On Mon, Nov 23, 2009 at 5:47 PM, Faheem Mitha <faheem@xxxxxxxxxxxxx> wrote: > > Hi everybody, > > I've got two queries that needs optimizing. Actually, there are others, but > these are pretty representative. > > You can see the queries and the corresponding plans at > > http://bulldog.duhs.duke.edu/~faheem/snpdb/opt.pdf > > or > > http://bulldog.duhs.duke.edu/~faheem/snpdb/opt.tex > > if you prefer text (latex file, effectively text in this case) > > The background to this is at > http://bulldog.duhs.duke.edu/~faheem/snpdb/diag.pdf > > If more details are required, let me know and I can add them. I'd appreciate > suggestions about how to make these queries go faster. > > Please CC this email address on any replies. I've found that a good way to approach optimizing queries of this type is to look at the EXPLAIN ANALYZE results and figure out which parts of the query are slow. Then simplify the rest of the query as much as possible without eliminating the slowness. Then try to figure out how to optimize the simplified query: rewrite the logic, add indices, change the schema, etc. Lastly start adding the other bits back in. It looks like the dedup_patient_anno CTE is part of your problem. Try pulling that piece out and optimizing it separately. I wonder if that could be rewritten to use SELECT DISTINCT ON (...) and whether that would be any faster. If not, you might want to look at some way of pre-marking the non-duplicate rows so that you don't have to recompute that each time. Then you might be able to use the underlying table directly in the next CTE, which will usually permit better optimization, more use of indices, etc. It seems pretty unfortunate that dedup_patient_anno joins against geno and then patient_geno does what appears to be the same join again. Is there some way to eliminate that? If so it will probably help. Once you've got those parts of the query as well-optimized as you can, add the next pieces in and start hacking on those. ...Robert -- Sent via pgsql-performance mailing list (pgsql-performance@xxxxxxxxxxxxxx) To make changes to your subscription: http://www.postgresql.org/mailpref/pgsql-performance
