My Experience in English Class

            By now, you should have learned about the types of distributed computing available, the latest and greatest hardware presently and the benefits of folding for a community. I have shared the knowledge that I have accumulated gradually into a series of short but informative and not too nitty-gritty blog entries. Short and sweet. To the readers who felt persuaded or motivated by my posts, I want to offer my appreciation to you because you were willing to take time to read them even if it didn’t make sense.

            I would like to acknowledge and offer advice to a few individuals to those who introduced me to blogging and saw me get to where I am today. First and foremost is Professor Wong, the smiling English teacher who is always happy to see you. I probably spent several hours during the course of the semester talking about random topics rather than the blog itself.

Second, overclock.net members, we, as individuals, may be separated geographically but as long we have a forum to discuss folding, the distance between us means nothing. I make a thread and within minutes, I usually have my answer. To the heavy hitting folders with the dedication and deep pockets to fold nonstop, I want to shake your hand. It’s really awesome, the actual definition, not the overused and cliché meaning if you know what I mean. On a side note, this feels like an acceptance speech for an award of some sort, ha-ha.

Finally, to the lucky students that will enroll in Professor Wong’s class, my advice to you guys is to have fun. The end of a semester will approach before you know it so make the most out of it. Her class is really enjoyable and she’s really lenient and laid back about deadlines although she says it’ll get more challenging next year. I would guess she’s probably bluffing. Kidding aside, even if the class is more difficult, it's still worth it. Think of it as a challenge for the future.

            From writing blogs, I realize that I got a lot out this type of writing. It allows the writer to be free of formal essay constraints, and without restrictions on topics and personal style, I was able to flourish and speak my mind. It felt good writing them because there’s an actual audience for you to target instead of an English teacher. Like my professor’s first time assigning blogs in her class and my first time as a novice blogger, I believe we both share a similar idea on it: a learning experience. For me, I didn’t know what the expectations were lengthwise and format wise. Near the end of the class, I realized and knew for a while that a timed on the spot essay does not determine your skills as a writer. From what I’ve been told, I’m a “talented” writer. Hopefully, it’s not all praise and no substance. On a final note, I would like to thank Professor Wong and the responsive members of overclock.net for answering all my questions and concerns, online and offline, hardware or non-hardware related.

Building From Scratch or Retrofitting an Existing Rig

            After reading my previous blog entry, you are probably touched by Syrillian’s unexpected passing or persuaded by me to get your feet wet in the world of computers, from learning about the hardware to having the ability to have an intelligent conversation with a computer geek. This first step by you will surely impress your family and friends alike. If you can’t tell, I was only making fun but if you seriously have a genuine interest in Folding, let’s begin from scratch.           

            First, you have to decide on a budget to construct a dedicated folding rig. Also bear in mind about what you learned earlier. As a review, there are two types of approach to FoldingatHome, CPU and GPU. For the CPU, the 2600k provides the best point to watt ratio and for the GPU, I’m not certain on what provides the most bang for buck. The problem is whether you want to buy newer hardware compared to older hardware.

Older hardware in the computer world are seen as outdated and not the latest and greatest. There’s nothing wrong with outdated hardware, it’s just the fact that present technology grows leaps and bounds compared to six months ago. I’ll use an example of my own. My mom recently replaced her 2002 Honda Odyssey that had 160,000 miles on the odometer with a 2011 model. The newer model is vastly roomer and is more fuel efficient compared to its predecessor. I hand calculated the miles per gallon to be somewhere from 16-18 on the premise that she fills up every four days and drives 60 miles roundtrip. Compare that to the improved version that features cylinder deactivation, a gas saving feature that allows a car to disable half its cylinders when cruising at a steady speed, which achieves almost 26 MPG. The same analogy applies to video cards as well. I purchased a second hand GTX275, featuring 240 stream processors, that can produce about 7000 PPD for $60 shipped. That was a quite a steal right there when you browse at the cards for sale with less power consumption, die shrinks and higher clocks. For the price you pay, you may receive the said benefits at the expense of stream processors, a must for folding.

For the budget builder who is going to mainly utilize graphics cards to fold, you really need a cheap, low-end processor manufactured by AMD, another CPU company. Next you need an AMD compatible motherboard with multiple PCI Express slots where the cards will fit into. The arguably most critical component is the power supply. Think of it as the heart of the machine and if it blows, your entire computer goes bye-bye. Some of the reputable brands include Seasonic, Antec, Corsair and PC Power & Cooling. The other peripherals such as the hard drive, ram and the enclosure isn’t a top priority; in fact, most folders run caseless as it improves the airflow.

