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Wouldn't it be nice to split workloads? - Page 3

post #21 of 33
Wouldn't a cluster computing hurt Folding performance?

From my understanding, Folding is attempting to collapse a protein into the most efficent package. That means you have hundred/thousands of molecules interacting with each other. GPU Folding works well because you have so many cores processing all these interdependent interactions. CPU Folding works well because you have so many powerful cores capable of out-of-order operation.

If you place the Folding workload on a cluster, the network latency would KILL performance as each interdependent change would have to be passed through a few interconnects adding at least 1-2ms of latency instead of ~1ns.

Cluster computing is good for when you have groups of parallel threads that can be processed completely independently and then merged at intervals.
Edited by DuckieHo - 6/10/10 at 11:32am
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post #22 of 33
Awww, the folding on multiple cheap proc's has gone down the drain
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post #23 of 33
Thread Starter 
yes, i read through most of the performance issues with cluster setups and i think it might just be a nag to get it going. if it was designed with the concept in mind it might yield great results, as for the setup of these nodes and patches to the kernels its way too complex to do if your end result is worse than your standalone.

zodac, yes i would make this a definite no

oh well, tried and tested .

bye
post #24 of 33
Thank you for trying
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post #25 of 33
not that the average person has it or could even think of ever having it, but a fiber network would provide next to no latency for it to work?
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post #26 of 33
Thread Starter 
yeah that could work
post #27 of 33
Quote:
Originally Posted by Magus2727 View Post
not that the average person has it or could even think of ever having it, but a fiber network would provide next to no latency for it to work?
A fiber network provides bandwidth (which isn't needed) and some reduction in latency (which isn't enough).


The inter-node communication is still above .1ms. That is still a 100-1000s times slower than L1, L2, L3, and RAM.
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post #28 of 33
what about server boards? they have logical different chips (while I am sure the latency is still smaller then on a network, it has to be larger then a single chip) and can use all the cores very efficently...

the protein is folded in a bunch of different ways to see what happens right? these folding patterns are independent of the previous results? it would require a large WU payload to recive, but if "flags" were used for start and stop points of folding, is there any reason why the two computers (or more) could start at opposit ends and work their way to the middle while using the network to update the sections done in the samw WU?

this would require a complete different client programing and could not be just software based on the computers running it, but the client would need to be programed such to run this way, along with the WU's being packaged in a was that this is possible from Stanford.
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post #29 of 33
Quote:
Originally Posted by Magus2727 View Post
what about server boards? they have logical different chips (while I am sure the latency is still smaller then on a network, it has to be larger then a single chip) and can use all the cores very efficently...
Yes, that would work. It is very different from cluster computing.

Quote:
Originally Posted by Magus2727 View Post
the protein is folded in a bunch of different ways to see what happens right? these folding patterns are independent of the previous results?
Protein folding when a random protein coil collapses into a structure. The structure is generally the lowest "resistence" state. Each protein will always collapse into this state... unless something goes wrong. When something goes wrong, it can lead/cause a disease. The Folding pattern is absolutely dependent on the previous result. From my understanding of the process, is each WU is a tiny time slice of the process. The PC is trying to figure the best possible way all the molecules can arrange themselves. Once figured out, it returns the result so the next WU can be based on that. (I think.)

Quote:
Originally Posted by Magus2727 View Post
it would require a large WU payload to recive, but if "flags" were used for start and stop points of folding, is there any reason why the two computers (or more) could start at opposit ends and work their way to the middle while using the network to update the sections done in the samw WU?
The point of Folding is attempting to find the end or solution of best possible configuration of all the molecules. It is basically a "Traveling Saleman Problem" and is a NP-Hard problem. Once you have the solution, it is relatively easy to check but getting to it is VERY hard. Figuring out how two molecules interact is easy. Figuring out three is a bit harder. Figure out ten is MUCH harder. Figuring out one hundred is EXTREMELY hard. Folding is even harder than the TSP because it is in 3-D....


(The Travelling Saleman Problem is trying to find the shortest route between "cities" while still visiting all the cities. It gets much much harder as you add "cities".)
Edited by DuckieHo - 6/11/10 at 11:10am
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post #30 of 33
Awww... I guess it would only be practicle if the next state, did not depended on the previous state, you could brake it up very easy if that was the case.
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