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Tuesday August 7, 2007
Folding@Home
An Interview with Prof. Vijay Pande

Folding@Home
• An Interview with Prof. Vijay Pande
•  Robert and the DL.TV crew trekked on down to Stanford University in Palo Alto to talk to the man who made Folding@Home a reality.
• For more Folding@Home info go to http://folding.stanford.edu/
Folding@Home Instructions

We kid, because, well, that's what we do.

Occasionally, tho, we get serious.

Robert, for example, is very serious about Stanford's Folding@Home (FAH) project, a worldwide distributed computing project working to map out the process of protein folding.

Why do you care? Per the Folding@Home page, "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."

Robert's rallied thousands of DL.TV viewers to download the Folding@Home software and join in.

You can, too.

Just download and install the Folding@Home software and let it run when you're not using your Mac, PC, PS3 or Linux machine. We track the stats regularly on the show.


Want to join the DL.TV Folding@Home crew? Here is what you need to know:

The DL.TV Folding@Home team number is 57391! Configure your FAH client with this team number to join our team!

Use the same unique user name with all instances of FAH that you run so you can track your personal progress.

Programs like FAH stress system hardware - insure your gear is adequately ventilated!

Lots of useful/interesting information can be found on the FAH FAQ page.

Extreme Overclocking's sweet FAH stats page


Which version of FAH is right for you?

Well, here are our recommendations based on relative FAH performance:


PlayStation 3

Go online and update the console's system software. FAH can be found in the PS3's Network column of the XMB. More details here.


PC equipped with ATI X1900-class graphics card w/256MB+ of on-board video memory

Use the GPU version (use multi-GPU version w/X1900 CrossFire setup).

Don't have an X1900-series graphics card? Then skip the GPU version and use a CPU version.


CPU versions

Use the text only (non-graphical) "console version" for best performance.

Console version user guide: http://folding.stanford.edu/console-userguide.html


PC equipped with an Intel quad core CPU

Download the Windows 2000/XP/Vista SMP client console version

Dual core/hyperthreaded PCs should not use the SMP version!!

Detailed SMP install instructions/FAQ here.


PC equipped with an Intel Core Duo/Core 2 Duo/AMD X2 CPU (dual core/hyperthreaded CPUs)

Create two instances of the FAH program that can be run simultaneously so that each core (virtual or physical) is working at 100%

Download: Windows NT/2000/XP/Vista "No nonsense" text-only console

Create a folder named "Folding At Home" and two sub folders called "FAH1" and "FAH2"

Copy the downloaded FAH executable file into each of the two FAH folders.

You must have each FAH executable in a separate folder!

Create a shortcut to each of the two FAH executables.

Suggest naming shortcuts FAH1 and FAH2.

Launch and configure FAH1.

Launch and configure FAH2, but when you get to the Advanced Settings option enter "yes" and change the Machine ID number option to "2". [FAH1 defaulted to Machine ID 1].


Tips
• Windows users should install all Windows Updates - .NET framework v2.0 is the most important, and this is already included with Vista.
• When configuring the FAH software, select the option to receive 5MB+ (large) work units! This will earn you (and the team!) more points per completed work unit than are awarded for completing regular-sized work units. The large work units do take longer to complete, but it's worth it.
• Tip suggestion? Email us at dl.tv@ziffdavis.com with "FAH Tip" in the subject line.
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Got a Question? A Comment? A product you want reviewed or something you want us to check out? Email us at dl.tv@ziffdavis.com

Posted By:  Scott Asnault
Posted by: reddragon72
August 7, 2007 5:52 PM

Ok I'm confused, why should we NOT run the SMTP version on dual cores??? if we do run SMTP and select the 5mb or greater workloads then it always says 500000 units, and if we loadup the normal client 250000 is the max per client, but they give less of the large workloads to the regular client. If you want points then loadup the SMTP and you will always get the 5mb or bigger work units. if you run two instances of the normal client on the same PC you run a lesser chance of getting the 5mb or greater workloads. So I say run the SMTP if you want points. I have been running 8 systems for over two months now with SMTP on core duo/core2 duo's and it really shows im in 14th in our group.

Posted by: dp
August 7, 2007 8:23 PM

I started F@H a couple of days ago, and i'm not even on any stat list. What's up with that?