Alternatively, if you wish to go the CPU route, you will be focused on achieving a high overclock and to do so, you need to ensure that the operating temperature is as low as possible. To accomplish the extreme overclock, you have to look at aftermarket cooling as the stock heatsink supplied is inadequate of cooling the processor properly, even at stock settings. There is a plethora of options available from low end and high end air coolers to all-in-one water cooling system to a full blown one. Most folders use their main rigs to fold instead of one from bare parts because it’s more cost efficient. Who in the front mind would invest hundreds of dollars for a watercooling loop for strictly folding when you can do the same in a computer you can use for gaming or watching movies? Like in the previous paragraph, the power supply is significant, not so much for the other parts including the video card. You would need a cheapo one to provide video input and I think that onboard video (no graphics cards) might also work.

 The best option, in my opinion, is to upgrade your computer given it isn’t a prebuilt computer from Dell or HP. Do you know why it’s so cheap? The companies mass produce them and are after profit so they skimp on computer essentials using no name power supplies, ram and motherboards. To put it plainly, you have really limited options when it comes to expanding. First, the motherboard settings are locked so you cannot alter the voltage and frequencies. Second, the power supply is cheap so unless you swap it out for a higher capacity one, you are restricted to low power consumption video cards. Third, most of the computer cases are fanless, other than the processor heatsink fan internally and the power supply fan externally. There are no air intake fans or exhaust fans so most of the heat produced by the system remains inside, not that it’s any danger to the hardware but us overclockers, are overachievers when trying to maximize the distance between the thermal threshold.

If this is your first time folding, you can decide to fold for an existing team, create your own team or fold for anonymous (default). Looking at the stats, I gather that most of the folders belong to one team or another. The main benefit for me personally by folding for a team is that you belong in a tight knit community. Take for overclock.net for example, if you have a questions regarding folding or hardware issues, the members of the forums are extremely helpful and will answer all your questions promptly. Aside from questions, it provides a place for folders and potential folders to address issues, chat or goof off, to a certain extent.

Folders and Non-Folders Unite!

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Syrillian's avatar, an Ensō, a Japanese word meaning "circle."

      After the unexpected passing of Syrillian, the word spread like wildfire on overclock.net. Immediately, the thread that was previously created for accepting donations in his honor was renamed to “R.I.P Syrillian” in remembrance of him. Countless members paid their condolences to the man, leaving messages of from the simple words “Rest in Peace” to heartfelt stories or events Syrillian changed their lives, on the website or in real life. Even guests, called “lurkers,” who wanted their voices heard, created an account on the website to bid farewell. I remember reading someone’s encounter with him. A new registered user posted a question or comment, probably silly to those that have computer know-how, was repeatedly harassed and taunted by other more knowledgeable members and one person step forward and defended the one who posted the question. Obviously, it was the moral thing to do and although I didn’t see the said thread but I absolutely saw something wrong with this. It was no way to treat a person who took the time to get registered on the website to get help but instead finding unwanted and unnecessary treatment from fellow members; it would also leave a bad impression that the members of overclock.net is snobby and unhelpful. I would bet that Syrillian felt the same way and gave a reputation point to the person who defended the first person, leaving the comment, “Stand and deliver.” There was another user that needed advice on something about case modding. If I recall correctly, it was about the type of screws needed. Anyway, Syrillian mailed the said screws to him, insisting that it was free of charge and that it should be kept a secret. Those two stories is probably one of hundreds, if not thousands, that have had the privilege of being touched by Syrillian’s kindness. 
     Soon news popped up that there would be a memorial service dedicated to the great man. It was determined that the service would be located in San Francisco.  A lot of members wanted to attend, some more than others I suppose, hoping to share their stories of him and meeting some of the people closed to Syrillian’s life. A member as far away as St. Louis met up with another member in San Diego and together, they rented a truck and drove up here. A third member from Portland flew into San Jose airport got picked up along the way. The fourth and final member was local, from San Francisco. After attending the memorial service, they had dinner in a restaurant where people could speak with each other and reflect on how Syrillian changed their lives. Take a step back and you can instantly see or sense that there is unity, woven into the fabric that is overclock.net. When one of its members falters, the rest of the team will join together and support the fallen. Imagine how much it means to the person who would fork money out of his own pocket to attend the service. Forget the monetary value for a moment and instead, focus on the sentimental value. That’s what unity and being an overclock.net member truly means.

