Useful Websites

[David Hosobuchi]

Use this thread for posting other websites relevent to this forum....:)

[linniec]

Protein Folding

http://folding.stanford.edu/

[mbhinz]

How do I join?
To join the Team:

We are Team number: 36047

You need to install and run a software client for the Stanford Project, Folding@Home (F@H) You can download the F@H clients Here (http://www.stanford.edu/group/pandegroup/folding/download.html)


Here are several good FAQS with "how to" instructions for installing this software:


For the Windows "No-nonsense" text-only console: How do I install and set up the Windows console client? (http://brain.hastypastry.net/forums/showthread.php?p=27759#poststop)

For the Windows Graphical User Interface Client: How do I install and configure the Graphical User Interface (GUI) Client ? (http://brain.hastypastry.net/forums/showthread.php?p=27761#poststop)

For MAC OS/X F@H Client: How do I install and set up F@H on MAC OS X? (http://folding.stanford.edu/OSX/OSX.html)


Once the client is installed and running, you are on your way.

[mbhinz]

How do I install and configure the Windows console client?


Create a folder on your computer and name it Fahconsole.

Click here to download Console client for your OS and save it in that folder.

Navigate to the folder and double click the file named Fah***-Console.exe, where *** will be the current version number of the client.Currently the final, non-beta version number for Win 2000/NT/XP is 504.

A DOS like window will open.

http://brain.hastypastry.net/forums/attachment.php?attachmentid=268&stc=1&d=1164053371

The first time you run the console client, you will be prompted for your specific configuration information. You have the option of leaving the settings at the default, which is indicated by the information located within the . This is accomplished by pressing the return key for each prompt; however, in most cases you will want to enter your individual information.

[B]User name [Anonymous]?
Enter your username here and press enter.
This username is case sensitive.
For example 'john' and 'John' will be considered 2 different names on Stanford stats server. It is advisable to use your BTC username so as not to confuse third party stats. It is probably best not to use a space as this will be interpreted as an underscore rather than a space.

Team Number[0]? 36047
We are Team 36047

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

If you enter yes, FAH***.exe will then run as a service, and you will see the following message: The program will continue in non-service mode now, working in C:\Program Files\FAH504 (Or whatever you named the folder you put the client in,).
The next time the computer is starts up, you should see work automatically continue there. Note that when this service is running, you should not try to manually run F@H from that directory at the same time.

Ask before fetching/sending work [no] (yes/no)?
Entering yes here will cause the client to prompt you before sending completed, or retrieving new, work units.

Use Internet Explorer Settings [no] (yes/no)?
If you enter yes here, the client will use whatever proxy settings are currently used by Internet Explorer and you will not be prompted for "Use proxy [no] (yes/no)?" next.
See Recent Changes from Stanford

Use proxy [no] (yes/no)?
You will only be prompted for this if you responded no to the previous prompt. If you enter yes here, you will receive these additional prompts:

Proxy Name [localhost]?
If your Proxy name is "localhost" press enter; otherwise,
enter the appropriate information.

Proxy Port [8080]?
If port 8080 is the proxy port you are using press
enter; otherwise, enter the appropriate port
information.

Use username & password with proxy (yes/no)?
Enter the appropriate response for your configuration.
If you respond with yes, you will be prompted for:

Proxy Username?
Enter your Proxy username.

Proxy Password?
Enter your Proxy Password.

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]

Change advanced options [no] (yes/no)?
If you answer yes, you can set the following options.

Core Priority [idle] (idle/low)?

idle = priority 34 and nice level 19

low = priority 28 and nice level 13
Low is actually at higher level of priority than idle.

CPU usage requested (5-100)?
Defaults to 100% which will use all CPU time if nothing else is running. Since the client will "play nicely with others and yield CPU time to other applications as needed, there is generally no need to modify this setting. Please note, changing this setting unnecessarily may actually cause the waste of valuable CPU cycles.

Disable highly optimized assembly code [no] (no/yes)?
This is a opposite of -forceasm as this will disable Gromacs optimizations.

This should be set to no to utilize optimal code when the Gromacs WUs are available.

Pause if battery power is being used (useful for laptops) (no/yes) [no]?
Only used if you are Folding on a laptop.

Interval, in minutes, between checkpoints (3-30) [15]?
Sets how often the client saves checkpoints onto the Hard Drive.

Request work units without deadlines (no-pref/no/yes) [no-pref]?
Allows you the option to work on either Regular FAH WUS (no),
To receive only FAH wus without a deadline (yes), (for slower machines)
Or to recieve whatever Stanford sends (no-pref)

Ignore deadline information (mainly useful if system clock frequently has errors) [no]? (no/yes)

Deadline information included with work (Printed to unitinfo.txt and available in queueinfo). Active units checked for expiration periodically all others checked for expiration at autosend time. Configuration option of ignoring deadline information (to use if system clock is bad -- not just telling incorrect absolute time, but having an incorrect conception of what one second is, for instance) if so desired.
See Recent Changes from Stanford

Machine ID (1-8) [1]?
This setting is intended only for dual processor machines.

