Messages from Prof. Vijay Pande

[Cirozorro]

All you have to do is add more systems to the one's you have.

Very true, D0M1N4T0R if you can't make it up to Number 1 you can join the rest of us vying for Number 10 spot at around 26-28000 ppd. I am sure next month the prize will be allocated randomly(so don't worry). That's usually how scott has done it, at least for the contest I have been in. I always have a hard time meeting the post requirement to be entered in though. This forum just isn't active enough for me to find enough opportunities to chime in, and I hate posting for posting sake.

I figure with only about 50 people to compete with, everyone will win something eventually.

[D0M1N4T0R]

Well, I mean right now I have over 100 discrete computers folding for me and that's still not enough to even come close to Vijay. I don't have unlimited resources. Obviously this is about cancer research and not just winning stuff, but I don't realistically see myself going beyond second place this month, despite my massive growth over the past little bit. The whole thing just seems stacked towards people with insane money for folding/render farms.

[Cirozorro]

Well, I mean right now I have over 100 discrete computers folding for me and that's still not enough to even come close to Vijay. I don't have unlimited resources. Obviously this is about cancer research and not just winning stuff, but I don't realistically see myself going beyond second place this month, despite my massive growth over the past little bit. The whole thing just seems stacked towards people with insane money for folding/render farms.

A couple High level Nvidia cards and Intel CPU's(990x, drool) would be more than enough to do it. You get insane bonuses for bigadv WU. Leganfuh is one of the top folders(he individually is in the top 10). He isn't using hundreds of clients(only 19) He deserves to win with those numbers, no render farm here.
He is getting an average of 2 million ppd with each one of his clients. Nothing but respect, and with a prize this nice, I don't blame him.( I only get 8k ppd with a quad amd, 7k with a radeon 6850, and I am seeing how the zacate e-350 folds right now.)

[Blacksmith1]

not trying to be nasty, but this is getting wayyy , to the point of being , so perhaps this conversation could be moved to it's own thread?

[Leganfuh]

Folding@home

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu
(c) 2007 Vijay Pande



May 01, 2011

One physical server down (vsp09), bringing down CS's

One physical machine (vsp09) is down, bringing down all of its related VM's (vsp09*). We're working on it and hopefully will be able to get it back up today, unless there's a more serious issue.
UPDATE: The machine is now back up and the main CS (vsp09a) is running. We are keeping the other CS's down, since the other CS's are now obsolete and have been integrated into vsp09a.

[Leganfuh]

Folding@home

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu
(c) 2007 Vijay Pande May 16, 2011

Best Practices FAQ

Folding@home (FAH) is a major scientific endeavor, but is also a kind of contest for some donors to see who can donate the most points. In order to keep a sense of fair competition, we asked donors to help us establish a list of rules, summarized on this FAQ page: http://folding.stanford.edu/English/FAQ-BestPractices .
These rules are stated below to engender the spirit of competition in a way that is impartial for all donors. We thank everyone for their contributions and hope they will enjoy competing and donating to the project.

[Leganfuh]

Folding@home

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu

June 15, 2011

update on v7 client progress

It's been a little while since our last v7 beta release (v7.1.24) and so I wanted to give donors some sense of what's going on. We've been working on internal testing of two releases past the current beta release and fixing bugs along the way. While we could in principle release v7.1.25 to open beta, there are enough todo items that we've decided to hold off a bit until it's a bit cleaner and further along. However, we're not going to hold off forever of course, just long enough for our developers to make some significant progress, especially since doing a release generates a lot of feedback, which takes developers away from coding.
To give some sense of where we are, here's the internal release notes for two recent builds (v7.1.25 and v7.1.26). Note that v7.1.26 is still in progress. Also, the #'s after the comment refer to our bug tracker. We have opened up the bug tracker, so one can see progress directly there on a daily basis if you're interested.

v7.1.26 (still under development):
* Failed upload attempt could cause WU to dump before it was expired. #679.
* Added AMD Radeon HD 6600 Series to GPU white-list.
* Fix failure to restart FAHControl in OSX when 'start minimized'. #649.
* Fixed a socket bug that could cause the loss of the end of a message.
* Build OSX client in 32-bit mode with Intel compiler.

v7.1.25:
* Hide 'Quit on window close' option in OSX.
* Fixed some problems with WU assign time and time offset calculations.
* Detect and ignore invalid assign time from older WS.
* Log computed WS time offset.
* Removed warning from Slot configuration about changing threads mid-run.
* Catch and log error accessing battery info in /sys on Linux
* Fix grayed out name and IP in client add after viewing local client. #640.
* Remove 'RS480 PCI-X Root Port' from GPU whitelist. #635
* Added a few new Radeon HD 6xxx cards.
* Added Nvidia GTX 590 device ID 0x1088 to whitelist.
* Increase Radeon HD 5xxxx and 6xxxx GPU type level by one. #653.
* Don't fail WS connections if all data was recieved even on net error.
* Print IP Address with 'Uploading' message.
* Fixes for OSX minimize and quit bugs. #649 & #659.
* Limit max CPUs per slot to system count. #652.
* Attempt to fix #654.
* Release system resources when querying OSX battery status. #650.
* Don't send 'auth' command from FAHControl if empty. #658.
* Fixed 'slot-add' NULL pointer exception. #666.
* Fixed 'log-updates start' error. #671.
* Fixed FAHClient script parsing bug. #676.
* Show 'Remote Access' tab in advanced mode. #648.
* Don't allow minimizing to sys-tray if it is not there. #670.
* Also print core return code numbers in hex. #677.
* Print times in ISO 8601 format. #664.
* Expire WUs in sending status.

