“UbuntuHelp:FoldingAtHome”的版本间的差异

2007年12月8日 (六) 09:38的版本

文章出处:

https://help.ubuntu.com/community/FoldingAtHome

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English

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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.

Installation

Three installers are mentioned here. fah_install is an installer/init script that works with Debian systems (including Ubuntu). finstall seems to be the all-purpose Unix installer. Also, folding.sh is a newer project that tries to automate installation, configuration and even removal. folding.sh is supported on nearly any Linux Distritubion (currently tested on Ubuntu, Fedora, RHEL, SUSE, OEL and *BSD). You can also do things by hand, by just downloading the client and running it some directory. I recommend fah_install, but I'm biased because I wrote it <wink>. (I Christer Edwards recommend folding.sh because I wrote it. Before using either installer, 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. The default for both username and team is anonymous.

Running the client manually

This is the simplest way. You get the client from http://folding.stanford.edu/download.html, save it to some directory (you will want to make one specifically for F@H, because it makes a bunch of files), and run it. The trouble is, you need to start it by hand. It is far more convenient and correct to make it start at boot-time, because you shouldn't have to think about it. Say you put it in `$HOME/foldingathome`. Then to start it, you will want to use

cd $HOME/foldingathome
(exec fah5 >& /dev/null &)

You must run the client from its directory, since it always looks for files in the current directory (and creates them if they don't exist). The parentheses fork a new shell, the exec replaces the new shell process with the client (not strictly necessary), the redirect supresses output, and the ampersand puts the process into the background. This all means you can safely close the terminal after starting the client this way.

fah_install

See FoldingAtHome/Install for step-by-step instructions. Edgy users: Due to the change from bash to dash in Edgy, previous init scripts don't work. The fix is easy: download the latest installer, untar it, and run sudo ./install.sh update. It will replace the old init script with a new one. You do not have to stop a running client to do this update, but it is probably a good idea to stop it anyway. Please report any Edgy problems to the how-to thread. SMP Users: The 6.00(beta1) version of the client needs a runtime option "-smp" in order to get SMP work units. You must add CLIENT_OPTIONS="-smp" to `/etc/default/foldingathome`. If you update with the latest version of `fah_install`, this will be done for you as long as you allow it to overwrite this file. The following script will download the latest client from the Folding@Home website, and install it to opt/foldingathome, either in / or $HOME. It will ask you to set up the client (the defaults are usually sufficient), and copy that configuration for every CPU in your machine.

• https://help.ubuntu.com/community/FoldingAtHome?action=AttachFile&do=get&target=fah_install-20071014.tar.gz

It is not possible to provide a .deb package for Folding@Home, because the client must be downloaded from Stanford's website. This is to ensure the integrity of the research. (Maybe it is possible to have a .deb; after all, this is how Macromedia Flash works. The point is that the executable has to be downloaded from Stanford.) To install, download the tarball and do

tar zxvf fah_install-20061219.tar.gz

This should extract the archive to a directory called fah_install/. Then

cd fah_install
less README

to read the documentation. Finally,

sudo ./install.sh install

to install the client. You can also install to your $HOME, in case you do not have root access to the computer. Clearly, you would not have to prefix the command with sudo in this case. If you install to your $HOME, a cron job will be created to start the client automatically. If you install to the system, the client will automatically start when your computer boots up. You can reconfigure the client using the supplied reconfigure script, which is placed in opt/foldingathome. You can also give the client command line options in /etc/default/foldingathome. See the README for more details. Should you choose to uninstall the client, it's easy. The first installation script contains an uninstalling script too. Just go to the directory fah_install and run install.sh with uninstall parameter. Use sudo to uninstall if you used sudo to install. The README file provides instructions for manual uninstall.

sudo ./install.sh uninstall

finstall

1. Download the finstall script with wget:

cd ~
wget -c http://www.vendomar.ee/~ivo/finstall

2.#2 Make the script runnable:

chmod +x finstall

3.#3 Start it:

./finstall

After the client is installed You can start/stop/... FAH client with ./foldingathome/folding script. For Example(s)

~/foldingathome/folding start

or

~/foldingathome/folding stop

or

~/foldingathome/folding status

For me this was all I needed as it automatically created the init scripts I needed to start after reboot. However the init scripts don't seem to work for everyone, so if you need to do it manually:

1. Make a file called foldingathome in the /etc/init.d directory:

gksudo gedit /etc/init.d/foldingathome

2.#2 Paste this in:

#!/bin/sh
# /etc/init.d/foldingathome for Ubuntu
# Start the F@H service.

pushd /home/YOUR_USERNAME_HERE/foldingathome/
su YOUR_USERNAME_HERE -c "screen -d -m ./folding start"
popd

3.#3 Save and exit

1. Make a symlink into the /etc/rc2.d directory:

sudo ln -s /etc/init.d/foldingathome /etc/rc2.d/S99fah

folding.sh

I wrote folding.sh to make Folding @ Home feel more native on Linux systems. I did not like how the process generally ran as your user, did not have an init script, and cluttered your home folder with all its data. All of those issues are resolved with folding.sh. To download the latest version of folding.sh (as of this writing, 0.5.2.1) visit: Folding on Linux. You can also checkout the latest builds via bzr on Launchpad:

bzr branch http://bazaar.launchpad.net/~christer.edwards/folding/main

Once you have the latest version downloaded, all you need to do to install and start the folding client is run:

sudo ./folding.sh --install

If you want to change the username and team information, folding.sh also comes with a function for changing that information at any time:

sudo ./folding.sh --rename

I've also written a network deployment tool to install the folding client to a network range of machines. This requires root access via ssh. To deploy folding across a network of machines simply use:

sudo ./folding --deploy

Finally, if you'd like to stop folding and wipe all trace of folding.sh and the folding client from your machine simply:

sudo ./folding --erase

If you have any questions, comments, concerns, bugs, etc please report them on launchpad Folding on Launchpad. I am also very actively pursuing packaging this for Ubuntu & Debian. My goal is to have this implemented in time for Ubuntu 8.04 "Hardy Heron".

General Tips

1. Pick a username before you start, to see if your username is in use visit this page first [1]. There is a search box at the top that you can use to see if your selected username is in use.
2. Have your team number ready, it is question two right after your username. You should use 45104 for this.
3. 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.
4. Finally here is a link to the original thread for using the finstall script from the folding community forums, it is where I found my answers and definitely the easiest way to get this working under Dapper Drake. [2]

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.

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.

Breezy and older

Edit /etc/acpi/power.sh. Inside the if [ $? = 0 ] && [ x$1 != xstop ]; then block, add

    # stop folding at home
    if [[ -x /etc/init.d/foldingathome ]] ; then
        /etc/init.d/foldingathome stop
    fi

and inside the else block, add

    if [[ -x /etc/init.d/foldingathome ]] ; then
        /etc/init.d/foldingathome start
    fi

Dapper and newer

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