Linux & Folding FAQ (Draft)

[Time to Paws]

Ok all after a chat with Daniel, he recommended that I post it here. This is version .01, so please feel free to comment, and I'll make the changes.

When I mentioned to Daniel, that I would like to post a few messages about running Folding under Linux, he suggested that I write up something a little longer. Well here goes. I am not expert, but I really wanted to make the switch to Linux on my desktop, as I had gone completley to linux on the laptop. The main item that was holding me back was of course Folding. I have already joined 'Folders Anomynous' and freely admit I am an addict.

I am running SuSE version 9.0 on the desktop with the 2.4.215 kernel and KDE 3.2.X It gets upgraded to often to lock it down to a version number, but most of what I'll write should work with any distribution.

The first thing to know is, yes you to can fold using Linux! There are two ways that I know to fold, the first being to run the native Linux client that can be found here: http://www.stanford.edu/group/pandeg.../download.html
You, of course want the Linux (x86)Console. The second way to Fold is to run it under a program called wine. Wine ("Wine is not an emulator") allows you to run some windows programs in a Linux enviroment. More information on running Wine can be found here: http://www.winehq.com/ although this is a general site and not Folding specific. I do not run Wine so I will leave this method to someone that does.

The client, when downloaded should have the name: FAH4Console-Linux.exe (why they would put an exe at the end I don't know, as Linux doesn't use file endings to determine what the file is/does. Using, in my case, Konqueror, check and make sure the file is listed as an executable. If not then go into advance permissions and add Exec, so that it will run.

This can also be done in a shell. Call up your distributions' console, you'll not need to go into root. Create a directory where you'll want to do your folding. To give you and example mine is /home/paws-1/productivity/folding. Place FAH4Console-Linux.exe into the dir. At this point if you are using the shell I would also rename it to something easier to type (i.e. fah-4), actually rename it no matter how you've gotten to this point. To make it executable from the shell type: "chmod 700 FAH4Console-Linux.exe" (without the quotes of course, also remember that Linux IS case sensitive). This will allow the owner of the program (well not the real owner of course, but just the possesser of the program on your system, I hope) to run it.

Regardless of how you got to this point, you'll need to go into the console (Hmmm..That's why they call it the console version ;^).
cd to the directory you put the program in, as an aside to Linux, if you type in the first character of the directory or file and hit <tab> it will complete the name of the directory or file as long as it is unique. I type pr<tab>f<tab>, and it puts me in the directory.
Your almost done. Type in a dot and forward slash (This is important, as that tells Linux the file you want to run is in this directory) and the name of the client (that's why I renamed it, cause I get lazy) with the config option (or config only if you want to configure the client and then exit).

./fah-4 -configonly (in my case, replace whatever you renamed it, like 'myaddiction')

The client will ask you some questions
1. User name (the same one you've used in the past or a new one)
2. Team: of course this will be 45, or I'll come haunt you!!!!! ;^)
3. Ask before sending work (up to you. I selected no as I am on DSL)
4. Use a proxy
5. Change advanced options (This defaults to no, and this will exit the config, Yes takes you to other options)
*6. Client type (I have no preference, I guess I should ask someday which will get me the most points for time spent ;^)
*7. Core priority (idle/low)
**** This is not the same as cpu throttleing that the windows version has. This only tells the client client what kind of cpu scheduling to use. Not much use to me, but I'll write more about this later.*******
*8. Disable highly optimized assembly code (I have mine set for no)
*9. Interval, in minutes, between checkpoints: (3-30)[15]. Depends how much you shut your system down. When I am doing a lot of upgrading I set it for 3, when I don't plan on making changes to the system and I'm not worried about lightnening (I live in Florida) I set it for 30.
*10. Ignore deadline (if your clock is messed up)
*11. Machine ID: defaults to 1. You'll need to change it if your running mutiple clients on the same machine.

And that's it!
Now for some startup options:
You can find the whole list at: http://www.stanford.edu/group/pandeg...userguide.html

The main ones I use are:
1. -forceSSE as I have an AMD processor, and this will use the optimized code for AMD's. What I think it does is download the FAH_78 core if you don't use it and the FAH_65 core if you do. Anyone can correct me if this is wrong.

