Hi Greg,
> What these are telling you is that the second query is not using the index:
> it's a sequential scan, so it has to test all rows of the database. This
> happens because the index is defined for the operator %, but not for the
> function tanimoto_sml(). There may be an approach to get the index set up
> using that function, but there we reach the limits of my expertise.
Well, I will stick to the recommended operator use then!
> One final advanced topic: if you are planning on making regular use of the
> similarity features in the cartridge and are running on a linux system or
> Mac I would recommend recompiling the cartridge with some optimizations for
> tanimoto similarity. To do this, you need to edit the cartridge Makefile
> from:
> PG_CPPFLAGS = -I${BOOSTHOME} -I${RDKIT}/Code -DRDKITVER='"007200"'
> ${INCHIFLAGS} #-DUSE_BUILTIN_POPCOUNT -msse4.2
>
> to:
> PG_CPPFLAGS = -I${BOOSTHOME} -I${RDKIT}/Code -DRDKITVER='"007200"'
> ${INCHIFLAGS} -DUSE_BUILTIN_POPCOUNT -msse4.2
>
> (I just removed a comment character here). This speeds the Tanimoto
> calculation up a fair bit (it's still not nearly as fast as Andrew's
> chemfp, but it's better than the default behavior).
I'm on linux (Ubuntu), and have just re-built with the above recommendation.
I'll see what the speeds look like afterwards (out of interest, I presume the
timings in your examples were with this optimisation in place?).
Does this also affect dice?
And final question - after rebuilding the cartridge, does the extension need to
be dropped and then re-created in all databases; does postgreSQL server need
restarting; or neither?
> Hope this helps,
> -greg
It does - thanks!
Kind regards
James
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