Folding@Home
Folding at Home is a project run by Standford University, which is almost exactly halfway between San Francisco and San Jose in the state of California. I’ll be honest, the exact science is way over my head but in principle they study Proteins in our bodies do what they have to do to allow us to live. Apparently these proteins can actually change shape, or Fold, in terms of the atomic structure. This seems to allow them to complete the tasks they need to. However, very occasionally they can “misfold”. It would seems that in most cases a misfold is just cast away with no consequences. However there are those very few occasions where the misfold actually starts up something we would rather not have, such as a number of Cancers, such as Breast Cancer. Some virus’ cause a misfold which lead to diseases such as Dengue Fever, Zika Virus, Hepatitis C, Ebola Virus. Other conditions lead to misfolds that brings us well known conditions such as Alzheimer’s Disease. This one is particularly close to me as my Mother is plagued with it, as was her mother before her.
Hey, look, instead of me telling you how this works, when you are done here, going and have a look yourself by clicking here –> Diseases at Folding.
So, what do they do there at Standford? They simulate protein folding in a computer environment. I’m guessing that if the model is done right then the misfold can be created. Then, if you know how the misfold started then perhaps you can figure out how to stop it happening in the first place. As I said, way above my head. But the computing is not above my head so let’s look at this problem.
The modeling of folding a protein is hugely mathematical, and here lies the actual problem, computational power. If Standford could buy the most powerful supercomputer in the world (Currently the Chinese hold that record) they still wouldn’t have enough power to do the work they need to do. The “Deep thought” approach of Seven and Half Million years is simply too long to wait. So how they get round this is to harness a tiny amount of all the millions of microprocessors in our computers. A computer cannot stop, so if there is nothing to do it has to literally twiddle its thumbs, in what is known as the “Idle task”. The idle task is the lowest priority process, so when you run your programs they come in a lot higher priority, stopping the idle task while your program runs.
So what Standford has done is to run a program on your computer that is one priority notch above the idle task. This program accepts a tasking from Standfords servers, then as your computer idles, instead of twiddling thumbs, to works on the cure for cancer!!. All that is required is an Internet connection and regular running of your computer. I will explore you running this yourself in a while.
This method is known as “Distributed Computing”. It’s not a new idea. There are other examples, such as SETI, that look for aliens; and the BONIC platform runs all sorts of projects. Folding is different, Folding could make a difference.
To make things interesting Standford have instigated a scoring system. The difficulty of the “Work Unit (WU)” and how quickly your computer gets the result back to them, adds to an accumulating score for you, as a Donor. So you can join a little competition, as it were, against the rest of the donors around the world. Now some large companies are rolling the Folding client out on all their employees computers and are contributing as a group. That’ll take a bit of beating, but I’m up for a challenge!! And as we have this friendly battle we are all helping. Maybe your work unit is the one that makes the difference.
Statistics. There are currently just under 2 million donors, but I think a fair number of that figure are idle accounts, the individuals having given up a long time ago. So you can either just quietly donate computer time and not worry about the score; or you can get competitive and “put the hammer down” in the race for No. 1. I am sort of in the latter group, let me tell you my story.
The story of Dwarflord
I actually got into Folding in around 2012, when I started running the client on my Intel Dual-Core, under my Internet name of “Darmain”. A short while later I acquired some old PCs from my employer and had three Pentium machines running. This was fine until Stanford realised that PCs were getting faster, so they made the work units more difficult. There is a time limit under which the work unit must be returned or else it is abandoned and the job realigned. My poor little machines couldn’t keep up so I had to eventually retire them. Now a revival, but why?
During the last twelve months I have taken an interest into the design and operation of “Data centres”. When someone talks about storing your files on the “Cloud”, what is the “Cloud”? It is essentially someone else’s computer. More specifically it is racks of powerful computers known as “Enterprise servers”. The big players sell them. IBM, Dell, Sun, and Hewlett Packard. The big names operate them. Google, Amazon, and Facebook, although Facebook are moving away to their own proprietary “open server” technology now.
I decided to get my hands on one, well, actually two, and this is growing, but let’s not digress. My target was Hewlett Packard and for various reasons a machine known as the DL380, generation 6, which I have called “Dwarflord”. The G6 machines had reached end of life and HP support was ending. The commercial operators were upgrading to the latest hardware. To buy a brand new G10 machine equivalent to my G6 would be about £10,000.
