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Official QJ.Net Folding@Home Team FAQ

This is a discussion on Official QJ.Net Folding@Home Team FAQ within the Everything Windows forums, part of the General PC Forums category; What is Folding? Spoiler for What is Folding? : Want to help find cures to Cancer, Alzheimer's, Parkinson's, Mad Cow ...

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Old 11-05-2006, 08:59 PM   #1
 
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Default Official QJ.Net Folding@Home Team FAQ

What is Folding?
Spoiler for What is Folding?:

Want to help find cures to Cancer, Alzheimer's, Parkinson's, Mad Cow (BSE) and numerous other diseases? ... how about joining the QJ.Net folding team (#52781)!

With a simple program installed on your PC (takes a few minutes), your computer will start working on research to find out how these diseases work and how to stop them. The program is designed not to have a noticeable impact on the performance of your CPU. The program only uses the CPU when it is idle (e.g. the CPU is about 90% idle when just reading web pages). Use your computer as you always have.

When proteins do not fold correctly there can be serious effects including many well known diseases, such as Alzheimer's, Mad Cow (BSE), Parkinson's disease, and cancer.
Stanford University Folding research (the research is non-profit and publicly available) into these diseases requires lots of computing power. With having much of the calculation done on regular PCs, what would take a supercomputer years, takes days. These regular PCs run a small program in the background that works whenever the CPU isn't busy.
This folding project is to help find causes and cures for these (and other) diseases. And it is working.
e.g. a recent paper came out based on the folding project research of protein p53. Roughly half of all known cancers result from mutations of this protein. By predicting how p53 folds we then know which amino acid mutations are important. Experimentation agreed with the computer simulation. This is an important step in finding out how to cure many types of cancer. Future projects will be to combine this with new drug design methods.

From the site: "FoldingsHome is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases. We use novel computational methods and large scale distributed computing, to simulate timescales thousands to millions of times longer than previously achieved. This has allowed us to simulate folding for the first time, and to now direct our approach to examine folding related disease."

And if you haven't join the team and want to, just do it! Help us to help beat cancer and other diseases.


Installation Instructions
Spoiler for Installation Instructions:

First you'll need to pick your folding name. For me it is NEvolution.
I'd suggest that you use your QJ.Net user name.
You can check http://vspx27.stanford.edu/cgi-bin/m...type=userstats to make sure someone hasn't already taken that name.

Notes:
- if the PC is overclocked, make sure it is stable first (e.g. run Prime overnight) and that it is not on the edge of overheating.
- only run folding on a computer you own or have written/email permission. It is illegal to install programs on other peoples PCs without them knowing about it.
- in the download area you'll see different ways to run folding. One of them is the windows graphic version. It is a nice client but as it is a real 3D program, Windows does not like to run it plus a full screen program. So either turn it off while gaming/benchmarking/full screen app (and have an icon to turn it back on afterwards), or use the prefered (but not so pretty) windows console client. Also for those with dual core/cpu or HT, and want to use more than one client (folding only uses one real/virtual core), you also will want to use the windows console client.
- these instructions are for Windows 98/NT/2000/XP console folding program. For other OSes and folding programs, go to http://folding.stanford.edu/download.html
- I'd suggest that the minimum PC for folding is a PIII (and Celerons based on PIIIs) or a Athlon/Duron. A Pentium, PII, K6 (including K6-III+) or VIA CPU is likely going to be too slow to complete the work on time.

The eight steps for installing:
Step 1. Create the directory c:\folding.

Step 2. Click on the following link to download the tiny program (248K) and save it in c:\folding
http://www.stanford.edu/group/pandeg...02-Console.exe

Step 3. Go to the c:\folding directory. Right click on FAH502-Console and select Create Shortcut.

Step 4. Right click on the newly created shortcut and select properties.

Step 5. A window will pop-up. The first line you can modify is called 'Target'. Add the flags -configonly -local so that it looks like C:\Folding\FAH502-Console.exe -configonly -local and then click Ok.

