News

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

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)

ATI/AMD GPU support in FAH, and what awaits with Core 16

By , the in Folding@Home Project - No comment
The project team is currently working on improved support for AMD and ATI GPUs. Originally, the Brook programming language was used to program on GPUs, but AMD have decided to support just OpenCL and drop all support for Brook. This has meant that the core has had to be completely rewritten to use OpenCL instead of Brook. This was a huge challenge, but that project is now bearing fruit (see the OpenMM site for more information). Because of AMD's decision to abandon support for Brook in favour of OpenCL, future developments of the AMD/ATI core will be made for OpenCL only, and will only run on graphics cards that support OpenCL.

This means that some currently supported cards will drop out of the project, as follows:
  • HD2xxx and HD3xxx series do not support OpenCL and thus will not be supported once FAHcore 11 is mothballed.
  • HD4xxx series is able to execute OpenCL code but lacks some hardware features necessary to make the new code run at an efficient speed, and so will also not be supported by the new core.
  • HD5xxx and HD6xxx series support the full range of necessary OpenCL functions, and will be fully supported by the new core.

In the short term, both FAHcore 11 and FAHcore 16 will be used in parallel so as not to leave people in the lurch. Unfortunately this situation cannot last forever, and support for FAHcore 11 is scheduled to end on September 1st 2011. This date may be postponed, but there is no guarantee that will happen. Stopping support of a platform is obviously never a popular decision, but in this instance the project has been left with little choice due to AMD ending support for the older cards.

The good news is that AMD/ATI is heavily involved in supporting OpenCL and the Pande Group are very excited by the prospects of the new core. This core will be released publicly after the release of the v7 client, which is necessary to run the new core.

Source : Vijay's blog

State of the v7 client

By , the in Folding@Home Project - No comment
A lot of work on the v7 client has been quietly been going on behind the scenes. The development process has taken longer than expected, but Vijay Pande settles for nothing less than 100% completion. The developer in charge of writing the new client, Joseph Coffland, has been working hard to add new features and eliminating bugs reported by the testers. The details are many, and too numerous to detail here, so we invite you to read the full changelog, which is linked to below. This will give you a good idea of ​​the client's development process.

Joe and Vijay believe that a public release is near, and if the internal testing of version 7.1.18 goes well, it will become the base used for the client's public beta.

Source: Vijay Pande's Blog

The bonus system is being tested on uniprocessor clients

By , the in Folding@Home Project - No comment
As you probably know, the SMP2 and bigadv sections of the project have been subject to a quick return bonus, where points are awarded on an exponentially increasing scale for fast returns of units.

The system is currently being tested on a limited number of uniprocessor projects with a view to potentially rolling it out to all uniprocessor projects too. Currently the only uniprocessor projects subject to the QRB are projects 10436 and 10437.

We must stress that this remains a test: with a project the size of Folding@home many unplanned complications are possible. The system may change so as to best reflect the scientific needs of the project.

Source: Vijay Pande's blog

New SMP a3 projects p7100-7154

By , the in Folding@Home Project - No comment
A new series of 55 projects has been made available: project numbers 7100-7154. They are the responsibility of a new researcher: Per Larsson. Per is currently working as a post-doctoral researcher in Peter Kasson's team at the University of Virginia, having studied for his doctorate in physics at the University of Stockholm with Erik Lindahl.

These projects are studying the flu virus and more specifically how certain mutations affect the virus. They are the first to require version 2.27 of the Gromacs a3 core and are distributed from the server at 128.143.199.96. Characteristics are as follows...
  • Approximately 77,200 atoms (+/-100 atoms depending on the project)
  • 585 points
  • Bonus factor of 3.23
  • Preferred Deadline of 2.66 days
  • Final Deadline of 4 days

These projects are available on -advmethods for Windows and Linux clients.

Source : Official Forum

New A4 uniprocessor projects: p10436 and p10437

By , the in Folding@Home Project - No comment
Kyle Beauchamps has launched two projects for the single core clients using Gromacs core a4: p10436 and 10437.

These projects simulate the pinhead of the Villin protein in the amber99sb-ildn forcefield at 300K (p10436) and 278K (p10437) in a solution of 3 Mol of GdmCL (guanidinium chloride) denaturant.

Still with us? ;)

These projects are testing the bonus system many of you will be familiar with from SMP clients, on uniprocessor clients. Project 10436 is served from the server 171.64.65.80 and project 10437 from 171.64.65.81. Besides the different servers their characteristics are identical:

  • 576 atoms
  • 311 points
  • Bonus factor : 0.69
  • Preferred Deadline : 8 jours
  • Final deadline : 12 jours

Project 10436 is available to all clients, while project 10437 is restricted to -advmethods for now.

Source : Official Forum