Обсуждение: query optimization
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. Regards, Faheem.
2009/11/23 Faheem Mitha <faheem@email.unc.edu>
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.
Regards, Faheem.
Hi Faheem,
There appears to be a discrepancy between the 2 PDFs you provided. One says you're using PostgreSQL 8.3, and the other shows you using common table expressions, which are only available in 8.4+.
Thom
On Mon, 23 Nov 2009, Thom Brown wrote: > Hi Faheem, > > There appears to be a discrepancy between the 2 PDFs you provided. One > says you're using PostgreSQL 8.3, and the other shows you using common > table expressions, which are only available in 8.4+. Yes, sorry. I'm using Postgresql 8.4. I guess I should go through diag.pdf and make sure all the information is current. Thanks for pointing out my error. Regards, Faheem.
On Tue, Nov 24, 2009 at 12:49 AM, Faheem Mitha <faheem@email.unc.edu> wrote: > > Yes, sorry. I'm using Postgresql 8.4. I guess I should go through diag.pdf > and make sure all the information is current. Thanks for pointing out my > error. > excellent report! about the copy problem: You seem to have created the primary key before doing the copy (at least that`s what the dump before copy says). This is bad. Create it after the copy. Greetings Marcin
How often are the tables you query from updated?
Rgds
Sebastian
Rgds
Sebastian
On Tue, Nov 24, 2009 at 12:52 AM, marcin mank <marcin.mank@gmail.com> wrote:
On Tue, Nov 24, 2009 at 12:49 AM, Faheem Mitha <faheem@email.unc.edu> wrote:excellent report!
>
> Yes, sorry. I'm using Postgresql 8.4. I guess I should go through diag.pdf
> and make sure all the information is current. Thanks for pointing out my
> error.
>
about the copy problem: You seem to have created the primary key
before doing the copy (at least that`s what the dump before copy
says). This is bad. Create it after the copy.
Greetings
Marcin
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On Tue, 24 Nov 2009, Sebastian Jörgensen wrote: > How often are the tables you query from updated? Quite rarely. Once in a while. The large tables, eg. geno, are basically static. Regards, Faheem. > Rgds > Sebastian > > On Tue, Nov 24, 2009 at 12:52 AM, marcin mank <marcin.mank@gmail.com> wrote: > On Tue, Nov 24, 2009 at 12:49 AM, Faheem Mitha <faheem@email.unc.edu> wrote: > > > > Yes, sorry. I'm using Postgresql 8.4. I guess I should go through diag.pdf > > and make sure all the information is current. Thanks for pointing out my > > error. > > > > excellent report! > > about the copy problem: You seem to have created the primary key > before doing the copy (at least that`s what the dump before copy > says). This is bad. Create it after the copy. > > Greetings > Marcin > > -- > Sent via pgsql-performance mailing list (pgsql-performance@postgresql.org) > To make changes to your subscription: > http://www.postgresql.org/mailpref/pgsql-performance > > > >
On Mon, Nov 23, 2009 at 5:47 PM, Faheem Mitha <faheem@email.unc.edu> 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
Hi Robert, Thanks very much for your suggestions. On Wed, 25 Nov 2009, Robert Haas wrote: > On Mon, Nov 23, 2009 at 5:47 PM, Faheem Mitha <faheem@email.unc.edu> 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. Good strategy. Now I just have to understand EXPLAIN ANALYZE well enough to figure out which bits are slow. :-) > 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. Isn't SELECT DISTINCT supposed to be evil, since in general the result is not deterministic? I think I had SELECT DISTINCT earlier, and removed it because of that, with the help of Andrew (RhodiumToad on #postgresql) I didn't compare the corresponding subqueries separately, so don't know what speed difference this made. > 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. What are the options re pre-marking? > 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. You don't say whether you are looking at the PED or TPED query, so I'll assume PED. They are similar anyway. I see your point re the joins. You mean anno INNER JOIN geno followed by geno INNER JOIN dedup_patient_anno ? I think the point of the first join is to reduce the anno table based on information from the geno table. The result is basically a subset of the anno table with some potential duplication removed, which is then re-joined to the geno table. I agree this seems a bit suboptimal, and there might be a better way to do this. > 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. Regards, Faheem.
