Re: Query taking long time

Hello,

I have changed the multicolumn index from:
"entity2document_name_qualifier_index" btree (name, qualifier)
to:
"document_qualifier_name_index" btree (qualifier, name)

And now the planner doesn't "Recheck cond:" (there are only three different qualifiers vs. millions of names...)

But still taking long time

Limit (cost=384043.64..384043.66 rows=10 width=313) (actual time=80555.930..80555.934 rows=10 loops=1)
-> Sort (cost=384043.64..384081.19 rows=15020 width=313) (actual time=80555.928..80555.931 rows=10 loops=1)
Sort Key: d1_.hepval
Sort Method: top-N heapsort Memory: 29kB
-> Nested Loop (cost=0.00..383719.06 rows=15020 width=313) (actual time=223.778..80547.196 rows=3170 loops=1)
-> Index Scan using document_qualifier_name_index on entity2document e0_ (cost=0.00..52505.40 rows=15020 width=59) (actual time=126.880..11549.392 rows=3170 loops=1)
Index Cond: (((qualifier)::text = 'CompoundDict'::text) AND ((name)::text = 'galactosamine'::text))
-> Index Scan using "DocumentOLD_pkey" on documentold d1_ (cost=0.00..22.04 rows=1 width=254) (actual time=21.747..21.764 rows=1 loops=3170)
Index Cond: (d1_.id = e0_.document_id)
Filter: (d1_.hepval IS NOT NULL)
Total runtime: 80556.027 ms

Any help/point to any direction, would be very appreciated.
Thank you,
Andrés

El Feb 26, 2014, a las 4:41 PM, acanada escribió:

