Re: [Rdkit-discuss] GIL Lock in BulkTanimotoSimilarity

2022-10-22 Thread David Cosgrove
Hi Greg, Thanks for the pointer. I’ll take a look. If it could go in the next patch release that would be really useful. Dave On Sat, 22 Oct 2022 at 10:52, Greg Landrum wrote: > > Hi Dave, > > We have multiple examples of this in the code, here’s one: > >

Re: [Rdkit-discuss] GIL Lock in BulkTanimotoSimilarity

2022-10-22 Thread Greg Landrum
Hi Dave, We have multiple examples of this in the code, here’s one: https://github.com/rdkit/rdkit/blob/b208da471f8edc88e07c77ed7d7868649ac75100/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp#L40 I’m not sure how this would interact with the call to Python::extract that’s in the bulk

[Rdkit-discuss] GIL Lock in BulkTanimotoSimilarity

2022-10-22 Thread David Cosgrove
Hi, I'm doing a lot of tanimoto similarity calculations on large datasets using BulkTanimotoSimilarity. It is an obvious candidate for parallelisation, so I am using concurrent.futures to do so. If I use ProcessPoolExectuor, I get good speed-up but each process needs a copy of the fingerprint