FoldingAtHome

Differences between revisions 1 and 3 (spanning 2 versions)
Revision 1 as of 2005-10-09 20:48:38
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Editor: 70-57-196-186
Comment:
Revision 3 as of 2005-10-09 21:00:29
Size: 2736
Editor: 70-57-196-186
Comment:
Deletions are marked like this. Additions are marked like this.
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Download these scripts to the same directory, and name them folding_install.sh and foldingathome, respectively. Then do Save these scripts to the same directory, and name them folding_install.sh and foldingathome, respectively. Then do
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=== Install Script ===
{{{
#!/bin/sh

# to do:
# add foldingathome user
# no password, shell /bin/true, only has access to fah_dir
# add option of running from $HOME
# uninstall

fah_dir=/opt/foldingathome
this_dir=$PWD
#fah_dir=$HOME/opt/foldingathome
config_dir=$fah_dir/config
executable=FAH502-Linux.exe

# check if installed
if [[ ! -d $fah_dir || ! -d $config_dir || ! -x $config_dir/$executable ]] ; then
    echo
    echo "Creating directory structure..."
    
    test -d $fah_dir || /bin/mkdir $fah_dir
    test -d $config_dir || /bin/mkdir $config_dir
    cd $config_dir
    
    echo
    echo "It appears that you have not installed Folding@Home yet. Would you like me to download it for you?"
    select resp in {yes,no} ; do
        if [[ $resp == "yes" ]] ; then
            if ! wget http://www.stanford.edu/group/pandegroup/release/$executable ; then
                echo "Downloading Folding@Home failed."
                exit 1
            else
                /bin/chmod 555 $executable
            fi
        else
     echo
     echo "Please download the executable and save it to $config_dir."
     echo "Then re-run this script."
     exit 1
 fi
        break
    done
fi

cd $config_dir
if [[ -x $executable ]] ; then
    ./$executable -configonly
else
    # should never get here
    echo
    echo "Could not find $executable!"
    echo "If you have already downloaded it, put it in $config_dir."
    echo "If it is in $config_dir, check that it is named $executable. If not, modify $0."
    exit 1
fi

# setup a client for each processor
num_cpus=`/bin/grep '^processor[[:space:]]*:' /proc/cpuinfo | wc -l`
echo
echo "Found $num_cpus cpus. I will create one client for every cpu."
for cpu_num in `seq -w 1 $num_cpus`; do
    echo debug
    echo cpu_num = $cpu_num
    client_dir=$fah_dir/$cpu_num
    test -d $client_dir || /bin/mkdir $client_dir
    /bin/cp -f $config_dir/* $client_dir
    /bin/sed -i -e "s/machineid=.*/machineid=$cpu_num/" $client_dir/client.cfg
    cpu_num=$((++cpu_num))
done

# install the startup scripts
echo
echo "How do you want to run Folding@Home?"
echo " Daemon = Run at boot up"
echo " Manual = Copy the startup script to the Folding@Home directory ($fah_dir)."
select resp in {daemon,manual} ; do
    if [[ $resp == "daemon" ]] ; then
        if [[ $UID != 0 ]] ; then
     echo
            echo "You must be root to install as a daemon."
            exit 1
        fi
 echo
        echo "Adding startup script to /etc/init.d"
        if ! /bin/cp -vf $this_dir/foldingathome /etc/init.d/ ; then
            echo "Could not copy startup script to /etc/init.d"
            exit 1
        fi
        # hopefully 2 is the default runlevel
        runlevel=2
 echo
        echo "Adding foldingathome to runlevel $runlevel."
        if ! /bin/ln -sf /etc/init.d/foldingathome /etc/rc${runlevel}.d/S99foldingathome ; then
            echo
     echo "Could not add to runlevel $runlevel."
            exit 1
        fi
        echo
        echo "To start folding right now, run /etc/init.d/foldingathome as root."
 break
    elif [[ $resp == "manual" ]] ; then
        echo "Copying startup script to $fah_dir"
        if ! /bin/cp -fv $this_dir/foldingathome $fah_dir ; then
            echo "Could not copy startup script to $fah_dir"
            exit 1
        fi
        echo "To start folding right now, run `$fah_dir/foldingathome start`"
 break
    fi
    
done
}}}

=== Startup Script ===
{{{
#!/bin/sh

# TO DO:
# a foldingathome user

PATH=/sbin:/bin:/usr/bin
. /lib/lsb/init-functions

fah_dir=/opt/foldingathome
config_dir=$fah_dir/config
executable=FAH502-Linux.exe

# check if folding at home has been configured yet
cd $fah_dir
if [[ ! -d 1 ]] ; then
    # there will always be at least one client
    log_error_msg "Could not find client directory."
fi

num_cpu=`grep '^processor[[:space:]]*:' /proc/cpuinfo | wc --lines`

function kill_clients()
{ for cpu_num in `seq -w 1 $num_cpu` ; do
        client_dir=$fah_dir/$cpu_num
        if [[ ! -d $client_dir ]] ; then
            continue
        elif [[ $client_dir == $config_dir ]] ; then
            continue
        fi
        
        cd $client_dir
        
        log_begin_msg "Stopping Client $cpu_num."
        for client in FahCore*.exe ; do
            killall -q $client >& /dev/null
        done
        killall -q $client_dir/$executable >& /dev/null
        sleep 1
        if ps -ef | grep "$client_dir[/]$executable" >& /dev/null ; then
            # failed
            log_end_msg 1
        else
            # success
            log_end_msg 0
        fi
    done
}

function start_clients()
{ for cpu_num in `seq -w 1 $num_cpu` ; do
        client_dir=$fah_dir/$cpu_num
        if [[ ! -d $client_dir ]] ; then
            continue
        elif [[ $client_dir == $config_dir ]] ; then
            continue
        fi
        
        cd $client_dir
        log_begin_msg "Starting Client $cpu_num."
        nice -n 19 $client_dir/$executable >& /dev/null &
        log_end_msg $?
    done
}

case "$1" in
    start|force-reload)
        log_begin_msg "Starting Folding@Home"
        start_clients
        log_end_msg $?
        ;;
    restart|reload)
        log_begin_msg "Restarting Folding@Home"
        kill_clients && start_clients
        log_end_msg $?
        ;;
    stop)
        log_begin_msg "Stopping Folding@Home"
        kill_clients
        log_end_msg $?
        ;;
    *)
        log_success_msg "Usage: /etc/init.d/foldingathome {start|stop|restart}"
        exit 1
        ;;
esac

exit 0
}}}
attachement:folding_install.sh-10092005
attachement:foldingathome-10092005

Overview

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 develope new drugs, cure diseases, etc.

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.

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.

Installation

The following script will download the latest client from the Folding@Home website, and install it to /opt/foldingathome. It will ask you to set up the client (the defaults are usually sufficient), and copy that configuration for every CPU in your machine.

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.

Save these scripts to the same directory, and name them folding_install.sh and foldingathome, respectively. Then do

chmod 500 foldingathome folding_install

to make them executable. Finally, do

sudo ./folding_install.sh

to install the client.

attachement:folding_install.sh-10092005 attachement:foldingathome-10092005

Future Plans

Some people don't have root access to their computers. To accomodate them, a way to install to the $HOME directory should be added.

There should be a way to easily uninstall the client.

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. I will add this feature in the future.

http://folding.stanford.edu/

FoldingAtHome (last edited 2008-08-06 17:00:30 by localhost)