Step 6. Double click on that shortcut. You can reuse this shortcut whenever you want to change the settings (e.g. in winter to increase CPU usage).

Step 7. Answer a set of question (with suggested answers):
- Qn 1. It will ask you what User name. Enter the user name you want to use.
- Qn 2. It will ask you what Team Number. Enter 52781 (the QJ.net Team number)
- Qn 3. Launch automatically at machine startup. Answer yes. Note if you have already installed this as a service, this question will change to ask if you want to remove the service (in this case select yes only if you want to uninstall the program).
- Qn 4. Ask before fetching/sending work (no/yes)? Answer no.
- Qn 5. Use Internet Explorer Settings (no/yes)? Answer yes. It will then ask about proxys - answer no, unless your network has proxies (it will ask about it if you say yes to proxys).
- Qn 6. Allow receipt of work assignments ... greater than 5MB ... (no/yes)? Set this to no except if the PC has lots of free memory. Yes means accept “large work units” (you get bonus points for these). These large work units can use up to 150MB of RAM instead of just 5MB. You should answer no if:
> If using Windows 95/98/ME (due to memory manager issues)
> If you use a modem or have limited bandwidth (e.g. 1GB per month)
> If you have less than 512MB (256MB if the machine only does folding)
> If you do video & photoshop editing work on your machine and have less than 1GB
> If this is your gaming machine and you want to play the latest games such as Battlefield 2 and have less than 1.5GB (e.g. Battlefield 2 wants 1.1 GB) (unless you’re ok to stop & start the service as needed).
- Qn 7. Change advanced options (yes/no)? answer yes
- Qn 8. Core Priority (idle/low)? set this to idle
- Qn 9. CPU usage requested (5-100)? set this to 100.
- Qn 10. Disable highly optimized assembly code (no/yes)? set this to no.
- Qn 11. Pause if battery power... (no/yes)? set this to no (except if a laptop then set to yes)
- Qn 12. Interval in minutes, between checkpoints (3-30)? set this to 15 minutes.
- Qn 13. Request work units without deadlines (no-pref/no/yes) - Answer no-pref (can also answer no - it doesn't make a difference). Do not answer yes as you won't get any projects (those projects are no longer available!).
- Qn 14: Ignore any deadline information (mainly useful if system clock frequently has errors) (no/yes)? Enter no
- Qn 15. Machine ID ( 1-8 )? set this to 1 (this number is if running multiple clients on the same computer such as dual core. Each client on a specific machine needs to have a unique number.)

Step 8. After the last question, the window will automatically close. Reboot the computer.

And that's it! Folding will then start up automatically. There are no special steps. Shutdown and startup the PC with normally (i.e. don’t turn it off by pulling the plug).

Want to change the answers? Just reclick on the shortcut created and follow steps 7 and 8. Note that the big work unit and no deadline flag will only be applicable when your computer completes the current project.

If you want to set up a second folding program (if you have a dual core/cpu/HT), then do the above instructions except use c:\folding2 instead, and for question 14 set it to 2. You will also need to set the -local flag (see "How to change flags for a service" in the following post).

You can check the progress on a project at any time by looking in the file c:\folding\unitinfo.txt.
And you can check how the team and you are doing (completed projects only) on http://fah-web.stanford.edu/cgi-bin/...&teamnum=52781. There should be no noticeable change in any program that you run with that PC. You can test that with running any benchmark.

For a great utility (optional) to get more details about how the work on your PC is progressing, check out FAHmon at http://fahmon.silent-blade.org/


Troubleshooting and Additional Info
Spoiler for Troubleshooting and Additional Info:

This post is for those that are having trouble or that want more info/control of folding.

