Hi Chris, On 12.07.2012 13:16, Geoff Hutchison wrote:
I've just seen a demo of the impact of running applications on the GPU and it does seem for some operations you can get striking performance gains. Would it be worth considering porting openbabel to OpenCL?Much like muti-threading, it's not clear how some operations in Open Babel would work in OpenCL.
As Geoff points out they are couple of factors to consider in this regard. Sometimes making algorithmic changes can boost performance even more than going the GPU way. In my case however, I'm interested in optimization through parallel approaches. That's why I'm researching on GPU and I will be very glad to hear whatever ideas you might have.
That said, there are certain types of code which make clear sense as multi-threaded and/or OpenCL, for example the force fields and conformer generation code, or the charge assignment. There's actually a student in Ireland sponsored by Noel who's investigating this as we speak. (You may have seen some posts from Omar already.)
I have look at force fields and conformer generation codes since they are both related. When you are doing conformational search you also need to asses the energy of the conformer to decide if you are going to keep it. Improving forcefields calculation should also improve performance for conformer generation.
Conformer generation also looks promising, Attached you can find a plot of the time spent generating conformers for several different drug like molecules using Confab [1]. I used the optimized Borodina set that you can get from Confab's article [2]. As you can appreciate from the plot as the number of conformers involved increases, execution times for conformational search increases noticeably. I will be happy if I can shave those numbers by a half factor offloading some operations to the GPU.
Cheers, -- Omar [1] Confab - http://confab.googlecode.com/[2] Confab Article (Borodina Optimized Set) - http://www.jcheminf.com/content/3/1/8
conformers_vs_generation_time.png
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