FAH vijesti

Esh · Nov 7, 2008

Folding@home/PS3 wins "gold" award at the Good Design Award competition

We're happy to announce that the PS3 client for Folding@home has won a prestigious design award:

The PS3's Folding@home service has nabbed a prestigious Good Design Award, AKA "G-Mark." Since 1957, the Good Design Award has been instituted by the Japanese Ministry of International Trade and Industry to award outstanding design in industrial and consumer products.
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http://www.scei.co.jp/corporate/release/081106de.html

Esh · Nov 12, 2008

Engineers at NVIDIA (notably Scott LeGrand) have come up with a theory for the EUE's seen in core 1.15 (and a few others in the 1.15 to 1.18 range) on certain hardware. They found that this core had code optimizations that drove the GPU so hard that it would draw a lot more electricity (one sign of this was running hotter). In some boxes, this was too much electricity and this lead to numerical instabilities. When the same machine was given a beefier power supply, the problem went away.

We've been told that 8800's require 600W power supplies, but we're finding that even a little bigger (eg at least 650W) is important to leave some room for error. We are working to see if there is some way to detect this issue in software, but for now, if you're getting EUE's on the NV GPU client, this is something to consider.

By the way, this will be very important for us to consider future code optimizations. NV core v1.19 removed some optimizations to solve this problem, but there are many cards which would run fine w/this more optimized code. If we can find a way to detect whether the card can draw enough power, we may be able to choose different code paths to allow for greater optimization for cards which can handle it.

We're still looking into this. For now, if you're seeing issues with your card, please consider trying out a bigger power supply. We will continue to look to see if this is indeed the problem and what we can do to help the situation such that the code runs stably on all machines.
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GW · Nov 12, 2008

Ovo je smiješno. Ne smiju optimizirati kod zbog prevelike potrošnje. Možda zato ATI neće da optimizira drivere za folding. Da se ne zapuše kartice.

Stevie_Ray · Nov 12, 2008

Hm, to je nesto novo, ili samo ukazuje na problem?

Taman mi stize 8800GTS 512, pa ne bih da ubije ubogog Corsaira.

nFare · Nov 12, 2008

Ne znam je li iko od vas vec dobio jednu ovakvu jedinicu, ali kako redovno dobijam ove "25 000" neki dan primjetih "10 000" u trayu i doslovno je trebalo nekoliko sekundi da se otvori media player a kamoli sta drugo, nije se moglo normalno raditi za kompom, temp grafe sa uobicajenih 78c je skocila na 86c sto bas pokazuje veliko opterecenje. Kontao sam postaviti pitanje kako se odbacuje neka jedinica ali eto pustio sam da to odradi i prezivjelo je sve
Zasigurno bi izgubili veci broj "foldasa" ako bi nastavili sa tim optimiziranim jedinicama.

dino73n · Nov 12, 2008

Ja evo upravo meljem jednu takvu od 10 000 i sijalice u kuci mi zmire :mrgreen: ,jedva surfam sve se vuce ko prebijena macka temperatura grafe nikad veca .

artemis · Nov 12, 2008

Poceo sam dobivati te velike od 10.000.Temp. grafe neznatno visa,ali zato cvrci od muke...

Moncho · Nov 13, 2008

a ppd je znatno nizi za te 'nove', sto je razumljivo sasvim

Mah neka oni prave, pa ko nema 1kW napajanje doma, neka si odmah puca u potiljak

Esh · Dec 6, 2008

Long term vision for FAH: Science, clients, etc

It's been a while since I've posted on this topic, so I thought it would be a good time to talk about the long term vision for FAH. In the first few years, we have done a lot to build up methodology (novel distributed computing algorithms, tests of methods), especially in the last years working to bring GPU's, PS3's, and tightly coupled SMP calculations to a distributed computing platform. While all of this has been going on, there has been a lot of work which would have a direct impact to disease and human health, and donors should see more results (i.e. papers) coming out in this direction soon. In particular, results on Alzheimer's Disease, Huntington's Disease, and some other surprises in the works (sorry, some details are best left until peer review is done).

In terms of a long term vision for the FAH software, our short term goals is to shore up the SMP client. Just as there was a big improvement from the GPU1 -> GPU2 client, we have been working steadily on an SMP2 client -- a version which is much easier to use, requires less donor effort, and scales much better. This really is a combination of a modified client and (especially) new cores. This effort has been going on for about a year and it's far enough along that I'm starting to talk about it publicly.

