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[Ubuntu] Setting up big-bigadv (P6903) for dedicated 2600k

post #1 of 771
Thread Starter 
Important Note!!
Please be advised, Stanford is no longer assigning bigadv work units to 8 or 12 core machines. You can modify the information in this guide to simulate a 16 core machine, however you will not be able to complete these work units within the deadline with any 4c HT CPU's any more. Therefore this guide is no longer valid for current folding conditions. I will leave the guide intact for those who wish to view it, or utilize portions of it for their own purpose.




Digigami's guide to setting up a dedicated 2600k for the new big-bigadv WU's (P6903)

This configuration will also install Langouste decoupler, provide the required script to 'trick' the client into thinking you have as many cores as you wish, and have everything run automatically at bootup without intervention.

I have written this right from installing OS, so to assume a fresh install. Modify this procedure at your own risk.

I have found Ubuntu 10.10 to work best, but only if the ext3 file system is used. You will need to specify this during installation. If you are unsure of how to do that, use the comprehensive guide and a spare hard drive you don't have anything important on.

Tested via VMware Player and native install. Anywhere you see username, enter your ubuntu username instead tongue.gif

There are two copies of this guide available to you. The quick n'dirty guide for those who have experience with Ubuntu/Linux, and a comprehensive guide, with screenshots for almost all steps along the way for those who aren't familiar with this enviroment. Expand the spoiler for which version of the guide you would like to work off from.

For either guide, first go here: http://releases.ubuntu.com/10.10/ and download the 64bit desktop release.
Or, use this direct link: http://releases.ubuntu.com/10.10/ubuntu-10.10-desktop-amd64.iso

Once downloaded, you will have to burn it to a DVD or bootable USB. For this, I reccomend ImgBurn http://www.imgburn.com/

Once you have your bootable media ready to go, open a spoiler and let the fun begin!

Quick n'dirty guide for advanced users Warning: Spoiler! (Click to show)
All information in code tags is entered into the terminal, all information in quote tags is entered into a text editor or described field. Please do this in the order outlined.

- Install Ubuntu 10.10, using ext3 partition
Check "log in automatically" when setting username
Do all updates for Ubuntu
Disable automatic updates (optional)


- Install FAH6.34 (don't run or configure yet..) (download url is Case Sensitive!)
Code:
cd /home/username/
mkdir fah
cd fah
wget http://www.stanford.edu/group/pandegroup/folding/release/FAH6.34-Linux64-SMP.exe
mv FAH6.34-Linux64-SMP.exe fah6
chmod +x fah6

- Enable sharing for fah folder (for monitoring via HFM on another local machine, disregard if not neccesary)
USE GUI - just easier, Ubuntu will need to install service

- Install Langouste decoupler (manages work units, lets client work on next WU right away)
Code:
cd /home/username/fah/
wget http://darkswarm.org/langouste3-0.15.6.tar.gz
tar xvfz langouste*.*
mv langouste3-0.15.7 langouste
rm langouste3-0.15.6.tar.gz
cd langouste
make dep
make
cp /home/username/fah/langouste/dist/linux/langouste-helper.sh /home/username/fah

- Setup script for core-fixin ;)(requires entering your user password into script)
Code:
cd /home/username/fah
gedit
- use editor, create file with this (edit NCPUS=x to whatever you want client to see, here we use 12 to get the big-bigadv WU's)
Quote:
echo "yourpassword" | sudo -S cat /proc/stat | awk 'BEGIN { TARGET_NCPUS=12 } ; { if ($1 == "intr") { for (i=NR-2;i<=NF;i++) S=S " " $i ; print }' > /tmp/stat.save
echo "yourpassword" | sudo -S mount --bind /tmp/stat.save /proc/stat
save file as corefix.sh in the fah directory


- Setup auto-run scripts

- Create new terminal profile called langouste. Do this from an open terminal window, select File, New Profile.
Select second tab "Title and Command"
check "Run command as a login shell"
check "Run a custom command instead of my shell"

which points to this command
Quote:
/home/username/fah/langouste/langouste3 -l 8880

- Create new terminal profile called fah6smp, which points to this command
also set it so that terminal stays open after command executed. Note - smp "X" here, use your actual thread count for best performance
Quote:
/home/username/fah/fah6 -smp X -bigadv

- Now back in the terminal
Code:
cd /home/username/fah
gedit
use editor, create file with this
Quote:
gnome-terminal --profile=langouste
save file as langouste.sh in the fah directory
Code:
gedit

use editor, create file with this
Quote:
sleep 5
cd /home/username/fah
gnome-terminal --profile=fah6smp
save file as fah6smp.sh in the fah directory

