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[email protected] Beginners Guide

Posted: Fri Apr 02, 2004 9:52 pm
by haysdb
What is [email protected]?
How to Begin Folding for SPCR
  1. Download the [email protected] software from HERE
  2. Install the software per the Install info link on the download page
  3. During the configuration step, enter 31574 for the team number
Frequently Asked Questions Where can I get more information?

Posted: Fri Apr 02, 2004 9:55 pm
by haysdb
Which client should I use?
  • Graphical client (aka GUI client)

    I am not a big fan of the GUI client, but it's arguably the best choice for someone just starting with [email protected] since it gives you something to look at, something to "watch," since it displays a picture of the protein being folded.
  • No-nonsense text-only console (aka CLI client)

    This is what the "serious folders" use. It's not geewhiz, but it provides more feedback about what's going on and doesn't waste cpu cycles displaying a pretty interface.
  • Screensaver

    The screensaver is "not recommended". The screensaver only runs when you aren't using your computer, but even when you are using your computer, your computer's cpu spends most of it's time doing nothing. On a powerful computer, most tasks use only a tiny fraction of the available cpu cycles. The unused cycles get "absorbed" by something called the 'idle process'. The screensave is unable to utilize these wasted cycles. A second reason NOT to use the ScreenSaver version is that it cannot be "configured" in ways the GUI and CLI clients can. I recommend using either the GUI or CLI clients and setting your screensaver to either 'none' or to a blank screen (so that the screensaver doesn't take cpu time away from FAH.)

    But if I use the GUI or CLI clients, won't FAH slow down my computer? No. FAH runs at a very low priority, just above that of the System Idle Process, so the only cpu cycles FAH will use are those that would have otherwise been wasted. You won't even know it's there.
What is a WU?

WU is shorthand for 'Work Unit'.
Work-units: The data that is sent by [email protected] servers to users running the software. The work-units are pieces that a computer will process in its idle time and then send back to [email protected]
The flowchart for [email protected] goes something like this:
  1. Download a work unit from Stanford
  2. Crunch crunch crunch crunch
  3. Upload the completed work to Stanford
  4. Rinse lather and repeat.
How do I monitor my progress on the project?
How do I monitor the progress of [email protected] on my computer?

Even if you are folding on only a single computer, but especially if you have more than one, there are a couple of programs for monitoring [email protected] which can be very useful. I'm not going to choose sides because I use both of the following programs, because they each offer features I like and use. What are Gromacs and Tinker?

Each work unit or 'WU' requires one of three 'cores'. The core is the "computation engine" that actually does the work. The GUI and CLI version of the client use the exact same cores.
  • Tinker - Generally slower and usually fewer points, becasue this older core does not support the SSE instructions found on modern WU's. If you have a relatively modern cpu, you want to try to avoid Tinkers if you can, by using the -advmethods command-line flag, explained elsewhere in this guide. For some older processors (those which do not have SSE), Tinkers are OK.
  • Gromacs - Generally faster and usually more points than Tinkers, because this newer core is optimized for processors with SSE instructions.
  • DGromacs - Double-precision Gromacs. Uses SSE2 instructions found on Pentium 4's, and recent generation Athlon processors.

Posted: Fri Apr 02, 2004 9:56 pm
by haysdb
How do I add the LiquidNinjas thing to my sig?
  • Click the 'Profile' link at the top of the page
  • In the 'Signature' block, cut-and-paste the following:

    Code: Select all

  • Replace XXX with your FAH username.

Posted: Fri Apr 02, 2004 10:21 pm
by peteamer
Looking Good David 8)

It's time we had some centralised resource for our pooled knowledge.

Should make things a lot easier for all answer hunters old and new.

Well done 8)

Pete (Wish it had been here when I started) Amer

Folding under Linux

Posted: Sat Apr 03, 2004 2:12 am
by dukla2000
If you have Linux and want to fold then things are much easier. You only need to (manually) download 1 file which is the finstall script that is maintained here.

You do NOT need to directly download anything from Stanford; you do NOT need to download any monitoring utilities. finstall will do all this for you.

