Jim Clark & John Hennessy visit Folding@Home offices

Just before Christmas, on the December 22, 2008, Entrepreneur Jim Clark and current President of Stanford University - John Hennessy visited the offices of Vijay Pande and his Folding@Home team.

Jim Clark, formerly a Professor of Computer Science at SU and founder of many Silicon Valley tech companies has contributed much back to his former stomping ground, with one of his more notable donations being a sum of $100M towards building the Clark Center, a Uni-wide center for interdisciplinary Biology.

Vijay posted on his blog about the visit, saying:

"Today, Dr. Clark along with John Hennessy (the President of Stanford University) visited our offices to hear about our recent work. They both were heavily involved in computer architecture in the past, so they were interested to hear about our work with GPUs and the success we are seeing there (in particular, the significant speed increases). Also, they are both interested in neuroscience and so I was excited to tell them about our recent Alzheimer's work.

Anyway, I was excited to give them both an update and some idea of where we're going, and it was great fun for me to tell them all about how much we've done."

Both Jim Clark's and John Hennessy's Wikipedia pages are interesting reads.

Possiblity for an Alzheimer's Drug to be made from new Folding@Home results

Vijay Pande posted on his blog back on the 18th December, 2008 about a Possible New Alzheimer's Disease Drug to be made from new Folding@Home results.

Vijay warns that although it's very exciting, this is still preliminary news:

"On Tuesday, we presented our results regarding new possible drugs (small molecule leads) to fight Alzheimer's Disease at a recent meeting at Stanford. This meeting was part of the NIH Roadmap Nanomedicine center retreat and was supported by NIH grants to Folding@home.

It's very early (so we are not publicly talking about the details until this has passed peer review), but we are very excited that it looks like we may have multiple small molecules which appear to inhibit toxicity of Abeta, the protein which is the toxic element in Alzheimer's Disease.

This is exciting in many ways. It's been a long road for FAH to get to this point, but we are starting to see the possibility of seeing these results published easily before our 10th birthday (October 2010). Considering all the technology development that had to be done in the first five years, these results have come very quickly (in the last 3 years), which is exciting. In particular, we are now looking to apply these methods to other protein misfolding diseases (we have pilot projects for Huntington's Disease underway).

Finally, I should stress that while we're very excited about this, it's still early and a lot can go wrong between where we are and having a drug that doctors can prescribe. Over the holidays, we will be double checking the experimental data, crossing t's and dotting i's to make sure there is nothing missed before we think about submitting this for peer reviewed publication. Also, there is still a long way from an interesting possible drug (where we are now) to something which has passed FDA clinical trials (where we'd love to be), and a lot can go wrong in clinical trials in particular.

Thus, this is an important milestone for FAH and we are very grateful to all who have contributed."

Hopefully all goes well and we can have a Alzheimer's Disease Drug on the market soon with Folding@Home to thank!

Folding@Home Stats Server updates to be quicker in 2009

Folding@Home's Statistics Server, used to provide all Team and Donor stats etc. will receive an update sometime in 2009 to speed up the time it takes to update the stats database, meaning that instead of waiting the first 45 minutes of each 2 hour update cycle just to see our Team stats page, it might only take the first 15 minutes, and hopefully with an hourly update cycle.

Currently you see this message in approximately the first 45 minutes of the current 2 hour update cycle:

Stats update in progress

External access to the Folding@home stats server is currently not available in order to expedite the stats input process. This was started on the hour and we expect this to take about 45 minutes. The stats updates run in 2 hour cycles.

An intention to update message is currently sitting beneath the lines above, telling us:

"In 2009, we will be upgrading our stats server such that the whole database will fit in RAM (this used to be the case, but FAH has gotten quite big over the last few years and the related databases require over 20GB). We expect that this new stats server should greatly speed up stats updates."

It's good to see that the Folding@Home team works to constantly improve their systems.

Stanford's Winter Holidays Schedule

Vijay Pande has informed us of the Winter Holidays Schedule for Stanford University on his blog recently. SU will be closed until January 5, 2009, however Folding@Home will still be operating as always, but there is warning that should problems arise, the corresponding response will be slower than normal due to reduced staffing during the holidays.

Most of the F@H team finished up on the 20th, however they worked very hard to add more jobs to the Servers, clear out hard drive space of previously returned work units etc. so that this holiday period can be as problem-free as possible.

