Folding@Home in Debian GNU/Linux Squeeze amd64 as a service

I think distributed computing is fascinating, these days I have been learning about MPI, clusters and related stuff. The power of a lot of machines working collaboratively to solve a problem... amazing!, I love computing :-)

You know that a mayor part of time your CPU is not fully used because your processes are not all heavyweight all the time, lots of IO locks, dead times, etc. I mean, rarely ours CPUs are 100% used.


Folding@Home is a distributed computing project where protein folding is studied doing complex simulations, so complex and CPU demanding that the scientists turn to ask for help to the whole world. You can share some cycles of your CPU to the Science.

"Protein folding is linked to disease, such as Alzheimer's, ALS, Huntington's, Parkinson's disease, and many Cancers. Moreover, when proteins do not fold correctly (i.e. "misfold"), there can be serious consequences, including many well known diseases, such as Alzheimer's, Mad Cow (BSE), CJD, ALS, Huntington's, Parkinson's disease, and many Cancers and cancer-related syndromes."

I joined to help anonymously some years ago and I hope you can join us, create a team or just add yourself to the default group.

Check the webpage, they have been awarded and several results have been published.

I have installed the client in my dual boot machines (Windows/Linux) and in my home server.

I will show you how to install FAH in Debian GNU/Linux Lenny in a machine without X and in a service mode. Setting FAH as a service will allow it to start automatically every time the system boots up and you still are in charge because you can disable or even uninstall the service.

Log in as root or sudo as you like.

You should create a new user account by security reasons and according with the best practices suggested here (or here), the best place to put our client is /opt/fah.

# groupadd fah
# useradd -g fah fah --shell /bin/bash -d /opt/fah -m

From here you can download the installer, I chose FAH6.34-Linux64.tgz bacause my linux box is:

uname -a

Linux blogger 2.6.32-5-amd64 #1 SMP Tue Jun 14 09:42:28 UTC 2011 x86_64 GNU/Linux

wget http://www.stanford.edu/group/pandegroup/folding/release/FAH6.34-Linux64.tgz

tar xzf FAH6.34-Linux64.tgz

chmod u+x fah6

After that we may configure the client, buy we should do this as the fah user (will create configuration files and data):

su fah 

Then, we run the executable:

$ ./fah6

Note: Please read the license agreement (fah6 -license). Further
use of this software requires that you have read and accepted this agreement.



--- Opening Log file [July 22 00:10:47 UTC]


# Linux Console Edition #######################################################
###############################################################################

                       Folding@Home Client Version 6.34

                          http://folding.stanford.edu

###############################################################################
###############################################################################

Launch directory: /opt/fah
Executable: ./fah6


[00:10:47] Configuring Folding@Home...

User name [Anonymous]? blogger (any username you like)
Team Number [0]? (The default team, create your team or join any one)
Passkey []?
Ask before fetching/sending work (no/yes) [no]? (this should be no as a service)
Use proxy (yes/no) [no]?
Acceptable size of work assignment and work result packets (bigger units
 may have large memory demands) -- 'small' is <5MB, 'normal' is <10MB, and
 'big' is >10MB (small/normal/big) [normal]?
Change advanced options (yes/no) [no]?

[00:12:18] - Ask before connecting: No
[00:12:18] - User name: blogger (Team 0)
[00:12:18] - User ID not found locally
[00:12:18] + Requesting User ID from server
[00:12:19] - Machine ID: 1
[00:12:19]
[00:12:19] Work directory not found. Creating...
[00:12:19] Could not open work queue, generating new queue...
[00:12:19] - Preparing to get new work unit...
[00:12:19] Cleaning up work directory
[00:12:19] + Attempting to get work packet
[00:12:19] - Connecting to assignment server
[00:12:21] - Successful: assigned to (171.67.108.52).
[00:12:21] + News From Folding@Home: Welcome to Folding@Home
[00:12:21] Loaded queue successfully.
[00:12:26] + Closed connections
[00:12:26]
[00:12:26] + Processing work unit
[00:12:26] Core required: FahCore_78.exe
[00:12:26] Core not found.
[00:12:26] - Core is not present or corrupted.
[00:12:26] - Attempting to download new core...
[00:12:26] + Downloading new core: FahCore_78.exe
[00:12:28] + 10240 bytes downloaded
(many bytes downloaded here...)

[00:12:38] + 1134407 bytes downloaded
[00:12:38] Verifying core Core_78.fah...
[00:12:38] Signature is VALID
[00:12:38]
[00:12:38] Trying to unzip core FahCore_78.exe
[00:12:39] Decompressed FahCore_78.exe (3435296 bytes) successfully
[00:12:39] + Core successfully engaged
[00:12:45]
[00:12:45] + Processing work unit
[00:12:45] Core required: FahCore_78.exe
[00:12:45] Core found.
[00:12:45] Working on queue slot 01 [July 22 00:12:45 UTC]
[00:12:45] + Working ...
[00:12:45]
[00:12:45] *------------------------------*
[00:12:45] Folding@Home Gromacs Core
[00:12:45] Version 1.90 (March 8, 2006)
[00:12:45]
[00:12:45] Preparing to commence simulation
[00:12:45] - Looking at optimizations...
[00:12:45] - Created dyn
[00:12:45] - Files status OK
[00:12:46] - Expanded 374844 -> 1805564 (decompressed 481.6 percent)
[00:12:46] - Starting from initial work packet
[00:12:46]
[00:12:46] Project: 6888 (Run 876, Clone 0, Gen 3)
[00:12:46]
[00:12:46] Assembly optimizations on if available.
[00:12:46] Entering M.D.

