News

New Gromacs 4 project: p10433

By , the in Folding@Home Project - No comment
Kyle Beauchamps has released a new project using the Gromacs 4 core: p10433. This project simulates the NTL9 protein in explicit solvent using the tip3p model, at 300K. This project is designed to complement the results of some GPU projects, which simulated the same protein but in implicit solvent.

The GPU results allowed the construction of the following model:



Project 10433 is distributed from the server at 171.64.65.80, is worth 425 points, and has a preferred deadline of 8 days with a final deadline of 16 days. This project uses the bonus system with a bonus factor of 0.7.

Source : Official Forum

New Gromacs A4 projects: p10720-10722

By , the in Folding@Home Project - No comment
Dan Vanetta has released several new projects concentrated on studying Vancomycin, a Glycopeptide class antibiotic, and the peptide to which it binds. Vancomycin is an antibiotic of last resort used to treat infections which are resistant to Methicillin, a penicillin used to treat non-resistant Staphylococcus aureus. Recently, examples of Vancomycin resistance have been discovered, so these projects aim to study the method of resistance.


A Vancomycin molecule.



Project 10720 : Vancomycin
  • 984 points
  • Preferred Deadline : 16 days
  • Final deadline : 24 days
  • Bonus factor : 0.75


Project 10721 : Peptide
  • 654 points
  • Preferred deadline : 8 days
  • Final deadline : 16 days
  • Bonus factor : 0.75


These projects are distributed from the server at 171.67.108.42.

Source : Official Forum

Update on 05/28 at 3:30pm:
A new project has been added to complete the study, p10722 which is also using the Gromcas A4 core, with the following characteristics :
  • 12098 atoms
  • 2244 points
  • Preferred deadline : 32 days
  • Final deadline : 56 days
  • Bonus factor : 0.75

Changes to the stats system

By , the in Folding@Home Project - No comment
Recently the Folding@home project has decided to make some changes to the way passkeys are handled in ordering the contributions of donors on the website, and in the flat text files used by third party stats sites.

Passkeys are a relatively new part of Folding@home, as they were introduced with the v6 clients in 2007. They are used to tie contributions to an individual user, providing an extra level of identification beyond a simple username. The intention was to prevent people from cheating using your username.

In order to ensure that the flat files match the website, changes were necessary to both. The issue is how to handle passkeys: the website stats currently ignore passkeys in order to speed up to the SQL count(*) command, while the flat files aggregate all passkey accounts into one donorname then orders by the aggregate points for that donorname.

The proposal is to change the system to make each username+passkey combination count as a unique user in the stats system, on both the website and the flat files. This is the only method that meets the two goals of consistency between the website and the flat files, and keeping the speediness of the stats system. As revealing the entire passkey would rather miss the point of having a passkey at all, only the last two characters of the passkey will be published to permit differentiation between passkeys.

The flat files will transition to the new format soon if they have not already, while a target date of May 1st has been set for the switchover on the web stats.

Source: Vijay's blog

OpenMM OpenCL (Core 16) available for ATI/AMD

By , the in Folding@Home Project - 1 Comment
With the release of the v7 client necessary to support this core a few days ago, it was only a matter of time: the Pande Group are rolling out Core 16 (OpenCL OpenMM) to open beta.

Firstly a warning: the beta tag is there for a reason, the core is not finished and may crash more often than usual or otherwise degrade system performance.

To receive these units you must have a v7 client set up in GPU mode with advmethods, a GPU and drivers with support for OpenCL (all 11.x series drivers contain the APP package necessary for this). Under these conditions, it is possible that you may receive the test project 11293, though the number of units available is limited for the first phase of the test and so many clients will be assigned Core 11 units instead.

This project simulates a complete amyloid beta peptide at high temperature. These simulations are very similar to those already performed using the CUDA OpenMM Core 15, and serve as scientific validation for Core 16. The project has the following characteristics (with the reference card being a GTX460 as with Core 15 projects):

  • 627 atoms (a relatively small protein)
  • Server 171.67.108.44
  • Preferred Deadline: 6 days
  • Final Deadline: 10 days
  • 1835 points

We tested the core and this project with a HD5770 (800 shader processors overclocked at 960MHz), powered by an Intel Core i7 920 overclocked to 3.5GHz running Windows XP with the 11.3 drivers package. With this setup we get 6650PPD with 100% GPU usage. This gives efficiency of about 70 PPD/W, which is almost twice what we achieved running this test with a Core 11 project. This is also comparable to the efficiency of the recently released nVidia GeForce GTX590.