Posted by: AE
August 8, 2007 4:31 AM

I agree with reddragon72. Use the SMP version if you have a fast enough computer. It does not matter if you only have two or even one core as long at it can finish the work unit before the deadline. I use it on my Macbook (core2duo 2GHz) and it works great.

dp: You have to finish a work unit before you show up on the list. Also it takes some time before the list is updated.

Posted by: Constitution-Bound
August 8, 2007 10:52 AM

dp,

You may need to have one WU done before F@H will list you on our DL.TV team score list. Even then you will need to break the top 1000 to see yourself on our team's front page'.

Check the "Fast Teampage URL" link on our F@H team page for a more complete list of DL.TV contributers.


C-Bound

Posted by: Jac Goudsmit
August 9, 2007 12:56 PM

reddragon72: You can run the SMP (That's SMP, not SMTP: SMP=Symmetric Multi Processor, SMTP=Simple Mail Transfer Protocol) version if your system is fast enough to meet the short deadlines. SMP deadlines are only a few days, non-SMP deadlines are much longer. This was done to discourage people from using the SMP client on machines that don't get any benefit from it.

My 3.6GHz Prescott Pentium4 with 2GB RAM is unable to meet the SMP deadlines, even when I run it at 100% CPU all the time. If you run the SMP client and it does one frame every half hour or so, you'll be okay. Mine takes an hour and a half per frame on the SMP client so SMP is a no-go for me; I have two instances of the command line version running.

Posted by: reddragon72
August 9, 2007 3:50 PM

sorry about that, but sometimes when you get to typing during break time, you rush and start typing the wrong thing. Silly about the SMTP though HAHAHAHA....

I run the SMP on core duo's and core2 duo's from 1.7Ghz to 2.33Ghz all in laptops(yonah and merom). My only worry is internet connectivity going down when I'm not here on the weekends and the extra day or so causes a late entry that wont count. But anyone running a Core duo or core 2 duo should be fine as well as the "new" Pentium dual core processors, as they use the Merom and Conroe(core2duo) cores just with less cache.

Posted by: Subwayfox
August 14, 2007 1:20 PM

You can also accept advanced simulations. I checked yes for it when it set up the non-graffical console version.

I heard they give extra points for it. I am running to machines at my work now. They keep giving me

p3402_dpdp-ii TIP3P ff whaters

Are they giving me it because it works best for my machines or do they just need to fold at lot of these.

I also want to see more results from all the folding that the Folding@home project has been doing. Maybe a little video of a large molecule folding up in real time would be nice.

GO DL.TV, I love watching our team rank keep going up and up

Posted by: Threader
September 11, 2007 4:40 PM

Go F@H DL.TV team! Woohoo!

Anandtech F@H Team just got owned

Team Engadget next for the kill!

Peace

Threader

Posted by: hasan
September 12, 2007 2:12 AM

we are climbing the ranks!

i've recently made it into the top 400 on the team too :)

Posted by: Sakimori
September 13, 2007 7:17 PM

OMG, the DL.TV team is ranked #8! That's amazing!

Posted by: Daine
September 15, 2007 11:52 PM

From http://folding.stanford.edu/FAQ-SMP.html

"We strongly suggest people run this client on 4-core boxes. While it will run on 2-core boxes, we have noticed some potential problems (we are looking into these issues now)."

But hey, if it works for you, go right ahead.

Posted by: Jim
September 26, 2007 5:18 PM

I am running the SMP client on my dual core laptop (Core 2 Duo), and it seems to work fine. I am completing 1700 point work units on my laptop faster than I am completing 500 point work units on my desktop (P4 3.4e). Also, the SMP work units are supposedly better for science (the real reason we do this).

If you want to help DL.TV's score, and you have a dual core system, use the SMP client.

The SMP client has an install process (unlike the regular console client), so please read up on the Folding@Home website.

Keep Folding!

Posted by: Constitution-Bound
October 10, 2007 11:11 PM

Hey! Our team is losing active participants!

Mr. Heron, please encourage DL.TV's F@H team members to restart their F@H endeavors.

Posted by: shinji
October 13, 2007 8:49 PM

I just downloaded the SMP client to use on my dual-core processor in my laptop. I did see the note about how there may be issues so I will be on the lookout but it seems to of started up ok. Downloading first workload now. Oh and I also joined the team so my work will help to improve team standing. ;)

P.S. - I've installed it as a service but instructed the application to halt work when I am running on battery as it is bad enough already when the cpu isn't working at full load (about 1.5 hours).