  Gromacs is Copyright (c) 1991-2003, University of Groningen, The Netherlands
        This inclusion of Gromacs code in the Folding@Home Core is under
        a special license (see http://folding.stanford.edu/gromacs.html)
         specially granted to Stanford by the copyright holders. If you
          are interested in using Gromacs, visit www.gromacs.org where
                you can download a free version of Gromacs under
         the terms of the GNU General Public License (GPL) as published
       by the Free Software Foundation; either version 2 of the License,
                     or (at your option) any later version.

[00:12:52] Protein: ALZHEIMER DISEASE AMYLOID
[00:12:52]
[00:12:52] Writing local files
[00:13:01] Extra SSE boost OK.
[00:13:01] Writing local files
[00:13:01] Completed 0 out of 250000 steps  (0%)

Ok, here we break the download of unit works [CONTROL+C] because we should setup fah as a service. It will continue from here when the binary be executed again anyway.

As root again, let's create /etc/init.d/fah with this content:

#!/bin/sh
### BEGIN INIT INFO
# Provides:          Service script for Folding@Home.
# Required-Start:    $syslog
# Required-Stop:     $syslog
# Default-Start:     2 3 4 5
# Default-Stop:      0 1 6
# Short-Description: This manages the service for client of the distributed computing project Folding@Home.
# Description:       Service script for Folding@Home.
#
### END INIT INFO

check_config()
{
        if [ ! -e /opt/fah/client.cfg ]; then
                echo "FAH has not been configured!!!"
                exit 1
        fi
}

case "$1" in
        start)
                check_config
                echo -n "Starting FAH..."
                cd /opt/fah
                start-stop-daemon --start --quiet --chdir /opt/fah -b --chuid fah --exec /opt/fah/fah6
                echo "."
        ;;

        stop)
                echo -n "Stopping FAH..."
                start-stop-daemon --stop --quiet --oknodo --user fah
                echo "."                                                                                     
        ;;                                                                                                   
                                                                                                             
        *)                                                                                                   
                echo "Usage: /etc/init.d/fah {start|stop}"                                                   
                exit 1
esac

exit 0

We make it executable:

chmod u+x /etc/init.d/fah

And we setup the service but this is Squeeze so we use insserv instead of update-rc.d (check this).

insserv /etc/init.d/fah

Now, we start our new service for the first time:

invoke-rc.d fah start

We can see what is happening in the background using tail:

$ cd /op/fah
$ ls -ltr
total 3864
-rwx------ 1 fah fah  314840 Feb 23 20:33 fah6
-rw-r--r-- 1 fah fah  146345 Feb 23 20:33 FAH6.34-Linux64.tgz
-rwxr-x--- 1 fah fah     110 Jul 21 20:12 client.cfg
-rw-r--r-- 1 fah fah    5214 Jul 21 20:12 MyFolding.html
-rw-r--r-- 1 fah fah       8 Jul 21 20:12 machinedependent.dat
-rw-r--r-- 1 fah fah    7168 Jul 21 20:12 queue.dat
-rwxr-x--- 1 fah fah 3435296 Jul 21 20:12 FahCore_78.exe
drwxr-x--- 2 fah fah    4096 Jul 21 20:39 work
-rw-r--r-- 1 fah fah     163 Jul 21 20:39 unitinfo.txt
-rw-r--r-- 1 fah fah    8527 Jul 21 20:39 FAHlog.txt
$ tail -f FAHlog.txt
[00:39:10] Project: 6888 (Run 876, Clone 0, Gen 3)
[00:39:10]
[00:39:10] Assembly optimizations on if available.
[00:39:10] Entering M.D.
[00:39:30] (Starting from checkpoint)
[00:39:30] Protein: ALZHEIMER DISEASE AMYLOID
[00:39:30]
[00:39:30] Writing local files
[00:39:39] Completed 2500 out of 250000 steps  (1%)
[00:39:39] Extra SSE boost OK.


(This continues... [CONTROL+C])

And that is all. Top will show you the process a FahCore using 100% of one of your cores but with the highest nice value, that is to say, with the lowest scheduling priority. So, if you don't use the CPU, FAH will do and you will be helping some scientist to find the cure to some ugly illness.























Take a look at this ranking, these papers (78!), these awards or these videos. Finally meet Vijay Pande!

So, Will you join Folding@Home?