2. -forceasm "Instruct the core to use SSE/3DNow assembly instructions if possible", this is from the users guide. I just know MY sysetems seems to process WU's faster with this option.
3. -advmethods This allows you to be assigned new cores &/or WUs, look in the forums for discussion on this feature.

and the last one is specfic for those that want to run freeBSD. -freeBSD (Duhhh)


Now that we have the client up and running (we hope, it is a computer after all), it will down load the core (as specfied above) and your first WU, and your off and running.

Now for some specfic Linux things:

The Linux version of the client doesn't have a cpu regulator like the windows version. This is extremely distressing to people like me that have heat problems with their systems. I live in South Florida and my computer spends the majority of it's time at ambient tempature. So folding at 100% cpu usage would shortly fry my system (good excuse to upgrade, BUT.....donations are excepted ;^). Thanks to fellow folder and Team 45 member Pratt for pointing me in the right direction. There is a program called fahlimit written by Kevin Bernhagen. What this program does is to take over the 'thread' that your folding is being run on and force it to pause, with the amount of time based on the percentage you optioned. I found 50% keeps my temps below the 55C mark even on hot days. My CPU meter looks like a ocilliscope wave function, but it works. I deeply appreciate his writing this, as it allowed the whole migration to linux.

Now, there is not a compiled program but you can get the code here: http://calxalot.homeip.net/downloads/fahlimit.c
What I did was copy all from my browser and copy it to a text file. I saved it in my folding directy. Go into the folding directory from a console window. Type "gcc -ofahlimit fahlimit.c", gcc needs to be installed of course, however on most systems it is. This creates the fahlimit executable. Now start a second console, start the folding client (./fah-4), then go to the console where you compiled fahlimit and type
./fahlimit [options].
The options are:
-percent XX 20-90% with a default of 70%
-daemon This allows the program to run as a daemon, and you can close the console. To stop the daemon type "killall fahlimit"

Running automagically:
Along with some things I did cover this web site http://www.vendomar.ee/~ivo/FAHLinux.txt has a way to start the client when you boot, but this means running it as root, and I really, really do not like to do this.
As I said I run KDE, but I'm sure most of the window mangers are pretty much the same. Create two text files in your folding directory:
#fahstart
#Bash
cd /home/paws-1/productivity/folding/
./fah-4 -forceSSE

and
#limitstart
#Bash
cd /home/paws-1/productivity/folding/
./fahlimit -percent 50 -daemon

then from the desktop create an icon, name whatever you want, in application:
sh /home/paws-1/productivity/folding/limstart (Make sure you put the sh in front)
under advance click 'run in terminal'
Create another icon and do the same.
Now you can start them both with the icon.
If you want to start them automagically everytime you start KDE go into the hidden directory .kde and put the icons in the autostart folder (this should work).
mine is: /home/paws-1/.kde/Autostart



Wheeew, This is a lot longer then I thought it would be. Any and ALL mistakes are mine, with no warranty expressed or implied, remeber we are dealing with computers, so if it don't work... play with it!!!!!!

I hope you found this useful, all I ask is if you have multiple CPUs you put one under my username, I'm tired of getting passed!!!!!
Keep folding....

More info can also be found from the wonderful fellow members on the AOA folding forum and at http://forum.folding-community.org/viewtopic.php?t=7021

[Daniel ~]

Very well done Time to paws! Front page stuff!

www.aoaforums.com

I've also copied your guide to our FAQ Topic. Thank you very much, this should be a real resource to our Linux users!!

[Daniel ~]

I can't get this link to work properly:

http://www.stanford.edu/group/pande...g/download.html

[Gizmo]

The text that shows in the link is truncated by Explorer, I think (or maybe the forum software). If you hover your mouse over the original link, you should see the actual link in your status bar at the bottom of explorer. That original link works for me just fine.

[Daniel ~]

I got it work by copying from properties. Strange,... I've never seen this before! Works now though. ":O}

[RussianMissile1]

perhaps the linux FAH boot from CD or USB stick could be added here from overclockers.com, with credit to them of course.
this is so you dont need a hard drive to fold. this is what i will be doing soon.

[Allan]

Thank you, Time to Paws!

[stigweed]

Thanks for the guide. My client is finally working after a week or two of deleting WUs after completing them. Folding became and addiction - now I've combined it with my new addiction, Linux. Next step: switching from KDE to a lightweight DE to eeek out the last few MHz for folding.

[SteveI]

Nice guide..
I have no clue with linux, but your instructions look very useful, and easy to follow. I've been thinking linux for years, but never did take the leap. Just one more reason to give it a shot.