Posted by: shinji
October 13, 2007 8:59 PM

BTW, I just looked at the process list with the smp version. The smp daemon for fah loads up 4 fah processes to work on the load. I hope my system can get it done fast enough. ;) I'm listening to music while I work and my processor is running at 66C and holding steady at full load. I'm going to try to find something to monitor my progress. I've opted for advanced scientific workloads too.... My config run...

# SMP Client ##################################################################
###############################################################################

Folding@Home Client Version 5.91beta5

http://folding.stanford.edu

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

Launch directory: C:\Program Files\Folding@Home Windows SMP Client V1.01
Executable: fah


[00:43:37] Configuring Folding@Home...

User name [Anonymous]? shinji
Team Number [0]? 57391
Launch automatically at machine startup, installing this as a
service (yes/no) [no]? yes

The program will continue in non-service mode now, working in C:\Program Files\F
olding@Home Windows SMP Client V1.01.
The next time the computer is starts up, you should see work automatically
continue there. Note that when this service is running, you should not try
to manually run F@H from that directory at the same time.

Use Internet Explorer Settings (no/yes) [no]?
Use proxy (yes/no) [no]?
Allow receipt of work assignments greater than 5MB in size (no/yes) [no]?yes
Change advanced options (yes/no) [no]? yes
Core Priority (idle/low) [idle]?
CPU usage requested (5-100) [100]?
Disable highly optimized assembly code (no/yes) [no]?
Pause if battery power is being used (useful for laptops) (no/yes) [no]? yes
Interval, in minutes, between checkpoints (3-30) [15]?
Memory, in MB, to indicate (2046 available) [2046]?
Request work units without deadlines (no/yes) [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]?
Machine ID (1-16) [1]?

I think this will be the most benefit to the team. Especially if my system can make deadline for the work. I will be leaving it on as much as I can.

Posted by: shinji
October 13, 2007 9:24 PM

Just one last thing here. It appears that one of the issue may be that when you load the smp client as a service it doesn't create enough processes. In interactive mode it created 4 on my dual-core processor which was enough to load it to 100%. When I halted it and started the service it only created 1 process which used only about 25% (not even) cpu load. I'll just stick to running 2 processes of the basic version and monitoring them with an application like fahmon.

Posted by: shinji
October 13, 2007 9:56 PM

One last note. I found that it will get stuck if you run it as a service (hence the one process when it is a service). The easiest way I found to work around that is to manually modify the account the service runs under. Set it to run as the same username and password that you gave the install.bat file. This will make it so that it works properly. Now it runs with 4 processes fully loading my processor. Might have something to do with the way that mpiexec.exe and smpd.exe communicate with each other or something.

Posted by: Dylan Fahey
October 27, 2007 3:51 AM

I'm joining the 57391 team. I've got a Q6600 mildly over-clocked to 2.65GHz for home game use on a Asus P5N-E motherboard. I'm running temps of 59/57/55/50C on my 4 cores at full load with ambient temp of 20c.
If you are running this stuff on a laptop, I would suggest a temp monitoring program like coretemp, speedfan or similar to make sure you've got adequate air flow through it. I'm using MBM to monitor my temps, but anything will do to protect your machine. Usually anthing under 60c is OK. If you are going over that, I would also suggest you go to some of the overclocker sites and see what you can do to improve/lower your system temps.

Posted by: KingFish00
November 3, 2007 12:06 PM

Does dl.tv have some dedicated folding forums? If so, where are they?

Posted by: shinji
November 13, 2007 1:06 PM

I had joined your team a while back. I have been running 2 processes of the regular client on my intel core 2 duo. Since then I have now started to get work units that use the double gromacs core. Anyone else? I still get mostly the regular ones but the doubles have a higher point value. My computer chews threw them like they are candy. ;)

P.S. - My cpu temps vary depending on where they i am at but here are current values as reported by i8kfangui (temp monitoring for dell laptops)

CPU -- 77C
GPU -- 51C
Memory -- 62C
Chipset -- 60C

yes a bit high but it keep stable there and the system holds up well. Been doing this for 2 weeks like this at least. It is setup to move aside to any other tasks and to temporarily pause/halt when I am on battery so it don't lessen the battery life.

