Dedicated Folding@Home AMD Based Research Node

Jason Newman's computer projects

User avatar

Site Admin

Posts: 178

Joined: Sat Oct 29, 2016 2:06 pm

Post Wed Dec 14, 2016 9:28 pm

Dedicated Folding@Home AMD Based Research Node

For many years I have supported the Folding@Home project run by Stanford University in the USA.

Image

For those unaware of the project, here is a brief overview:

Folding@home (FAH or F@h) is a distributed computing project for disease research that simulates protein folding, computational drug design, and other types of molecular dynamics. The project uses the idle processing resources of thousands of personal computers owned by volunteers who have installed the software on their systems. Its main purpose is to determine the mechanisms of protein folding, which is the process by which proteins reach their final three-dimensional structure, and to examine the causes of protein misfolding. This is of significant academic interest with major implications for medical research into Alzheimer's disease, Huntington's disease, and many forms of cancer, among other diseases. To a lesser extent, Folding@home also tries to predict a protein's final structure and determine how other molecules may interact with it, which has applications in drug design. Folding@home is developed and operated by the Pande Laboratory at Stanford University, under the direction of Prof. Vijay Pande, and is shared by various scientific institutions and research laboratories across the world.


As of 14/12/2016 I have processed 1264 work units for this project and now I plan to put an old system I've recently brought back to life to use and make it do this 24/7.

Image

The specifications for this machine are not mind blowing, but should be enough to produce some good numbers for the project while at the same time keeping energy costs down.

The specs are:

AMD Athlon X2 4600 overclocked to 2.7Ghz
2GB Samsung DDR2 RAM
8GB Kingston USB Stick (for Ubuntu OS)
400W PSU

Image
User avatar

Site Admin

Posts: 178

Joined: Sat Oct 29, 2016 2:06 pm

Post Wed Dec 14, 2016 10:12 pm

Re: Dedicated Folding@Home AMD Based Research Node

Firstly I installed Ubuntu server onto a USB stick, as this isn't all that interesting I've skipped this part.

Once into Ubuntu I SSH'ed into the machine over the LAN and setup the Folding@Home client.

Image

Configured the client.

Image

All installed and ready to run!

Image

After a brief moment, the machine began downloading it's first work unit and eventually, the 2 CPU cores went flat out 100% processing the data.

Image

Now I ran this for awhile to test stability but I plan to try overclocking this CPU on this machine to get that little bit extra performance out of it. I also want to install 'xfce' desktop environment a I want to be able to view the folding@home client status. Granted you can do this from the command line but it looks a lot nicer in a GUI.
User avatar

Site Admin

Posts: 178

Joined: Sat Oct 29, 2016 2:06 pm

Post Thu Dec 15, 2016 12:03 am

Re: Dedicated Folding@Home AMD Based Research Node

Next up, install the GUI so i can keep track of what the client is doing.

I installed xfce as it's extremely lightweight and also supports xrdp which is windows remote desktop protocol, my favorite remote desktop program.

xfce took ages as it's rather big but after i installed xrdp

Image

SSL 2048bit key generation and all the other final steps...

Image

once complete i connected via one of my Windows boxes

Image

Next it was time to install Fahviewer and Fahcontrol, both of which needed a ton of dependencies but this was easily fixed with 'apt-get -f install'

Image

Once this was done I logged into the machine via xrdp and took a look at the status, the machine was performing around 1474 points per day. Fairly slow in comparison to many more modern machines such as an Intel i5 or something. I will now overclock it and see what more i can get out of it.

Image

Once in the BIOS i went to the FSB settings to have a play around with them and see what this machine can handle

Image

Once i got to the stage where it wouldn't take anymore I took the settings back down a bit and left it at that

Image

Here are the final overclock settings i got out of the machine

Image

The result was from 2400mhz to 2734mhz a pretty nice increase

Once again i headed back into the OS and remote connected and now the machine is doing 3479 points per day. A massive increase although i think part of this was due to the machine settling down. It takes awhile for the machine to calculate the points per day rate but I'm sure the overclocking plays a part too.

That's the machine all configured and ready to go, next i will mount it on a board so it can go up on the wall in my workshop as well as also having silent fans installed as it is currently pretty loud. I may also get a Pico PSU for it so i can use a external transformer and do away with the huge power supply.
User avatar

Site Admin

Posts: 178

Joined: Sat Oct 29, 2016 2:06 pm

Post Thu Dec 15, 2016 12:11 am

Re: Dedicated Folding@Home AMD Based Research Node

Little side note, I've increased the number of work units worked on at one time. The program typically makes you run both cores (or however many cores you have) on one work unit. I prefer 2 work units running, one per core. As i find this gives me more completed work units overall.

Image
User avatar

Site Admin

Posts: 178

Joined: Sat Oct 29, 2016 2:06 pm

Post Thu Dec 15, 2016 1:42 pm

Re: Dedicated Folding@Home AMD Based Research Node

Finishing touches, a rather crude case!

Image

Image

Image

It is now running in my closet under the stairs 24/7 for Folding@home.

Image
User avatar

Site Admin

Posts: 178

Joined: Sat Oct 29, 2016 2:06 pm

Post Thu Dec 15, 2016 2:56 pm

Re: Dedicated Folding@Home AMD Based Research Node

One last thing to install, lm-sensors so i can keep track of the temperatures.

Image

All installed

Image

66c, pretty warm but not bad for a heavily overclocked CPU fully maxed out constantly.

Want to join the research project? https://folding.stanford.edu

Image
User avatar

Site Admin

Posts: 178

Joined: Sat Oct 29, 2016 2:06 pm

Post Sat Dec 24, 2016 4:25 pm

Re: Dedicated Folding@Home AMD Based Research Node

This machine has now been retired for a much faster and less power hungry i5 based laptop.

I got a cheap core 2 duo laptop with a nice big 17 inch screen and although it's not nearly as fast as my i5 it is great for my eyes.

Image

So i'm now using it as my general use laptop. The i5 can process well and it only uses 35w vs the AMD's 65w so this is a great way to increase research and also lower the cost of electric use.

I've removed the SSD and a few other non essential items from the laptop to save even more power.

Image

Image

it is now folding 24/7 at a much higher rate! The AMD machine did 1300 points per day whereas this i5 laptop is doing 6501 points per day, a massive increase at almost half the cost of electric!

Image
User avatar

Site Admin

Posts: 178

Joined: Sat Oct 29, 2016 2:06 pm

Post Mon Apr 03, 2017 10:40 pm

Re: Dedicated Folding@Home AMD Based Research Node

This machine has now been removed as well as my rack server has taken over the research effort.

AMD was running at 1,300 points per day

i5 laptop was 6,501 points per day

The 8 core beast is doing it at 17,320 points per day!

Image

Not bad for older 2.33Ghz Xeon processors (when you consider my much newer and better i7 3770 3.4Ghz processor does it at around 20,000... not too far behind at all!)

Image

Return to Computer Projects



cron