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Among other things, this has lots of applications for molecular dynamics (computational chemistry simulations) [1]. Before you had to transfer data over to the
by pvnick 13y ago
Among other things, this has lots of applications for molecular dynamics (computational chemistry simulations) [1]. Before you had to transfer data over to the GPU, which if you're dealing with small data sets and only computationally limited is no big deal. But when you get bigger data sets that becomes a problem. Integrating the GPU and the CPU means they both have access to the same memory, which makes parallelization a lot easier. If, as someone else here said, AMD is partnering with Oracle to abstract the HSA architecture with something more high-level like java [2], then you don't need to go learn CUDA or Mantle or whatever GPU language gets cooked up just for using that hardware.
I'm personally hoping that not only will we get to see more effective medicines in less time, maybe some chemistry research professors will get to go home sooner to spend time with their kids.
[1] http://www.ks.uiuc.edu/Research/gpu/ http://www.ks.uiuc.edu/Research/gpu/
[2] http://semiaccurate.com/2013/11/11/amd-charts-path-java-gpu/ http://semiaccurate.com/2013/11/11/amd-charts-path-java-gpu/
- higherpurpose 13y agoHSA will also be compatible with LLVM, so you get all the languages supported by that, too.
- reitzensteinm 13y agoAs to your last point, I suspect there's a sort of Jevons' Paradox for scientific research (and creative problem solving fields in general). Which is to say that when you're seeing progress more quickly, you'll spend more hours working on the problem, not less. Determining whether this is good or bad is left as an exercise to the reader :)
- vanderZwan 13y agoDoesn't that kind of imply we're screwed when it comes to sustainability?
- blah32497 13y agoCan you give examples of medicines developed thanks to computational chemistry simulations? I'm rather ignorant about this area of research, but it always seemed to me kinda fruitless? Sorta like high throughput screening - a ton of resources and computation is dedicated because it sounds like a good idea... but ultimately there is very little to show for it all. Way too little signal and way too much noise.
- akiselev 13y agohttp://en.wikipedia.org/wiki/Drug_design#Rational_drug_discovery http://en.wikipedia.org/wiki/Drug_design#Rational_drug_disco... Scroll down to Examples.
- sp332 13y agoWhy not just link there? https://en.wikipedia.org/wiki/Drug_design#Examples https://en.wikipedia.org/wiki/Drug_design#Examples
- cma 13y agoI'm not giving you what you want, but here's a visual example of using a computational microscope to understand how drug actually works and finds its binding site: http://www.youtube.com/watch?v=PGqCeSjNuTY&t=50m27s http://www.youtube.com/watch?v=PGqCeSjNuTY&t=50m27s If you can't see a difference between that and say, X-Ray crystallography then well..
- caycep 13y agoI would be interested in seeing publications on this - the last time I checked, I think the algorithms and software were being treated as in-house intellectual property by pfizer, novartis, and co
- rotskoff 13y agoActually, the "algorithms" are usually fairly straight-forward and well documented integrators for Newtonian dynamics, usually some form of Verlet Integration. The most popular and efficient Molecular Dynamics packages are open source, some GPL (e.g., NAMD, Gromacs). The technology is nowhere near in silico drug design, but we're converging on useful tools to measure important quantities like free energies of binding. Pharmaceutical companies have some interest in this technology, but at this point, don't direct too much effort into atomistic simulations.
- dogmatix 13y agoMantle's is a graphics, not a compute API. For compute AMD uses OpenCL and HSAIL.
- Arelius 13y agoI'd be surprised if Mantle did not have a way to issue compute shaders.
- sn0v 13y agoI've worked with CUDA before (and hit issues with large datasets, like you've mentioned). While HSA is presumably going to make things a lot easier, I'm curious about AMD's partnership with Oracle - how much of a performance hit do you reckon we'll see if Java is implemented? And wouldn't it have been easier to go with something like Python that also supports multithreading and (to the best of my limited knowledge) has better scientific libraries?
- nitrogen 13y agoIt's likely their implementation of Java will add constructs to aid parallelization, but Java already has very robust threading support with no GIL.
- sn0v 13y agoYeah perhaps I could have worded my comment better. I meant Python (just like Java) supports parallelization as well, plus it seems to have better scientific libraries.