General
Folding expects the CPU to work 100% correctly. Most other programs (games, video, etc.) can handle a fair number of CPU errors without any noticeable impact. Different projects use different parts of the CPU, so maybe there might not be any error with one project, but with another there may be many errors. Some core types are TINKER (FPU intensive), GROMACS/DGROMACS (SSE intensive) and QMD (bandwidth intensive).
PRIME95's torture test (blend) for 12 hours at priority 10 and real-time will usually find out if there are any CPU problems and heat problems. I recommend this even for non overclocked PCs. For overclocked PCs, after finding the max stable FSB (using Prime) and verifying the memory using memtest (2 passes should be fine), I strongly suggest dropping the FSB by a little (e.g. on mine, I dropped the FSB from 219 to 216) as different applications (e.g. folding) might have slightly different results, plus power is never 100% perfect. On some of the older motherboards, they don't have PCI lock - beware of pushing the PCI bus as it can cause unpredictable errors (I corrupted a hard drive at PCI bus speed of only 38 !).
Prime95 is found at: http://www.mersenne.org/freesoft.htm Click Advanced, password is 9876. Click Advanced, priority and set it to 10. Then click options, Torture Test and select blend. When running the torture test, the computer will act hesitant.
memtest is found at: http://www.memtest86.com/ the best method is to get the ISO image and burn it to a CD and boot-up on that CD.

Spyware and viruses
You think you don't have any. Maybe, maybe not. I had Adaware, spybot and Microsoft spyware with zonealarm, hardware firewall and AVG. Pity none of them caught the keyboard logger, the password catcher and the credit card tracker programs that I found on my PC! (and I don't even go to suspicious sites!). My computer was acting a little strange (nothing that I could see, more of intuition?) so I downloaded (from cnet) Spy Sweeper and CounterSpy that both immediately found them. I also downloaded a few more malware and spyware trial programs but nothing else was found. So... if things are going a bit strange with folding, or even if it isn't, it is worth trying other spyware/malware programs.

If you are using the windows client (instead of the console client), and have problems with graphics... uninstall the windows client and install the console client (see the 4th post).

The log file
Check the fahlog.txt file
Errors would be noted in here.

Here are some of the lines to look at (comments are indicated with a >>>)

# Windows Console Edition ######################### ######################### ###
>>> Specifies the type - the Windows Console (when in service mode) is normally considered the best as it is fast, uses up little room and doesn't cause problems with some graphic cards. It is however not as easy to setup as the problematic Windows Graphic version.

FoldingbHome Client Version 5.02
>>> Specifies the version - 5.02 is the latest Windows Console version

Service: C:\folding\FAH502-Console.exe
Arguments: -svcstart -local -forceasm
Launched as a service.
Entered C:\folding to do work.
>>> Looks good - it is starting up in service mode with those flags. If you don't see all those flags, see the instructions in the changing flags in a service paragraph later in this post. The -forceasm -local flags are optional if folding is running fine and not using a dual cpu/core. Note that with the -forceasm flag, it gives a warning message about the dangers of using this flag if you are not very sure your overclock is stable.

[15:41:54] Core required: FahCore_78.exe
[15:41:54] FoldingbHome Gromacs Core
>>> The core type. See the first paragraph in this post about the different core types. Folding will automatically download the appropriate core if it is not on your PC.

[15:42:03] Project: 1150 (Run 52, Clone 28, Gen 6)
>>> So this is the project your computer is working on. The Run/Clone/Gen is variation of that project.

[15:42:53] Extra SSE boost OK.
>>> You MUST see this unless you are running an old Athlon/Duron (before the XP), a PII, K6 series or older CPU for Gromac projects (other projects may or may not display it). If you don't (for a Gromac project), that mean the folding program had ended abruptly (e.g. power failure, crash, etc.) and has gone to a slow safe mode. Make sure your PC is running ok (see the second paragraph of this post). You can force it back to SSE boost by adding the -forceasm flag. See the changing flags in a service paragraph later in this post. If not using the service, just add -forceasm (with a space in front of the -) to the end of the shortcut (outside of any " marks if any).

[17:16:52] Completed 172500 out of 250000 steps (69)
>>> How much is completed in the current project.

