@Home Monitor and Farm (FAHMF) : http://home.cogeco.ca/~fahmf/
FahMon : http://fahmon.silent-blade.org/
Electron Microscope 3 (EMIII) : http://www.em-dc.com/

PROTIEN VISUALIZATION

JMOL : http://www.jmol.org/

UTILITES

Dick Howell’s Utilites (QD, QFIX, QGEN) : http://linuxminded.xs4all.nl/mirror/www.boston.quik.com/rph/fah.html

Folding@Home Links

http://folding.stanford.edu/ - Folding@Home Homepage
http://folding.stanford.edu/download.html - Folding@Home Client Download page
http://forum.folding-community.org/ - Official Folding@Home forums
http://fah-web.stanford.edu/psummary.html - Currently running public work units
http://forum.folding-community.org/viewtopic.php?t=11700 - Folding@home master tools list
http://fahwiki.net/index.php?title=Main_Page - The Folding@Home Wiki
http://fahstats.com/ - A good stats page
http://fah-web.stanford.edu/cgi-bin/main.py?qtype=userstats - Official User Statistics
http://fah-web.stanford.edu/cgi-bin/main.py?qtype=teamstats - Official Team Statistics
http://folding.stanford.edu/faq.html - Official Folding@home FAQ
http://forum.folding-community.org/viewtopic.php?t=4824 - Folding@home Common Errors
http://fahinfo.org/ - CPU comparisons using folding@home

5

Folding@home Cores

Tinker - FahCore_65
http://dasher.wustl.edu/tinker/

Tinker units do not use SSE. These units can take a long time and make up a large portion of the “timeless” units. Tinker units perform well on AMD CPU’s

Windows v2.53 (MD5=90140efc066fca1856ed71532e229675)(Size=1,314,816)

Linux v2.53 (MD5=b7b92c2cafeb2d080f85723b486e3a49)(Size=2,264,152)

Mac v2.53 (MD5=bfa9df1d88daafa089816d08bb46878e)(Size=705,836)

Gromacs - FahCore_78
http://www.gromacs.org/

Gromacs unit are among the most common. They take advantage of the SSE instruction set which will improve folding time by up to 3 times. They also can take advantage of AltiVec with Macs.

Windows v1.86 (MD5=92540be84fc0d48436c5e9c271797709)(Size=2,322,432)
Windows v1.90 (MD5=19dc2c337c2d568d30217d5619b36371)(size=2,338,816)

Linux v1.80 (MD5=99ec546ee3cdfb99d8c2e89e4f126755)(Size=3,461,632)
Linux v1.86 (MD5=1b38a016b706fe7b8fd91d2b380db134)(Size=3,435,296)
Linux v1.90 (MD5=140afc16f2393d044f1e5b3daa4b2a23)(Size=3,452,908)

Mac v1.86 (MD5=0f549bf8d86dfb7978af78fb9f01ffd0 )(Size=2,718,444)
Mac v1.90 (MD5=01d7f5dcc698c65f001725c26f7d8dcd)(Size=2,718,444)

Double Gromacs (DGROMACS) - FahCore_79
http://www.gromacs.org

Similar to the gromacs core, DGROMACS performs double precision calculations as opposed to single. It also takes advantage of SSE2 found in P4’s and Athlon64’s

Windows v1.72 (MD5=8689d0508abcd1f857f76c4f52e6857a)(Size=2,326,528)
Windows v1.91 (MD5=c76a8c58b6d1d6d83eee3bcda2d74889)(Size=2,334,720)

Linux v1.72 (MD5=a4bcaefef41feecc2c8522be2cf40870)(Size=3,440,948)
Linux v1.91 (MD5=20786fe7e0133b7d9d364f08c3a4afa6)(Size=3,452,908)

Mac v1.72 (MD5=35f0fca7bb3635acfa234d50360c13f9)(Size=2,144,820)
Mac v1.91 (MD5=80483c6e53f6be7e32e40d4b84b097e4)(Size=2,148,956)

GBGromacs - FahCore_7a
http://www.gromacs.org/

Similar to the Gromacs core with modifications from Pande Group.

Windows v1.90 (MD5=48319bc38b8fdc2e01dfcb13f8c8601c)(Size=2,387,968)

Linux v1.86 (MD5=f381bce945b47f55d353518be71bcd35)(Size=3,486,728)
Linux v1.87 (MD5=4dea05d33733eb24437058fb47f5eda3)(Size=3,486,728)
Linux v1.90 (MD5=1ad38f95a897066aac657ddd877e8398)(Size=3,102,232)

Gromacs33 - FahCore_A0
http://www.gromacs.org/

The gromacs33 core contains more recent gromacs features that have been ported to folding@home. The gromacs33 core is currently only available to linux users.

Linux 1.70 (MD5=3540b9a3d5e6d185f49c8472f68de512)(Size=3,166,376)
Linux 1.71 (MD5=065fdc86dbcde184720eed1faa24c71a)(Size=3,165,800)

Amber/PMD - FahCore_82
http://folding.stanford.edu/AMBER.html

AMBER (Assisted Model Building and Energy Refinement) does not use SSE but furture versions may use SSE2.

