News

New SMP Gromacs a3 projects: p11020 and p11021

By , the in Folding@Home Project - No comment
Dan Vanatta has released two new projects for the Gromacs SMP A3 core.

These projects are examining the conformational changes during a transition from the active state to the inactive state of the Nitrogen regulator protein C.

These projects are distributed from the server at 171.64.65.55, and have the following characteristics...
  • 25,192 atoms
  • 310 points
  • Bonus factor of 0.75
  • Preferred Deadline: 8 days
  • Final Deadline: 12 days

These projects are currently available to clients with the -advmethods flag and only available to Windows machines, though they should be rolled out to Linux shortly.

Updated 29th March:
Project 11020 has left -advmethods and is now available to all folders.

Source: Official Forum

The SMP gromacs A3 core reaches v2.27

By , the in Folding@Home Project - No comment
Kyle Beauchamps has deployed version 2.27 of the Gromacs a3 core for SMP clients on all platforms.

This version primarily exists to update the science code to the latest version, v4.5.3 of the Gromacs package. The update adds some new scientific analysis methods which will be useful in upcoming projects.

No current projects require the update, but when you receive a project that requires the update, it will be performed automatically.

Source : Official Forum

The holy grail of linux users has arrived: Core A5 and the return of BigAdv

By , the in Folding@Home Project - 1 Comment
The holy grail of linux users has arrived: Core A5 and the return of BigAdv
It's official now, Linux is back in favour for BigAdv after a long absence.

For many months, folding BigAdv units on Linux was not possible due to a curious bug that caused the results to be incorrect.

The new A5 core appears to have fixed the gremlin allowing Linux BigAdv once again, and indeed significant performance gains.

To use the new core:
It is necessary to have a new version of the client (6.34) plus all the usual pre-requisites for BigAdv as before.
All BigAdv units will migrate to A5 in the coming weeks, so it is necessary to migrate to the 6.34 client on all platforms or you will only receive standard SMP units using the a3 core.

To compare your performances with the new and old cores the forum has set up an official comparison thread: here.

Publication #78: the role of water in membrane fusion

By , the in Folding@Home Project - No comment
The research team at Folding@home recently published the 78th peer reviewed paper to be produced using the project's work, in the Journal of the American Chemical Society (JACS). The paper, entitled "Water Ordering at Membrane Interfaces Controls Fusion Dynamics" is the result of a collaboration between Peter Kasson (University of Virginia), Erik Lindahl (University of Stockholm and the Royal Institute of Technology), and Vijay Pande, of Stanford University.


The ordering of molecules at the interface controls the dynamics of membrane fusion.


Based on previous simulations of membrane fusion, the Folding@home team used the network to systematically analyze the fusion reaction between two cells, and specifically the role of water in this reaction. To achieve a reasonable simulation time, many simulations use an implied model of water to save the processing time that would be required if the water molecules were explicitly modeled. In this simulation, the researchers have shown that water does in fact have a direct effect on both the thermodynamics and dynamics of the reaction. This has important consequences for future simulations of membrane fusion, and the researchers provided a further example of two flexible hydrophilic surfaces. This structure of water could be important in many cellular interactions.

For the record, the units that contributed to this paper were the BigAdv p268x series.

Source: JACS *

*Access to the paper is paid for the first year under the publishing agreement with JACS unfortunately. For those at academic institutions it may be worth checking if your university/college has paid for access to the site.

SMP v6.34 client available for download

By , the in Folding@Home Project - No comment
Version 6.34 of the SMP client is now available for download on FAH's high-performance clients page, for both Windows and Linux.

It is provided as an executable file, which should be placed in the main directory of an already installed client. For safety and data stability reasons, it is recommended that this update be applied when no partially-completed units are present.

The main new feature in this version is support for the new A5 core, which should be making its public appearance in the near future.

This new core will be used exclusively by BigAdv projects. It's identical to A3 core, but it is built from a different code branch which is specific to BigAdv projects to improve compatibility and stability.

Source: Vijay Pande's Blog

Updated on 02/25 at 11:30 :
Project 6901 has just started being assigned. It is identical to project 6900, the only difference being the use of the new A5 core.

The Gromacs 4 core reaches version 2.27

By , the in Folding@Home Project - No comment
Kyle Beauchamps has released a new version of the Gromacs 4 core, more commonly known as Core a4. This version upgrades the Gromacs software to version 4.5.3, giving the researchers more analysis methods.

This core is available for Windows (32-bit) and Linux (32-bit and 64-bit). For the avoidance of doubt the Windows core runs fine on 64-bit Windows ;)

No projects currently require the new revision, however if you wish to force the update then deleting your copy of the a4 core will cause the new version to be downloaded for the next unit that requires core a4.

If you choose not to upgrade now, it will be performed automatically the first time you receive a project needing the newer core.

Source: Official Forum

GPU3 client reaches version 6.40r1; featuring Compute Capability support

By , the in Folding@Home Project - 3 Comments
Original news on 10/31/10:
Mark Friedrichs has just put version 6.40r1 of the GPU3 client online.

The main change in this version is the replacement of the previous method checking for CUDA support, namely by checking the version of CUDA installed on the computer, if it was at all. The client now achieves this end by directly checking the Compute Capability value on the GPU chip itself.

Possible values for detected versions are:

Citation:
v1.0 -> 10
v1.1 -> 11
v1.2 -> 12
v1.3 -> 13
v2.0 -> 20
v2.1 -> 21
Unknown -> 0


The main reason for this change is due to an incompatibility between Core 15 (OpenMM) and cards that only support Compute Capability 1.0 (which means a G8x chip). The change should now prevent unpleasant crashes for owners of these cards, and pave the way towards better hardware detection, perhaps with some specialised optimizations based on the chip capabilities.

This new version comes in the form of an executable file replacement. Quit out of your client and replace its executable with that of the new vesion.

Console version: http://www.stanford.edu/~friedrim/Folding@home.exe_console
Systray version: http://www.stanford.edu/~friedrim/Folding@home.exe_systray

Remember to remove the trailing _console or _systray from the file name!

Updated on 01/27/11:
The Systray version of the 6.40r1 (also known as 6.41) client is now available on the High Performance clients download page.

Change log:
  • A new value for -forcegpu flag has been added : nvidia_g80_1.0 will force Compute Capabilities 1.0 (species=10)
  • The old -forcegpu nvidia_g80 value will force Compute Capabilities 1.1 (species=11)
  • If the -forcegpu value is not recognized, the client will give a pop-up warning then exit.


Source: Vijay's blog

Updated on 02/15/11:
The v6.41 console client is now available on the High Peformance client download page.

New projects roundup : p6801, 6805, 6883 and 6887

By , the in Folding@Home Project - No comment
During the second half of December, not many new projects are typically added for processing due to Stanford's winter break, though the first half of January usually helps to redress the balance somewhat. In the last month, only Yu-Shan Lin has added new projects, as follows:

p6801: OpenMM for Fermi
This project simulates the amyloid beta in a mutant configuration, as with other p6800 series projects. The units are worth 1348 points and simulate a system of 634 atoms. The preferred deadline is 5 days, with the final deadline 5 days later. These projects are served from 171.64.65.64.

p6805: OpenMM for Fermi
This project continues the p6800 series of amyloid beta studies, but this time not in a mutant configuration. The units are worth 1280 points and comprise 598 atoms. Deadlines and the server are identical to p6801.

p6883: Uniprocessor Gromacs 3 (Core 78)
This project simulates the abeta peptide in explicit water. The unit comprises 12,226 atoms, is worth 69 points and has a preferred deadline of 14 days, with the final deadline a week later. These units are served from 171.67.108.33.

p6887: Uniprocessor Gromacs 3 (Core 78)
This project also simulates the abeta peptide in explicit water. The unit comprises 12,219 atoms and is worth 69 points. Deadlines and the server are the same as p6883.

Happy Folding :)

Happy New Year! Time to take stock... and look forward to 2011!

By , the in Folding@Home Project - No comment
OK so we were a bit late translating this news and its already the 4th of January. However, we wish you all a belated happy new year and hope you haven't failed your resolutions yet ;)

A new year means it is time to look back at what the project has achieved over the previous year, and whether we predicted the year correctly.


How did we do with our predictions for 2010?


2010: Year of the v5 server code: Correct: (OK this wasn't exactly the hardest prediction to make we admit)
The vast majority of the project's servers have now been switched to the much more reliable v5 server code, meaning fewer dropouts (once some teething problems were ironed out). Some servers even began migrating to the further improved v6 server code in the later stages of the year.

A new, more reliable statistics system: Correct
With both new hardware and new software, the statistics system underwent a major revamp in 2010, and most statistics features that had been deactivated are now enabled once again. Combined with some rather more aggressive IP banning by Stanford University, this has resulted in a major performance boost.

The launch of the long-awaited brand new client: Wrong
The v7 client did not make an appearance in 2010, so unfortunately our prediction that it would was proved wrong. However, the v6 client made some important leaps, particularly the abandoning of MPI for the SMP client, helping to make the project easier to contribute to.

A new version of the Assignment Server (AS) code: Correct
While not visible to donors, the code that the ASes run has been updated. As it is impossible to be assigned work without first being referred to a work server by the AS, the improved reliability of the ASes has helped to reduce headaches for donors.

The GPU3 client to reach maturity: Kind of...
In terms of the algorithms needed to make this happen, OpenMM on CUDA is ready and is being used as a kind of GPU2.5 client for nVidia GPUs (as it stands it is the only way to fold using Fermi cards). Unfortunately OpenMM on OpenCL is not quite ready, despite the fact that it is desperately needed by ATI users to replace the current ATI core.

SMP2 making its appearance: Correct
SMP2 has rapidly replaced SMP and added much to the project: more reliability, more speed, Windows compatibility, simpler operation, the latest Gromacs developments... but we have lost Linux BigAdv!

SMP2 to gain more cores: Wrong
Desmond has not yet appeared. 2011?

So 2010 has been a big year for development behind the scenes at folding@home, but SMP2 excepted, not much of a revolution for users.

Consulting FAH-Addict's crystal ball...


2011 year of v7: this time for sure! The key word: usability.
2011 year of GPU3 on ATI: OpenCL should finally bring up the goods and allow GPU3 on ATI.
2011 year of BigAdv Linux: we predict that the bug that is currently preventing BigAdv on Linux will be fixed this year, allowing it to return. We certainly hope so :P

Folding@home's v7 client expected for Q1 2011

By , the in Folding@Home Project - No comment
It is now official, Vijay Pande has announced that the v7 client has a target release date, namely the first quarter of 2011.

Of course, this gives a wide range for the release, and last minute bugs may well appear that may delay the release beyond the target date. However the fact that a date has been announced in advance at all is a good sign that no such issues are expected.

To recap, the new client has been designed with usability in mind. The current clients might best be described as functional, and the new client is intended to address the usability deficiencies and make contributing much easier. For the developers, the new code is intended to be much easier to maintain and more logical to add to, allowing faster development of further improvements.

As a result it should be easier for the client to be modified to support new client types or methods than it has been with the current clients.

We will keep you updated of any news on this release.

Source: Official Forums