News

Help, my CPU slot no longer folds !

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Help, my CPU slot no longer folds !
Recently, your CPU slot might have stopped folding with the following messages in the log :

Citation:
Connecting to 171.67.108.45:8080
Failed to get assignment from '171.67.108.45:8080': Empty work server assignment
Connecting to 171.64.65.35:80
Failed to get assignment from '171.64.65.35:80': Empty work server assignment
Exception: Could not get an assignment

In its default behaviour, the client always configure automatically the CPU slot to use fewer threads of the CPU than the total available :

  • if you have a GPU slot, the client reserves 1 thread to feed it
  • if you use little aggressive settings (Folding Power set to Light or Medium), the client will not use all threads

This behaviour usually creates a non even number of threads to be used for the CPU slot (if you have an 8 threads CPU, the client will attempt to use at most 7) which implies compatibility issues with a lot of simulated systems when this odd number is a prime number. This limitation comes from algorithms used by Gromacs (the science code) to decompose the system in parts computed by each thread. To determine the supported combinations, the researchers relied on returns from testers for each project and set up the assignment servers accordingly. Gromacs used to work well from 1 to 8 threads, then for every value that didn't contain a prime greater than 7 when factored (this means that all prime numbers greater than 7 were excluded).

Lately, the Folding@Home project started to follow official Gromacs recommendations more strictly, which exclude odd prime numbers greater than or equal to 7 from supported decompositions.

If you are in this situation with you CPU slot, the workaround is quite simple. You just have to change the automatic behaviour of the client (-1 value) to a forced setup (6 threads instead of 7 if you use an 8 threads CPU for instance) with the following method :
In FAHControl, click on Configure.
In Slots tab, select the CPU slot and click on Edit.
Near the top of the window, change the number of CPUs.
Click on OK then on Save.

If you need further assistance to configure your client, do not hesitate to post on our forum.

Ongoing maintenance on Folding@Home servers

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As mentioned on the official Twitter account :

A few key servers for Folding@Home project (the AS ones) are in maintenance for a few hours. Don't freak out, everything will be back online soon !

Source : Vijay's blog

EDIT : 27/08/2013 12:30pm UTC

Maintenance has been longer than expected due to network hiccups encountered after the servers were restarted. But today at about 2 am UTC, almost everything has been reactivated and things have been progressively doing better. Vijay Pande has officially announced it on Twitter after two intermediate messages :


You should keep in mind that some type of WUs are still causing issues : for instance, I’m still unable to send or get work for my old nVidia GPUs (pre-Fermi).

Source: Vijay’s blog

EDIT : 27/08/2013 8:00pm UTC

As we already noticed in previous update, VSP07 server, which handles WUs mainly for core 11, is still broken. System administrator of University are still working hard to fix it and put it back on line.


Source : Vijay's blog

FAHcon 2012 : Professor Peter Kasson

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During Folding@Home conference 2012, Professor Peter Kasson of University of Virginia presented his work on the influenza virus and he explained why this virus attracted so much attention.

First, the influenza virus kills about 40 000 people in the USA every year and many more worldwide. These are mostly children under 2 and adults over 60. This is obviously something that concerns us because everyone hopes to have children in good health and to live beyond the age of 60 … Second, influenza has proven track records of causing global mass-mortality, such as in 1918. A similar virus today could easily kill much more than 60 million people and we’d like to be prepared. Finally, the influenza virus is an interesting model for understanding other viruses such as HIV and cancer-causing viruses such as HPV (Human papillomavirus), Heptatitis C, and Epstein-Barr virus. It might surprise you, but many cancers are associated to a virus and these form an important area of prevention.

Folding@home has done a lot of work on how influenza virus enters into cells to replicate. This is an important therapeutic target and it is critical to understand why some viruses like H5N1 (“bird flu”;) have not become efficiently transmissible between people. Some of the recent work on the topic focuses on the folding of the cell membrane which is necessary for viral entry. Professor Kasson’s team obtained interesting results and we will post a news article when they are published.