In the previous post, I also mentioned about some of our work behind the scenes in revamping the backened of FAH, i.e. a whole new set of server codes. We have code for the workserver and collection servers, but in time we expect the full backend to be cleanly rewritten from scratch.

Longer term, with a more solid GPU2 and SMP2 clients done, we can then move on to other areas. 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. We still have a ways to go, but I am excited that projects that were started some time ago are now looking like they will see the light of day.
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Link: http://folding.typepad.com/news/2008/12 ... s-etc.html

Stevie_Ray · Dec 6, 2008

Yup, zbilja fali posten SMP klijent. :|

Esh · Dec 9, 2008

Folding@home Alzheimer's Simulation work published

Za oni koji cekaju na "konkretne rezultate" FAH projekta:

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

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 (2008); DOI:10.1063/1.3010881

url: http://link.aip.org/link/?JCP/129/214707
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Abeta misfolding and aggregation is believed to be the cause of Alzheimer's Disease. Simulations, like Folding@home, are a natural way to understand this process. However, there are several key challenges for simulating the key step -- oligomerization. This work represents a new way to simulate Abeta oligomerization, with a key advance of being able to simulate experimentally relevant timescales and concentrations, using a novel method. We use this new method and the power provided by Folding@home donors to simulate oligomerization in all-atom detail. This has lead to specific predictions about the process, which we are now testing experimentally.

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.

GW · Dec 9, 2008

Odlično je kad znaš da si dao doprinos za ovakve stvari.

kolinsb · Dec 12, 2008

potpisujem! evo vec mi herc tandrce, kad znam da sam doprinio necemu ovog tipa :smt003

Esh · Dec 13, 2008

New paper #59: Ribosome gate

Jos dobrih rezultata FAH projekta pa ko voli znati:

Side-chain recognition and gating in the ribosome exit tunnel by Paula M. Petrone, Christopher D. Snow, Del Lucent, and Vijay S. Pande. Proceedings of the National Academy of Sciences, USA 2008

http://folding.stanford.edu/English/Papers (#59)

This one deals with the ribosome. 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). One of the questions revolving around ribosome function is why is there a large tunnel inside the ribosome, through which proteins exit after being synthesized. In this paper, we used "bigWU" classic clients (clients which allow larger systems to run) since the ribosome is so huge that it would not run on regular classic clients.

The primary goal of this paper was to analyze the surface of the ribosome tunnel. Understanding the nature of this surface would be useful for both understanding the fundamental nature of protein synthesis as well as how key antibiotics interact with the ribosome. An interesting related discovery was the identification of a potential "ribosome gate" which can open and close selectively, based on what is interacting with the gate. This suggests novel hypotheses for several aspects of ribosome function as well as interesting new directions for work on studying the ribosome and for new routes for antibiotics.
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Esh · Dec 13, 2008

Accelerating Molecular Dynamic Simulation on the Cell proces

Evo dobar rad na temu kako je Cell procesor pomogao u istrazivanju:

Accelerating Molecular Dynamic Simulation on the Cell processor and PlayStation 3
by Edgar Luttmann, Daniel L. Ensign, Vishal Vaidyanathan, Mike Houston, Noam Rimon, Jeppe Øland, Guha Jayachandran, Mark Friedrichs, Vijay S. Pande.

http://folding.stanford.edu/English/Papers (#60)

'In this paper, we detail how we were able to get great speed increases for Folding@home (and actually certain molecular dynamics calculations in general) on the PS3. This is our first paper using the PS3, laying out the "how does it work," with a follow up paper in the works describing the results obtained in FAH from PS3 clients.

It is also worth noting that this paper is a collaboration between FAH team members (Luttmann, Ensign, Vaidyanathan, Houston [now at AMD], Jayachandran, Friedrichs, and Pande) with developers at Sony (Rimon and Øland and their coworkers).

Here's the more technical abstract as well:

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.
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Esh · Dec 22, 2008

Nakupilo se par zanimljivih vijesti pa idemo redom:

Novi klijent za ATI kartice:

We have made several bug fixes and speed improvements wrapped into a new ATI GPU client (version 6.23). We strongly suggest that everyone upgrade. While current (and new cores, especially ATI GPU core version 1.22) should work with other clients, we are seeing some possible issues which the new client fixes.

As always, we suggest that one backup their machine before upgrading software, especially in case you would like to go back to the previous version. You can download the new client at

http://folding.stanford.edu/English/DownloadATI

and as always, please post comments in the forum (http://foldingforum.org).

