Howto setup Folding@Home

[ndhskp]

This first post is outdated, please see: https://help.ubuntu.com/community/FoldingAtHome and https://help.ubuntu.com/community/FoldingAtHome/Install
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• I should note this howto is geared to 1 cpu however multi-cpu systems can still use this howto. But each cpu in multi-cpu systems must have it's own machine id.

• Laptop users are encouraged to see the Folding@Home wiki for special information. I don't use an laptop so that info probably will not show up here.

• For information on the issue of Intel HT cpu's (HyperThreading) see this post at the stanford forums

• I want to make sure that everyone knows that the author of the script used in this howto is jpkotta. User jpkotta is to blame. wink wink.

This is a howto for Folding@Home on Ubuntu. Works great on Breezy-5.10 & Dapper-Drake-6.06.



Is Folding@Home for you? (Old & New Computers welcome)
It is a distributed computing project to understand protein folding, misfolding, and related diseases. It is run by or associated with (not sure) Stanford University. This software will benefit best if you leave your computer on 24/7. However the computer does not actually need to be on 24/7 however it will take a longer time to complete the job and if the time is long enough then you may miss the due date there by causing the WU (work unit) to be reasigned to someone else and causing delays. Remember that this project is about getting work units back to the researchers as fast as possible. So at the very least 4 to 6 hours a day of operation.




Step 1. Do not download the folding@home executable from the folding.stanford.edu website. Actually you can download it if you really want. Just run the script first to create the proper folders and then place the Folding@Home executable in No sudo /home/username/opt/foldingathome/config With sudo /opt/foldingathome/config

However I recomend that you download the single install script to your/home/username directory. If the link below ever stops working just get the file from the wiki.

File:<removed link per OP's request>
Click on the link ^ to download




Step 2. Extract the archive in your /home/username directory

• Do this by opening your terminal. In Gnome this is Applications/Accessories/Terminal.

KDE and others you need to find and open your terminal version. For those that don't have X or boot directly to console I'll assume you know what to do.

Replacing "fah_install-version" with the current name.

tar zxvf fah_install-version.tar.gz

Note the following info is just to let you know about 2 files they are not needed for this howto.When you extract the script you will see 2 files called "client.options" and "system.options". These files allow you to pass arguments (options) to the client so those arguments become persistent where as before those arguments had to be added manually every time you started the client. Note (client is higher precedence than system). Syntax is bash. Example of syntax:

CLIENT_OPTS='-forceasm'

If you need a list of options the link is at end of howto. I don't provide support for these 2 files.

Step 3. Navigate to the new folder in /home/username/folding and read the documentation.

cd fah_install
less README

Press the letter q to quit reading the documentation.





Step 4. Install the Folding@Home client. Please note that if you don't have root access (su or sudo) you can't use sudo or su, so in that case just use the command without sudo or su.


Install command

sudo ./folding_install.sh install

At this point you will be asked if you want to install to the system or user. Remember that if you don't have root (su or sudo) access to the computer you will need to choose user (1). Note that I personally strongly recomend that if you have root access (su or sudo) to your computer that you choose number (2) "system".




Step 5. Configuring the client. The client will ask you some questions and you will give it some answers to optimize it for your computer. Note that defaults will be shown in brackets [] and you may just hit enter to accept defaults.

• User name [Anonymous]? Make up one.

• Team Number [0]? Only if you want to be a part of a team. However I recommend that you join team "TeamUbuntu" just enter the number 45104.

• Ask before fetching/sending work (no/yes) [no]? Best to say no here.

• Use proxy (yes/no) [no]? Most people will probably say no here. If not just enter your proxy info.

• 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]? Less than 1GB RAM no, 1GB or more yes. Remember you need to take into account your operating system and programs. Large units can exceed 500MB in ram requirements. Also if you are on dial-up modem service you should say no here.

• Change advanced options (yes/no) [no]? Type no here if you want to keep it simple.

Step 5a. Advanced options

• Core Priority (idle/low) [idle]? Type idle here. There is no benefit to putting in low and in fact could actually interfere with your computers operation.

• Disable highly optimized assembly code (no/yes) [no]? Type no here

• Interval, in minutes, between checkpoints (3-30) [15]? I chose 30. This is how often to save the state. You should enter 3 to 5 minutes if you have a notebook or laptop, I myself use a desktop on battery backup. If you reboot, shutdown or crash and your state has not been saved your computer has to start over from the last saved state.

• Request work units without deadlines (no-pref/no/yes) [no-pref]? If you have an older computer or a computer that's not on all the time you might want to choose yes here.

• Ignore any deadline information (mainly useful if system clock frequently has errors) (no/yes) [no]? Type no here. But from time to time make sure your computer clock is fairly accurate.

• Machine ID ( 1-8 ) [1]? Type 1 here. If you have a multi-cpu system then each cpu must have it's own machine id. It is very important to make sure that under the "Advanced Settings" option each copy is given a unique machine ID ( from 1 to 8 ). The first copy (cpu 1) will default to a machine ID of 1, so additional copies should be given IDs of 2 (cpu 2), 3 (cpu 3), 4, etc.