On Wed, Nov 25, 2009 at 5:54 PM, Faheem Mitha <faheem@email.unc.edu> wrote: > > Hi Robert, > > Thanks very much for your suggestions. > >>> 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. > > Good strategy. Now I just have to understand EXPLAIN ANALYZE well enough to > figure out which bits are slow. :-) Well, you basically just look for the big numbers. The "actual" numbers are in ms, and each node includes the times for the things beneath it, so usually my approach is to just look at lower and lower levels of the tree (i.e. the parts that are more indented) until I find the lowest level that is slow. Then I look at the query bits presented there to figure out which piece of the SQL it corresponds to. Looking at the estimates (which are not in ms or any other particular unit) can be helpful too, in that it can help you find places where the planner thought it would be fast but it was actually slow. To do this, look at the top level of the query and get a sense of what the ratio between estimated-cost-units and actual-ms is. Then look for big (order of magnitude) deviations from this throughout the plan. Those are places where you want to either gather better statistics, or rewrite the query so that it can make better use of statistics. The latter is more of an art than a science - I or someone else on this list can help you with it if we find a specific case to look at. >> 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. > > Isn't SELECT DISTINCT supposed to be evil, since in general the result is > not deterministic? I think I had SELECT DISTINCT earlier, and removed it > because of that, with the help of Andrew (RhodiumToad on #postgresql) I > didn't compare the corresponding subqueries separately, so don't know what > speed difference this made. Well, any method of DISTINCT-ifying is likely to be somewhat slow, but I've had good luck with SELECT DISTINCT ON (...) in the past, as compared with other methods. YMMV - the only way to find out is to benchmark it. I don't think it's non-deterministic if you order by the DISTINCT-ON columns and enough extras to break any ties - you should get the first one of each set. >> 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. > > What are the options re pre-marking? Well, what I usually do is - if I'm going to do the same distinct-ification frequently, I add an extra column (say, a boolean) and set it to true for all and only those rows which will pass the distinct-ification filter. Then I can just say WHERE <that column name>. >> 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. > > You don't say whether you are looking at the PED or TPED query, so I'll > assume PED. They are similar anyway. > > I see your point re the joins. You mean > > anno INNER JOIN geno > > followed by > > geno INNER JOIN dedup_patient_anno > > ? I think the point of the first join is to reduce the anno table based on > information from the geno table. The result is basically a subset of the > anno table with some potential duplication removed, which is then re-joined > to the geno table. I agree this seems a bit suboptimal, and there might be a > better way to do this. Yeah, I didn't think about it in detail, but it looks like it should be possible. Eliminating joins can sometimes have *dramatic* effects on query performance, and it never hurts. ...Robert
On Wed, 25 Nov 2009, Robert Haas wrote: > On Wed, Nov 25, 2009 at 5:54 PM, Faheem Mitha <faheem@email.unc.edu> wrote: > Well, any method of DISTINCT-ifying is likely to be somewhat slow, but > I've had good luck with SELECT DISTINCT ON (...) in the past, as > compared with other methods. YMMV - the only way to find out is to > benchmark it. I don't think it's non-deterministic if you order by > the DISTINCT-ON columns and enough extras to break any ties - you > should get the first one of each set. Right, but adding enough extras to break ties is up to the user, and the language doesn't guarantee anything, so it feels more fragile. >>> 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. >> >> What are the options re pre-marking? > > Well, what I usually do is - if I'm going to do the same > distinct-ification frequently, I add an extra column (say, a boolean) > and set it to true for all and only those rows which will pass the > distinct-ification filter. Then I can just say WHERE <that column > name>. Yes, I see. The problem with is premarking is that the selection is somewhat dynamic, in the sense that this depends on the idlink table, which depends on patient data, which can change. >>> 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. >> >> You don't say whether you are looking at the PED or TPED query, so I'll >> assume PED. They are similar anyway. >> >> I see your point re the joins. You mean >> >> anno INNER JOIN geno >> >> followed by >> >> geno INNER JOIN dedup_patient_anno >> >> ? I think the point of the first join is to reduce the anno table based on >> information from the geno table. The result is basically a subset of the >> anno table with some potential duplication removed, which is then re-joined >> to the geno table. I agree this seems a bit suboptimal, and there might be a >> better way to do this. > > Yeah, I didn't think about it in detail, but it looks like it should > be possible. Eliminating joins can sometimes have *dramatic* effects > on query performance, and it never hurts. Failing all else, couldn't I smoosh together the two queries and do a triple join? For reference, the two CTEs in question, from the PED query, are as follows. dedup_patient_anno AS ( SELECT * FROM (SELECT *, row_number() OVER(PARTITION BY anno.rsid ORDER BY anno.id) FROM anno INNER JOIN geno ON anno.id = geno.anno_id WHERE idlink_id = (SELECT MIN(id) FROM idlink ) ) AS s WHERE row_number = '1' ), patient_geno AS ( SELECT geno.idlink_id AS idlink_id, geno.anno_id AS anno_id, geno.snpval_id AS snpval_id, allelea_id, alleleb_id FROM geno INNER JOIN dedup_patient_anno ON geno.anno_id = dedup_patient_anno.id ), Regards, Faheem.