PS For those with NVIDIA GPUs, you could also consider upgrading to client version 6.23 (from http://folding.stanford.edu/English/DownloadWinOther ) as it also fixes some issues. However, this is less of a critical at the moment for NVIDIA than ATI.
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Kroz naredne dvije sedmice najavljeni su kratkokrajni prekidi, ne bi bilo utjecati na proces obrade/slanja/primanja

Planned maintenance for Stanford network over the next 2 weeks
During the next two weeks (December 20 - January 4), the Backbone Networking group plans to schedule a backbone maintenance window every morning from 4-8am pacific time to implement improvements in the network, as they did last year. In most cases, the changes should not affect the connectivity of the networks used by Folding@home. In cases where they might, any interruption in service should be under 5 minutes.
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I za kraj najvaznija vijest od svih, o znacajnom napretku u pronalasku lijekova za borbu protiv Alzheimerove bolesti!

This is very preliminary news, but something I'm very, very excited about, so I'll give some advance 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 (http://proteinfoldingcenter.org/) 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. Happy holidays to all!
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GW · Dec 22, 2008

Stvarno dobre vijesti.

Esh · Jan 4, 2009

Computational screen to identify important mutations in infl

We're happy to announce a new Pande Group paper (paper #61 at http://folding.stanford.edu/English/Papers). This paper describes a new computational screen to identify important mutations in influenza:

Combining Mutual Information with Structural Analysis to Screen for Functionally Important Residues in Influenza Hemagglutinin.
Peter M. Kasson and Vijay S. Pande. Pacific Symposium on Biocomputing 14:492-503(2009).
Download URL: http://psb.stanford.edu/psb-online/proc ... kasson.pdf

The influenza hemagglutinin protein performs several important functions, including attaching the virus to cells it will infect and releasing the viral genome into the interior of the cell. Most protective antibodies against influenza also bind to the hemagglutinin protein. We wish to understand how mutations to hemagglutinin affect viral function, including what keeps avian influenza ("bird flu") from being readily transmissible between humans. In this paper, we have applied a technique from information theory known as mutual information to genetic sequence data to predict important mutation sites on the hemagglutinin protein. In follow-up work, we are combining this technique with other methods to refine these predictions and test some of them using Folding@Home.
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PS For those curious out in more details, check out the paper (see link above) or the technical abstract:

Influenza hemagglutinin mediates both cell-surface binding and cell entry by the virus. Mutations to hemagglutinin are thus critical in determining host species specificity and viral infectivity. Previous approaches have primarily considered point mutations and sequence conservation; here we develop a complementary approach using mutual information to examine concerted mutations. For hemagglutinin, several overlapping selective pressures can cause such concerted mutations, including the host immune response, ligand recognition and host specificity, and functional requirements for pH-induced activation and membrane fusion. Using sequence mutual information as a metric, we extracted clusters of concerted mutation sites and analyzed them in the context of crystallographic data. Comparison of influenza isolates from two subtypes—human H3N2 strains and human and avian H5N1 strains—yielded substantial differences in spatial localization of the clustered residues. We hypothesize that the clusters on the globular head of H3N2 hemagglutinin may relate to antibody recognition (as many protective antibodies are known to bind in that region), while the clusters in common to H3N2 and H5N1 hemagglutinin may indicate shared functional roles. We propose that these shared sites may be particularly fruitful for mutagenesis studies in understanding the infectivity of this common human pathogen. The combination of sequence mutual information and structural analysis thus helps generate novel functional hypotheses that would not be apparent via either method alone.
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hurmash1ca · Jan 6, 2009

We have switched the stats (points) update to occur every 3 hours instead of every 2 hours. The reasoning here is that it takes about an hour to update the stats, and so doing this every 2 hours means that the stats are accessible only 1 out of every 2 hours. However, doing the stats update every 3 hours doesn't take that much longer to update the stats (1 hour and 15 minutes vs 1 hour) and so this should make the stats more available. The reason it doesn't take that much longer is that the stats update is done in batches by project to help db thrashing in and out of memory and so once a project db is in memory, it doesn't hurt to push through more stats.

We're going to try out this new schedule to see if this bears out. If not, we'll go back to the old schedule.
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Odsada update na oficijelnoj F@h statistici svaka 3 sata, umjesto 2 dosada. Dobar potez, uvijek kad hocu otici na oficijelnu statistiku - potkaci me update i sipak, nema.

GW · Jan 6, 2009

Meni i sad potrefi update. :x

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