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New Core/Work Available

T

Tobit

[H]ard|DCer of the Month - March 2010/May 2011
Joined
Dec 12, 2005
Messages
5,145
There are some new work units out there that use a newly released core. These do not appear in psummary yet so don't be alarmed when FAH-mon or HFM.net report unknowns for the client and core along with the inability to calculate points.

Found on fah-addict.net:

The Protomol core for uniprocessor clients has just entered the public testing phase for –advmethods flag users. It comes along with two new projects: 10000 and 10001.

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.


Happy folding!
 
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One minor issue with these new WUs but they are working as expected here. I've reported my issue already.

One tip I can pass along already, however. If you happen to notice it not make it to 100% and finishes early.. this is not a bug. It was mentioned this could happen and it's expected. The trajectory just fails at that point, there is no further computation possible but it's not an EUE caused by a bug so it's not outputting it as such.
 
Yup, I've figured it out already Zero.. thanks. :cool:
 
Tobit said:
Only 200 to 400 PpD.. this is pretty typical of most uniprocessor work, so it's all about the same.
Click to expand...
I think it's closer to the PPD of the bonus uniprocessor WUs compared to the regular P4400s, but I have only folded on one unit so far.
 
thats why you should get HDCoTY zero, you are everywhere with answers to everything
 
Mr. Pedantic said:
Why is this out first?! Why is the new SMP client not out!?
Click to expand...
Coding for new cores already used by others is easy. Coding an entirely new clients is much harder than most users give Stanford credit for. ProtoMol is an established core.. coding for it is therefore quite easy. SMP3 is a major re-write of the client.
 
Coding for new cores already used by others is easy. Coding an entirely new clients is much harder than most users give Stanford credit for. ProtoMol is an established core.. coding for it is therefore quite easy. SMP3 is a major re-write of the client.
Click to expand...
That was a rhetorical question. And you were supposed to say something like, 'yeah!' 'get the SMP3 client out!' or some other comment dripping with self-righteous indignation.
 
For those of you who read the part in the announcement that said there might be some incompatibility issues with AMD processors, the following from John Naylor, a private beta tester, may shed some light on this topic some more.

Intel and AMD have reached an agreement that will shortly allow the Intel compiler that Joe has used for this core to properly support all these optimisations for AMD chips. Once Intel release the updated version it should be a matter of a simple recompile to add support for those extensions on AMD processors. The Intel compiler produced code which is still 5-10% faster on AMD than any other compiler Joe tried, but it should be faster still once AMD support is added to the Intel compiler. Therefore for once it is not the Pande Group who are the blockage, but Intel.
Click to expand...
 
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Vijay Pande has finally made an official announcement on his blog regarding these WU's -

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)!
 
Tobit said:
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)!
Click to expand...
Looking forward to the additional improvements to be introduced in 2010. However, I scaled down my uniprocessor clients from a peak of nearly 20 clients to about 4 clients now. After migrating to single SMP VMs and dropping their priority to idle, it made little sense to continue running the classic client on most of these systems.
 
APOLLO said:
Looking forward to the additional improvements to be introduced in 2010. However, I scaled down my uniprocessor clients from a peak of nearly 20 clients to about 4 clients now. After migrating to single SMP VMs and dropping their priority to idle, it made little sense to continue running the classic client on most of these systems.
Click to expand...
Agreed, the Uniprocessors always seem to get the least amount of love when it comes to points but there is still a lot of valuable work they can provide to Stanford. There is a surprising number of configurations out there that still run the standard uniprocessor client.

If you want to maximize points, don't run the uniprocessor client. However, one will benefit science quite a bit by running it. :confused: There is a definite line between points and science and it's becoming broader every day.
 
There are some issues with this new core.
It has been reported to the devs so hopefully after the holidays there will be a fix available.
 
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