- back to terminal
Code:
cd /home/username/fah
chmod +x langouste.sh
chmod +x fah6smp.sh
chmod +x corefix.sh

- Add langouste.sh, corefix.sh, fah6smp.sh to user auto-run programs

SYSTEM-PREFERENCES-STARTUP APPLICATIONS
ADD, browse to script file

cross your fingers.. hope we did this right

restart client machine, it should boot right into desktop, two terminal windows open. One for langouste and one for fah client.

verify client identified desired number of cores

enter your details into client setup,

when client asks for proxy, say YES!!

use 127.0.0.1 for host

use 8880 for port

no user/pass neccesary

finish client config

client should start looking for work now, monitor langouste terminal window and make sure it sees the request

win!


Comprehensive guide with screenshots Warning: Spoiler! (Click to show)
Full Ubuntu 10.10 installation with EXT3 filesystem

Required - 1 empty HD or HD with free partition. Steps we will be taking can be dangerous if you use a HD with multiple paritions, one of which has data you wish to preserve. If you are going to use a drive with good data on it, please fully understand how to manage partitions. That is out of scope of this guide.

This guide and screenshots are from a trial run in a VM, so it shows as a single empty partition of 21.5GB

1 - With our downloaded ISO file ready to go on bootable media, fire up the machine. Here is the first screen we come up to. Click "Install Ubuntu"

ub1.jpg

2 - Second screen, check off "Download updates while installing" and then hit forward.

ub2.jpg

3 - Ok, here the important bits come. On this screen we must choose "Specify partitions manually".

ub3.jpg

4 - My screenshot here shows the device as a directory within my drive. This is due to the VM installation, yours may list the HD itself. Important point here, is we have no partitions existing, just an undefined space. If your drive has existing partitions, so long as you are sure you don't need anything on them, Delete them so you have nothing defined like this.

Now click "New Partition Table"

ub4.jpg

5 - Click through the warning...

ub5.jpg

6 - Now we have available free space. But we still have to define partitions. Highlite the free space, and click "Add"

ub6.jpg

7 - Ok, now we setup our first of two partitions. We want to assign all but about 2GB to the first partition. The second partition will be reserved for swap file space.

The critical step here, is to make sure under the partition option "Use as:" we select Ext3 journaling file system instead of Ext4 as shown below.

Also, you must select the mount point as root "/"


To review:

Partition size is 2GB less than my total space available. 21474 - 2000 = 19474
Ext3 File System
Mount at root "/"

ub7.jpg

8 - Ok, now highlite the remaining free space and click "Add"

ub8.jpg

9 - Change partition option "Use as:" to "swap area". It should have already choosen the size. Click OK

ub9.jpg

10 - Alright, if your patition table looks like mine, with different sizes of course we are good to go. Click "Install Now"

ub10.jpg

Ubuntu will now configure itself and start installing. Meanwhile it does the usual;

Select your timezone,
Select keyboard layout,

Next it will ask you for your username and password. You also have the option of selecting "Log in automatically" For a dedicated folder you would want to check this. If security is of a concern, then you may not want to. Otherwise, enter your choosen username and password. I reccomend using a different password here than you would use for anything that needs to be secure. Later in the guide we have to enter your password into a script to make things work right, so keep that in mind.

Once you are satisfied, move along and Ubuntu will finish installation.
Grab a coffee, light a smoke, check your PM's.. whatever.. you have a few minutes to kill.

11 - After a prompt to restart, you should boot right into Ubuntu.

If you sit there and stare at it for a minute or so, this might pop up.. Select "Don't Upgrade" We just installed 10.10 because it works faster for Folding at Home!


ub11.jpg

12 - Either give it another minute, or navigate your way to Update Manager via "SYSTEM, ADMINISTRATION" Although Ubuntu downloaded some updates while installing, it did not do them all. Take the time now to get everthing updated. Once the updates are done, reboot again.


ub12.jpg

13 - This step is optional, but highly reccomended. I go back into update manager, click on settings in the bottom left, and disable automatic updates and release upgrade notices. Don't forget to manually check for updates once in a while.

ub13.jpg



FAH 6.34 Install Guide


1 - This portion of the guide will almost all be done in the terminal. (CTL-ALT-T) is the fastest way to open up the terminal from your desktop. Also, I would suggest opening up this guide on your machine, so you can easily copy and paste the entrys. If you choose to type them out, remember it's case sensitive. (Mozilla Firefox button in the top bar)


fah1.jpg

2 - Enter each line of code one at a time followed by enter. Replace /username/ with your Ubuntu username.