[Leganfuh]

Folding@home

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.eduJune 22, 2011

Changes to donor ranking on the Stanford stats web pages

We have been making changes to the donor ranking on the Stanford stats pages to work to reconcile them with the 3rd party stats. The central issue at hand is how does a given stats system handle accounts with multiple passkeys. A more detailed discussion can be found in this discussion thread.
We are working directly with 3rd party stats to come up with a solution that works for all. For now, we have made one change which brings them closer, but not completely in agreement. However, donors who pay close attention to the Stanford site will likely see a big change in their ranking. We're posting this blog post to give donors a heads up on this issue and some information of what's going on behind the scenes.

[Leganfuh]

Folding@home

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu
June 25, 2011

Stats db reset this morning – stats updates running again now

The stats db hung last night around midnight pacific time. We saw that it was down this morning (we get emails from the stats system when there hasn't been an update in over 2 hours) and we restarted the stats db. A stats update is now in progress and should continue to run.
We will keep an eye on this over the weekend in case there's some greater systemic problem here. Please note that we have a reduced admin staff on the weekends, so response will be a bit slower.

[Leganfuh]

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu

July 02, 2011

Change in the points system for bigadv work units

For new bigadv WUs, we have changed how the points are calculated to bring them back into balance with the rest of the points in Folding@home. There are more details in this post:
http://foldingforum.org/viewtopic.php?f=24&t=19059
The main jist of the change is that we are decreasing the points associated with bigadv WUs, from 50% over SMP to 20% over SMP. As with previous points changes, this deals with only new WUs to go out, not with WUs that have be collected, etc. I want to stress that the bigadv program is still continuing, but that, as we've mentioned before, this is an experimental program and subject to changes.
It's clear that any change to the points system is controversial, but this one has been raised as a very serious problem by many donors. After investigating the issues raised, we agreed that this was significantly out of balance, and made this change. Moreover, the feedback we have gotten is that we make a change soon and do so quickly, like "removing a bandaid" rather than drag out the pain. I'm sorry to have to make any changes at all, since any change is disruptive, but we (and many donors) felt very strongly that this change was very important.
The other change that we have in mind to do is to bring all classic and GPU WUs into the Quick Return Bonus (QRB) system. This would help further bring all FAH projects into balance. There may be some issues with GPUs and QRB, so we are looking to see what we can do to minimize problems with that before making a change in the points for GPU WUs.
Finally, I would like to remind all that we do listen to donors and take their input very seriously. There has been extensive discussions about the problems with the points system with the huge PPD's seen with bigadv (sometimes reaching 500,000PPD) and the lack of QRB for GPUs being major shortcommings.
Considering the great variety of donor opinions on this matter, it is no surprise that we agree with some donors and disagree with others. Moreover, with points, there will never be any system which makes everyone happy, but our goal is to try our best to balance the project as a whole, taking donor input seriously, and making hard calls when we feel it is necessary. This was definitely a hard call, but hopefully in time donors who disgaree now will come to understand the issues raised by the other donors and appreciate their point of view.

[Blacksmith1]

Not to offend anyone,but it's about time. the points thing has stuck in my craw since they first started giving those huge bonuses to the bigadv projects. of course I was more than happy to take my SMP bonuses which those on gpu only or uni clients probably thought was unfair.

[James86]

we might see a big drop in Leg's PPD

[Blacksmith1]

Not so much, this is more to slow down the guys that are doing the magny-cours servers and getting 500,000 PPD from one box, Mike's farm should still produce a decent amount of PPD ( tho' it will take a hit)

[Leganfuh]

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu

July 25, 2011

New serverstats page

We've developed a new serverstat page, which we're now suggesting as a replacement for the old one. The new one is more asthetically pleasing but also has a lot of changes under the hood to allow for more reliable and faster updates.
We're keeping the old serverstat page link pointing to the old page (i.e. no change) in case there were scripts that were parsing the old page. However, we've set the new page to update every 10 minutes and the old one to only update every hour. We will keep the old page up for at least two months to give 3rd party utilities a chance to update their code and to give us feedback (please post feedback to http://foldingforum.org ).

[Leganfuh]

A blog all about Folding@home, from its Director, Prof. Vijay Pande
http://folding.stanford.edu

August 05, 2011
Results page updated – new key result published in our work in Alzheimer's Disease
We have made a major update to the Results page on the Folding@home web site. We now list 95 papers that have directly resulted from Folding@home, although we note that there are 193 papers from the Pande group in general. There are many new results to talk about, but I will just highlight a few below.
One major result is in the area of Alzheimer's Disease (paper #95). It is believed that Alzheimer's Disease results from the misfolding of the Abeta peptide. Understanding how Abeta misfolds could give us some key insights into how to cure Alzheimer's Disease. This paper experimentally tests a key prediction made in an earlier paper (paper #58: "Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach" by Nicholas W. Kelley, V. Vishal, Grant A. Krafft, and Vijay S. Pande. J. Chem. Phys. 129, 214707 (200; DOI:10.1063/1.3010881). In this paper, we show experimentally that there appears to be a beta turn in the Abeta as predicted. This leads to a very stable form of misfolded Abeta which could be used as a starting point for a new Alzheimer's therapy. We are heavily pursuing this research direction at the moment.
Another key result is in the area of methods (paper #93). We are constantly honing our methods to improve Folding@home's ability to predict the behavior of proteins. This paper demonstrates the current state of the art in terms of both sampling and analysis. When compared to detailed TTET experiments, we show that our methods can piece out even fairly detailed aspects of folding. However, we also see the ways in which our models are not perfect, suggesting how we can improve our methods even further.
We'll highlight other papers as time goes on. I'm particuarly excited about these results. In particular, the results from paper #95 were first discovered several years ago, but we carried out several followup studies to verify them, etc. As always, I'm most excited about what we're doing now and hope to get some of our current key results in theses areas out from peer review soon.