On behalf of the F@H team, Vijay writes:

"We'd like to wish all the FAH donors a happy holiday and thank all of you for all your great help with our project."

Important Update to Folding@Home's End User License Agreement (EULA)

Vijay Pande has posted on his blog a very important notice about an update to the Folding@Home End User License Agreement (EULA).

Straight from Vijay:

"We added the word "written" to this sentence:

"You may use this software on a computer system only if you own the system or have the written permission of the owner."

We felt that this was an important addition in order to avoid any confusion. There have been a few situations where donors felt that they had permission, but the owners of the computers did not. Having written permission is the best way to make sure that there is no doubt. It also gives protection to the donor in that he/she would then have proof of permission, avoiding problems involving oral agreements."

I'd like to re-affirm that you could find yourself in a situation of getting sued for installing and running this program unauthorised, as many people have gotten into trouble setting up multiple computers at they're place of work (such as a school I.T. Administrator setting up tens to hundreds of computers) when they weren't authorised to do so, and have in some cases been ordered to pay damages for things such as increases in power bills, internet bills etc. Also, not having sufficient knowledge about the program and how it can affect different computers etc. (such as Notebooks being advised to run at no more than 90% CPU usage due to their less than optimal cooling systems) can lead to a bit of a blame game as far as what caused the computer to pack itself in and who is going to pay for it!

So guys, make sure you get written consent to run Folding@Home on computers or machines that are not your own. And be sure to inform those owners or bill-payers of the potential to have slightly higher power and internet bills whilst running this program (not a big deal for one or two machines, but any more, the extra power and internet usage quickly adds up!). Providing you do the right thing by the owner, i'm sure they will enjoy helping out a Distributed Computing Project such as Folding@Home.

New Paper published on the Playstation 3 Folding@Home client

Vijay Pande's blog yet again brings good news with yet another Paper being published, this time about the Playstation 3 Folding@Home client - Accelerating Molecular Dynamic Simulation on the Cell processor and PlayStation 3.

A collaborated effort between the Folding@Home and Sony Development teams, this is the first paper resulting from the Playstation 3's involvement in the Project. The paper is more of a 'how does it work' with details about how the PS3 accelerates simulations through use of it's powerful streaming processor, the CELL Broadband Engine.

The abstract reads:

"Implementation of molecular dynamics (MD) calculations on novel architectures will vastly increase its power to calculate the physical properties of complex systems. Herein, we detail algorithmic advances developed to accelerate MD simulations on the Cell processor, a commodity processor found in PlayStation 3 (PS3). In particular, we discuss issues regarding memory access versus computation and the types of calculations which are best suited for streaming processors such as the Cell, focusing on implicit solvation models. We conclude with a comparison of improved performance on the PS3's Cell processor over more traditional processors."

Papers of this type not only help the Folding@Home team at Stanford, but can potentially help many others outside of the Project. Whether it helps out others involved in the field of Molecular Dynamics, or people that intend to use and program for the CELL processor, knowledge gained can be knowledge shared!

Another new Paper! Ribosome Gate

Only on Tuesday Vijay Pande announced on his blog that the Project published New Alzheimer's Disease Work. Now another paper, Folding@Home's 59th to be exact, has been published - 'Side-chain recognition and gating in the ribosome exit tunnel'.

The Ribosome plays a very important role in Protein research says Vijay:

"The ribosome is a fascinating molecular machine, responsible for the synthesis of proteins. For this reason it is of fundamental importance to protein folding (as the last step in the central dogma of biology) as well as to human health (since the ribosome is the target of a very large fraction of antibiotics)."

Vijay mentions that this paper has been made possible by the contributions of folders running 'bigWU' enabled classic clients stating:

"the ribosome is so huge that it would not run on regular classic clients."

It's certainly good to see a couple more important research papers come out lately, and only a day after another! I can't wait to see what other papers get released and how they can help us move forward in the Protein research field.

New Alzheimer's Disease Work published

The latest news from Vijay Pande's blog is about the publication of a key paper relating to Alzheimer's Disease - 'Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach'.

Vijay comments saying:

"I am very happy to announce that a first key work from the Folding@home project on Alzheimer's Disease (AD) was just published"

"In many ways, this paper is the "tip of the iceberg" for the Folding@home activities in AD, with a lot more interesting results to come, especially in terms of experimental tests of our predictions and interesting new possibilities for new drugs and AD therapeutics. So, while we're excited that this result is now past peer review, we're even more excited for what's coming down the pipeline, waiting peer review. We'll keep you posted as more results become public, hopefully with some even bigger announcements in 2009."