[Toro]

Originally Posted by SteveI

Nice guide..
I have no clue with linux, but your instructions look very useful, and easy to follow. I've been thinking linux for years, but never did take the leap. Just one more reason to give it a shot.

you go get 'em tiger!

all i need is a guide to get ur mouse t work in linux and im laughin'

[dod]

Originally Posted by Time to Paws

The first thing to know is, yes you to can fold using Linux! There are two ways that I know to fold, the first being to run the native Linux client that can be found here: http://www.stanford.edu/group/pandeg.../download.html
You, of course want the Linux (x86)Console. The second way to Fold is to run it under a program called wine. Wine ("Wine is not an emulator") allows you to run some windows programs in a Linux enviroment. More information on running Wine can be found here: http://www.winehq.com/ although this is a general site and not Folding specific. I do not run Wine so I will leave this method to someone that does.

The client, when downloaded should have the name: FAH4Console-Linux.exe (why they would put an exe at the end I don't know, as Linux doesn't use file endings to determine what the file is/does. Using, in my case, Konqueror, check and make sure the file is listed as an executable. If not then go into advance permissions and add Exec, so that it will run.

Okay, I'm with you up to there. When I click the executable I get a message coming up saying what do I want to open the program with. When I right click the program itself it says it IS an executable.

Unfortunately fool proof didn't make allowances for me

[Daniel ~]

Originally Posted by SteveI

Nice guide..
I have no clue with linux, but your instructions look very useful, and easy to follow. I've been thinking linux for years, but never did take the leap. Just one more reason to give it a shot.

STEVEI! Why not join dod and a few others of us as we try out SUSE 9.1? See thread in Alternative OS Topic":O}

[BuiesCreek847]

1. -forceSSE as I have an AMD processor, and this will use the optimized code for AMD's. What I think it does is download the FAH_78 core if you don't use it and the FAH_65 core if you do. Anyone can correct me if this is wrong.

2. -forceasm "Instruct the core to use SSE/3DNow assembly instructions if possible", this is from the users guide. I just know MY sysetems seems to process WU's faster with this option.
3. -advmethods This allows you to be assigned new cores &/or WUs, look in the forums for discussion on this feature.

As found in the F@H FAQ about switches:

-forceasm
Instruct the core to use SSE/3DNow assembly instructions if possible, even if it has previously made the determination that the machine may not be handling this well.
-forceSSE
On machines with an AMD processor, Core_78 gives priority to 3DNow over SSE -- this overrides that.
-advmethods
Request to be assigned work units from new projects, before they are broadly released to the rest of Folding@home. As among the first to try out new advanced simulations, you may wish to post any observations (positive or negative), questions, or issues at the user Forum.

See HERE

-forceasm: This forces your rig to run tha advanced assembly methods that are available with the newer CPUs. The F@H client, by default will turn those off should it see any problems during crunching. I'll stay off till you restart the client after making adjustments. This switch simply forces them to stay on. If there are continued problems, the client will most likely do the early unit end thing.

-forceSSE: When it comes to crunching Gromacs WUs, SSE instructions are way faster than 3DNow instructions. This switch forces the SSE over the 3DNow. The client, by default starts with 3DNow. This switch will be phased out for -forceasm with the next client release.

-Advmethods: As you may know, most all of us do the regular WUs. Well, to get to us, there are some folks who do initial testing of Clients, cores, and WUs. Those folks are in the BETA stages of testing. When most of the kinks are worked out, they take the testing one step further, and open them to those who run the advmethods switch. With that, those still experimental clients, cores, and WUs have the chance to work with some of the wild equipment that you and I run, and see if things still hold up. If more bugs are found, they are corrected and then finally released to the general public. If one is to run the -advmethods switch, they should understand that they are working with clients, cores, and/or WUs who may crash, or act stupid otherwise. If there is anything weird about them, it should be reported to www.folding-community.org so that said info can be forwarded to Stanford.


There was a time that, one could get a lot more points, very fast by running with the -advmethods switch. That was once true in that Gromacs were just coming out. They were still mostly experimental, still though, many were jumping on that switch just for the points. The problem was, and still is, that with running the -advmethods switch, you much contact the scientists about any problem found. You must watch things much closer. If you ain't into all that, don't bother running the switch.



Further, the _65core is exclusive to Tinker WUs. The _78core is exclusive to Gromacs. I can't remember what the Genome core was.