Folding@Home - reaching final target soon.

Nothing makes my inner geek happier than saying "My hobby is computational chemistry." For the last few years I have been taking part in the distributed computation Folding@home project. This Stanford University project uses donated computer time to study protein folding. A better understanding of protein folding will advance medical research looking for solutions to diseases such as Alzheimers, Huntingtons, Parkingsons and many cancers.

I kind of fell into the project in 2008 when looking for a worthwhile activity for my Mac G5 that had the problem of crashing when waking from sleep mode. The folding@home project kept the system busy and the cause is worthwhile. The CPU donations don't come for free as a flat out computer (or two) adds noticeably to the quarterly electric bill, offset somewhat by a set of PV Solar panels on the roof.

One feature of the project is the donation stats generated from returning completed work units. Donors join teams and those teams compete for ranking and placement on the donation stats boards. These stats are post-processed by a couple of web sites ExtremeOverclocking and KoaoStats give a sense of community and competition. There are also a good set of forums to get help and support for running the work units.

Folding@home can be done on wide variety of machines and operating systems. Work units can also be done on higher spec graphics cards using a CUDA compatible folding client. Folding can use all or just part of a machine's capacity by setting values in a configuration files. When running on all CPUs the power supply, motherboard and cooling are throughly tested. At one stage I had Mac, Windows 7 and Ubuntu folding side by side with a GPU client. The best performance numbers from a single machine, with an Intel Gulftown Hexacore cpu was ...

NODE (s) Real (s) (%)

Time: 17278.673 17278.673 100.0

4h47:58

(Mnbf/s) (GFlops) (ns/day) (hour/ns)

Performance: 711.518 36.599 10.001 2.400

That kind of performance from a PC size machine in 2011 puts it along side a Cray T94 from the mid 90s.

There is lots to learn running a small group of high performance folding systems. Mostly that problems occur when you are not looking or just after you left on holiday. Other issues that required some technical attention....

• Software configuration control
• Power supply reliability both domestic input supply and ACtoDC converter
• PC System building, especially over clocking.
• CPU performance and CPU cooling
• Wine the PC on Linux environment
• Remote access for administration

I have enjoyed my time with the folding crew at Team MacOS X but having reached 12,000 work units and 30,000,000 folding points it's time to move on to other research projects. Posted here are my folding stats graph showing monthly output.

If you have some cpu cycles spare be it on a Mac, PC or even a Playstation 3 check out the Folding@home project.

Overclocking is the new hot-rodding

Back in the days when you could improve a car using a set of spanners and a trolly jack the craze for Hot rodding was all over the streets. These days the testosterone filled teens ( and other geeky enthusiasts) overclock their PCs instead. There are many similarities, both activities are all about getting the best performance from what starts as commodity equipment; both interests involve a combination of detailed information, home engineering, trial and error tuning, and of course those manly pursuits of bragging and racing.

The purchase of carefully selected bolt-on goodies from RipSpeed, Demon Tweeks has been replaced these days by Corsair and Zalman specialities. "Throwing a rod" has been replaced by a catastrophic meltdowns as the cost of getting it wrong. Unlike racing on the public road to compare performance, Lan parties and folding teams are where system performance are compared and debated.

My first overclock in 1992 was pushing a Mac IIsi from 20Mhz back to the 25Mhz the motherboard was designed for. A hardware hack described here. These days pushing cpu clocks from 2.8Ghz to over 5Ghz ( 5000Mhz) is not routine but possible.

The pattern for both hot rodding cars and overclocking PC follows the same levels, use stock parts, get the best replacement parts, swap out the weaker parts with reengineered parts, buy or build exotic replacement parts. Tweak tune and adjust at each level to get the best performance and discover the weakest link.

The common fascination of tweaking and tuning, pushing a set of carefully assembled kit up to and beyond the meltdown limit joins the hot rodder from previous generations to the PC overclocker of today.

Cheers

Gannett

Had a better week Mac wise

Defiantly had a better week last week and got a few long standing issues resolved.

Firstly I have a Mustek A3 USB Scanner that had been stuck on an old Mac G3 B&W. I Finally found a blog which guided the way to get the SANE drivers and files needed to get it up an running. Ok so the blog references a previous ( now defunct ) blog but thats was all I needed. See PJ Holdens blog. The scanner works OK on 150 dpi but scrubs on higher resolutions. Integrated into Photoshop CS as File -> Import -> SANE. Sorted.

Secondly Creating Disk Images on OSX for use as bundled backup files. Found the Application DropDMG at $20. Neatly packaged, command line options and quite configurable.

Also found the code hackable BuildDMG.pl perl module over at this location. It needed a bit of work, mostly to swap out /Developer/Tools/CpMac and replace it with /bin/cp that preserves special Mac file attributes from OSX 10.4 onwards. Find this bit in the perl an change to the following ...

# copy the files onto the dmg
# use /bin/cp rather than /Developer/Tools/CpMac Only works on OSx > 10.4.x and beyond
print "Copying files to $dest...\n";
print "> /bin/cp -R $files \"$dest\"\n" if $debug;
$output = `/bin/cp -R $files \"$dest\"`;
$err = $?;

Put the perl in /Applications/BuildDMG/BuildDMG.pl then you can create a script+crontab to build the images on demand and drop them on your backup drive. A kind of TimeCapsule if you like :-) Have not yet managed to figure out how to drive it for directories with spaces in the name yet.

Thirdly since installing Leopard I have been suffering panic on wake-up. Let the system drift off to deep sleep then 1 time in 4 it will system panic on wake up. Looks like a USB or IO stack and It's all documented on the support boards here but not really made much progress. The solution is not green, but sometimes you have to give something away to get what you want. In this case I wanted "no panics" so installed Folding_At_home and donated a CPU. The distributed science application has a small memory footprint and is niced down so gets out the way when you need the horsepower.

And finally found a really good Mac based uk Tivo file extractor. The Java based TySuite has gui & command line & web interfaces and will pull as MP2 ready for conversion to MP4/AVI. Not quite as convienet as TivoTool but is better on Leopard and can pull Mode 0 recorded files at 720 * 576.


Cheers

Gannett