Folding@home

Frontiers in Biotechnology inverview

Frontiers in Biotech is a radio interview show.  Some time ago I recorded an interview with them and it's now available.  You can hear it at http://twit.tv/fib27 .  I've put their summary of the interview below as well.  I enjoyed the chat -- it was very lively and went back and forth between the world of computers/technology and that of drug design/biotech.  Marc is an expert in biotech (CSO at a biotech) and Steve is a well known expert in computer security, which made the conversation pretty diverse and interesting.

Futures in Biotech 27: Folding@Home at 1.3 Petaflops

Hosts:  Marc Pelletier and Steve Gibson

Guest: Dr. Vijay S. Pande, Director of Folding@Home and Associate Professor of Chemistry and of Structural Biology, Stanford University

Steve Gibson joins me in interviewing a true visionary of biotechnology: Dr. Vijay Pande. Dr. Pande is the creator and Director of Folding@Home, the world's largest distributed computing project (Stanford University) that seeks to address some of the most difficult problems in biology.

It is indeed a pretty amazing story: Sony PS3s are the largest component of the world's fastest computer, running approximately 3x faster than IBM's Blue Gene/L. And, the largest computations are being performed to simulate biology at the atomic level...

                    

Outage over, servers going back up

The power is back at our server room that had to go down.  The critical servers are back up and we'll bring the rest up later tonight or tomorrow (it's midnight pacific time, so it's getting late).

Planned power outage tomorrow (12/27)

One of our server rooms will be undergoing a planned power outage on December 27, starting in the morning pacific time.  We expect the outage to last about 5 hours.  We are on minimal staff right now due to the holidays, but we'll do all we can to keep FAH going.  Roughly about 40% of the FAH work servers will be affected during the outage, but the AS, stats, web page, etc will all be up.

New FoldingForum.org Update

The Mods at the Folding Forum have updated the forum with new functionality and a new look.  The URL is http://foldingforum.org (but the old url will go the new forum as well).

The mods are also working to get the content from the previous form so we can refer to it.  There's lots of information there (and it's referenced by other tools, such as the fahwiki).  Also, it's interesting to look back at the old days -- it's amazing how far FAH has come!

FAH PS3 update

A new version of Folding@home for the PS3 was released today.  You can learn more about it here:
http://blog.us.playstation.com/2007/12/18/new-foldinghome-features-coming/
but I'll post the update below as well in verbatim. 

Noam Rimon is the lead of the development team we work with at Sony and has played a critical role in the development of FAH/PS3 (in fact, he was the one who contacted me to consider the port in the first place and then helped push for it to happen).

Posted by Noam Rimon // Sr. Development Manager SCEA R&D

As we approach one million PLAYSTATION 3 consoles participating in the Folding@Home program, we continue to improve the FAH client. With the new Firmware v2.1 we also prepared an updated version of FAH, which can soon be automatically downloaded by clicking on the FAH icon. This updated version includes the following new features:

If you happen to be one of the people that wants to leave their machine running after they finished their late-night gaming session, but wish to shut it down after a limited period of time, we have a great tip for you:

• Go to Settings menu, select Automatic Shutdown and then After Current. You will see a little clock appearing on the top right hand corner of the screen. When this clock reaches zero, the machine will power off completely so you can sleep quietly through the night. In this option the machine will power off after sending the data back to Stanford University so your contribution to the project is maximized.
• You may also choose to shut down after a limited period of time (for example, 3 or 4 hours). To do that choose the Automatic Shutdown option and click on the “In 01h:00m” timer. You will now be able to change the timer settings. After rotating the timer to a new time, you should now see your selected timer appear at the top right corner of the screen. This timer will count all the way down to 0 and then power off the system.
• To disable active timer at any time, go to Settings, choose Automatic Shutdown and then Disable.

What’s a better Holiday addition to Folding than playing music? We’ve added a great feature in this version in the form of a background music player:

• To activate the music player select Music and then a channel. The channels are automatically populated with songs you have stored on your Hard Disk Drive! For holiday music I prefer to choose Dramatic (yeah!) and voila - music is playing.
• If you wish to skip to another track, just use a combination of X + left or right arrow. You can also change the channel by choosing X + up or down arrow. Happy listening!
• To stop music from playing, select Music again from the main menu and choose “disable.”
• Your music playback selection will be saved between consecutive runs of Folding@home.

We hope that these enhancements help improve your FAH experience. The response from PS3 owners really has been spectacular, and thanks to you, the most powerful distributed computer network in the world continues to grow.

          

FoldingForum.org forum upgrade

Forum mods have been working to improve the new forum and plan on upgrading the forum to phpBB3 on tuesday evening UTC (about 1800).  They will need to take the forum down for a couple of hours to do this, to make sure that a) we don't loose anything, b) that they don't break anything.

While the upgrade is in progress, they''ll set up a redirect that gives an info message with a link pointing people to the google group so people know what's going on.

Still digging out from the campus-wide power outage

We're still digging out from the campus-wide power outage.  This was as major disaster as Stanford could ever have, as the whole campus was out for a while, and chilled water was out even after power came back on.  Moreover, this hapened as everyone was sleeping (I logged off at ~11:30pm and this happened at 11:58pm), so there wasn't anything we could do to fix it until ~8 hours later.

We're pushing to get the CS's back first.  It looks like the main CS (171.65.103.100) is having hardware issues and we're working on that.  Having such a large-scale disaster has given us some ideas on how we can be more ready for this in the future, although there's already major investigations at Stanford to figure out what happened and how to prevent it (a campus-wide power outage is really not acceptable for an institution like Stanford).

Power outage throughout Stanford

There was a campus-wide power outage at Stanford last night.  According to facilities:

At approximately 11:55 PM Stanford lost power to all buildings on campus.  Power was restored at approximately 2:30 AM.

UPS's are wonderful things, but this really pushes the limits -- it's hard to keep FAH up if the whole campus is down.  Anyway, it looks like the backup systems did well and we have minimal clean up to deal with, from what we can tell.  We're still looking into this to see if there's anything we missed.

New forum

We've created a new forum at  http://foldingforum.org/ .  The plan is for this one to be a temporary forum, until we can get the old one back up.  However, we'll keep it around to serve as a temporary forum when the main one goes down.  The only caveat is that you'll have to re-register (sorry).  However, the FAH team and Mods are already set up there, so we're ready to welcome your posts.  Sorry to take so long with this -- many people (esp Bruce, Py, WW and some other mods and FAH team members) have been working hard behind the scenes to make this all possible.

I think we have a plan which will work long term.  This backup forum will always be there, and if needed, it could become the primary forum if we can't get the main one back up.