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pengxingang / Pocket2Mol

Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets
MIT License
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Question about CPU usage #14

Open SejeongPark8354 opened 1 year ago

SejeongPark8354 commented 1 year ago

First of all, thank you for sharing your wonderful research. After I run the Pocket2Mol, I have a question about CPU usage. I think that Pocket2Mol doesn't require large memory in GPU but uses CPU a lot. Is there any reason for specifying Pocket2Mol use CPU a lot rather than GPU? Wouldn't it cause a problem if I change the code to run process mainly using GPU?

pengxingang commented 1 year ago

Thanks for your interest in the work. Some parts of the algorithm use multiple CPUs , e.g. calculation of the KNN graph edges. However, actually we found that the sampling also worked well if we restricted it only on one CPU using the command taskset -c 0 python samplexxx.py. It seemed that the number of CPUs did not influence sampling too much. So we actually recommend using one CPU for sampling.