On our test machine, we did not notice any degrading of performance, even when playing videos.

Unfortunately not all is well with this core. Firstly there is the high CPU and RAM usage in our test machine: Core 16 uses an entire thread at 100% and requires 375MB of system memory to operate. Hopefully these figures will improve as the core is optimised better, much as happened with the Core 11 variants in the past. The second point is more problematic: some users have reported crashes when folding in parallel with certain apps (notably Flash). These problems do however seem to be limited to cards based on the Cayman chip (HD6900). The developers have been able to reproduce the problem and are working on a fix.

Please let us know how the core is working for you...

Source: Official Forum

v7 Client Reaches Open Beta

By , the in Folding@Home Project - No comment
At long last, after many months of development and testing the new version 7 Folding@home client software is now available for open-beta testing. The V7 client is a complete rewrite of the previous client for Windows, OS-X and Linux with the following goals:

  • To make the installation and startup user-friendly for the novice. (before the project consumes their life and they become FAH-Addicts ;) )
  • To integrate the user interface into a single Monitor/Control program that manages the functionality previously contained in separate clients.
  • To create a forward-looking design that can be readily expanded to incorporate new Folding Cores without the need to issue new client releases.
  • To greatly improve previously problematic aspects including support for SMP, GPU, and the 3D viewer.

Getting Started
Please consider reading one of the guides listed in the documentation section, but if you want to dive right in you can start by downloading and installing the new client.

Documentation
Install and user guides can be found here:

https://fah-web.stanford.edu/projects/FAHClient/
There are also some additional quick start FAQ items here
http://foldingforum.org/viewtopic.php?f=67&t=18043

Features
The new client has too many features to list but here are some of the highlights:
  • Improved Windows installer with support for Windows XP, Vista, 2008 and Windows 7.
  • 64-bit OS-X install package. (32-bit in the works).
  • Debian/Ubuntu and RedHat/Fedora/CentOS 32-bit and 64-bit Linux packages.
  • Low priority background operation has very little impact on your computers usability. You should hardly notice Folding@home is running when using other applications.
  • A more compatible and stable 3D protein viewer with several view modes, rotation, zoom, online help and interpolated protein animations.
  • Separate but integrated console client (FAHClient), user interface (FAHControl) and 3D protein viewer (FAHViewer).
  • Novice, Advanced & Expert user interface modes. (See drop down list in FAHControl.)
  • Support for more than one Folding Slot (UNI, SMP or GPU).
  • Ability to monitor, configure and control many remote folding clients from a single computer.
  • Very low CPU overhead for FAHClient, FAHControl and FAHViewer. 3D viewer overhead can be minimized by disabling rotating and protein animation.
  • Single client for normal (Uniprocessor), SMP (Multiple CPUs) and GPU (Graphics Processors) folding.


Bugs/Tickets
The V7 client has undergone months of testing but due to the complex nature of distributed computing, the many features provided by the Folding@home client and the difficulties of simultaneously supporting software on Windows, OS-X and Linux there are still some open bugs, feature requests and likely other as of yet undiscovered issues. The beta testing process will help the Pande Group test new features and fix any remaining bugs before a full public release is made. That said the open-beta V7 client is very usable and has many advantages over the previous client releases.

In an effort to increase the transparency of our development process it has been decided to open read-only access to our bug tracking system. The system chosen for this purpose is Trac, a Web based system which, among other things, manages a database of tickets. Each ticket represents either a bug or feature request of some component of the Folding@home client software. You can view the list of open tickets here:
https://fah-web.stanford.edu/projects/FAHClient/report/3

Getting Help
The documentation remains the best place to get help but if you still run into trouble further assistance is available from one of the v7 client forums:


Final Notes from Vijay Pande
We are very excited to see this software make its way around the world improving and expanding Folding@home and thereby increasing our understanding of how proteins fold and ultimately helping to find cures for some of our societies scariest diseases. We greatly appreciate your participation and understand that without your generous contributions of time and computing resources there would be no Folding@home.

Note: The ATI/AMD core 16 is to be released seperately at a later stage.

Note 2: Currently only FAHControl can monitor v7 clients... 3rd party software needs updating to use the new monitoring methods used by v7.