What can I do with it? Well, I’m a geek, so lets leave it there. However it is designed to provide Internet services. I could do that but then it will spend a great deal of time idling…. Wait a minute, can it Fold? Can it Fold? Darn right it can and fold like no other machine could get close to.
So, to set up such a machine is a little involved. It doesn’t run Windows, rather preferring the much more reliable and faster Ubuntu Linux server operating system. It sits on the home network and fetches and returns work units like the old Pentium machines used to. But, of so much quicker. My donor name is now within the top 5% in the world on the score table as a result. I have processed over 1,200 work units in total and half of them have been done in the last two months, by Dwarflord.
So lots of advantages, whats the catch? Well there are one or two. Firstly it is physically big. It is designed to be held in a rack so its only 85mm tall, but it is 480mm wide and 700mm deep. Yarp, the better part of a metre. Second, the noise. It has eight fans and it knows how to use them. Thirdly they are incredibly power hungry, as in electrical power. Mine is using about 230 watts of power continuously, but I see it a donation to charity. A £1 a day donation, but surely its worth it, Yes? There is an advantage here. All that power is converted to heat, which warms the house. I’ve seen a back off in the gas central heating as a result. Okay, its not a like for like exchange but you do get a bit back.
Folding on your own computer
You can run folding on most personal computers or Macs, and even on a Android phone or tablet. You do not need to have a monster DL380 to fold, but if you feel the need then go and look on Ebay. The absolutely best tool to conduct Folding on is a PC with one, or more, high performance Video Cards fitted. The folding client can use the Graphics Processing Units (GPU) in the Video Card to Fold. The vector processors in a GPU are vastly more efficient at this job than a standard Central Processor (CPU). Unfortunately high performance Video Cards are also very good at mining crypto-currencies, which in turn makes money for the owner. The Video card manufactures have got wise to this and are pushing up the price of Video Card in order to get a slice of the action. So that kind of removes that as a viable option for folding, or playing games for that matter.
You can fold on a laptop but I advise caution. When you set the software up it will give you the option to how intensive it can use the CPU, I recommend you do not select the highest setting as laptops were not really designed to do this kind of thing and could overheat. Also make sure it is set to suspend folding if you are running the machine on battery, otherwise your battery will go flat rather rapidly.
Before you can do any of this you will need to go on to the Folding@home website and set yourself up an account. Then follow the instructions. Together we shall beat Cancer.
Extra bits
For giggles, this web site is actually be served off of the very same Dwarflord. Getting a little technical, Dwarflord runs an application called “Virtual Box”, which allows me to create “Virtual servers”. Using this I have created another Linux server called “Webonics”. On this machine I run an application call “Apache” which is probably the most well known web server in the world, a database manager called “Mysql” and a server side scripting language called “PHP”. This site is then hosted via the framework known as “Word Press”. Using virtual servers isolates functionality. It was what the DL380 was born to do.
As you may have picked up I “was” upgrading Dwarflords processors. The new processors didn’t work in Dwarflord and eventually I discovered that the lowest level of software, which is programmed into the motherboard [Techie – Geeky stuff, the BIOS] was too old to support the new processor architecture. HP think these old machines still pose a threat to their market so I would have to sign a support agreement with them to get the firmware upgraded. This simply wasn’t going to happen. So I was either going to send the new processor back, or come up with plan B. Like yourself, I am not a quitter, so plan B it was. I bought a second server from a company in Reading. These great guys built me a machine with low spec processors but a motherboard that could support the new devices I already had. After taking delivery and a quick check out I swapped the processors. It was then a case of installing all the disks and loading the Linux server operating system. This part involves the naming ceremony. Sticking with the dwarf theme I named this one after “Thorin Oakenshield” from the Hobbit. Dwarflord was the most powerful machine I have every owned. Thorin has faster processor cores and more of them, probably doubling its power. Folding through put is staggering. In fact I had to throttle it back to stop it overheating. Unfortunately it also demands 100W more electrical power than Dwarflord and the fans scream like a jet engine when its folding at full power. This can only be happening when I am at home, as a result. Dwarflord will remain running the 24 hour attack and official web server.