Windows v1.03 (MD5=266eeb7a4c0035688e21adf638c74ba3)(Size=1,683,456)

Linux v1.03 (MD5=bb6762b68c82ecf3c9bd42fa1ab8ac01)(Size=2,542,532)

QMD - FahCore_92
http://www.cpmd.org/

The QMD core requires a lot of memory 512MB+. The QMD work units are currently offline while pandegroup reviews
the results from the previous batch. QMD Units are not available for AMD CPU’s. The core is multi-thread capable.

Windows v1.04 (MD5=d14e7ea0b6bd546a2fbf16ec5b3b84cd)(Size=8,441,856)

Linux v1.04 (MD5=4f92e4e31d4ed132b8db461545df3630)(Size=9,110,072)

GPU Core - FahCore_10
http://

The GPU core uses a graphics card core to perform the calculations.

6

Running Folding@home as a Windows Service

  1. During the initial setup of your client (or by running the client configuration -configonly) answer yes to the third question:

–>Launch automatically at machine startup, installing this as a service (yes/no) [no]? YES

  1. Reboot the computer.

VERY IMPORTANT!!! Make sure you don’t have any shortcuts in your startup folder that will start the “service” client when you boot.
Loading 2 instances of the same fah client/core will result in loss of work.

  1. Now that you have the client set as a service, you will wan’t to add your flags (arguments). First you must shutdown the service. Click
    START->RUN->“services.msc”, or Click START->SETTINGS->CONTROL PANEL->ADMINISTRATIVE TOOLS->SERVICES. Next locate the service. It will start
    with FAH@ followed by the location of the client. Right Click and select stop.

  2. Click START->RUN->“regedit”. Navigate the registry to HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services<service name>

  3. Right Click “Image Path” and click Modify.

  4. Make sure you leave the -svcstart flag as it is necessary for the service client to function correctly. Add your flags after it.

  5. Restart the service and voila! You can confirm that flags you added are activated by looking at the fahlog.txt at the top. Look for:

Arguments: -svcstart -local -verbosity 9 -forceasm -advmethods

Note: You can do this for multiple clients. Once the service is activated you will not see the console anymore. You can view the
fahlog.txt file at any time, or download a 3rd party monitoring tool (See above).

Switching from the GUI client to the Console client

  1. Shutdown the GUI client completly.

  2. Download the console client from http://folding.stanford.edu/download.html

  3. Copy the console client to your GUI clients folder.

  4. Modify all your shortcuts including any in the startup folder so that you don’t start the client twice by accident.

  5. Follow the instructions above for configuring the client.

Folding@home and Windows 98

The last folding@home client for windows 98 was 4.00. Since then clients 5.02 and 5.04b have been released. While not specifically for Windows 98 these clients can in fact be used on your windows 98 machines. There are two key things to note when using them however. First you cannot install the 5.x clients as a service under windows 98, and you cannot run the 5.x clients with the “big WU” option. In other words, during the clients configuration answer no to:

–>Launch automatically at machine startup, installing this as a service (yes/no) [no]? NO

–>Allow receipt of work assignments and return of work results greater than 5MB in size (such work units may have large memory demands (no/yes) [no]? NO

I also personally don’t reccomend using the 5.03 graphical client under windows 98. Instead run the console client.

Using a proxy server with Folding@home

To setup your proxy server run he clients configuration (-configonly). When you get to the question:

Use Internet Explorer Settings (no/yes) [no]?

you have a descision to make. If Internet Explorer is configured to used the proxy you can answer yes here, however with later versions of IE it has been reported that this doesn’t work so well with the proxy server.

If you choose to answer no to the above question, you will have to setup your proxy manually. Here are the questions that you will encounter during this procedure:

Use proxy (yes/no) [no]?
Proxy Name [localhost]?
Proxy Port [8080]?
Use username & password with proxy (yes/no)?
Proxy Username?
Proxy Password?

You will have to ensure that port 8080 is not being blocked by your firewall. That should work for you, remember if you are using some of the newer IE’s setup your proxy manually. Even if your not using a proxy, answer no and then no to “Use Proxy”.

7

Folding@home Sneakernetting Guide

Sneakernetting is the process of download a work unit on one machine and then transfering it to another machine. This is handy if a machine does not have a connection to the internet, or for moving large units off slow machines.

For the purposes of this guide I will label our two machines as Machine A and Machine B

Machine A - Has internet.
Machine B - Has no Internet

  1. Assuming Machine A is already folding, create another folder for downloading your units that you wish to sneakernet. Copy the client to this folder and set it up however you like. Make sure you use the -local flag on both your clients at this point.

  2. Copy everything on machine A’s sneakernet folder to machine B.

  3. Now you must copy the registry key from machine A to machine B. Click Start->Run->“regedit” and navigate to HKEY_LOCAL_MACHINE\SOFTWARE\PandeGroup\

  4. Right click “PandeGroup” and click export. Call it fold.reg

  5. Now copy the key you exported from Machine A to Machine B

  6. On machine B, double-click fold.reg and click Yes to add the key to your registry.

  7. To download work, on Machine A run the client (with the -local flag and any others you wish. The client will download a core and a work unit. Once downloaded, it will start folding. Stop this process by pressing CTRL-C.

  8. Now you must transfer your work to Machine B. There are several files which you will now need to copy (listed below).

FahCore_xx.exe -> The core. xx represents the core needed (ie 78, 7a etc)
\WORK -> The entire work folder. This is the work unit.
queue.dat -> The queue.dat file contains the deadline information as well other important information.