On Fri, Nov 27, 2009 at 4:47 PM, Faheem Mitha <faheem@email.unc.edu> wrote: >>>> 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. >>> >>> What are the options re pre-marking? >> >> Well, what I usually do is - if I'm going to do the same >> distinct-ification frequently, I add an extra column (say, a boolean) >> and set it to true for all and only those rows which will pass the >> distinct-ification filter. Then I can just say WHERE <that column >> name>. > > Yes, I see. The problem with is premarking is that the selection is somewhat > dynamic, in the sense that this depends on the idlink table, which depends > on patient data, which can change. Yeah. For things like this I find you have to think hard about how to organize your schema so that you can optimize the queries you care about. There are no "just do this and it works" solutions to performance problems of this type. Still, many of them are solvable by making the right decisions elsewhere. Sometimes you can use triggers to recompute your premarks when the data in the other table changes. Another strategy is to keep a cache of precomputed results somewhere. When the underlying data changes, you use triggers to invalidate anything in the cache that might now be wrong, and set things up so that it will be recomputed when next it is used. But in either case you have to figure out the right place to do the computation so that it gains you more than it saves you, and adjusting your schema is often necessary. >>>> 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. >>> >>> You don't say whether you are looking at the PED or TPED query, so I'll >>> assume PED. They are similar anyway. >>> >>> I see your point re the joins. You mean >>> >>> anno INNER JOIN geno >>> >>> followed by >>> >>> geno INNER JOIN dedup_patient_anno >>> >>> ? I think the point of the first join is to reduce the anno table based >>> on >>> information from the geno table. The result is basically a subset of the >>> anno table with some potential duplication removed, which is then >>> re-joined >>> to the geno table. I agree this seems a bit suboptimal, and there might >>> be a >>> better way to do this. >> >> Yeah, I didn't think about it in detail, but it looks like it should >> be possible. Eliminating joins can sometimes have *dramatic* effects >> on query performance, and it never hurts. > > Failing all else, couldn't I smoosh together the two queries and do a triple > join? For reference, the two CTEs in question, from the PED query, are as > follows. > > dedup_patient_anno AS > ( SELECT * > FROM > (SELECT *, > row_number() OVER(PARTITION BY anno.rsid ORDER BY > anno.id) > FROM anno > INNER JOIN geno > ON anno.id = geno.anno_id > WHERE idlink_id = > (SELECT MIN(id) > FROM idlink > ) > ) AS s > WHERE row_number = '1' > ), > patient_geno AS > ( SELECT geno.idlink_id AS idlink_id, > geno.anno_id AS anno_id, > geno.snpval_id AS snpval_id, > allelea_id, alleleb_id > FROM geno > INNER JOIN dedup_patient_anno > ON geno.anno_id = dedup_patient_anno.id > ), If that will give the same results, which I'm not immediately certain about, then I highly recommend it. In general I would recommend only using CTEs to express concepts that can't sensibly be expressed in other ways, not to beautify your queries. Keep in mind that joins can be reordered and/or executed using different methods but most other operations can't be, so trying to get your joins together in one place is usually a good strategy, in my experience. And of course if that lets you reduce the total number of joins, that's even better. ...Robert