* For use with dual processors please refer to this link »folding.stanford.edu/faq.html#run.dual.

* For use with clusters, please refer to this link »folding.stanford.edu/faq.html#run.cluster

Once all the information is entered and you are connected to the Internet FAH client will download a scientific core, fetch a work Unit and start folding.

If you installed it as a service, FAH will run in background after you restart the computer. (step three in configuration)

If you installed it as console, The window can be minimized and run in Taskbar.

Note:If for some reason client needs to be shut down, do a Ctrl+c and client will shutdown properly.

Congratulations on being a proud member of the Team.

[mbhinz]

How do I install and configure the Graphical User Interface (GUI) Client ?


Click here (http://folding.stanford.edu/download.html) to download the GUI client for your operating system and save it in a folder on your computer.
Double click the executable and installation will begin.

http://brain.hastypastry.net/forums/attachment.php?attachmentid=269&d=1164063216

Click 'Next'


On the next screen read and accept license agreement by clicking 'yes'.

Next screen will bring 'Readme information'. It is advisable to read through this information as it contains important information about the client.

Clicking next will bring the following screen where you input your user info.


http://brain.hastypastry.net/forums/attachment.php?attachmentid=270&stc=1&d=1164063571


Here you will enter your username. This username is case sensitive.
For example 'john' and 'John' will be considered 2 different names on Stanford stats server. It is advisable to use your BTC username so as not to confuse third party stats. It is probably best not to use a space as this will be interpreted as an underscore rather than a space.

Click 'Next' and installation will begin.


http://brain.hastypastry.net/forums/attachment.php?attachmentid=271&stc=1&d=1164063728


Choose a folder to extract files to and click next. After installation is complete, navigate to FAH folder and double click file named winFAH***.exe, where *** will be the version number of the FAH Client. For example for Windows NT/2000/XP, the final, non beta, version number is currently 5.03.

FAH Control Panel will open.


http://brain.hastypastry.net/forums/attachment.php?attachmentid=272&stc=1&d=1164063886


You will see the FAH icon in Windows System Tray.

http://brain.hastypastry.net/forums/attachment.php?attachmentid=273&stc=1&d=1164064079


The three buttons labeled 'View Team statistics', 'View User Statistics' and 'View log file' can be used after configuration is complete and the client has fetched a Work Unit. FAH control panel will close after configuration and will run in System Tray. Control panel can be accessed again by right clicking the Tray Icon. Here you can also open the Client Window. Right clicking anywhere on the client Window will also open the FAH Control Panel.

Enter the Team Number. We are Team: 36047


Click on 'Connection' tab.


Connection Settings. Here you will configure your connection settings.


Ask before using network ?
It is advisable to leave this blank.

Use Internet Explorer settings ?
Check if you have Broadband connection. You will not need to enter any proxy settings.

Proxy settings ?
Enter appropriate setting provided by your Network Administrator or ISP.

Allow receipt of work assignments and return results of greater than 5MB.
Check only if you have a faster processor and at least 300MB of memory for each client you will run on the box. A single processor box should run only one client and have at least 300MB RAM installed. A dually can run two clients, but should have a minimum of 600MB installed to run the big WUs.

Click on 'Display' tab.

These settings are purely cosmetic and have no effect on the performance of the client unless you like to keep the Client Window open on desktop in which case these settings can be used.


Molecular Draw Rate:
Can be used to set the rate of draw of Protein Simulations (Graphics Intensive).

Screen Saver:
Can be checked if you wish to run the FAH Client as a screensaver. (Not advisable as this eats into CPU cycles).

Title:
Check this if you wish to display a text message in Client window.

Logos:
Here you can enable a gif image as a company logo or your favorite pet.
Warning: These settings are graphics intensive and purely cosmetic. Always run the client in System Tray.


Click the 'Advanced Tab'.


Scientific Core:
Set Core Priority to 'Slightly Higher'.
Set CPU Usage Percent to 100.
Do not disable 'Highly Optimized Assembly' Code.
Set Checkpoint Frequency to 10 minutes. ( The range is from 3 mins to 30 mins ).

Power:
Useful if you use a notebook computer.

Deadlines:
If you have a slower machine set it to 'deadlineless', otherwise set this to 'No Preference'.


Click 'OK' and the control panel will close and client will connect to Stanford Assignment Server, download a scientific Core and fetch a Work Unit.
Congratulations, you are now a proud member of the BTC Team.

[mbhinz]

Here is a third party application that you can use to keep track of your folding at a glance.

The Electron Microscope (http://www.dslreports.com/faq/thfaq/4.1_Electron_Microscope)

Enjoy!