[00:20:10] Foldingbhome Core Shutdown: INTERRUPTED
[00:20:15] CoreStatus = 66 (102)
[00:20:15] + Shutdown requested by user. Exiting.
FoldingbHome Client Shutdown.
>>> I did a regular shutdown of the computer. These are normal exit messages.

Checking folding on your system
1) Run the task manager. You can see it by hitting ctrl-alt-del and selecting "Task Manager", or hit Start button then click on run and then type taskmgr.
Click on the "Processes" tab. Click on the "Image Name" heading. That will sort the list of processes. Scroll down to where you should see FAH502-Console.exe and FahCore_XX.exe (the XX varies - e.g it can be FahCore_82.exe). You should not see more than one of each of these (unless you are running dual core/cpu). If you are, it is normally a bad thing and you should remove it. See the instructions on how to remove a folding service later in this post.

2) Check the services. In the windows control panel, select click "Administrative Tools" and then select "Services" ( or you can also just go Start->Run->Services.msc). You should only see one folding program e.g. (unless running two for dual cpu/core)FAHbC:+folding+FAH50 2-Console.exe . If you see more, note all of them down. Check to see what ones are running, and what directory they specify. If more than one has the status of "Started" and is pointing to the same directory (even with dual core/cpu), that is a problem. Stop all of them (right click on the service and select Stop). Remove the extra ones (see How to remove a service section in this post).

To Stop & Start a service
Go to Start->Run and enter services.msc or click "Administrative Tools" and then select "Services"
You will see the list of services. Find the one that you wish to start or stop e.g. FAHbC:+folding+FAH502-Console.exe The current status will be listed beside the description. Right click on the service and select either stop or start (depending on what you want to do). It can take up to a minute to start or stop a service.
If the Startup Type for the service is listed as Automatic, that means it will start again when the computer is rebooted. In the properties for the service, that can be changed to Manual or Disabled if you wish.
Note: Check the 5th post of this thread for an very easy way to stop and start folding with an icon.

How to remove a service
If you don't have a problem with folding, just use the instructions mentioned in the 8th post of this thread to remove the service. If that doesn't work, then come back here.

If you are running this as a service, stop the service. (see the above section "To Stop & Start a service" on how to do that). If you are not familiar with regedit, do this with someone who is.
Start regedit (Start->Run).
Go to HKEY_LOCAL_MACHINE\SYSTEM \CurrentControlSet\Servic es and find the folding service you want to delete.
Right click on it and select delete.

How to change flags for a service
Stop the service. (see the above section "To Stop & Start a service"). Again, if you are not familiar with regedit, do this with someone who is.
Start regedit (Start->Run).
Go to HKEY_LOCAL_MACHINE\SYSTEM \CurrentControlSet\Servic es and find the folding service you want
You will see a item called ImagePath. Edit this such as adding the additional parameters you want (don't delete -svcstart) (don't put -config or -configonly either) and click OK to save it.
e.g. C:\folding\FAH502-Console.exe -svcstart -forceasm
Then reboot the computer.

Flags available for folding
Most flags are applicable for different type of folding programs (e.g. windows graphic, service console mode)

Here are some of the available flags are:
-local Run in the current directory instead of using the registry settings. Used primarily for dual core/cpu for the second folding client
-forceasm If the folding program has crashed (primarily due to CPU OC pushed too far), the folding program will run in a significantly slower safe mode. This forces the fast mode to be used in any case.
-advmethods Used to get beta projects
-verbosity 9 Gives extra info in the log file

-configonly After it asks the questions, it exists instead of starting to fold in the window. DON'T add this to the registry settings!

And in DOS/Command windows mode (e.g. Start->Run->command), you can do the following commands to delete problem projects. If you are not familiar with DOS/Command windows mode, do it with someone who is.
-queueinfo Lists what there the current project is in the queue
-delete x Deletes a troublesome project from the queue (x being the queue number)

Other notes
1. Cool n' quiet and speed step are not known to cause problems. As folding is the lowest priority, the cpu may go to a slower speed. If this is the case, for question 8 (in the 4th post), answer low priority instead of idle.
2. Windows XP64 is not well tested. It should normally work, but there is no guarantee.
3. If you have a project that is just not working well (e.g. the AMBER core based projects sometimes seems to cause problems), you can use the -delete flag (see the section on flags available for folding).