> Hello to everybody and thanks in advance to take a look to this message.
> I'm new in this list and with PostgreSQL.
> My queries are taking too much time to complete and I don't know what to do right now. I think I'm providing all the info required for you to help me. If you need extra info please tell me.
>
> I am using DQL included in the last version of symfony2 (2.4.2). This is the query, formed by DQL, but coppied-pasted to the psql client (9.1.11, server 8.3.8)
>
> explain analyze SELECT e0_.id AS id0, e0_.name AS name1, e0_.qualifier AS qualifier2, e0_."tagMethod" AS tagmethod3, e0_.curation AS curation4, e0_.created AS created5, e0_.updated AS updated6, d1_.id AS id7, d1_.kind AS kind8, d1_.uid AS uid9, d1_."sentenceId" AS sentenceid10, d1_.text AS text11, d1_.hepval AS hepval12, d1_.cardval AS cardval13, d1_.nephval AS nephval14, d1_.phosval AS phosval15, d1_."patternCount" AS patterncount16, d1_."ruleScore" AS rulescore17, d1_."hepTermNormScore" AS heptermnormscore18, d1_."hepTermVarScore" AS heptermvarscore19, d1_.created AS created20, d1_.updated AS updated21, e0_.document_id AS document_id22 FROM Entity2Document e0_ INNER JOIN documentold d1_ ON e0_.document_id = d1_.id WHERE e0_.name ='ranitidine' AND e0_.qualifier = 'CompoundDict' AND d1_.hepval IS NOT NULL ORDER BY d1_.hepval DESC limit 10;
>
>
> limtox=> \d+ documentold;
> Table "public.documentold"
> Column | Type | Modifiers | Storage | Description
> ------------------+--------------------------------+-----------+----------+-------------
> id | integer | not null | plain |
> kind | character varying(255) | not null | extended |
> uid | character varying(255) | not null | extended |
> sentenceId | character varying(255) | not null | extended |
> text | text | not null | extended |
> hepval | double precision | | plain |
> created | timestamp(0) without time zone | not null | plain |
> updated | timestamp(0) without time zone | | plain |
> cardval | double precision | | plain |
> nephval | double precision | | plain |
> phosval | double precision | | plain |
> patternCount | double precision | | plain |
> ruleScore | double precision | | plain |
> hepTermNormScore | double precision | | plain |
> hepTermVarScore | double precision | | plain |
> Indexes:
> "DocumentOLD_pkey" PRIMARY KEY, btree (id)
> "document_cardval_index" btree (cardval)
> "document_heptermnorm_index" btree ("hepTermNormScore" DESC NULLS LAST)
> "document_heptermvar_index" btree ("hepTermVarScore" DESC NULLS LAST)
> "document_hepval_index" btree (hepval DESC NULLS LAST)
> "document_kind_index" btree (kind)
> "document_nephval_index" btree (nephval DESC NULLS LAST)
> "document_patterncount_index" btree ("patternCount" DESC NULLS LAST)
> "document_phosval_index" btree (phosval DESC NULLS LAST)
> "document_rulescore_index" btree ("ruleScore" DESC NULLS LAST)
> "document_sentenceid_index" btree ("sentenceId")
> "document_uid_index" btree (uid)
> Referenced by:
> TABLE "hepkeywordtermnorm2document" CONSTRAINT "fk_1c19bcd0c33f7837" FOREIGN KEY (document_id) REFERENCES documentold(id)
> TABLE "cytochrome2document" CONSTRAINT "fk_21f7636fc33f7837" FOREIGN KEY (document_id) REFERENCES documentold(id)
> TABLE "hepkeywordtermvariant2document" CONSTRAINT "fk_a316e36bc33f7837" FOREIGN KEY (document_id) REFERENCES documentold(id)
> TABLE "entity2document" CONSTRAINT "fk_a6020c0dc33f7837" FOREIGN KEY (document_id) REFERENCES documentold(id)
> TABLE "specie2document" CONSTRAINT "fk_b6e551c8c33f7837" FOREIGN KEY (document_id) REFERENCES documentold(id)
> Has OIDs: no
>
>
>
>
> limtox=> \d+ entity2document; Table "public.entity2document" Column | Type | Modifiers | Storage | Description -------------+--------------------------------+---------------------------------+----------+------------- id | integer | not null | plain |
> document_id | integer | | plain |
> name | character varying(255) | not null | extended |
> qualifier | character varying(255) | not null | extended |
> tagMethod | character varying(255) | default NULL::character varying | extended |
> created | timestamp(0) without time zone | not null | plain |
> updated | timestamp(0) without time zone | | plain |
> curation | integer | | plain |
> Indexes:
> "Entity2Document_pkey" PRIMARY KEY, btree (id)
> "entity2Document_name_index" btree (name)
> "entity2document_name_qualifier_index" btree (name, qualifier)
> "idx_a6020c0dc33f7837" btree (document_id)
> "qualifier_index" btree (qualifier)
> Foreign-key constraints:
> "fk_a6020c0dc33f7837" FOREIGN KEY (document_id) REFERENCES documentold(id)
> Has OIDs: no
>
>
>
>
>
>
> Table metadata:
> documentold: 124.515.592 of rows. It has several columns with a large proportion of NULLs(updated, patternCount, ruleScore, hepTermNormScore, hepTermVarScore)
> entity2document: 93.785.968 of rows. It has two columns with a large proportion of NULLs (updated, curation)
>
> None of the tables receive updates or deletes regularly
>
>
> QUERY PLAN
> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> Limit (cost=387929.02..387929.05 rows=10 width=313) (actual time=55980.472..55980.476 rows=10 loops=1)
> -> Sort (cost=387929.02..387966.75 rows=15090 width=313) (actual time=55980.471..55980.473 rows=10 loops=1)
> Sort Key: d1_.hepval
> Sort Method: top-N heapsort Memory: 28kB
> -> Nested Loop (cost=469.14..387602.93 rows=15090 width=313) (actual time=96.716..55974.004 rows=2774 loops=1)
> -> Bitmap Heap Scan on entity2document e0_ (cost=469.14..54851.25 rows=15090 width=59) (actual time=51.299..8452.592 rows=2774 loops=1)
> Recheck Cond: (((name)::text = 'Cimetidine'::text) AND ((qualifier)::text = 'CompoundDict'::text))
> -> Bitmap Index Scan on entity2document_name_qualifier_index (cost=0.00..465.36 rows=15090 width=0) (actual time=36.467..36.467 rows=2774 loops=1)
> Index Cond: (((name)::text = 'Cimetidine'::text) AND ((qualifier)::text = 'CompoundDict'::text))
> -> Index Scan using "DocumentOLD_pkey" on documentold d1_ (cost=0.00..22.04 rows=1 width=254) (actual time=17.113..17.129 rows=1 loops=2774)
> Index Cond: (d1_.id = e0_.document_id)
> Filter: (d1_.hepval IS NOT NULL)
> Total runtime: 55980.554 ms
> (13 rows)
>
> version
> -----------------------------------------------------------------------------------------------------
> PostgreSQL 8.3.8 on x86_64-pc-linux-gnu, compiled by GCC gcc-4.4.real (Ubuntu 10.4.1-3ubuntu3) 10.4.1
>
> This query has been always slow. It's fast only when it's cached. Vacuum and analyze have been done manually very recently
>
>
>
>
> SELECT name, current_setting(name), source
> FROM pg_settings
> WHERE source NOT IN ('default', 'override');
>
> name | current_setting | source
> ----------------------------+--------------------+----------------------
> client_encoding | UTF8 | client
> DateStyle | ISO, DMY | configuration file
> default_text_search_config | pg_catalog.spanish | configuration file
> effective_cache_size | 7500MB | configuration file
> lc_messages | es_ES.UTF-8 | configuration file
> lc_monetary | es_ES.UTF-8 | configuration file
> lc_numeric | C | configuration file
> lc_time | es_ES.UTF-8 | configuration file
> listen_addresses | * | configuration file
> log_line_prefix | %t | configuration file
> log_timezone | localtime | command line
> maintenance_work_mem | 2000MB | configuration file
> max_connections | 100 | configuration file
> max_fsm_pages | 63217760 | configuration file
> max_stack_depth | 2MB | environment variable
> port | 5432 | configuration file
> shared_buffers | 1500MB | configuration file
> ssl | on | configuration file
> tcp_keepalives_count | 9 | configuration file
> tcp_keepalives_idle | 7200 | configuration file
> tcp_keepalives_interval | 75 | configuration file
> TimeZone | localtime | command line
> timezone_abbreviations | Default | command line
> work_mem | 50MB | configuration file
>
> Setting the work_mem to 3000MB doesn't change anything...
>
> Everything seems good to me but the Recheck Cond, because of the large ammount of rows, is slowing the query too much. I have read that is not a good point to try to get rid of recheck cond (maybe even not possible, I don't know, I'm new to PostgreSQL). I'd like to know what I am doing wrong and how can I solve it...
>
> Any help please?
>
> Thank you very much,
>
> Andrés
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