As per the finstall page you should copy the entire contents of that webpage and save them in a file called finstall. The comments at the top of finstall are better maintained than this post so I will say no more, except:
1) Say 'yes' to retrieve the utilities (qd etc)
2) Dont forget team 31574
3) Under SuSE 9, after running finstall I just edit
a) ~/foldingathome/CPU1/FaH script to add -advmethods -forceSSE to the default flags (I have Athlons)
b) /etc/init.d/boot.local to add
cd ~/foldingathome
./folding start
to get folding to automatically start with Linux. (Replace ~ with path to your folding, probably /home/username)

Re: Folding under Linux

Posted: Sat Apr 03, 2004 3:06 am
by CharlieChan
dukla2000 wrote: a) ~/foldingathome/CPU1/FaH script to add -advmethods -forceSSE to the default flags (I have Athlons)
You can add the extra parameters in a file called 'fah_config' located in the foldingathome directory.
b) /etc/init.d/boot.local to add
cd ~/foldingathome
./folding start
There is now a installService script which you can run as root to install folding as a service/daemon.

Posted: Mon Apr 05, 2004 10:43 am
by mormakil
When you have time David, why don't you add a quick how to optimize [email protected] with flags section? Mostly for the AMD's user which may not be using -forceSSE as it's been discussed in other threads. Also you could add a link to that thread when you explain how to install [email protected] as a service.
And I think we should make this thread sticky.

Posted: Mon Apr 05, 2004 12:39 pm
by haysdb
Yes, a section on optimizing FAH with -advmethods and -forcesse is overdo. If there is a well written "how to" on this somewhere, especially with pictures, then I could just do a short blurb and say "click this link for details on exactly how to add these flags". I remember having a lot of difficulty with just exactly WHERE to add the flags when I first got started, and I think of myself as a reasonably savy Windows guy. :oops:


Measuring [email protected]'s Performance Impact

Posted: Mon Apr 05, 2004 8:05 pm
Hey guys,

A lot of new folders question the performance impact on their systems when running [email protected] Many folks are skeptical and refuse to try folding because they just don't believe it when they read, or are told, that the [email protected] client will not slow down their systems. So this link is for those fence-sitters who need to get off the fence and get folding for SPCR!
So Start Folding Already... We've got some MacOS X butt to kick :twisted:

Posted: Tue Apr 06, 2004 10:23 am
by ColdFlame
[email protected]:
Whether you see [email protected] running in the background depends a lot on what you are doing. When I run [email protected] on my server and do some massive file copying I see huge slowdowns. When I play a game on my desktop that takes 100% CPU time itself I see some slowdowns but not much. I prefer to kill [email protected] client before launching a game anyway.

I was kidding about putting this into the guide, yes :) However, I'm not sure if this is really evil given the deadlines Stanford gives out. I don't think it is worth my time on a larger scale however. Too much babysitting.

Posted: Tue Apr 06, 2004 10:48 am
by haysdb
ColdFlame wrote:haysdb:
I was kidding about putting this into the guide, yes :) However, I'm not sure if this is really evil given the deadlines Stanford gives out. I don't think it is worth my time on a larger scale however. Too much babysitting.
It's a worthwhile topic, but one a bit "politially charged," so it's one we have to be careful with. For example, when someone loses a few WUs due to folding instability, nobody says anything, but wantonly delete one because you "don't want it", and people will be all over you. It becomes an ethical debate of "right" and "wrong". In fact, it's an interesting topic, and I'd love to debate it, but perhaps on a "neutral site" such as Just my $.02.


Posted: Tue Apr 06, 2004 12:57 pm
by ColdFlame
Sorry for polluting your thread again David but my point was that if a deadline for a particular WU is like (I actually don't know how much it is) XXX days (where XXX is a lot like 150?) then this particular WU is not very urgent.

Also I think Stanford sends out many copies of a WU out and they can monitor how many replies they got. So as long as they got 45/50 Tinker WUs that they sent out they keep assigning Tinkers till they got all 50 WUs processed.

I guess what I'm trying to say is that I don't see that there is any loss for the science or anything like that.

I think assignment algorithms that Stanford uses should account for folding instability and loss of a WU (as David noted) so there isn't much we can do to hurt the science :)

Posted: Tue Apr 06, 2004 1:04 pm
by dasman
I always thought the deadline was based on how long it took a celery 500 to finish the WU and not on the "urgency" of the WU.