Hopefully this will mean Folding@Home as a Project will start to see some real fruit for all it's labour!

UPDATE:

"It was asked which clients participated. This work started several years ago and took some time to analyze and then publish. So, it ran exclusively on classic clients. For the follow up simulations, we are using a mixture of GPU, SMP, and classic clients. Due to the large number of classic clients, they allow us to calculations not possible on the other platforms. However, the raw speed (but smaller number) of the GPU and SMP clients allow us to get a good rough idea quickly, refining later with classic clients."

Where Folding@Home is heading

Vijay Pande has posted a 'Long term vision' on his blog about Folding@Home about where it is heading and what sort of results we can expect Science wise.

He mentions the fact that the first few years of the project was spent working out the right types of methods to use to enable a functional Distributed Computing network.

The next step was to work in the latest range of clients (Playstation 3, SMP and GPU) which has been a big task to accomplish and still not perfected as of yet. An 'SMP2' client is the next target for the development team, with hopes that it will be similar to the transformation of the GPU to GPU2 client. Vijay comments saying -

"Our goal is to be bleeding edge in the nature of our science, but get back to the simplicity and stability found in the classic client"

Science wise, we are to expect some pretty big results very soon, with many research papers to be published after peer review is completed. Vijay comments -

"In particular, results on Alzheimer's Disease, Huntington's Disease, and some other surprises in the works"

So there you go guys, the real reason we are all folding hasn't been forgotten. Hopefully a lot can be learned from these future publicly-released research papers, and we can see the benefit gained from lending our CPU cycles!

Folding@Home Server changes plan to reduce downtime

Vijay Pande has posted some news on his blog about recent changes regarding the Collection Servers (CS), and also about plans for Server upgrades in the near future.

The Collection Servers have gotten a bit of tweaking, and have been moved onto a new network as the old one has had quite a few problems. Both Servers (171.67.108.17 & 171.67.108.25) are reportedly doing well for now. These servers act as backups when the Work Servers (where you download work units from) can't handle all the completed/uploaded work units, or when they are down.

The Folding@Home team also plan to issue general server upgrades with v5 code (currently in beta testing with Project 3798) early next year, with production Work Servers likely to be updated starting in January. This v5 code is being built from scratch and hopefully will result in much more stable servers for a more reliable Project network.

Increase in 'active' PS3 folders pushes Folding@Home past 4 Petaflops!

Sony's recent release of 'Life with Playstation' has played the major factor in Folding@Home passing the 4 Petaflops mark. The new update for the folding application on the PS3 has attracted many more 'active' PS3 folders than in recent months. The last time the PS3 had ~ 60,000 active folders would have been when Metal Gear Solid 4 came out, and since then, the numbers have slowly declined back to an average of ~40,000.

At the time of the 3 Petaflop breakthrough, The GPU guys were the major factor, and it has to be said, they've kept up consistent 'active' folder numbers, and even added ~ 300 Teraflops worth since then.

I personally would like to see 'active' PS3 numbers rise to ~ 100,000 and consistently stay there. Considering there is well over 10 million PS3 systems out there, i'm only asking for just 1%!

Taken from the OS Stats page -

Client statistics by OS

OS Type	Current TFLOPS*	Active CPUs	Total CPUs
Windows	207	217288	2191266
Mac OS X/PowerPC	6	7455	120622
Mac OS X/Intel	23	7580	64552
Linux	57	33374	333719
ATI GPU	494	4490	11195
NVIDIA GPU	1518	13802	32137
PLAYSTATION®3	1716	60867	621405
Total	4021	344856	3374896

Total number of non-Anonymous donators = 1085872

Last updated at Sun, 28 Sep 2008 05:04:09

DB date 2008-09-28 05:00:01

Problems with certain PS3 WUs? Server VSP06 was down

If your PS3 has had trouble returning work units from Projects 4044, 4045 (the big 1,250 pointers) & 4900 (310 points) then it's because a few days ago one of the four PS3 Servers, VSP06 - 171.64.122.73 was down. Vijay Pande had reported the server's downtime on his blog.