How to stop and start folding easily on Windows XP
Spoiler for How to stop and start folding easily on Windows XP:

For those (hopefully most of you) with the console client in service mode, here is an easy way to turn off & on folding (i.e. when you need every last MB, especially when playing BF2 or have a 512MB system) using two icons on your desk (one that says Stop Folding, the other that says Start Folding. (note that Dual core/HT client would need to add a second set of icons.)

The example should work for those that followed the original instructions (currently in the FAQ).
If not, then if you are using FAH504 instead of FAH502, just correct the name.
And if not using C:\folding, then just adjust the directory name.
Can also just check in the service list (Control Panel->AdminstrativeTools->Services and look for the service starting with FAH and use that text instead of the one in this example.
If you have two folding clients on your system, just do these instructions twice to create two pairs of icons, one pair for the first folding client, the second pair for the second folding client.

1) Right click on your desktop. Select New->Shortcut.

2) In the box that says Type the Location of the Item, put the following (quotes and all) (that is the "at" symbol not the letter "a" in "FAHaC:")
net.exe stop "FAHaC:+folding+FAH50 2-Console.exe"

3) Click on next

4) In the box that says Type a name for this shortcut, put Stop Folding

5) Right click on your desktop. Select New->Shortcut.

6) In the box that says Type the Location of the Item, put the following (quotes and all)
net.exe start "FAHaC:+folding+FAH50 2-Console.exe"

7) Click on next

8) In the box that says Type a name for this shortcut, put Start Folding

Done! Now whenever you need to stop folding to get that extra memory, just click on the “Stop Folding” icon. And when you’re done, click on the “Start Folding” icon!


Some notes about console version 5.04
Spoiler for Some notes about console version 5.04:

Almost identical to version 5.02 but modified for better control memory usage (can specify the maximum memory to be used starting at 64MB).

Here is the suggested settings:

User name [Anonymous]? put your folding name here
Team Number [0]? 52781
Launch automatically at machine startup, installing this as a service (yes/no) [no]? yes
Ask before fetching/sending work (no/yes) [no]? no
Use Internet Explorer Settings (no/yes) [no]? yes
Allow receipt of work assignments and return of work results greater than 5MB in size (such work units may have large memory demands) (no/yes) [no]? yes
Change advanced options (yes/no) [no]? yes
Core Priority (idle/low) [idle]? idle
CPU usage requested (5-100) [100]? 100
Disable highly optimized assembly code (no/yes) [no]? no
Pause if battery power is being used (useful for laptops) (no/yes) [no]? no
Interval, in minutes, between checkpoints (3-30) [15]? 15
Memory, in MB, to indicate (511 available) [511]? 500
Request work units without deadlines (no/yes) [no]? no
Set -advmethods flag always, requesting new advanced scientific cores and/or work units if available (no/yes) [no]? yes
Ignore any deadline information (mainly useful if system clock frequently has errors) (no/yes) [no]? no
Machine ID (1-8) [1]? 1


Adapted and Edited from NCIX Folding Team FAQ


Other questions:
Spoiler for Other questions:

Quote:
Originally Posted by Cortès The Killer
Is it possible to be a member of more than one team? I'm kinda dedicated to the ATi team... :|
Quote:
Originally Posted by NEvolution
Yes it is possible. I'm currently in Overclock.net, NCIX, and QJ.Net
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Last edited by NEvolution; 11-13-2006 at 05:45 PM..
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Old 11-05-2006, 09:06 PM   #2
 
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I didnt know this kind of thing could be done... Anyway, I'll set it up tomoro when Im on my Windows computer.
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Old 11-05-2006, 09:08 PM   #3
 
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I had did this with the SETI program....