The big WU's always have longer deadlines than the little ones...


Posted: Tue Apr 06, 2004 3:20 pm
by haysdb
From what I have been reading on this subject at, Stanford does NOT actually send out multiple copies of the same WU, at least not right away. There are apparently TWO deadlines, one for when the WU must be completed, but there is a shorter "reassign" deadline. If they don't get the WU back within a certain time, it gets reassigned. So I guess you could say "if I don't do it, someone else will", and you would be right, but it's also true that if you don't do it, it means someone else has to, and it does delay the entire project (for this particular protein).

What I am told is that the folding of a protein follows a "trajectory", and that the work is actually linear: the next state of the protein cannot be determined until the previous state is determined. This doesn't make sense either though. I mean, how would the folding of a protein ever be simulated completely if the next frame cannot be started until the previous one is completed?

I admit to having spotty knowledge on the subject, but I do believe that WU's aborted or deleted ARE detrimental to the project. It's just a fact of life that a certain amount of WU's will be trashed, but I make a distinction between "accidents" and "I don't want that WU because it's not worth enough points".

See, now here we are talking about it, when I said we shouldn't. ;)

What was this thread about anyway? :lol:


Posted: Sat Jun 12, 2004 3:06 am
by shathal
Well, I've joined the fold... (so to say).

2 questions I've got so far that don't seem to be answered:

* Hyper Threading - best to run 1 instance or 2?
* How do I "save" work, as I'll likely have to reformat my PC one or more times in the near future. Obviously, I'd rather not lose any work. Is it as easy as "just copy the directory"?

* Hmm - seems like I can't run the GUI-version of [email protected] in 2 instances ... bummer.

Urm... I think that's it for now. Hello all :).

Posted: Sat Jun 12, 2004 7:26 pm
by haysdb
Run two instances on a HyperThreaded cpu.

You can only run one GUI client, so the second MUST be a CLI client. I recommend running BOTH as CLI clients and using monitoring software such as Electron Microscope to monitor their progress. I further recommend running them as a service, so they start automatically when the computer is booted, and are not visible (and in the way).

To save work, make a copy or "backup" of the entire FAH directory.


Posted: Sun Jun 13, 2004 3:57 am
by shathal
Thanks Dave :).

I'll keep running only 1 instance for a while, as I've noticed some weird behaviour, (whole machine slowed down for no good reason), and I'm trying to figure out what wonkiness caused it.

I doubt it's [email protected] but ... never know. The Debug continues... :)

Posted: Fri Jun 18, 2004 7:36 am
by peteamer
Flags and their meaning/use :

From EOC Forums Here
What are flags?
Flags are special instructions given to the client at launch.

You can see the complete list HERE

How do I use flags?
Append them to the target line in the shortcut that launches your folding client.

Which flags should I use?
AMD Single processor rig: -advmethods -forceSSE -verbosity 9
Intel Single processor rig: -advmethods -forceasm -verbosity 9
AMD Multiprocessor rig: -local -advmethods -forceSSE -verbosity 9
Intel MP/HT rig: -local -advmethods -forceasm -verbosity 9

-advmethods: "Request to be assigned any new Cores or work units." In effect, you get gromacs most of the time. You will still get the occasional Tinker.

In April of 2004, the points awarded for many WUs, including tinkers, were increased. As a result, there is better ppd parity between tinkers and gromacs and the -advmethods flag now provides less benefit than it once did. In fact, some folders no longer use it.

-forceSSE: "On machines with an AMD processor, Core_78 gives priority to 3DNow over SSE -- this overrides that." NOTE: AMD TBird processors do NOT support SSE.

-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."

-verbosity 9
: Sets the level of output detail (0=Least 9=Most) that is written to the log file


Adding Flags in Windows :

Left click, 'Start/programs/[email protected]'

RIGHT click, '[email protected] 4' and select (left click) 'Properties,

In the box to the right of 'Target' it will say (Assuming you installed to the C-Drive)

"C:\Program Files\[email protected]\winFAH.exe"

You need to add your flags to the right of that . There should be a space before each subsequent entry i.e. it should look like:

"C:\Program Files\[email protected]\winFAH.exe" -advmethods -forceasm -forceSSE -verbosity 9

Depending on which flags you use.