  1. Transfer these files to machine B and start the client. The client will now fold the unit.

  2. Once the unit is complete, you must copy the \work and queue.dat folder and file back to Machine A. It is not necessary to copy the core back to machine A. Make sure you transfer the work to the sneakernet client on Machine A and not Machine A’s own folding client

  3. To send the results, run the sneakernet client on Machine A with the -send all flag. The unit will now upload and a new unit will download another. Repeat this process. Make sure that if the unit downloads a new core that you move the core to Machine B as well.

It’s important that you keep the files in their correct folders. This guide assumes two machines, one with connectivity and one without, however you can sneakernet to as many machines as you like. Its not necessary for the sneakernet clients on Machine A to have different Machine ID’s either.

8

Folding@home Error Guide

EUE - Early_Unit_End

There are many different types of EUE’s. Some EUE’s are a natural end to the folding simulation, others are a result of machine instability. The general rule of thumb when determining if your machine is unstable and producing EUE’s is the frequency of the EUE’s. If you experience EUE’s often, or one after another, this is a major sign of instability. If you experience an EUE every now and again (once or twice a month) then there is probably nothing to worry about.

Machine Instability can be caused by a number of reasons. The first thing to look at would be your CPU temperature. First, find out from your CPU manufacturer what the “safe” operating temperature is for your machine. Then compare it with readings while your CPU is at full load (folding). You can download software such as Motherboard Monitor 5 ( http://mbm.livewiredev.com/ ) to monitor your CPU temperature from windows. If you determine that your CPU is running hot, a good cleaning is in order. Clean all fans and ducts with compressed air and a vaccuum. You should also consider cleaning your heat sink on your CPU. Dirt and dust often collects on the top of the heat sink and obstructs air flow through the fins. You may also consider replacing the thermal compound seperating the CPU core and the heat sink core. Follow the instructions from your manufacturer closely.

Another possible explanation for machine instability is bad overclocking. If you are overclocking and getting EUE’s, consider returning the settings to normal and restart folding. If the EUE’s stop, then your previous attempts to overclock didn’t work. Try different settings for your overclocking or consider not overclocking. Some CPU’s don’t overclock as well as others.

Memory can also be a cause of EUE’s. Memory Stress tests can help determine if your memory is bad. Memtest86 is a good choice for doing this ( http://www.memtest86.com/ ). You can also run SSE stress tests and CPU stress test ( http://forum.folding-community.org/viewtopic.php?t=11700 - Under “Testing Your System Stability” ). If you find that hardware is not functioning correctly it may be necessary to replace it.

Gromacs EUE’s (Including GBGromacs, Gromacs33, DGromacs)

“Gromacs cannot continue further” - Most likely a natural end to a folding simulation however can be hardware related.
“Quit 101 - Fatal error: NaN detected: (ener[xx])” NaN stands for Not a Number. More likely machine instability.
“Quit 101 - Fatal error (LINCS warnings)” - Unit violated the minimum distance between atoms necessary for a correct calculation.
“Quit 101 - Fatal error: XTC Error” - “It could be something physical, very large numbers, e.g. due to bad minimization” - Groeten, David.

Amber EUE’s

“NaN/Inf detected e[0]” - Inf is short for infinity

There are a number of other errors that are less common. Remember the rule of thumb. Every now and again is expected, but frequent EUE’s could be a result of machine instability.

Note for people running Advanced Methods (-advmethods): Advanced Methods work units are units that have just come out of the testing processess. During the initial testing process EUE’s are quite common and used to design better simulations. After a while, units are moved to the advanced methods catagory. These are public units but do run the risk of EUEing slightly more often than units you would get if you didn’t use the flag.

Error 0x0 and 0x1

Error’s 0x0 and 0x1 true cause is unknown. If you experience one of these errors you should consider reporting it to Pande Group via the folding-community.org forums ( http://folding-community.org ).

CoreStatus Codes

CoreStatus = 0 (0) and CoreStatus = 1 (1) - See Error 0x0 and 0x1 above.
CoreStatus = 62 (98) - Core restart due to a change in settings
CoreStatus = 6E (110) - Core out-of-date. The core will then update.
CoreStatus = 63 (99) - An error occured when starting the core. This could be the result of the user not having sufficient permission to access the core.
CoreStatus = 64 (100) - Work unit completed successfully.
CoreStatus = 65 (101) - SPECIAL_EXIT
CoreStatus = 66 (102) - User requested core shutdown.
CoreStatus = 70 (112) - Work Unit is corrupted. BAD_FRAME_CHECKSUM
CoreStatus = 72 (114) - Bad_Work_Unit or Early_Unit_End.
CoreStatus = 75 (117) - An error reading the work from the hard disk or another I/O problem.
CoreStatus = 77 (119) - UNKNOWN_ERROR
CoreStatus = 79 (121) - UNKNOWN_ERROR. Disk may be full. The core could not write to a checkpoint file.
CoreStatus = 7E (126) - ERROR 0x7e Core failed to load. May be due to permission issues or a bad work unit.
CoreStatus = 89 (137) - ERROR 0x89 Insufficient memory.
CoreStatus = C0000005 - A known bug with the GUI client. Update video drivers or keep the client closed when folding is nearing completion.
CoreStatus = C000008F - No information available

9

Windows GUI (Graphical) Client Setup

The graphical version of the folding@home client offers a graphical interface in which the user can see a visualization of the protien being worked on. There is no difference in the way that GUI client folds when compared to the console client. The graphical client can also serve as a screensaver for windows.

