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Scientists create first billion-atom biomolecular simulation

lanl.gov

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Re: Scientists create first billion-atom biomolecular simulation

#31

Post by thatcat »

phkahler wrote: post #28
thatcat wrote: post #20

Earlier quoted context omitted.

What is the engineer publishing model?

One engineering model is to put the code on github under an open source license so people can use it. But please dont just put it out there and walk away. If you want to develop a useful piece of software, find a way to maintain it. Another model is to offer it for sale as a product. Either way, engineers dont really care about publishing, we care about making useful things and Shari g how-to.

Most engineering fields have journals and publish their research in the same manner as scientists. Whether they care about publishing or not is related to whether their position is in academia or industry.

Re: Scientists create first billion-atom biomolecular simulation

#33

Post by vo2maxer »

jryb wrote: post #8

Biologist's perspective: this paper is not about the biology. The simulation performed here has zero biological interest - the point of the paper was to show how efficient and scalable their software is. This article about the paper is terrible, but honestly I feel like they should be given a pass - it's hard to justify to a lay audience that understands neither DNA nor memory bandwidth why you would choose to study…

I don’t see how this would be of “zero biological interest.” Is it because presently it is not that useful or because it will never have any applicability?

Re: Scientists create first billion-atom biomolecular simulation

#34

Post by jryb »

vo2maxer wrote: post #33
jryb wrote: post #8

Biologist's perspective: this paper is not about the biology. The simulation performed here has zero biological interest - the point of the paper was to show how efficient and scalable their software is. This article about the paper is terrible, but honestly I feel like they should be given a pass - it's hard to justify to a lay audience that understands neither DNA nor memory bandwidth why you would choose to study…

I don’t see how this would be of “zero biological interest.” Is it because presently it is not that useful or because it will never have any applicability?

Because what they were examining is already very well understood.

Re: Scientists create first billion-atom biomolecular simulation

#35

Post by moonbug »

safsafsafa wrote: post #18
moonbug wrote: post #6

must be Gordon Bell prize time again.

1E9 atoms / 130 000 cores = 8000 atoms/core in 2011 I was building 40 000 atom models on a 2001 SGI Fuel simulating them on a single 8 core node at 1ns/week -> 8000 atoms/core. They're about 7 times faster then me 8 years later. So from a computation point, meh. From a tools point this is cool. It isn't trivial to build or analyze a model of 40 000 atoms, never mind 1E9 atoms.

weak scaling is easy.
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