Von: Deepti Gupta via Rdkit-discuss
Gesendet: Mittwoch, 26. Februar 2020 09:46
An: rdkit-discuss@lists.sourceforge.net ;
Tim Dudgeon
Betreff: Re: [Rdkit-discuss] RDkit in Python vs. on PostgreSQL?
Hi Tim,
Thank you!
I'll be more detailed in my post, sorry about
Well, as I mentioned previously the big difference is because from
Python you are iterating through the molecules, calculating the
fingerprints and then doing a comparison on the fingerprints. Whereas in
the PostgreSQL cartridge the fingerprints are already generated and
indexed so the search
Hi Tim,
Thank you!
I'll be more detailed in my post, sorry about that. As this was a PoC, I had a
spark cluster with 2 worker nodes with 4 vCPUs with disk size 500GB and memory
15GB on Google Cloud. I timed the response against 2 million data points
consisting of Chembl id, Smile structures.
I think you need to explain what benchmarks you are running and what is
really meant by "faster".
And what hardware (for Spark how many nodes, how big; for PostgreSQL
what size server, what settings esp. the shared_buffers setting).
A very obvious critique of what you reported is that what you
Hi Gurus,
I'm absolutely new to Chem-informatics domain. I've been assigned a PoC where
I've to compare RDKit in Python and RDKit on PostgreSQL. I've installed both
and am trying some hands-on exercises to understand the differences. What I've
understood that the structure searches are slower
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