  1. Download the graphical client from Stanford (5.03) at http://folding.stanford.edu/download.html

  2. Double-click the installer to begin the installation procedure.

  3. When asked for your name, choose your folding@home username. If you don’t have one, you can create one.

  4. Install the program in the default location. If you choose to move it elsewhere, remember where you put it so that you can access the logs later on.

  5. Once the installation is complete and the application has begun, the Folding@home Control Panel will open. Firstm is the username you selected during the setup. Next is the team number section. Enter 315.

  6. Click on the connection tab. If you wish to have the client ask you for permission when uploading and downloading work units, check the box “Ask before using network”. If you have a connection that is “always on” don’t bother checking this box. The client only requires bandwidth when uploading and downloading work units and will not use the internet all the time.

  7. The next box is “Use Internet Explorer Connection Settings”. With the new IE7 connection problems have been occuring while this box is clicked. Choose not to use these settings.

  8. If you wish to use a proxy server select “Set a proxy server” and fill in the information to connect through the proxy including a user name or password if it uses one.

  9. The last box on the connection page asks if you wish to recieve and return results greater than 5mb. Check this box only if you wish to get some of the larger DGromacs work units and QMD’s. These units can be much more taxing on your system.

  10. Next click the Display tab. You will see a slider called “Molecule draw rate”. This has nothing to do with the MD calculation but rather, the speed at which the screen refreshes the image of the protien. The higher this slider goes, the higher the CPU useage will be from the client, taking away CPU usage from the core which is what is doing the calculation. Next is the visualization type. There are two options (Ball&Stick and Spacefill). You can experiment with which one you like best.

  11. The “Turn on screensaver after xx minutes” option allows you to use folding@home as your screensaver. Click the box and then set the time the machine will sit idle before engaging the screensaver.

  12. The “Main title enabled” box is simply the display message at the top of the clients window. You can change or disable this if you like.

  13. The “Logos enabled” box shows several folding@home logos at the bottom of the client. You can turn these on or off and even add your own from the web by filling in the URL.

  14. Next, click the Advanced Tab. The first option is the “core priority” Choosing Lowest Possible will only activate the core when no other applications are usingthe cpu, chosing slightly higher will run the core all the time, but allow other applications to cut into the cores cpu cycles.

  15. Below is the CPU usage slider. Keep it at maximum all the time.

  16. The “Disable highly optimized assembly code” box should never be checked. This will disable SSE/SSE2 or equivalent.

  17. Next is the Checkpoint frequency slider. This slider should also be left where it is. The default is 15 minutes. Lowering it will increase the possibility of a checksum error when writing to disk.

  18. Next is the “Pause work while battery power is being used (for laptops)” It is reccomended to use this setting if you are in fact using a laptop. Otherwise the core will burn through your battery in under an hour.

  19. Finally is the “ignore deadlines locally” box. Keep it disabled for now.

  20. You may also wish to request units without time limits. These units can take as long as you wish to run. You can also choose to download them as a batch (up to 8) to work on for a long time. The normal setting is No preference, but I suggest switching it to standard.

10

Operating the Folding@home GUI client

Once the client is set up. There are a few other day-to-day operations you may wish to be aware of. This section of the guide will briefly describe the other options that are available to you.

The Main Screen

On the main screen, you see a representation of the protien being worked on. You can get more information about the protien from the following locations:

http://fah-web.stanford.edu/psummary.html - The Official Folding@home project summary page
http://fahwiki.net/index.php?title=Projects - The Folding@home WIKI project page
http://jmol.sourceforge.net/fah/ - Java based protien visualization
http://fah-web.stanford.edu/cgi-bin/fahproject - Project information from Pande Group.
http://www.rcsb.org/pdb/Welcome.do - RCSB Protien Data Bank

On the left you will see your user name (under “Donator”) as well as your team number (315 of course). After that is a finished work units count. This is a local count of the work units completed by this client only. After that is the current project being worked on as well as the core being used. The protien name usually cuts off but you can see the whole thing in the fahlog.txt file located in the folder where you installed this client.

The frames completed section is a progress counter for the current work unit. It differs somewhat from the console client, so be aware of that. Below this is a counter for the next frame completion. For this counter to be accurate, the client must complete a few frames first. Expect the number to vary depending on how long the client has been running. Finally is the WU end estimation. This estimation will also be way off initially. Again, the core needs to complete a few frames to get an idea of how long the work unit will take.

Right Clicking anywhere on the main screen will bring up an options menu. You can view the copywrite information by clicking “About”. Next is the “Switch display mode”. This option will switch between the window mode and full screen mode. If you have set the client up as a screen saver it will automatically switch to the full screen mode. Below that is the “Configure” option which will bring up the client configuration described in the previous section of the guide. You can change any of your options at any time. Finally is the “Quit” option that will close the client.

The System Tray

In the system tray (where the clock is) you will see a red gear. This is the folding@home clients system tray icon. Right clicking it will bring up more options, many of which have already been discussed. You will notice that there is an option to “Pause” the work unit. This option should not be used for long periods of time. There have been many reports of the work unit being trashed because the pause was left on. If you need to stop folding@home, then quit rather than pause. You can also choose to “Pause when done”. This will pause the client once the current work unit is complete.