Step 6. The install script will now tell you the command to start Folding@Home

If you did not use sudo, then use this command. Note you still need to enter this command even if you chose to install the cronjob to be absolutely sure it is started as it gives immediate feedback.

/home/username/opt/foldingathome/foldingathome start

If you did use sudo, then use this command.

sudo /etc/init.d/foldingathome start

If you ever want to reconfigure the options, use this command.

sudo /opt/foldingathome/reconfigure.sh
or if you did not use sudo
home/username/opt/foldingathome/reconfigure.sh
or
sudo ./folding_install.sh update

Step 7. Once you are done entering the command open up in Breezy-5.10 Applications>System Tools>System Monitor and Dapper-Drake-6.06 System>Administration>System Monitor click the Resources tab and check CPU history to make sure it's at 100% all the time. KDE and others I don't know where your GUI system monitor is. For the console or terminal people type "top".


Step 8. Open your file browser also known as Nautilus and go to this location: /home/username/opt/foldingathome or /opt/foldingathome here you can check several things. Such as to make sure one or more directory's were created. There are a minimum of 2 directory's called 1 and config respectively. Go into both and explore. In my 1 directory I have 3 files of interest they are: FAHlog.txt, MyFolding.html, unitinfo.txt. Check them out as they all have very interesting info. By the way the directorys that are numbers are the actual working clients. Number 1 would be cpu 1 and 2 would the second cpu and so on. So the config directory is just used for configuration, no actual work.

The HTML file will be the one you use the most from here on out as it will allow you to get to unitinfo.txt from within your web browser and you can bookmark it.

Leave the other files and directories alone for best safety!


Step 9. Give Folding@Home the best chance possible.
Disable all screensavers.




Special thanks to the script author jpkotta. Also user jpkotta has indicated that you may contact him via PM (Private Message) if you have problems with the script. Thank you to user: henriquemaia for pointing out some formatting tips.

Folding@Home links:
Team Ubuntu & chew the fat social talk
The main Stanford site
Official F.A.Q.
Dual core or cpu F.A.Q.
The Stanford Folding@Home forums
Version changes info
Lightweight userguide from Stanford
The one and only original Ubuntu wiki
Fahwiki
A complete list of Linux command line arguments.

User: WelterPelter has created a Folding@Home monitoring program. ProThink


Cheers.

[ToastedToad]

Thanks, I'll give it a try soon.

[ndhskp]

Let me know how it goes. Also you can choose from any number of teams out
there if you decide to go that route not just team Ubuntu. I should have
mentioned that even if you sign up with a team you still have individual
statistics.

[henriquemaia]

Thanks a lot for this. I had a friend that told me once about this, but I never installed before.

I followed your howto and everything went perfect. It's good to know my ubuntu is helping othes actively.

Thanks again.

[ndhskp]

henriquemaia, yes it is nice to know that this has a fairly direct impact on our lives as opposed to other projects that are big ifs. Not to say that others are not worthy but just that for some people a little bit more immediate benefit is important. Also projects like Folding@Home seem to go with the spirit of open source/free software. Anyway glad to hear every thing went well. I also cleaned up the howto a bit to make it easier for new users.

[henriquemaia]

I also cleaned up the howto a bit to make it easier for new users.

I would suggest you to give some spaces between lines on Step 6, to make it more readable. You could also add some bullets and bolds. Something like this:

Step 6. Configuring the client. The client will ask you some question and you
will give it some answers to optimize it for your computer.

• User name [enter a username] make up one
• Team number: only if you want to be a part of a team.
• Ask before fetching/sending [no] best to say no here.
• Use Proxy yes/no: most people will probably say no here.
• Allow receipt of work assignments and return of work results greater
  than 5MB in size (such work units may have large memory demands)
  yes/no: less than 256MB RAM no, 512MB or more yes.
• Change advanced options [yes] type yes here
• Core Priority [idle] type idle here
• CPU Usage [100] if this comes up type 100
• Disable highly optimized assembly code [no] type no here
• Interval, in minutes, between checkpoints (3-30) [I choose 15] you can choose more if you have battery backup and have a stable computer. This is how often to save the state.
• Request work units without deadlines [no] your choice but I chose no
• Ignore any deadline information (mainly useful if system clock has
  errors) [no] I chose no as my clock is accurate.
• Machine ID ( 1-8 ) [1] type 1 here

[ndhskp]

Thanks henriquemaia.

The formatting ideas really make the howto look better. I gave you credit for the formatting suggestion.

[D2X2903]

Thanks for the tutorial. I installed Ubuntu last week after my Windows installation on my secondary (and largely unmonitored) PC became unstable again. Since then, I've been trying to figure out how to set this thing up with Folding. I just found this this morning, and now I'm back online with the second box.

- InNeedofHelp from team 36057

[ndhskp]

User D2X2903, glad everything went well with Folding@Home. Ubuntu forums are really the best place to find out how to setup up your Ubuntu box. There is just so much good info here.

[drizek]

oops, wrong thread....

*bump*