UbuntuHelp:FoldingAtHome
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Overview
Folding@Home is a project from Stanford University that uses millions of networked PCs to form a supercomputer for protein folding simulations. The client software is loaded on a PC, it contacts the central servers, and receives "work units". The client then runs on spare CPU time, and uploads finished work units to the server. When proteins are created, they undergo a complex process known as folding, so-called because the protein molecule transforms from a long chain of amino acids to a complex shape (it "folds up"). The final shape of the protein is absolutely critical to determining its properties and function. Scientists have created software to simulate the folding process to better understand how proteins work, which in turn makes it possible to develop new drugs, cure diseases, etc. Folding@Home is a great way to make your computer do useful work even when you're not using it. Since it runs at a very low priority, you should never realize it's running when you're using the computer to do your work. Note that "using the computer" refers to doing heavy computations. Generally, tasks like web browsing and word processing involve very little CPU usage, so the Folding@Home client will be running at near 100% even when doing those kinds of tasks. It helps to leave your computer on at all times, but is not necessary, as the project will benefit from virtually any time that the client runs on your computer.
Contact
For support concerning installation, configuration and other use of the below installation methods please drop by IRC in #ubuntu-folding (freenode).
Installation
There are several ways to install the Folding@Home client. You can just run it manually, or you can use a number of scripts that will do certain things automatically. Each method has its own page to reduce clutter.
- Manual installation is simple, but the installer scripts solve the many problems with this method.
- finstall is the semi-official installer for Unix.
- fah_install is a script maintained by jpkotta, who is also the main maintainer of this page. Most things on this page are biased a bit towards fah_install for that reason.
- folding.sh is a frontend for finstall by Christer Edwards. It works quite well, especially for installing over a network, and now supports SMP clients!
Before using any installation method, you may want to pick a username and a team. Neither is necessary, but having a unique username lets you know how much you are folding, and folding for a team adds to the fun. Because you're a fan of Ubuntu, you probably want to fold for Team Ubuntu; the team number is 45104. You can pick any username you want, but if you pick one that's already being used, that will make it impossible to track your score and will inflate someone else's score, which may or may not be welcome. Search for unused names here. If you have an old computer you should run deadlineless work units. To select the option to do this select yes when asked if you want to set advanced options, then continue to select the defaults until you are asked about deadlineless workunits and select yes. Note: There are frequent shortages of the deadlineless WUs. If you haven't gotten one for several days, you might as well ask for both deadlineless and normal WUs.
Other Issues
Questions and Discussion
For technical questions and bug reports, go to the HowTo forum thread. For casual talk about Folding@Home, use the Ubuntu Team recruiting thread. Don't forget the Ubuntu Folding Team IRC channel: #ubuntu-folding (irc.freenode.net).
Security
Folding@Home is secure. The Stanford team has gone to great lengths to ensure security, both for the integrity of their research and the safety of donors' computers. However, the more secure the better. The Gentoo ebuild for Folding@Home creates a new user foldingathome whose sole purpose is to run the client. Now fah_install offers the same. It creates a user whose account is disabled, and runs the client as this user when the init script is run as root, so the client is never run as root.
Hyper Threading
For those with Hyper Threading CPUs, you probably know that an SMP kernel sees two processors. Then clearly, if you run two clients, you will get more work done than if you only run one (probably about 10-30% more). However, results that are done quickly are more useful than more results done slowly. The reason is that each work unit is a step in a giant simulation, with future steps depending on past ones. So the faster you get your work done, the faster the simulation can move along. Long story short, run one client for each physical CPU, not for each logical CPU. The installer should automatically count the number of CPUs in your system. See this post in the Folding@Home forums.
Laptop Systems
Because the client runs at low priority, the client should not cause the CPU governor to kick up the frequency. In other words, even though the client runs at 100% CPU usage, it should not cause the CPU frequency to go up, which keeps the fan slow and quiet. If this is not the case, then the frequency governor should be reconfigured.
Note: Feisty uses different default cpu governing method than Dapper (I don't know about Edgy). Feisty uses a kernelspace governor whereas Dapper uses a userspace one (powernowd). The consensus seems to be that kernelmode is the superior implementation. The trouble is that the default is not to ignore nice'd processes (i.e. low priority processes like the folding@home client) in kernelmode, while powernowd's default is to ignore nice'd processes in its calculations. To get powernowd behavior, you must do the following:
sudo -i echo 1 > /sys/devices/system/cpu/cpu0/cpufreq/ondemand/ignore_nice_load
To enable this behavior in the future, add the above (just the echo line, not the sudo one) to /etc/rc.local. For more about manipulating frequency governors, look at this link.