The “Status” section in the system tray pull-up is a handy information tool. It contains the following options:

My Folding : Pulls up the MyFolding.html file located in the folding@home client directory.
Queue Info : Pulls up information from the queue.dat file. This will contain all the work units currently downloaded as well as the completed ones. It will show all the units in a batch download as well.
Team Statistics : Will pull up the official Stanford team stats page for Team Phoenix Rising
User Statistics : Will pull up the official Stanford user stats page for your user name.
Log file : Will display your fahlog.txt file found in the folding@home client directory.

11

Reporting Errors or Problems with Folding@home

We all have questions from time to time. I am always willing to help anyone with folding@home. All they need to do is ask. However, having the correct information about a users problem will ensure that their problem is taken care of as quickly as possible. I am creating a form for team members to fill out when submitting a folding@home question or problem. Please take the time to fill out all of the form so your problem can be addressed in a swift manner. The form is also available as a plain text file from : http://home.cogeco.ca/~fahmf/tpr_helpform.txt To save time you can fill out parts of the form and have it saved so when you need it, most of the information is there.

A note about the QD output: The output from running QD can be very helpful in determining whats wrong with your client. To use QD, download a version from http://linuxminded.xs4all.nl/mirror/www.boston.quik.com/rph/fah.html#qd (scroll down for the executable). Put the QD.EXE file in the folding@home clients folder and click:

START->Run->CMD

Navigate to your folding@home client folder and type:

QD -i > fah.txt

The name of the .txt file can be anything you wish, copy and paste the contents of the .txt file created into the report below.

THE FORM:

Your General Setup

[b]
CPU:
Operating System:
Is this machine Overclocked:
If overclocked provide details:
Internet Connection:
Using a proxy:
Firewall:

Client Username:
Number of Clients Installed on this computer:
Client version: [/b]

Folding@home Information

[b]Current Work Unit (Project,Run,Clone,Gen ie Project 2100 (Run 1, Clone 2, Gen 3):

Fahlog Output (May be long. Post everything):

QD Output:[/b]

----END FORM-----

If need be, this information may be passed on to the experts at folding-community.org to help resolve your problems. This is the case for questions about work units not being credited as well as other questions that I’m not so sure on :wink:

12

Folding@home Files (console client)

client.cfg - The configuration file created by running the client for the first time or modified with the -config or -configonly arguments. DO NOT modify this file with a regular text editor!
FAH50x-Console.exe - The client executable. x represents the version number for the series 5 client.
FahCore_xx.exe - The folding core. the xx represents the version (see cores for descriptions and versions.
FAHlog.txt - The logfile. A direct copy of the clients output while running.
FAHlog-Prev.txt - The previous logfile. Created once Fahlog reaches a certain size.
MyFolding.html - A html file generated after the first run linking to your stats pages.
queue.dat - Critical information about the current and past work units worked on by this client.
unitinfo.txt - Text file showing the progress of the current work unit.
machinedependent.dat - Binary containing the userid. Used only on linux or mac. On Windows it is stored in the registry.

\WORK - The work folder. Contains the work unit.

The xx represents the wu’s designation in the queue.dat file (ie wudata_01.xxx)

wudata_xx.XXX - There may be multiple files called wudata_xx. The extension may be multiple different things, they can include .bed .bxv .dyn .goe .pdo .sas .xtc .xvg .xyz
wudata_xxCP.arc (.arc.b) - The checkpoint files for the current work unit.
wudata_xx.arc - Insight II Cartesian Coordinate Archive File
logfile_xx - Current work units log file
wudata_xx.chk - Binary file which is a newzmat Gaussian 03 checkpoint file.
wudata_xx.txt - Settings for current work unit
wuinfo_xx.dat - Current work units name and other information.
wudata_xx.dat - The work unit itself.
corexx.sta - Unknown. Usually contains 0 bytes.
current.xyz - The current atom possitions. Can be viewed with JMOL.
stepxxxx.pdb - Created under certain EUE conditions.
wuresults_xx - A binary containing the results of a finished work unit.

Note: Some of these files may not appear at all times.

13

The fahlog.txt file - part 1/2

Folding@home prints all the client output to a file called fahlog.txt (an fahlog-prev.txt when fahlog.txt is full). Understanding the log file is important to help diagnose troubles you are having, as well as understanding what is going on with your client.

The first part of this guide will deal with Gromacs (as well as Dgromacs, GBgromacs) type work units. The log files differ somewhat with other types of units (especially tinker). Since gromacs is the most common type of unit, we will take a look at this type of log first.

Note: Some of what is listed in this guide are only visible with the -verbosity 9 flag.

