James,
On Fri, May 9, 2014 at 10:25 AM, James Davidson <[email protected]>wrote:
>
> > 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?).
>
I would have thought so, but it turns out that I was using a build on my
Mac without the optimization. It's about 20% faster for those sample
queries when I use the rebuilt version.
> Does this also affect dice?
>
It should, but, stupidly, it looks like it doesn't. I'll fix that.
> 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?
>
You do not need to drop the extension. This is just a change to the shared
library and doesn't affect the API. You just need to do a "make install" to
copy in the new shared lib and then restart the server.
-greg
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