The researcher also presented a promising new software suite: Copernicus. Peter Kasson’s, Eric Lindhal’s and Vijay Pande’s teams published a paper back in 2011 on the topic and they have pursued developments. Copernicus essentially makes the back-end control of large-scale simulations much more transparent, so FAH researchers will be more easily able to integrate new methods. This software also works on supercomputers and cloud computing platforms which makes it easier to run simulations that complement the simulations run on Folding@Home. It also allows other researchers from outside FAH to gain access to the kind of simulations we run on FAH. All these changes are on server side, so the donors should not notice any difference in the client behaviour. But thanks to Copernicus, we should see new research areas appear.

Source: Vijay’s blog

FAHcon 2012 : Doctor Greg Bowman

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Doctor Greg Bowman of Berkeley University showed a project at Folding@Home conference (FAHcon) focused on new therapeutics applications of proteins. It is known that the interleukin 2 (IL-2) protein can help to stimulate an immune response, so in theory, this protein might be efficient to treat patients with immune deficiencies.

However in practice, prescribing IL-2 to these patients often leads to severe heart problems. To find a better solution, researchers at Stanford University designed a variant of IL-2 that can stimulate this immune response without any side effects. However, they were unable to understand how this mechanism worked because the two proteins had almost identical structures!

Using Folding@Home, Doctor Bowman’s team showed that IL-2 is a relatively floppy protein while the one designed at Stanford is locked in a structure that is poised to stimulate an immune response.

Source: Vijay’s blog

Folding@Home Consortium Conference 2012

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On May 25th 2012 at Stanford University, the first Folding@Home Consortium scientific conference was held. The goals were to discuss about recent scientific advances, to share new techniques for how to better use the resources available to FAH as well as to plan Folding@Home platform advancements for the next year.

A series of news will follow to summarize the main ideas that came out of this conference.

Here is a picture of most participants:


Click on the image to enlarge.


From top left to bottom right: TJ Lane (Stanford), Dr. Jason Wagoner (Stanford), Prof. Dr. Vincent Voelz (Temple), Dr. Sidney Elmer (Sandia National Lab), Dr. Fancesco Pontaggia (Brandeis), Dr. Lan Hua (UCSF), Bruce Borden (FoldingForum.org), Joseph Coffland (Cauldron Development), Dr. Diwakar Shukla (Stanford), Dr. Lee-Ping Wang (Stanford), Steven Kearnes (Stanford), Kyle Beauchamp (Stanford), Dr. Greg Bowman (UC Berkeley), Dr. Relly Brandman (UCSF), Robert McGibbon (Stanford), Prof. Dr. Yu-Shan Lin (Tuffs), Prof. Dr. Matt Jacobson (UCSF), Prof. Dr. Jesus Izaguirre (Notre Dame), Prof. Dr. Vijay Pande (Stanford), Prof. Dr. Michael Shirts (University of Virginia), Dr. John Chodera (UC Berkeley/QB3), Prof. Dr. Peter Kasson (University of Virginia), Prof. Dr. Xuhu Huang (Hong Kong).
Not pictured: Prof. Dr. Chris Snow.

Source: Vijay’s blog

Peptoids

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Peptoids
One of the projects that Prof. Vincent Voelz’s laboratory is excited about is molecular simulation of synthetic polymers called peptoids. These are biomimetic molucules that can fold like proteins, but with different strucutral properties. Several peptoids that can fold in a unique three dimensional structure have been identified, but a better computational model is needed to identify the driving forces for folding and to be able to predict stable structures of these peptoids. If the laboratory is able to develop tools to achieve it, peptoids have the potential to become an amazing platform that can be used in all kind of applications, from biotherapeutics to nanomaterials.

So far, the researchers have shown that modern forcefields can accurately fold peptoids (results available on http://dx.doi.org/10.1002/bip.21575) and they are working with experimental collaborators on blind predictions of peptoid structures (new results will be published soon). Folding@Home would contribute to large-scale simulations of peptoid folding to better understand peptoid folding mechanisms and design principles.


Source: Vijay’s blog

Folding@Home 7.3.6 final released, a new website and a video !