— Opening Log file [June 4 02:55:01] - The date the logfile was started (client start)
Launch directory: c:\Documents and Settings\Mike\Desktop\Folding\fah1 - The directory where the client was launched from.
Executable: C:\Documents and Settings\Mike\Desktop\Folding\fah1\FAH504-Console.exe - The location of the client executable.
Arguments: -local -verbosity 9 -oneunit -forceasm -advmethods - The arguments that the client was started with.
Warning:
By using the -forceasm flag, you are overriding
safeguards in the program. If you did not intend to
do this, please restart the program without -forceasm.
If work units are not completing fully (and particularly
if your machine is overclocked), then please discontinue
use of the flag. - A warning message if you are using the forceasm flag. Doesn’t appear otherwise

Entries after this point contain a timestamp in UTC time. (ie : [02:55:01] )

- Ask before connecting: No - In your configuration options, you can choose to ask before connecting to the internet or not.
- User name: fenix25 (Team 315) - Your username and team number (better be 315!!)
- User ID: A1A1A1A1A1A1A1A1A1 - Your unique user ID that ties your username to the machine the client is run on. Stored in the registry.
- Machine ID: 1 - The machine ID for this client.

The following two entries are first run only

Work directory not found. Creating… - Creates the \work directory for storing the work unit
Could not open work queue, generating new queue… - Generates the queue.dat file.
+ Benchmarking … - There was a time when this number was going to be used by assignment servers to issue units, but it isn’t used currently.
The benchmark result is 3116 - The higher the number, the faster the machine.

The following entries are for fetching work units

- Preparing to get new work unit… - Checks for connectivity
+ Attempting to get work packet - Connectivity has been confirmed. Will attempt a download now
- Will indicate memory of 1022 MB - The ammount of memory you set in the configuration for the client to use.
- Connecting to assignment server - Attempting an HTTP connect to the assignment server
Connecting to http://assign.stanford.edu:8080/ - The master assignment server. This will direct your client to the appropriate download server.
Posted data. - Passed your settings to the assignment server[/b]
Initial: 41AB; - Successful: assigned to (171.65.103.150). - The assignment server redirects you to a server to get work.
+ News From Folding@Home: Welcome to Folding@Home - Standard welcome message… haven’t ever seen it change.[/b]
Loaded queue successfully. - Your queue.dat file is loaded into memory and is prepared to accept an assignment[/b]
Connecting to http://171.65.103.xxx:8080/ - The client attempts to connect to the server given by the assignment server.
Posted data. - Passed your settings to this server.
Initial: 0000; - Receiving payload (expected size: 1084979) - The download has begun. The WU size is indicated (compressed).
- Downloaded at ~353 kB/s - The connection speed at the beggining of the transfer.
- Averaged speed for that direction ~353 kB/s - The average transfer speed for the download.
+ Received work. - Confirmation of the reciept of work.
+ Closed connections - The network connection closes.

Every six hours you will see the following message when the client attmpts to send any finished work units. This message is first seen when the client loads as well.

- Autosending finished units… - The attempt to send work is being made.
Trying to send all finished work units - The client checks the queue.dat file for any completed work units and attempts to send them.
+ No unsent completed units remaining. - If no units are waiting to be sent.
- Autosend completed The attempt to send work is complete.

The following messages are for the core startup

+ Processing work unit - The client signals that a unit is going to be processed
Core required: FahCore_xx.exe - The client indicates which core is required.

If the required core is not found or is corrupted or out of date. The client will attempt to download a new core.

Core not found. - The client inducates that the core is not found.
- Core is not present or corrupted. - Message Indicating that the core is not found or corrupted
- Attempting to download new core… - The client will attempt to connect to stanford.edu to download a new core.
+ Downloading new core: FahCore_79.exe - The connection has been established and a core is being downloaded.
Downloading core (/~pande/Win32/x86//Core_xx.fah from www.stanford.edu) - The client indicates which core is being downloaded and from where.
+ 10240 bytes downloaded - The client will count out the bytes recieved until the core is downloaded.
Verifying core Core_79.fah… - The client checks the integrity of the downloaded (compressed) core.
Signature is VALID - Indicates that the core downloaded is ok.
Trying to unzip core FahCore_xx.exe - The client attempts to unpack the core executable.
Decompressed FahCore_xx.exe (2334720 bytes) successfully - The client indicates that the core was unpacked successfully.

If core was present, or the new core is downloaded successfully…

+ Core successfully engaged - The core has been initiated

The client then passes the work to the core.

+ Processing work unit - The work unit begins to be processed.
Core required: FahCore_xx.exe - Message indicating the required core for the work unit.
Core found. - Message indicating that the core was found successfully and the unit can engage.
Working on Unit xx [June 2 20:01:33] - Message indicates which unit in the queue the core is working on as well as the time the core started work on the unit.
+ Working … - Working :slight_smile:
- Calling ‘FahCore_xx.exe -dir work/ -suffix 03 -priority 96 -checkpoint 15 -verbose -lifeline 2368 -version 504’ - Various settings given to the core to complete the unit.

14

The fahlog.txt file 2/2

The Simulation

Folding@Home Double Gromacs Core - The Core being used
Version 1.91 (April 11, 2006) - Core version and release date.
Preparing to commence simulation - Client is entering the simulation phase passsing the work to the core.
- Assembly optimizations manually forced on.
- Not checking prior termination. - Displayed if the -forceasm flag is being used.
- Looking at optimizations… - Checking for SSE/SSE2
- Files status OK - Status of the work unit file is OK
- Expanded 1313453 -> 4646037 (decompressed 353.7 percent) - Expanding the work unit file from original package
Project: xxxx (Run xx, Clone xx, Gen xx) - The project identification.
- Starting from initial work packet - Displayed if the work unit is new or if the checkpoints are corrupted.
Assembly optimizations on if available. - The SSE optimizations will be used

Previous termination of core was improper
Working with Standard loops this execution - The SSE optimizations have been turned off due to improper shutdown. Restart the client.

