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Better Ethernet Speeds Folding Simulations

post #1 of 12
Thread Starter 
From one of the trade magazines I am subscribed to, Drug Discovery and Development (dddmag.com)

To speed the performance of their cluster computing system used to run simulations that model the folding and unfolding of proteins, researchers at the Laboratory of Biophysics and Surface Anaysis (LBSA), University of Nottingham School of Pharmacy, Nottingham, UK, are using a new Ethernet technology to speed the transfer of data.

The technologu, called EtherFabric, from Level % Networks, Sunnyvale, CA, is, in esscence, a network interface card that is installed in the servers of a computing cluster. The card takes the task of transferring data away from the central processing unit (CPU) so it can concentrate on performing the intense calcualtions needed by the application.

Phillip Williams, PhD, a research fellow in the School of Pharmacy and a staff member of the LBSA, focuses on the protein folding process whereby LBSA researchers run single-molecule experiments that measure the force required to unfold a protein.

Completing analysis of a single folding or unfolding protein can require billions of calculations, over billions of time steps, among thousands of atoms, performed on thousands of computers in massively parallel computing clusters.

"We found that normal TCP Ethernet hardware is often a bottleneck in the calculation," says Williams, "and the CPUs spend their time running the network, which is of no use. With EtherFabric, the actual network hardware takes control of the communication and leaves the CPU to do the job that it was intended for - the calculation."

Report by Elizabeth Tochin, News Editor
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post #2 of 12
Woohoo, Nottingham! 10 miles from meeee...

But interesting nonethless. No mention of it coming out for the wider public?
post #3 of 12
Thread Starter 
I am assuming this EtherFabric card is waaay expensive for us enthusiasts. But it makes a lot of sense to me, free the CPU to calculate, let the network be handled by a secondary CPU.
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post #4 of 12
hmm, I wonder if a software implentation could be created for HT/dual core/dual processor systems - whereby one core/half (for HT) takes control of the network and the other purely folds.
post #5 of 12
Thread Starter 
Quote:
Originally Posted by muffin
hmm, I wonder if a software implentation could be created for HT/dual core/dual processor systems - whereby one core/half (for HT) takes control of the network and the other purely folds.
That is an interesting proposition for us, the financially challenged.
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post #6 of 12
Interesting. Found pricing estimates of $295 and $495.

I'll have to do some more research and see if it will fit my uses.
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post #7 of 12
Wow impressive this sounds..wish i had it.
post #8 of 12
Hmm...If they import it into the US, and prices fall, I may consider investing in one of those.
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post #9 of 12
Quote:
Originally Posted by muffin
Woohoo, Nottingham! 10 miles from meeee...

But interesting nonethless. No mention of it coming out for the wider public?
{OT} Muffin, I was just wondering, why do you say "miles" instead of "kilometers"? Is miles used as a general term in the UK, or is it something that you picked up from talking to us yanks for so long? {OT}
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post #10 of 12
Quote:
Originally Posted by Lando95
{OT} Muffin, I was just wondering, why do you say "miles" instead of "kilometers"? Is miles used as a general term in the UK, or is it something that you picked up from talking to us yanks for so long? {OT}
Screw metric. Its good for small stuff like millimetres and centimetres. Miles have just stuck around in Britain because its more familiar to us? I mean, all the road signs say miles, so if we changed to km then the sign makers would have a heart attack with changing every sign in the country
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