Looking at VSP06's log, the server was down between 7:45 PM PDT, Saturday 30 August and 3:10 PM PDT, Sunday 31 August. If your an East Coast Aussie like myself, then the times translate to 12:45 PM AEST, Sunday 31 August to 8:10 AM AEST, Monday 1st September.

So for approximatley 19 & 1/2 hours, the server was out of action, and it meant that if you had one of the above mentioned work units to return, you would've had to have waited for the server to start up again. Nobody should have had any problems receiving new work units however, as your PS3 would still have 3 different servers to download a work unit from.

PDT = Pacific Daylight Time = GMT-7
AEST = Australian Eastern Standard Time = GMT+10

Monitor your PS3 carefully!

Just as a warning, apparently a lot of PS3 folders have had troubles with certain work units, and experiencing funny things like title screens locking up, HDD activity taking way too long and more unfortunate results such as work units being lost, or a complete reset to default settings such as what I experienced!

It seems that Dan Ensign from the Pande Group has removed some problem work units saying:

'I'm going to pull projects 4026-4037 until I get a better sense of what's wrong, from our side. Sorry for the inconvenience.'

Watch these two threads (PS3 stalls at zero frames - various WUs & 4033 flatlined?) from the Folding Community Forum to keep updated on the situation.

GPUs push Folding@Home past 3 Petaflops!

Following a thread in the Folding Community Forums - Highwater Mark , it seems that the total project power of Folding@Home has now passed the 3 Petaflops mark!

This is quite a significant achievement for the project, as 1 Petaflop was only achieved back in September last year. It just goes to show how much the project has grown since then. The release of the more mature GPU2 client has been the significant factor in getting the project to the power it's at now and undoubtably it's also going to be the big push for the project in the next couple of years.

There has already been around 25,000 GPU2 client installs to date, with a healthy 16,000 of those currently 'active'. This easily gives the GPU clients the best active/total CPU ratio of any type. Most others are less than 1:10.

Now there was a bit of a discussion on whether this 3 Petaflops measurement was 'legit' as the whole Stats Server issue could have produced unrealistic figures, but thats seemed to have settled well and truly, and we are definitley past 3 Petaflops by more than a whisker!

The NVIDIA GPUs seem to have the most support at the moment, having ~9,000 more active folders than what the ATI camp has. This is most likely due to the fact that the NVIDIAs are being rewarded with a better PPD average than the ATIs, but then again NVIDIA does have a better market share in graphics cards. But they have also recently released a GeForce Power Pack (to show off special NVIDIA graphics card only features such as PhysX demos & CUDA-based programs) which includes the GPU2 Folding client. So that might have atleast spurred the last week or so's jump in total project power to over 3 Petaflops.

Looks like its time to invest in a little GPU folding action! Just a note though, the PS3 active numbers have really taken a dive lately, and i'd just like to indicate that although GPU systems now put out the most folding power for the project, the PS3 work units are still very important for the project's development, just like the old CPU client is still very valuable. So don't worry about the points too much, just fold however much you can, and know that your helping a very worthy project.

Taken from the OS Stats page -

Client statistics by OS

OS Type	Current TFLOPS*	Active CPUs	Total CPUs
Windows	199	209633	2138357
Mac OS X/PowerPC	7	8270	118934
Mac OS X/Intel	20	6468	59276
Linux	62	36482	326368
ATI GPU	366	3323	6439
NVIDIA GPU	1405	12774	18556
PLAYSTATION3	1111	39388	584773
Total	3170	316338	3252703

Total number of non-Anonymous donators = 1056777

Last updated at Thu, 21 Aug 2008 06:04:49

DB date 2008-08-21 06:00:03

Folding@Home over 2 Petaflops again and this time not stopping there

With the recent release of a GPU2 beta client for NVIDIA graphics cards, the OS Stats has soared ~250 Teraflops to a total project power of ~ 2.2 Petaflops!

The combined GPU stats (a GPU2 client already existed for ATI cards) now sit at around 450 Teraflops... Not bad for only ~4,000 active GPU folders. The good thing to see is that the project now has over 310,000 active folders, edging closer to 320,000.

Hopefully with more and more clients of different hardware compatibility, the project can accumulate more participants, push progress, and result in new research papers being released.

Congrats to Vijay's Folding@Home development team for the release of this latest client and also to those who are currently folding with a graphics card.