Adding Flags to Other Operating Systems :

Fraid i can't help there, you'll have to speak to the clever guys on this forum. :oops:

Hope this is of some use.


(David, feel free to copy/delete/move/use/ridicule/correct/rearrange/etc. as nec.)

the dumb newbie question

Posted: Thu Dec 23, 2004 12:22 am
by BigDu21
Hey all,
I just started this folding thing, and I've got a couple of dumb n00b questions:

I downloaded the console only client from the link in the first post, and ran it and told it to run as a service...and restarted, and I see it running in taskmanager.exe....but is it actually doing anything? When should I expect to see some kind of results?

Also, as a gamer, I'll probably at some point need or want to benchmark my games w/ and w/o the folding running, esp. if I notice a drop in frames. how do I go about shutting it off? Can a just stop the service, or is there some better way of doing it?

Thanks in advance for any answers.

and why isn't the sig displaying properly? is it because I haven't accomplished anything yet?

Posted: Thu Dec 23, 2004 12:33 am
by peteamer
Welcome to the team BigDu21 8) ,

Usually your first WU will be a big/long one and will be frustratingly slow. :wink:

Your sig will show after you return a WU and then Liquidninja's 'catch up'.

As to 'is it doing anything?/ can I stop a service', which operating system are you running?.

I'm off to work now but it will give us something to work from. 8)


Posted: Thu Dec 23, 2004 6:12 am
by BigDu21
D'OH!!! You know I've used forums before, really :oops: ....I usually remember to include all the useful info...

I'm running WinXP Home, SP1, however I will (shortly) be trying to really screw things up with SP2; so if there's any differences, or if SP2 screws things up w/ FAH, please let me know that too.

As for the first one being really long.... :D I'm fine with that--I leave for vacation today (I'll check these boards when I get home), so FAH will have a full week of time to use up all my processor power crunching. I just wanted to make sure it was performing like expected. Its kind of a really cool feeling when a program installs and does exactly what it's supposed to do without much input from me. :lol: :lol: :shock: 8)
Thanks for the info so far.

Posted: Fri Dec 31, 2004 11:03 am
by teknerd
Here is a great tool I found to allow you to install FAH as a service while adding the appropriate flags.

Posted: Wed Jan 19, 2005 11:09 am
by DyJohnnY
either i did something wrong or this
Image does not work on my profile, but it works in a browser.

This is a block of text that can be added to posts you make. There is a 300 character limit

HTML is OFF" do i need this?can i enable HTML code for my sig somewhere? i couldn't find where

Posted: Wed Jan 19, 2005 11:21 am
by peteamer
DyJohnnY, Welcome To Team SPCR !!! 8) 8)

Your answer can be found here ... :(

Fold on Mighty Brother :D


New Cores Automactically Detect 3dnow/sse and optimize

Posted: Wed May 17, 2006 5:50 pm
by fastturtle
Just started folding today and since I have broadband, decided to stick to larger files if possible. Heck my system can do a fair amount of work as it's not stressed enough on a normal basis and at least my idle CPU is being put to work. :lol:

Aint worried about personal ranking, just figured the inclusion of the liquidninja's link made sense. Now all I have to do is include it in several other locations where it's useful.

Posted: Sun Feb 11, 2007 2:44 pm
by mouse
I just began folding for the SPCR team!!!

Posted: Sun Feb 11, 2007 4:41 pm
by haysdb
Welcome to the team mouse.

Posted: Sat May 26, 2007 6:05 pm
by Thelonious Monk
i will start folding shortly, i always leave my computer on and this is a great way to make some use of it!

however, until then, i have a question: anyone know the song used in the flash intro? i really liked it. reminds me of my dirty pleasure, indian folk music. 8)

Posted: Sat May 26, 2007 11:33 pm
by peteamer
Thelonious Monk, Image to Team SPCR!!!

The song is 'American Dream' from the album Vision by Jakatta. Some details.

Any questions... just holla..... 8)


Posted: Thu Jun 07, 2007 3:52 pm
by kittle
Anyone know how you switch teams?

im spending more time here than on the website of my current team...