Syrillian Forever Remembered

            Cancer is a faceless killer with no conscience or morals, inflicting victims indiscriminately regardless of age and ethnicity. One day, you are at the top with the world in your palms but the next, you are having night sweats and intolerable pains out the blue. At first you brush it off, thinking you were just tired and it will eventually go away. But as time goes by, your condition progressively gets worse and decide to pay the doctor a visit. After a battery of tests of blood tests, MRIs and CT scans, the doctor speaks to you in a low, soft voice -almost a whisper- and stoically gives you your diagnosis: terminal cancer. Initially, you vehemently deny the truth and demand to get retested but deep down, you realize the diagnosis was accurate, explaining all the symptoms you are experiencing. Then all emotions are let loose in front of the doctor with uncontrollable sobbing and tears of anger and sadness rolling down your face. I must admit, the narrative I wrote somewhat portrays a typical movie scene out of Hollywood.

Syrillian, the great man himself.

In reality, I’ve known two people, my grandpa and Syrillian, another outstanding person on overclock.net, who have fought against cancer and lost. I have to believe there was a level of sadness involved but both men stood strong in light of their situations for they were role models to their families and acquaintances. Since this blog is Syrillian, I figured I will mention some of his extraordinary talents and endless contributions to the forum. I haven’t met him personally or even contacted him in any way so the information on his background is pretty limited. As a child, Mr. Daniel Costin moved around as a child from India to Hong Kong, living there most of his childhood. Later he joined the Marines where he served for some time and as a member on the forums, he always had that sense of professionalism and respect towards other members. He would intentionally go out of his way to help another member through tips on computer case building to actually mailing some nuts and bolts. Mr. Costin was a master of computer case modding, creating unique case designs that flowed in his mind out of scratch. Everything was done by hand; the guru would cut, drill and polish his own parts. Since I don’t know what case is made of aside from aluminum or steel, I won’t say much other than it takes a master to create a masterpiece. On one of his many builds, one particular one, dubbed “Silentium” made its way on the cover of CPU magazine. It’s truly a work of art and I can’t begin to imagine the dedication and man-hours placed in a project. In March 2011, he was diagnosed with large cell neuroendocrine lung cancer with symptoms of excruciating pain, depression and night sweats as early as January of the same year. He remained strong in his battle, splitting what little time he had with health problems to the website, trying to answer all well-wishers. Sadly, he passed away in August where the entire overclock.net community banded together to help the cause either by donating their computing power or funds, in honor of Syrillian. Mr. Costin, considered a legend on the forums, will live in memory of the hearts and minds of overclockers everywhere. Semper Fidelis, Syr.

"Silentium," constructed out of imagination and hard work, is displayed on the cover of CPU magazine in 2009.

The Folding Hardware

Photos/Diagrams to follow

The i7 2600k CPU may produce hefty points but costs a pretty penny.

            Time to get into the core of Folding at Home, the hardware that will serve as your army to rake in points like nobody’s business. To construct a rig that will maximize your points per day, you have to determine how your folding setup. Like previously stated, there are two ways to go about it, CPU and GPU folding. Let’s clear the pros and cons of each method of out the way first. The Sandy Bridge, king of the PPD, produces the highest amount while at the same time, is more efficient with a higher point to watt ratio. In addition, running only one piece of hardware can reduce the noise and heat that is produced. Like all advantages, there are disadvantages. To achieve the high amount of points, you have to push your system’s limit, over the original factory settings, to be able to complete the work unit for the bonuses. This approach also increases the instability of the entire system which can compromise the entire work units and also your points. A perfect analogy is putting your eggs in one basket. You can fit and overload your basket with them but when it breaks, all your eggs are broken. Losing a work unit like that can drastically affect your entire output because when you lose the work unit, you lose the point value of it as well as the time your system is spent running.

Atlas' folding farm in Aug 2009 contains 23 GTX295s and 32 9800GX2 video cards. Think of the heat output.

