Hi Gregori.
On Tue, Apr 23, 2013 at 1:57 PM, Gerebtzoff, Gregori
<[email protected]> wrote:
> Hi RDKitters,
>
> I'm facing some performance issue using the RDKit cartridge;
> the database contains roughly 170k small molecules, I use the cartridge
> version 0.20.0 on PostgreSQL 8.4.7, and the tanimoto_threshold is set to 0.5
> A simple similarity search takes at least 30 seconds to complete.
> The database has been recently vacuumed.
> Any hints are most welcome!
That's a pretty ancient version of both postgresql and the cartridge.
Any chance you could switch to a more up-to-date version of at least
the cartridge? The newer version may have better performance and will
certainly make it easier for me to help you track down the problem.
As a reference point, here's timing for a basic similarity search in a
table of 100k fingerprints :
fptest=# select count(*) from fps where
atompairbv_fp('O=C(NCCc1cccs1)c1cc(Cl)sc1Cl')%pairbv;
count
-------
31
(1 row)
Time: 328.503 ms
That's running on a VM, using postgresql 8.4.16 and a recent version
of the cartridge.
-greg
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