a. Makes sure we start in your home directory.
Code:
cd /home/username/

b. Make a new directory "fah"
Code:
mkdir fah

c. Go into the fah directory
Code:
cd fah

d. Downloads the Folding @ Home client from Standford servers. (remember, case sensitive!)
Code:
wget http://www.stanford.edu/group/pandegroup/folding/release/FAH6.34-Linux64-SMP.exe

e. Let's rename that awfully long file to something simpler..
Code:
mv FAH6.34-Linux64-SMP.exe fah6

f. Set file permissions for "fah6"
Code:
chmod +x fah6

Alright we can close the terminal window. The folding client is ready to go. But we're not ready to fire it up just yet..

3 - One thing that I like to do at this point before I forget, is to enable the sharing of the folder the client is now in. This is required if you want to monitor the client via HFM running on another machine in your network.

Open from the top bar "PLACES, HOME FOLDER" we now see our home folder, with the newly made fah client folder.

fah2.jpg

Right click on the fah folder and select "Sharing Options" when you click "Share this folder" you will be informed the service needs to be installed. Install it now.

fah3.jpg

Once it's done you will be asked to restart this session. Go ahead and do that, and every time I do I get this error while Ubuntu is trying to shut down. I suspect it's part of the installer still running. "Log Out Anyway" has yet to fail me wink.gif

fah4.jpg

Log back in, go back to your home folder, right click on fah and share the folder with whatever name you desire.



Langouste decoupler installation

This is all performed within the terminal again (CTL-ALT-T); each line of code followed by enter.

a - Goto our fah client directory
Code:
cd /home/username/fah/

b - Download Langouste Decoupler (case sensitive)
Code:
wget http://darkswarm.org/langouste3-0.15.6.tar.gz

c - decompress (unzip?) the download package
Code:
tar xvfz langouste*.*

d - rename the decompressed file directory to something more manageable. Note the version unpacked is 0.15.7 here, not 0.15.6
Code:
mv langouste3-0.15.7 langouste

e - remove the downloaded compressed file (we don't need anymore)
Code:
rm langouste3-0.15.6.tar.gz

f - goto langouste directory
Code:
cd langouste

g - build langouste dependencies
Code:
make dep

h - apply dependencies (I think.. not actually 100% sure on this one to be honest) I do know forgetting this step sucks
Code:
make

i - copies a script from langouste into the folding client folder
Code:
cp /home/username/fah/langouste/dist/linux/langouste-helper.sh /home/username/fah

Alright, Langouste is installed and ready to go now too! We're almost there!

Final part of the detailed guides. Here we will create our core count manipulation script, langouste startup script and folding client startup scripts.

Since we know how and it's easy, we're going to start in the terminal again (CTL-ALT-T)

1 - we want to create our scripts in our client's directory
Code:
cd /home/username/fah

2 - here we are going to launch a simple text editor from the terminal
Code:
gedit

This should open up the following window.

scripts1.jpg

3 - Ok, I suggest you copy/paste the following, replace "yourpassword" with your password, KEEP THE QUOTES!. If you are using this script for other purposes than the big-bigadv's, you may modify "TARGET_NCPUS=12" to how many cores you want the client to see. We're looking for 12 here smile.gif
p.s. I'm not even going to try and explain how this works.. I have no idea myself. Also, make sure the first line wraps, and you don't use the return key to separate lines.
Code:
echo "yourpassword" | sudo -S cat /proc/stat | awk 'BEGIN { TARGET_NCPUS=12 } ; { if ($1 == "intr") { for (i=NR-2;i<TARGET_NCPUS;i++) print "cpu" i S } ; S="" ; for (i=2;i<=NF;i++) S=S " " $i ; print }' > /tmp/stat.save
echo "yourpassword" | sudo -S mount --bind /tmp/stat.save /proc/stat

4 - click "FILE, SAVE-AS" and name it corefix.sh and make sure it saves it in the fah folder. Here you can see the completed script, filename and folder location. Click "Save" and close the text editor.

scripts2-1.jpg


5 - We should now still see the terminal we launched gedit from before. Click "EDIT, Profiles..." in the terminal's menu bar.

scripts3.jpg

6 - Create a new profile, called langouste, based on the default.

scripts4.jpg

7 - Click the "Title and Command" tab.
Check "Run command as a login shell"
Check "Run a custom command instead"
Now enter this for our custom command:
Code:
/home/username/fah/langouste/langouste3 -l 8880
When command exits: Change to Hold the terminal open.

all said and done it should look like this: if it's all good, click "Close"

scripts5.jpg

8 - Create one more new profile, called fah6smp, also based on default.

use the same options as the langouste profile, but use this for the custom command:
note "-smp X" Use your actual thread count for best performance. ie (2600k: -smp 8, x6's: -smp 6)
Code:
/home/username/fah/fah6 -smp X -bigadv

scripts6.jpg

9 - ok, almost done! Back to our terminal window, we need to make two more small scripts.