            Next up is the graphics processor that is able to finish smaller work units in a shorter timeframe. Think of it as a turbo mounted on an engine in a car. There are two types of turbo options available: small, fast spooling turbos or one big turbo. The former is able to generate ample power quickly while the latter takes a while to spin but is able to generate huge amounts of power. GPUs are flexible in the way that if your motherboard and power supply can handle the additional load, you can plug and have it running within a short time. They are also more consistent, meaning they can complete a work unit in a matter of hours instead of completing a work unit every few days for the central processor and by going this route, you have more leeway for setting up a folding schedule. Video cards are less volatile so if the work unit is incomplete due to stability issues, the work unit will end early and will be uploaded, giving you credit for what had been finished. Since the work units do not have high point values, the lost of points are minimum. There are downsides to this method as well, you will be earning less points per day than your processor counterpart and definitely, no doubt about it, earn less points per watt. The flagship Nvidia GPU is the GTX580, capable of producing around 17k points per day with a maximum consumption of 150W while an i7 processor can produce 34k points, consuming 125W. The more graphics cards you add to your computer, the more expensive the farm gets. Besides the money issue, the heat produced by the cards is tremendous. During the summer, the heat is unbearably hot but in the winter, the cards serve as a standalone heat source. Either approach is a double edged sword but is similar to a person working. Either the person has to work a double shift to earn his or her pay or he or she can set their own hours but receiving less pay. There is no clear winner between the two but in the end, science wins.

Work Units and Meeting Deadlines

Picking up where I left off, I’m going to write more about the work units and their deadlines, the energy bill and begin to mention some of the folding hardware. From the beginning, I stated that although I was going to explore distributive computing, I was going to emphasize in Folding@Home. From what I understand from photos, they all share a similar layout with an almost identical method of operation. When the program is first run by the user, he or she is asked to type in a username with “Anonymous” as default, next option is the team number where the user can create his or her’s own team or join an existing team. Other options that are not important includes: choosing to use a proxy, selecting the memory usage (small, medium or large) and indicate whether to be prompted before fetching a new work unit. Now comes the good part. The work unit is automatically downloaded into the computer where the computer (central processing unit or graphics processor unit) will crunch that data.

A bigadv work unit being run nets about 25000 points per day.

The fastest single Nvidia GPU today produces over 16,000 PPD. Notice each percentage of the WU is completed in 9 secs.

            There are two main ways to fold on a computer and only one on the PlayStation 3. For the PC, there is the CPU client and GPU client. As time progresses, so do advances in technology architecture. Take a look at the new high end CPU from Intel 2600k codenamed “Sandy Bridge” which utilizes hyperthreading, allowing simultaneous tasks to be done at once. It has four physical cores but eight threads for the computer to take advantage of. The SMP or Symmetric Multi-processing client is used by multicore processors. But running a 2600k on regular client is a waste of time and money, instead it is put to the test on bigadv units, a high point value and high priority work unit and require a minimum of eight cores. To be eligible to bonus points, the user must complete 10 WU first and also complete the bigadv one before the deadline, a feat that requires at least 16 hours of folding. The meat of the points originates from the bonuses and the faster you complete them, the more points you get. The GPU client, in my opinion is more simplistic in terms of setting up and getting it running. Another pro is the work units are short and manageable. What I mean is, with a pretty decent Nvidia video card, you can finish a work unit in more or less an hour. Sure, you won’t match a 2600k’s PPD but you also don’t need fold for hours on end. Lastly, the PS3 is also capable of producing using its Cell processor but as the name implies, it’s a gaming console, inadequate of mass completing units. A quick search indicates that it produces about 900 points a day and takes about 8 hours to complete one work unit.

With Fahmon, users are able to keep track of progress in realtime.

When you finish that particular unit, it will automatically upload the processed data back to Stanford’s servers and a new replacement is given. Not much info on the work unit is given unless you use a Folding monitor program such as FahMon; it is extremely helpful as it lists the type of unit, the point value, the preferred and final deadline and probably the most important feature: the estimated of completion. If it isn’t completed by the final deadline, the results are still uploaded but no credit is given to your name. A general rule is the faster the work units are finished, the more can be churned out. Now, there are hardcore folders out there that will run their systems day and night for the sole purpose of folding. Running your components at this rate will reduce the lifespan of your hardware to a certain extent but it’s probably going to be outdated and considered obsolete in the ever changing technology field. Since I fold when my computer is not in 3D mode and not nonstop, I can’t accurately determine how much electricity my computer consumes when folding. Furthermore, I fold sporadically and without any schedule on my video card. My next post will mention some of the hardware involved and folding farms.

What is Distributed Computing?

           When the term “distributed computing” comes up, something complex usually comes to mind. In fact, it’s quite simple despite the term not being used so often. I feel that once distributed computing is defined, everything will fall into place as I attempt to get my meaning across. Without ado, let’s begin.

