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.

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."

Scheduled Maintenance at SU during the Holidays

Vijay has given us a heads up on his blog about some Scheduled Maintenance that is going to be performed over the Holidays period at Stanford University.

The Network Backbone is to undergo improvements between maintenance windows - Every morning between 4 AM and 8 AM PST, December 20 to January 4 (For us East Coast Aussies - every night between 11 PM and 3 AM AEDT, December 21 to January 5) and it is hoped that normal operations should not be affected at all by the works. If users experience troubles though, it should only last up to around 5 minutes.


PST = Pacific Standard Time = UTC-8
AEDT = Australian Eastern Daylight Time = UTC+11

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.

Main Assignment Server was down temporarily

Reading Vijay Pande's blog (posts 1 & 2), it seems the Main Assignment Server was out of action for approximately an hour, which wasn't to worry as they have other backup servers in place for times like these. This all happened at approximately 4:30 PM PST November 21 (so just before lunch, 11:30 AM AEDT, November 22 here on the Aussie East Coast!)

The main consequence is that the Stats system had to hold off updating for a while, so the Team/Donor stats might not have appeared to update for a few hours. All work unit credits were still counted, but they just might have taken a while to get credited to the Stats system. All should be good now.


PST = Pacific Standard Time = UTC-8
AEDT = Australian Eastern Daylight Time = UTC+11

PS3 Server 171.64.65.83 Reset

Just over half an hour ago I switched on smASHer88_PS3 to successfully download a new work unit - Project 5308 Run 40 Clone 848 Generation 5. Lahm_Family_PS3 then downloaded Project 5308 as well, Run 35 Clone 854 Generation 8.

Reading Vijay Pande's blog, he's told us that they've reset server 171.64.65.83 and that seems to have fixed the PS3 downloading troubles we've been having. I dare say this particular server didn't boot up properly after the scheduled server outage they had a few days ago. There looks to be another scheduled server outage for 171.64.65.XX network on November 5, 7 AM to 8:30 AM PST (2 AM to 3:30 AM, November 6 for us on AEDT) so if ya have some issues then, hopefully it will pass quickly.

PST = Pacific Standard Time = GMT-8
AEDT = Australian Eastern Daylight Time = GMT+11

EDIT: Seemed to be a 3-4 hour period after my two 7hr work units finished where they wouldn't then download another new work unit! However i've turned them back on yet again to download new work units. I seriously hope these troubles are behind us now for the PS3! Haha

PS3 Servers seem to be down

If your PS3 is saying "can't connect to Server" then your not your own. It seems to be another small problem with the servers as many people have reported on the Folding Community Forum. Less than a fortnight ago, PS3 folders experienced the same problem, and it was given a short-term fix.

So hold tight guys, hopefully the Stanford guys are working on fixing this problem as we speak, as it is daytime there now. I'm sure Vijay will give us some official news soon. I have shutdown both my PS3s for now, and will keep checking one of them every now and then and post back when i have success in downloading a new work unit! Haha this doesn't really help our Foldathon, but oh well, gotta keep crunching away best we can!

PS3 work unit downloading issues given short-term fix

If you fold using a PS3, you probably would have noticed just lately, in the last few days or so that your system may have had troubles downloading a new work unit. It seems the servers have been temporarily out of 'jobs' or work units to dish out.

Reading Vijay Pande's blog, Stanford have implemented a short-term fix for the issues, but no comment as to exactly what is wrong.

I had both my PS3s switched off for two days, turning them back on every now and then to see if a new work unit could be downloaded. Last night both PS3s successfully downloaded new work units, one after 1 retry, the other straight away. As far as I can tell, both have been trouble free since. So if you currently have your PS3 down, waiting for these issues to pass, switch her back on, everything should be smooth sailing for now! lol

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

New Folding@Home Clients Installation Guides

A new page of Client Installation Guides has been added to the Folding@Home website, making it easier for newcomers to install anyone of the various types of folding clients that are now available.

Existing folders can also benefit, whether it's adding an SMP or GPU client to the mix, these new guides will certainly help ease the process! Remember you can always visit the Folding Community Forums as well should you need further help, or just want to provide some feedback on your experiences.

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.

Stats Update delayed due to Power Outage @ SU

Reading Vijay Pande's Blog (particular posts 1, 2 & 3), it seems just yesterday or so, Palo Alto (and therefore Stanford University) has had a pretty serious power outage! It took a fair few servers out of action for a short while, but most are back up now.

One exception though, the Stats Updates server is not operating at the moment. This server usually just updates the Team/Donor stats database every hour, but its just being put on delay for now. A back-logging server is keeping all this information however, so once the updates server starts back up, the database will get updated and you will notice your points and work units count go up two or three days worth to make up for this period of in-activity.

Geez, that'd be chaos at a University! But they seem to be able to fix things up pretty quick which is good.