Source: Vijay Pande's blog

New Gromacs A4 projects: p10063-10082

By , the in Folding@Home Project - No comment
With projects 10063 through 10082, Badi' Abdul-Wahid studies several WW mutant structures. These simulations are based on the structures discovered by Feng Liu in his article, entitled "An experimental survey of the Transition Between Two-state and downhill protein folding scenarios".

The projects have the following properties:

  • Server: 129.74.85.15
  • Points: 242
  • Preferred deadline: 4 days
  • Final deadline : 8 days

These projects are for for uniprocessor clients only.

Source : Official Forum

New Gromacs A3 core projects: p6952-6979

By , the in Folding@Home Project - No comment
Peter Kasson has put online a new series of projects, whose focus is the study of the influenza virus. These are projects 6952 through 6979, and complement existing studies by numerous projects, such as the p6050-6078 series. The virus is almost the mascot of the SMP client ;), and is Professor Kasson's main field of study.

These projects are currently available to clients running with the -advmethods enabled. They have the following properties:

  • Serer: 128.143.199.96
  • Atoms: 77,113
  • Points: 552
  • Preferred deadline: 2.7 days
  • Final deadline: 4 days
  • Bonus factor: 3.33


Source: Official Forum

GeForce GTX590: Warnings, and first Folding@home tests

By , the in Hardware - No comment
GeForce GTX590: Warnings, and first Folding@home tests
If you are the proud owner of a GTX590, it would be wise to pay close attention to the drivers installed on your machine.

It is essential to make sure you have driver version 267.85 (the only version which officially supports the GTX590), as this is the only driver which fully supports the card's OCP (over-current protection). Sadly nVidia have chosen to manage this through the drivers, as opposed to AMD who build a controller into each card to manage it in hardware.

The cards are currently shipped with a disk containing 267.52, which does not fully support OCP. This has led to the possibility of damage to your card, as demonstrated by this video:



On a rather more positive note, PCINpact has tested the GTX590 on Folding@home. The result was 13,000PPD per GPU on project 6801, for a total output of 26,000PPD per card. Power consumption for the system was 360W, giving 72PPD/W. It is still a long way from the efficiency of -bigadv...


Source: PCINpact (in French)

A little more information about AMD Bulldozer is revealed...

By , the in Hardware - 1 Comment
A little more information about AMD Bulldozer is revealed...
AMD plans to launch its first range of processors based on Bulldozer in June this year. The first batch of processors are codenamed Zambezi.

These processors will be manufactured on a 32nm process, using Socket AM3+. The naming of the range is fairly obvious, with two octocore processors named FX-8000, two hexcore processors named FX-6000 and two quad-core processors named FX-4000. For each of these pairs one will be a Black Edition with an unlocked multiplier. TDP is 95W, except for the top FX-8130P which will have a TDP of 125W. All processors have an integrated DDR3 controller, but none will have integrated graphics. Black Edition models will feature a Turbo mode, similar to those found on Intel's processors.

The processors have 1MB of L2 cache per core, so 8MB for octocore, 6MB for hexcore and 4MB for quadcores, which is joined by an 8MB L3 cache on all models. Operating frequencies remain unknown.

The Zambezi platform is intended to compete at the higher end of the market and is in competition with Intel's i7-2600 series. Prices remain unknown.

We hope that AMD will once again be competitive at Folding@home... and note that the FX-8000 series is AMD's first range of consumer processors which meets the 8-core requirement for -bigadv.

Source: Tom's Hardware (in French)

The boundary between uniprocessor and SMP is shrinking

By , the in Folding@Home Project - No comment
Following a small configuration error by Kyle Beauchamp in the settings of one of his projects, we have discovered a new feature of the A4 core.

Approximately 400 clients were given project 10437 units in SMP mode! The project is designed for uniprocessor clients, and the error has been corrected. If you were sent one of the incorrectly configured units, do not worry, the results remain usable.

Subsequently, Kyle has confirmed the functionality of the A4 core v2.27: it is able to operate both as a uniprocessor and SMP core. There are two conditions: the client must have the SMP flag specified, and the researcher must have allowed SMP mode when configuring the project. If only one of these parameters is met, the core will use uniprocessor mode regardless.

No project using this core has SMP mode enabled currently, but we hope this will change soon.

Sources: Official Forum: (1) and (2)