Posted by: HokieGrid2
November 13, 2007 4:07 PM

What happened to the FAH forum page, haven't been able to access for two days, i.e. Fehler 403 ist aufgetreten :-( Filename: /kunden/usr/local/apache/share/cgi-bin/error403.1.html

There isn't any apparent way to contact the Web Master on the FAH site.

Now that I found the problem that was causing FAH to freeze my PC I wanted to post it to my open question.

Make it a great day!

Posted by: JohnnyDoe2007
December 26, 2007 1:49 PM

Why all this hype about Folding at Home? Why not check out Berkeley Open Infrastructure for Network Computing or BOINC (for short):
http://boinc.berkeley.edu

Posted by: GGCAN
December 30, 2007 1:59 AM

I've got BOINC on my work laptop and Folding@Home on the PS3. Both seem to be working fine....PS3 has DL tvs number. BOINC actually is a program my workplace encourages us to run.

Posted by: leexgx
January 5, 2008 6:18 PM

FAH is an one only program
you should only run one project Bionc lets you use lots at once and can set how much cpu time each project gets, but that not work well for FAH as thay realy need doing as fast as it can

SMP works well on
Core 2 quad and c2duo and Xeon cpus(insanely fast on Xeons)
AMD systems any X4 CPU (phenom) can do them in an day (thats @ 2.2ghz X4)

AMD dual core best to use high speed ones 3.2Ghz(X2) can do an unit in 1.5 days
the 2ghz ones will put it close to the deadline and the CPU must have no other load on the pc or it may go over

an alot of the 3ghz P4 chips are HT not dual core chips thay are single core cant run SMP as thay take to long

Posted by: Leo
January 14, 2008 6:01 PM

WOOT we are in 13th place. Keep chugging along guys soon we will break the top ten. FOR PATRICK

Posted by: Dylan Fahey
January 25, 2008 2:58 PM

Score=41414 WU=35

Look at what a q6600 will do!!! I've also got an old P4 3.0 single core doing FAH on my linux server 24/7.
The q6600 is overclocked to 2.68MHz and the temps at full load are now at 66/64/60/58C for each cores. That's about as high as I want it to go. I'm taking off the CPU HS/Fan this weekend and doing some lapping: http://www.overclock.net/intel-air-cooling/225983-pictorial-hsf-ihs-lapping-guide-check.html , which is a really good guide which shows some of the finer points of lapping.
Long live the DL.TV FAH project!!!

Posted by: Dylan Fahey
January 25, 2008 9:19 PM

Score=41414 WU=35

Look at what a q6600 will do!!! I've also got an old P4 3.0 single core doing FAH on my linux server 24/7.
The q6600 is overclocked to 2.68MHz and the temps at full load are now at 66/64/60/58C for each cores. That's about as high as I want it to go. I'm taking off the CPU HS/Fan this weekend and doing some lapping: http://www.overclock.net/intel-air-cooling/225983-pictorial-hsf-ihs-lapping-guide-check.html , which is a really good guide which shows some of the finer points of lapping.
Long live the DL.TV FAH project!!!

Posted by: Pet-Cal
January 27, 2008 10:58 AM

Anyone know why this happened? it was my first attempt.. everything seemd to have gone well untill this point.

[15:43:44] + Attempting to send results
[15:43:50] Couldn't send HTTP request to server (wininet)
[15:43:50] + Could not connect to Work Server (results)
[15:43:50] (171.64.122.76:8080)
[15:43:50] Could not transmit unit 01 to Collection server; keeping in queue.
[15:43:50] + Closed connections

Posted by: Dylan Fahey
February 2, 2008 12:40 PM

Check your firewall or pg2 settings.

Posted by: Dylan Fahey
February 2, 2008 12:45 PM

Hi,
How do we do the 'sweet' signature thingy's that everyone else has, so we can proudly display our FAH stats???

Thanks,
Dylan

Posted by: Sandlapper
February 20, 2008 8:06 PM

2 things...

Can I just close these two instances of FAH and they'll pick back up where I left off?

2nd, I have a CPU usage meter on my desktop. It shows how much both cores are being used. One is pegged out to 100% , the other only to 43%. Any ideas why the second one is not at 100%?

Posted by: coercus
February 20, 2008 10:03 PM

two days and i have about 2k. i plan to pervert the cpu use around me. i have about 20 more servers i can involve and then maybe a few hundred pc's later this month. i'm obsessed. thanks dl.tv. i have an addiction. at least it may do some good and add to the dl.tv team score

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