Folding@home

Optimizations to stats web pages

In preparation for the migration to the new stats db, we have been doing some profiling on the stats db to see where we can get the most speed up.  We have found a few items that we're working on to increase speed.  The hardware improvement will make the biggest advantage in general, but now is a good time for us to try to get the stats system lean and efficient, since profiling afterwards will be harder (and any efficiencies we can squeeze out will help years from now when the new hardware is underpowered for the new stats load).

So, from the donor perspective, you will at first see the results of some experimenting on our side to improve the throughput (i.e. may be some bugs too), but hopefully there will be some throughput benefits even in the short term.

Finally, we have noticed that there are many web clients pounding our stats system, some doing 10,000 accesses per day and many doing 1,000.  These IPs will be banned, so please turn off any scripts you have doing automatic access.  "Normal" access is assumed to be up to 50 accesses a day.  There's no need to do 1,000 or more and it really bogs down the stats for everyone else.

If you're looking to get access to our stats system, please check out our FAQ entry on this issue.

UPDATE:

We've turned off certain stats page functions dealing with queries relating to the number of CPUs.  We have also stepped up the caching of team pages (all team pages are cached for 60 minutes).  This will make a major performance win in the stats db and so far is looking to help a lot.  

So, in fields which we are temporarily not showing on the web page, you will see a N/A.

This change is temporary since the cause is clear:  our db keeping track of items like specific cpus is way too big, due to the millions of CPUs that have participated in FAH.  This won't be a problem with the new servers, so we will just turn on these features after we migrate.  For now, turning off this parts of the stats pages will help a lot until we switch over.

Machine went down last night, affecting others. Reset this morning.

A machine went down last night, which brought down vspg1, vspg1v, and vspg1v2 (these are all different virtual interfaces on the same physical server).  Our admins (working during the holidays -- thanks to them for their hard work) reset the machine this morning and we got the machines going again.

While vspg1* were down, this lead to a much greater load on other machines, causing issues for vspg2v2, vspg4v2, and vsp07v.  These reset themselves some time around 7:30am pacific time (with the exception of vsp07v, which I reset).

So, it looks like the server farm is settling down.  I can't wait until we get the new, really powerful machines loaded up with jobs to help take over some of this load.  Some of the jobs being tested right now are on those machines, so that should be very soon.

Note that during the holidays (especially the next week or so), we have a limited staff in the office, but those that are working are diligently looking for problems.  Happy Holidays!

Release of new Protomol (Core B4) WUs

As announced some time ago we have been working on a new core (Protomol core B4), and it has been looking good in QA so we have started to release Promol core WUs more broadly.  We have a preliminary Protomol FAQ for those who are curious to get more information.

This new core implements the NML (Normal Mode Langevin) method which accelerates the long-time dynamics of the proteins by a factor that can reach speeds up to a hundred times faster than those of molecular dynamics. This method searches for low frequency directives by using normal mode analysis and projects the motion of the molecule along them while resolving the nearly instantaneous motion. If you want to learn more about this method, you should read this pre-publication: Multiscale Dynamics of Macromolecules Using Normal Mode Langevin.

Based on Protomol 3.1, this core and its associated projects have the following goals:

• To validate NML by simulating the folding and dynamics of the Fip35 WW domain.
• To understand the role of mutations on folding.
• To understand the activation of src Kinase, an enzyme that is involved in the onset of some kinds of cancer.
  

For more information about the Protomol core, you should visit the Protomol official site.

The new projects are distributed by a new server (129.74.85.48) which is located at the University of Notre Dame (Indiana) and have the following characteristics:

• p10000 : 544 atoms, 84.48 points, preferred deadline 3.07 days, final deadline 23.04 days. This project uses conventional simulation methods.
• p10001 : 544 atoms, 50.56 points, preferred deadline 1.84 days, final deadline 13.79 days. This project uses the NML simulation method.

We will be posting more information as time goes on.   I'm very excited about the new capabilities here, since NML allows us to algorithmically get an amazing speed up, i.e. without any additional CPU power.    That algorithmic speed up multiplied by the vast power of FAH could mean very significant advances shortly, making 2010 an exciting year for FAH (in many ways)!

New changes to psummary

We have made some changes to the psummary generation scripts so that they can support the v5 servers and in general fix some bugs.  This is a complete, clean rewrite of a very, very old script (10 year old perl mess), which also bodes well for future fixes and changes.

Joseph Coffland (a software developer on the FAH team) has been working on this and has opened a thread to discuss this with third party developers:

http://foldingforum.org/viewtopic.php?f=18&t=12489&start=0

IMAG meeting today -- The Impact of Modeling on Biomedical Research

I'm at NIH today for the IMAG meeting on the Impact of Modeling on Biomedical Research.  IMAG stands for the Interagency Modeling and Analysis Group and it constitutes all of the science major funding agencies in the US (NIH, NSF, DOE, and more).  It's a great idea to get these agencies together and well-coordinated in terms of their approach to computer simulation and modeling.

In the meeting, they've broken down all of modeling into 5 scales, and I'm chairing the atomic and molecule scale.  Our charge is to talk about the future of modeling and I'll be highlighting some of the key new results from Folding@home.

For more information, please check out:

http://www.imagwiki.org/mediawiki/index.php?title=IFM_Announcement

main web page issues

We're seeing some issues with the main http://folding.stanford.edu web page.  We have some ideas, but it's late here (11pm pacific time), so we'll have to wait for IT to get in to work in the morning to get a fix implemented.

For now, if you see "Access Denied", please try to reload the page: that should yield a working page.

UPDATE:  9am Dec 9 
Stanford ITS has sent me an email saying that this is now fixed, but it doesn't look like that to me (although it is better).  I have informed them that it isn't and am waiting on them.  For now, you can hit retry until you get the page you want, but clearly this is still broken badly.

UPDATE:  Looks like this has now been resolved.

SMP2 core update

We are excited to announce progress in our testing of new SMP2 cores. These cores use threads-based parallelization instead of MPI and, we hope, should be much more robust than our first-generation SMP cores. 

The SMP2 cores are currently in testing; watch for future announcements regarding their release. The first SMP2 core to be released will be a Gromacs-based core with core number A3. In conjunction with this release, we are implementing some updates to our points benchmarking system. In particular, we will use early-completion bonuses, which we have been testing with the bigadv work unit program, more extensively for SMP2 cores.