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There is another revolution at Stanford : after a resoundingly successful release of v7 client and the complete website redesign, the 7.3.6 client is starting a new approach, aimed at simplifying the client for potential new donors. This release comes together with a new site design and a promotional video.

The client


The following main features have been announced by client developer, Joseph Coffland:

  • Web control interface added
  • Control buttons removed from FAHControl interface
  • Simplified installation

For the time being we haven’t been able to test these new features, but we’ll take a closer look.

The website


This is again a big change : the three frames which were part of the already simple interface are gone, replaced by a new home page completely dedicated to education with an animation oriented graphic style.


The website also emphasizes social networks (well yes, we’re not alone :hehe )

The text emphasizes the principles of protein folding, the opportunity to participate and introduces the network machines (us ;)) already in place.

The video


To complete this release, a Youtube video has been posted to introduce its audience to the implication of misfolded proteins in a huge variety of diseases, and it explains how to participate in finding cures for them !



Let’s communicate !


Stanford has offered us great tools to promote the project more easily, the time has come to recruit. Your family, your friends, the forums and the online communities you’re involved in might be interested ! It would be a shame not to enjoy this beautiful dynamic !

Main source : Vijay’s blog

Introduction of Vincent Voelz laboratory at Temple University

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Introduction of Vincent Voelz laboratory at Temple University
The Professor Vincent Voelz laboratory has started in August 2011 at Temple University in Philadelphia, PA. Two servers for the Folding@Home project have been set up there and the first simulations hosted on them have started this summer. In the meantime, the team had an acces to high performance computing cluster of Temple university Institute for Computational Molecular Science to generate some initial data for these simulations.

One of the main goal of this laboratory is to use molecular simulations for computational design of folding and binding properties. This design requires folding for lots of different possible protein sequences, which is a natural task for the Folding@Home distributed computing platform. Vincent Voelz’ team works to consolidate Markov State Models of conformational dynamics to do efficient estimation of the effects of sequence perturbations. A good starting point to test these effects are to look at proteins for which many sequences have been characterized, to see if it is possible to predict sequence-dependent changes. Many of these sequence mutations are important in human diseases, so professor Voelz hopes to gain insight into these process as well.


High performance computing cluster at Temple University.



Source : Vijay’s blog

Understanding the folding of hIAPP, the peptide linked to the Type 2 diabetes

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Understanding the folding of hIAPP, the peptide linked to the Type 2 diabetes
Here’s an update from the Professor Xuhui Huang’s laboratory at University of Sciences and Technology of Hong Kong, another laboratory collaborating inside the Folding@Home consortium.

In addition to the study of molecular recognition process, another goal of this laboratory is tu use the Folding@Home platform to explore the folding of free energy landscape of the human islet amyloid polypeptide (hIAPP). hIAPP, also called amylin, is a 37-residue peptide and its aggregation reduces working beta-cells in patients with Type 2 diabetes. As an intrinsically disordered protéin, the hIAPP monomer doesn’t have a folded global minimum in its folding free energy landscape, but contains many stable local minimums. Thus, understanding these local stable states can help us to understand the amylin aggregation mechanisms and then design some small molecules to inhibit the amyloid formation.

As we have seen in Vijay Pande’s laboratory simulations on the alpha beta peptide involved in Alzheimer disease, this research may lead to potential therapeutic agents for the Type 2 diabete. On the Folding@Home platform, professor Huang’s team is running extensive simulations on molecular dynamics (MD) and they are building Markov state models to elucidate the free energy landscape of the hIAPP monomer. Projects 2974 and 2975 are related to this study. The laboratory team wishes to thank Folding@Home donors who make these research possible.

Source : Vijay’s blog

Receptor binding by the Influenza virus

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Professor Kasson's team has recently published an article in the Biochemistry journal detailing how the influenza virus binds to cell surface receptors. In this article, the researchers detail how simulation techniques can be used to further analyze the biochemical and structural data of glycan binding by the influenza virus. They also review the work done in collaboration with Professor Pande's team, including research completed using Folding@home. Previous articles on the same subject can be found here and here.


20 glycan molecule structures are connected to the receptor-binding pocket of hemagglutinin.



Source: Vijay's blog