Entering M.D. - The simulation has begun.
(Starting from checkpoint) - The simulation will continue from the last saved checkpoint
Protein: pxxxx_protien_name - The official protien designation including project number
Writing local files - Writes the necessary files for the simulation to disk.
GB activated - Displayed for GBGromacs units
Extra SSE/SSE2 boost OK - The SSE assembly optimizations are working correctly.
Completed xxxxxx out of xxxxxxxxxx (x) - The amount of steps completed and the percentage of the unit completed
Timered checkpoint triggered. - Checkpoint written to disk

Shutdown

***** Got a SIGTERM signal (2) - Client shutdown requested.
Killing all core threads - All threads including the core are shutdown
Folding@Home Client Shutdown. - The client has been shutdown.

Work Finished

Writing final coordinates. - The final results are written to wuresults_xx.dat
Past main M.D. loop - The simulation is complete.
Finished Work Unit:

  • Reading up to 9360 from “work/wudata_08.arc”: Read 9360
  • Reading up to 78172 from “work/wudata_08.xtc”: Read 78172
    goefile size: 0
    logfile size: 140583[/b] - The work unit results are being prepared.
    Leaving Run - The core begins to shutdown.
    - Writing 262683 bytes of core data to disk…
    … Done.     - The Core dumps the results to the disk to be sent.
    - Shutting down core - The core is shut down.
    Folding@home Core Shutdown: FINISHED_UNIT
    CoreStatus = 64 (100)     - The core completed the work unit successfully. If there is an error code it would appear here.
    Unit x finished with xx percent of time to deadline remaining. - The unit (represented by its number in the queue.dat file) is finished. The % time remaining to the deadline is also shown.

Sending Results

+ Attempting to send results - The client will attempt to send the results file.
- Reading file work/wuresults_08.dat from core - The results are loaded into the memory.
(Read 262683 bytes from disk) - The size of the results file loaded into memory.
Connecting to http://171.64.122.139:8080/ - The client attempts to connect to the results server.
Posted data. - The results server is informed of what it is going to recieve.
Initial: 0000; - Uploaded at ~85 kB/s - The upload speed at the beginning of the transfer.
- Averaged speed for that direction ~79 kB/s - The average speed for the upload.
+ Results successfully sent - The client confirms that the work unit has been sent.
Thank you for your contribution to Folding@Home. - Your welcome :wink:
+ Number of Units Completed: x - Local count of work units completed by this client. Doesn’t reflect your total.

+ -oneunit flag given and have now finished a unit. Exiting.***** Got a SIGTERM signal (2) - If you used the -oneunit flag the client will exit.

Keep checking back for updates. There are many more messages that will be added as I find examples of them. I will also work on versions of this guide for other cores.

15

This is a beta release and there will be several bugs, flaws, problems, etc – releasing software for GPU’s (Graphics Processing Units or Graphics Cards) is itself very new in the software industry in general and there will be problems at the start.

As in the use of any beta software, please make sure to back up your hard drive, and do not run this client on any machine which cannot tolerate even the slightest instability or problems.

Currently only ATI X19nn series cards are supported. For X1950 cards you MUST use the Catalyst 6.10 drivers. Cards in Crossfire mode are not supported.

There are two steps:

  1. Download the GPU client file from here . For the console client, just run it as normal. For the GUI client, unzip the file to its own folder and then run the winFAH binary. Command line options are identical to the CPU client and details are provided elsewhere in this sticky. We do not recommend this beta client for those who have never run FAH before, as in this beta test several parts of the client will not be working correctly and/or will require a knowledge of how FAH works.

  2. Download and install the necessary system software. Due to the complex nature of performing scientific calculations on GPUs, the FAH GPU client needs very specific system software to work. Stanford are working on a way to avoid this in the future, but for now, there is no way around this (please keep in mind that a Graphics Driver is really a compiler of sorts and thus any GPU code is very sensitive to this issue). Before installing the new system software, don’t forget to backup your computer’s hard drive (always a good idea in these situations) and then install the following components:

Catalyst driver version 6.5 download from ATI here. Version 6.10 download from ATI here with the newest core appears to be working now (but requires more testing to be sure). Versions 6.6 and 6.7 will work, but at a major performance hit; 6.8 and 6.9 will not work at all. Due to all the complexities of support, we will support only versions 6.5 and 6.10.
DirectX: 9.0c (4.09.0000.0904) or later, download from Microsoft here , which yields d3dx9_30.dll (the critical part for FAH)
This system software configuration is critical as a misconfiguration can lead to problems, such as excessive Early Unit Ends (EUE’s). EUE’s may also occur frequently in the current GPU cores due to testing of new types of WU’s. Stanford need the help of beta testers to help pin down this issue with more data.

It is a good idea to download, install and run ATITool. Version 0.25 build 15 works fine for me. This will allow you to set 3D clock speeds on your GPU whilst only running 2D applications. Doing so makes a significant difference to WU times. You must ensure that your GPU voltage is set to 1.4v and that you closely monitor GPU temperatures. It is ‘normal’ for the GPU to run at 80 - 85 degrees whilst running F@H. You may have to adjust fan speed settings to keep within these parameters.