There is a utility called cpulimit that will limit the CPU time of a given application. Look at this link for a quick how-to. If there is demand, I will add support for it to fah_install.
One can configure ACPI (the power regulation subsystem) to stop the client when the system goes on battery power, and to start it again when the power cord is plugged back in.
Simply create two scripts in the relevant directories.
sudo -i echo "/etc/init.d/foldingathome stop" > /etc/acpi/battery.d/fah.sh echo "/etc/init.d/foldingathome start" > /etc/acpi/ac.d/fah.sh exit
This assumes that the client has been installed for the entire system (as opposed to installing just for your user), which it should be if you are able to edit files in /etc in the first place!
TeamUbuntu (45104)
A competitive Folding@Home team called TeamUbuntu exists to represent the Ubuntu community and to have some fun while doing good. The team number is 45104. To join the team, simply enter 45104 when the setup dialog requests a team number.
FAQ
How do I uninstall?
If you used fah_install, the installer on this page, rerun the installation script with the "uninstall" option. The README file has a detailed description of what the uninstall command does. If you used finstall, cd to $HOME/foldingathome and run ./uninstallService. If you just downloaded it to some directory, just delete the client and the directory. See also the next question about random files.
Why does F@H write files to random directories?
If you use fah_install or finstall, it shouldn't. That was half of the reason why those scripts were written. The client writes a bunch of files to some directory, we'll call it the working directory or WD, if the WD doesn't have all of the files already. So if you have no F@H files in the WD, the client will write them. How do you figure out what the WD is? It is the current directory of the shell that starts the client; in other words, it could be anything. If you have a script of some sort that you wrote to start up the client, you need to cd to whatever directory you want all of those files to be written to before starting the client.
cd /working/directory /path/to/FAH502-Linux.exe
How do I find out how much I'm folding?
The client writes a log file in WD/FAHlog.txt. For fah_install, this is in /opt/foldingathome/#/FAHlog.txt or $HOME/opt/foldingathome/#/FAHlog.txt, where '#' is a digit from 1 to 9, but probably only 1 will exist unless you have a multiprocessor system. If you use finstall, it is in $HOME/foldingathome/CPU#.
There is also a more concise progress file unitinfo.txt, in the same directory as FAHlog.txt.
There are nice graphical programs that will display the information in these files, for example Protein Think. You can see how many points your current work unit is worth by looking up your protein on http://fah-web.stanford.edu/psummary.html
I don't seem to be making any progress.
If the log looks something like this:
[19:39:55] + Attempting to get work packet [19:39:55] - Connecting to assignment server [19:39:57] - Successful: assigned to (171.64.122.133). [19:39:57] + News From Folding@Home: Welcome to Folding@Home [19:39:57] Loaded queue successfully. [19:39:58] + Could not connect to Work Server [19:39:58] - Error: Attempt #9 to get work failed, and no other work to do.
then you probably have everything set up correctly, and the problem is on Stanford's side. Some people have encountered this when asking for deadlineless units, because there appears to be shortages of those. If you can't connect to the assignment server, then probably you're behind a firewall or proxy or something else that is preventing the connection. Ask your network administrator how to get around this. F@H can be set to use different TCP ports, but the default is 8080.
How do I backup my work?
It's a good idea to stop folding before making your backup, though it isn't absolutely necessary. Assuming you used fah_install, then make a tarball of foldingathome directory.
sudo tar zcvf fahbck.tar.gz /opt/foldingathome/ /etc/default/foldingathome
If you haven't modified the file /etc/default/foldingathome, then you don't need to add it. Clearly, /opt/foldingathome would become /home/$USER/opt/foldingathome if you installed it in your home directory.
How do I restore my backup?
cd / sudo tar zxvf /path/to/fahbck.tar.gz
If you somehow destroyed the /etc directory (e.g. you reinstalled the operating system), then use the installer with the "update" option to replace the init symlinks, so it can start automatically at boot time.
Links
- Folding@Home project home page
- Ubuntu Folding@Home Team home page
- Ubuntu Folding@Home Team recruiting, casual discussion at ubuntuforums.org
- Folding@Home on Ubuntu howto, technical discussion at ubuntuforums.org
- Protein Think, a folding progress monitor
- Report on the impact of F@H to the system
- Sneakernetting How to deal with non-networked machines.
- Current proteins summary. You can look up your current protein and see how many points a WU is worth.
- Team Ubuntu statistics at fah-web.stanford.edu
- Team Ubuntu statistics at fahstats.com
- Team Ubuntu statistics at folding.extremeoverclocking.com
