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Showing posts from September, 2014

Adding a simple cuda library to RDKit

There are many interesting things a chemist can do with a GPU. Think FastROCS as an example where GPU has greatly speed-up aligning two conformers.

A chemist, in addition to learning how to code on a GPU a little bit, has to distribute the code. One strategy would be to include the code in another software package that's widely used by the target audience. This can be a very tedious task... and so the task of this post will be to cover this 'boiler plate' part. The code presented here does nothing meaningful, it just shows you how to do the piping.

For the ubuntu users in the house, visit https://developer.nvidia.com/cuda-downloads. In my setup ubuntu 14.04 64bit DEB was the choice, then 'sudo apt-get install nvidia-cuda-toolkit'

Here is a simple 'hello world' program that truly does some work on the GPU.
Let's save that as hello-world.cu file. It can be anywhere – this will be independent of rdkit for now. That's all good. Now let's ma…