KNOWN BUGS, COMPATIBILITY ISSUES, AND RUNNING NOTES

Please note that the Windows GPU client for Folding@Home is a beta release. While Stanford have done lots of testing in house, there are limits to the bugs they can find in these limited tests (and hence the need for a beta test). As in the use of any beta software, please make sure to back up your hard drive, and do not run this client on any machine which cannot tolerate even the slightest instability or problems.

Thus, Stanford expect that there will be many problems with the client that need to be resolved. Below is a list of some of the relevant known issues or bugs for beta testers of this new client.

Known Bugs

  1. The GUI pause core command doesn’t work
  2. The GUI Client will automatically quit when running fullscreen directx apps (games), it may be a little slow at doing this though
  3. The console cannot be run as a service (must be run as a program)
  4. Screen saver mode in the GUI does not work
  5. Fast user switching problems: Turning fast user switching off and using the standard “ctrl+alt+del then lockout button” causes the gpu client to terminate as soon as I press the ctrl+alt+del combonation. GPU client terminated with the exact same error codes. This is a “feature” of XP: when switching users, the GPU context is taken away (this happens under locking (Windows+L or screen saver lock) or switching).
  6. There have been some reports that the GPU core does not save (checkpoint) correctly when quit
  7. Some people have posted logs showing GPU work going to Completed 85, then sending results. It appears that this is a reporting issue and that the core is actually working during this time (there is a two-hour lapse between 85% and the send, which is consistent with computing the last 15 % – about 8 min. per frame, and the returned log and xtc files seem to be just fine).
  8. In some rare situations, one needs to set the Hardware acceleration to max if the Catalyst install didn’t do this. To do this, go into the Display Properties/Settings/Advanced/TroubleShoot tab and double check that the Hardware acceleration was set to “Max”.

Known compatibility issues

  1. One must use specific Catalyst drivers (6.5 or 6.10) and a recent DX version-- see the HOW TO above
  2. The GPU core does not run under WINE in linux (nor do we have plans to support WINE)

Notes for running

  1. The GUI client will slow down the scientific core (since both use the GPU heavily). We do not recommend the GUI client for long term use, unless you have two graphics cards.
  2. Multiple GPUs are currently not supported (but will be supported in future releases); Crossfire is also not supported – Crossfire will make FAH run more slowly than using a single GPU (this isn’t a bug as much as a fundamental issue regarding the nature of a Crossfire/SLI type architecture).
  3. The GPU client is not meant to be run in the background while one uses the computer for applications with heavy GPU usage – it will greatly slow down the response of programs which make heavy use of a GPU
  4. Do not run multiple GPU clients simultaneously – there will be a huge (non-linear) slow down in performance. We currently do not support multiple GPU configurations, although a second GPU can help speed up the graphics of the GUI.
  5. Client looks like it is using lots of CPU time: Graphics drivers must poll the GPU to see if it is done. This will look like a lot of CPU time being used, but nothing is really being done, so one can run other relatively CPU heavy code at the same time. However, we do not recommend running multiple FAH clients, as this can significantly slow down the GPU client. A good rule of thumb: leave at least 25% of the CPU time available for the GPU client.

Trouble shooting EUE’s

Some Alpha testers have found an excessive number of Early Unit End’s (EUE’s) – these have not reproduced that at Stanford or ATI and they need help from beta testers to help track this down. If you see many EUE’s (i.e. more than 20%), please make a post in the GPU section of the Folding@Home forum with your system configuration (ATI driver version, DX version, OS) and hardware (card, CPU, motherboard type). With the help of beta testers, Stanford hope to nail down what’s going on.
If you are seeing lots of EUE’s, please download the ATItool application and check that your core voltage is set to 1.4V. This has been shown to lead to problems in certain cases (although we have seen it work without this set to 1.4V as well).
Be careful about overheating and/or overclocking the GPU.

Policy Notes

The client will stop working after 2 months (this is a limited release beta – new clients will be available before the current version ends its test period)
Deadlines will be set to be much shorter than normal, as we need to get data back quickly in this beta test and we are releasing to a very specific set of hardware. This will likely change in time, as we move from a beta test and as we move towards supporting other graphics cards.

16

GROMACS SREM - FahCore_80
http://www.gromacs.org/

The Gromacs Serial Replica Exchange Method core, also known as GroST (Gromacs Serial replica exchange with Temperatures), uses Replica Exchange Method in its simulations also known as REMD, Replica Exchange Molecular Dynamics.

huangx:
[i]"In the MD simulaitons of large molecules such as proteins, molecules are easy to be trapped in local free energy minima, which slows the sampling of phase space. In the Replica Exchange Method, a few simulations are performed at different temperatures simulatineously, and exchanges of configurations are tried every certain a period of time. Even if a trajectory is temporarily trapped in a local minimum, the simulation can escape by exchanging with a higher temperature configuration.

The usual implementation of REM requires parallel processors where the different replicas must be run synchronously which is not suitable for Folding@home. Serial Replica Exchange(SREM) is a method that is equivalent to standard REM in terms of effciency, yet runs asynchronously on a distributed network of computers."[/i]

Linux v1.00 (MD5=99594fa29b1745891ea7373ab6f465f0) 3,503,204 bytes
Windows v1.00 (MD5=)

17

Ummm, links no workeee any more, I was going to re-install it

18

links in first post are fixed now :slight_smile: