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New ProtoMol B4 Uniprocessor Core Released

LCB001

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Stanford just released the new Protomol B4 core for Uniprocessor client under advmethods. This new core is used by the two new projects p10000 (84.48pts) and p10001 (50.56pts).

Users of the Uniproc. client will need to update their FahMon to recognise the new WU's.

Prof. Vijay Pande explains;

Release of new Protomol (Core B4) WUs

As announced some time ago we have been working on a new core (Protomol core B4), and it has been looking good in QA so we have started to release Promol core WUs more broadly. We have a preliminary Protomol FAQ for those who are curious to get more information.
This new core implements the NML (Normal Mode Langevin) method which accelerates the long-time dynamics of the proteins by a factor that can reach speeds up to a hundred times faster than those of molecular dynamics. This method searches for low frequency directives by using normal mode analysis and projects the motion of the molecule along them while resolving the nearly instantaneous motion. If you want to learn more about this method, you should read this pre-publication: Multiscale Dynamics of Macromolecules Using Normal Mode Langevin.






Based on Protomol 3.1, this core and its associated projects have the following goals:
  • To validate NML by simulating the folding and dynamics of the Fip35 WW domain.
  • To understand the role of mutations on folding.
  • To understand the activation of src Kinase, an enzyme that is involved in the onset of some kinds of cancer.
On the technical side, this core is able to take advantage of most modern CPU optimizations (SSE2, SSE3, SSSE3, SSE4.1 and SSE4.2), however, a few compatibility issues are still present on AMD processors, resulting in the core only using SSE2 on these chips. This should change in the not-too-distant future when the issues have been worked out. If you have a processor that doesn’t have the above mentioned optimizations (Pentium 3, Athlon XP, etc.), please report the behavior and the performance of this core on your machine.

For more information about the Protomol core, you should visit the Protomol official site.






The new projects are distributed by a new server (129.74.85.48) which is located at the University of Notre Dame (Indiana) and have the following characteristics:
  • p10000 : 544 atoms, 84.48 points, preferred deadline 3.07 days, final deadline 23.04 days. This project uses conventional simulation methods.
  • p10001 : 544 atoms, 50.56 points, preferred deadline 1.84 days, final deadline 13.79 days. This project uses the NML simulation method.
We will be posting more information as time goes on. I'm very excited about the new capabilities here, since NML allows us to algorithmically get an amazing speed up, i.e. without any additional CPU power. That algorithmic speed up multiplied by the vast power of FAH could mean very significant advances shortly, making 2010 an exciting year for FAH (in many ways)!



Hopefully we get the rest of the new goodies soon...:thumb:


Edit; An Update, Got this from FAH-Addict : News

Updated on 22 Dec at 22H15 UTC :
The behaviour of Project 10001 has proven to be different from that which we usually see; sometimes, the simulation enters into a state where no further computation is possible, but which is not technically a folding error. This situation usually triggers, with other cores, an Early_Unit_End or an Unstable_Machine error. With the Protomol core, these states are expected and don't trigger an error. You'll see them with a WU reported as completed (Finished unit, core status = 64) before it reaches 100%. Don't worry if this phenomenon occurs on your machine; it is perfectly normal and expected.

Happy folding!


 
Last edited:

LCB001

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FahMon Fix-It

Ooops forgot this part,

For those having problems with FahMon recognizing the new projects this was posted on the [email protected] forums.

Posted by bollix47 from this thread; Folding Forum • View topic - New Project: 10001 ?

The psummary now has 3 pages for projects. If you look under Currently Running Projects at the top of the Project Summary page you will see the 3 choices.

In FAHMON open preferences and go to the advanced tab.

Change the Address to:

http://fah-web.stanford.edu/psummaryC.html

Click on OK and then in the Tools section of FAHMON select Download New Projects.

This will direct FAHMON to use the third page which lists all projects.
:canadianwave:
 

chrisk

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Looks like the AMD crowd gets screwed in the short-term. Looks like some good science will get done.
 

SugarJ

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AHA! That psummaryC page now updated my HFM.net so that it shows my bigadv PPD correctly, including the bonus!
 

Soultribunal

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Do not use this if you are running GPU clients at all.
I just tested it with and without and it drops the PPD of all your cards by 25-85% from what I've seen.

Bad Mojo lol.

ST
 

LCB001

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AHA! That psummaryC page now updated my HFM.net so that it shows my bigadv PPD correctly, including the bonus!
There is alot to like about HFM.net, the only thing I miss from FahSpy is the actual time of completion as opposed to a countdown ETA.

The link to realtime EOC stats is a nice bonus...
 

SugarJ

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Just hooked HFM.net up yesterday, very similar to Fahmon which I've always used, with a lot of extra features. One blip getting it to auto-load the config, and the other was it not recognizing the bigadv wu. I liked that it directly imported my clients from Fahmon.
 

LCB001

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Feb 19, 2008
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Just hooked HFM.net up yesterday, very similar to Fahmon which I've always used, with a lot of extra features. One blip getting it to auto-load the config, and the other was it not recognizing the bigadv wu. I liked that it directly imported my clients from Fahmon.
For some reason I never liked FahMon and have always used FahSpy, for one thing I found it to be more accurate as far as ppd figures went.

Unfortunatly I made the mistake of trying to update the WU database and the new psummary page revisions messed it up on my main rig.

Did you get the auto-load figured out?...
 

SugarJ

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I did.

for those trying to figure it out: Save your configuration file. then Edit>Preferences>Startup. Checkmark load configuration file, and browse to where you saved it.
 

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