Distributed computing is the linking of computers in either one area or around the world, collaborating to achieve a common goal. The workload is divided up between multiple systems. In our case, it’s going to use computers around the world to assist scientists in research from finding a cure for caner to finding life forms in outer space. There are many programs available depending on what your interests lie. Simply put, you run a piece of software downloaded from their website and thus, you’ve began to make a difference to benefit humanity.

Folding@Home running on a Nvidia GPU.

Folding@Home is a program created by Stanford used to study the folding of proteins. Proteins are essential to life because they carry out the many functions of the body such as defending your body from foreign invaders and speeding up chemical reactions to providing structural support like keratin, found in nails and hair. The macromolecules are created from various chains of amino acids, and depending on the sequence and chain length, it will have varying functions and coiled shape. Each one is specifically designed to complete a certain task within the body. To do that, the proteins fold themselves into a particular shape. Think about enzymes that speed up chemical reactions, there is a certain groove (active site) for the molecule (substrate) to sit in. This example can be described as a lock and key mechanism. When these proteins misfold, it’s believed by scientists to cause Alzheimer’s, Huntington’s and many types of cancers that aggregation related, meaning that they clump together.

Rosetta@Home

Rosetta@Home, formed by Baker Laboratory, is a similar program to Folding@Home but takes a different approach to the same solution. This program mainly focuses on the prediction of an unknown protein given the amino sequence whereas Folding@Home tries to understand how proteins fold in a specific timeframe. An example I can think of is the process of baking a cake. Rosetta is only interested in predicting the end product, the cake while Folding wants to understand each step on how it’s created.

Seti@Home, created by UC Berkeley, is dedicated to detecting life forms in outer space. One approach is to utilize radio telescopes to listen for radio signals from space. Since I’m not interested in extraterrestrials and don’t know much about Seti particularly, I will try to do a quick run-through.  From what I gathered, huge volumes of data are recorded from a telescope in Puerto Rico, filling about 35 gigbytes of data per day. Then the tape containing all the data is sent to Berkeley where the data is then divided into 0.25 megabyte chunks.  From there, they are sent from the Seti@Home server over the Internet and around the world for people to analyze using their computers.

Hopefully this post gives you an idea of some of the many distributed computing projects out there. From here I will dive deeper into the specifics of Folding@Home and use my own personal experience and knowledge to guide the reader from work units, points worth per WU and other small tidbits.

Conceptualization of My Curiosity

 Contextualization of My Curiosity

            Out of everyone in my family, I would say, without a doubt, that my grandpa was a hardworking, tireless man who deeply cared for his family. Don’t get me wrong, there are quite a number of diligent members but he is placed on top of my list. Grandpa worked in a Chinese restaurant as one of the chefs for many years, even several years past the age of retirement. Out of the blue, he had to be admitted to the hospital. At that time, our family didn’t think too much it since he was probably overworked or some minor issue. After a battery of tests, it turned out that Grandpa developed terminal lung cancer. Although surgery was an option, it was decided that it was not worthwhile. When I learned of the news, I was shocked beyond belief and could not accept that fact. Out of everyone in the world, what were the odds of having cancer? Previously, I always thought that everyone lived to at least 80, quite a long lifespan. Those that didn’t hit the milestone would be considered lucky. In a way, I was oblivious to reality until I was in for a rude awakening. Needless to say, we still deeply miss him but we won’t forget him. There are times after his passing that my dad would say “if” questions and comments like, “if he hadn’t developed cancer, he would still be alive today.” In one instance, my dad mentioned that Grandpa promised to help him with replacing the roof on our house after he was discharged from the hospital. Like the blink of an eye, my grandpa was gone.

            In late 2007, I decided it was time to build a new computer, this one by hand, to replace the aging system that had been used for seven years. I had enlisted a friend of mine to assist me in assembling the hardware since I had no idea how to do so myself. A few months of completing my new rig, I stumbled upon the website, overclock.net, a forum where enthusiasts of every kind came together to show off their expertise. As I lurked about, reading some posts, a particular section of the forum caught my eye: Overclock.net Folding@Home Team. The more I read, the more I became interested. It was understood by me that through the donation of computing power from distributed computing, research breakthroughs would be hopefully discovered and would ultimately lead to cures. I decided to combine my love of technology and with the gaping sadness of my grandpa’s passing to help contribute to finding a cure, not just to cancer but a laundry list of deadly diseases like Alzheimer’s, Huntington’s and MS. I feel that this would be the best way to remember my grandpa: by folding in his memory. Because running the program requires the computer to be on, it was taken a toll on the electric bill. Although I cannot fold at full capacity, I strive to reach the goal I’ve set at a million points.