-make sure we start in the right directory again
Code:
cd /home/username/fah

and then
Code:
gedit

10 - copy/paste this one liner into the blank editor window, then save the file as langouste.sh in the fah directory and close the editor.
Code:
gnome-terminal --profile=langouste

scripts7.jpg

11 - one more, launch the editor from the terminal again
Code:
gedit

12 - copy/paste this into the blank editor window, then save the file as fah6smp.sh in the fah directory and close the editor.
(yes I suggest sleep 5, but was testing sleep 10 when I took this screenshot. The reason we want it to wait, is to make sure our core-fixing script runs before the folding client starts)
Code:
sleep 5
cd /home/username/fah
gnome-terminal --profile=fah6smp

scripts8.jpg

13 - one last thing to do back in the terminal. We need to set permissions for the scripts we just made. One at a time:
Code:
chmod +x langouste.sh
Code:
chmod +x fah6smp.sh
Code:
chmod +x corefix.sh

And we can now close the terminal.

14 - Finally, we need to add our three scripts to Ubuntu's list of startup programs.

From the menu bar, select "SYSTEM, PREFERENCES, STARTUP APPLICATIONS"

scripts9.jpg

15 - Click "ADD" and enter langouste for the name, and browse to the langouste.sh script. Then click "Add" again

scripts10.jpg

16 - do this again for fah6smp.sh

17 - one more time for corefix.sh

18 - We're now done with setup except for fah client configuration, we just need to test our installation. If everything works we will configure the client on-the-fly.

19 - restart the computer. When it's restarted it should automagically start up one terminal window with langouste, and 5 seconds later one with the folding client awaiting your configuration details. Like so:


scripts11.jpg

20 - First, check and make sure the client "detected" 12 cores. If it worked, continue with configuring the client as per normal, except when it asks you to use proxy. To work with Langouste, we need to say yes!

Enter 127.0.0.1 for proxy Name
Enter 8880 for port
Say no for username and password.

scripts12.jpg

Finish the rest of the configuration, and the client should start looking for a work unit.

Watch the Langouste terminal window, and verify it is communicating with the Fah Client.

It will look something like this while it's working.

scripts13.jpg


With some luck, you downloaded a P6903 and are now folding a big-bigadv! Don't worry if you got a regular bigadv, the P6903's aren't always available.




I will elaborate where needed as things come up.. Please if anyone uses this be sure to let us know how it works out.
Edited by Digigami - 8/13/12 at 12:35pm
post #2 of 771
Wow! This has to be the most comprehensive guide yet.

After a quick glance through it I dont see a setup for AMD Phenom II x6. Would your guide work just the same for an x6?
post #3 of 771
Thread Starter 
Quote:
Originally Posted by Philistine;13960318 
Wow! This has to be the most comprehensive guide yet.

After a quick glance through it I dont see a setup for AMD Phenom II x6. Would your guide work just the same for an x6?

Yes, in theory it should all work the same. I was just talking to Zodac about adding the configuration for x6's and 2500k's. I don't have the hardware to test it myself at this point, so I'm going to do some research tomorrow and add it.

Feel free to give it a go, and let me know if it will work as is, or if more specific information is required.
post #4 of 771
I'll give it a go on my days off.
post #5 of 771
Great guide, I'll give it a try once I do a clean install of Windows 7 and I'll make sure I make a Linux partition. biggrin.gif
    
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post #6 of 771
Digi, Good job buddy on putting in the effort to make a guide for everyone. +1 =)
post #7 of 771
Will test this as soon as my current WU is done. Any problem using 10.04 instead, somehow I can't get 10.10 to work on my gear?
Frigg d.y.
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post #8 of 771
Good job, Digi! Guide looks good!
post #9 of 771
Good job thumb.gif
I'll try it ASAP.
post #10 of 771
If we weren't running a team challenge atm i'd totally try this on my quad just to see what kind of TPF i got. I'm assuming it would be over an hour per frame.
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