I hate leaving my computer on all the time so its really not for me anymore.

Good Luck!!!!
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Old 11-05-2006, 09:09 PM   #4
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I've got it going 24/7 on my pc at work.
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Old 11-05-2006, 09:11 PM   #5
 
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I have this on during 'waking' hours. And I'll be folding for QJ once I'm done my current WU's (Work Units).

Edit: Almost forgot, I may consider giving out points to weekly/monthly top Folders. Stay tuned for that.
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Last edited by NEvolution; 11-05-2006 at 09:31 PM..
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Old 11-05-2006, 09:13 PM   #6
 
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Is it possible to be a member of more than one team? I'm kinda dedicated to the ATi team... :|
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Old 11-05-2006, 09:14 PM   #7
 
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Yes it is possible. I'm currently in Overclock.net, NCIX, and QJ.Net
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Old 11-05-2006, 09:15 PM   #8
 
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lol. Im currently in... none...

Gonna be in QJ tomoro tho
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Old 11-05-2006, 09:16 PM   #9
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Quote:
Originally Posted by NEvolution
Almost forgot, I may consider giving out points to weekly/monthly top Folders. Stay tuned for that.
If you need more points, just pm or im me, I can get you a decent amount
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Old 11-05-2006, 09:17 PM   #10
 
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Quote:
Originally Posted by Macca
If you need more points, just pm or im me, I can get you a decent amount
Gotcha, thanks for the offer.
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Old 11-05-2006, 09:28 PM   #11
 
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how does this help with the research?
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Old 11-05-2006, 09:43 PM   #12
 
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Here you go, click the link for more info.

Folding@Home
Quote:
You can help by simply running a piece of software. Folding@Home is a distributed computing project -- people from through out the world download and run software to band together to make one of the largest supercomputers in the world. Every computer makes the project closer to our goals.

Folding@Home uses novel computational methods coupled to distributed computing, to simulate problems thousands to millions of times more challenging than previously achieved.
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Old 11-05-2006, 09:44 PM   #13
 
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EDIT: What he said ^^


Also, I'd like to add, if you use the GPU client version of folding@home you get about a 40% speed boost.
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Old 11-06-2006, 04:34 AM   #14
 

 
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Damn you nVidia! Why must you make me choose between proteins and Linux.
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Old 11-06-2006, 05:23 AM   #15

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is there a linux version? or should i just wine it?
-= Double Post =-
yes there is a linux version....

questions: will this eat bandwith? cz i torrent alot and need every kb i can get
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Last edited by Yev Kasem; 11-06-2006 at 05:23 AM.. Reason: Automerged Doublepost
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Old 11-06-2006, 12:58 PM   #16
 
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Ok, I set it up about an hour ago, It sayd 0 out of 500000 steps left, I just went back to thats computer and its still says the exact same thing, except now under it it says creating checkpoint files... Is it even doing anything?
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Old 11-06-2006, 01:24 PM   #17
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Yes it is working but the first work unit will take ages to do.
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Old 11-06-2006, 01:24 PM   #18
 
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Quote:
Originally Posted by Yev Kasem
questions: will this eat bandwith? cz i torrent alot and need every kb i can get
No, this does not eat bandwidth at all. All it needs bandwidth for is to download the work unit and when it's done it needs to upload the work unit, which is pretty much just a text file.

Quote:
Originally Posted by Maniakc
Ok, I set it up about an hour ago, It sayd 0 out of 500000 steps left, I just went back to thats computer and its still says the exact same thing, except now under it it says creating checkpoint files... Is it even doing anything?
The first Work Unit will take a long time and will display a ridiculous ETA.
Also, depending on the work unit and the number of points allocated to it, it may or may not take a long time. I recently got a few Amber work units and those finish in pretty much a day and a half.

Watch out for those Gromacs. They give quite a bit of points but they will take a long time. I had two of those for each of my cores and they it took about 6-7 days to finish.
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