Re: Query taking long time

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От acanada
Тема Re: Query taking long time
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Msg-id FA02E6B1-9C0A-4122-8642-7D497D7DBB42@cnio.es
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Ответ на Query taking long time  ("acanada")
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Query taking long time  ("acanada", )
 Re: Query taking long time  ("acanada", )
 Re: Query taking long time  ("acanada", )
  Re: Query taking long time  (Vladimir Sitnikov, )
  Re: Query taking long time  (Venkata Balaji Nagothi, )
   Re: Query taking long time  ("acanada", )
   Re: Query taking long time  ("acanada", )
    Re: Query taking long time  (Venkata Balaji Nagothi, )
     Re: Query taking long time  (desmodemone, )
      Re: Query taking long time  ("acanada", )
       Re: Query taking long time  (Evgeniy Shishkin, )
        Re: Query taking long time  ("acanada", )
         Re: Query taking long time  (Evgeniy Shishkin, )
          Re: Query taking long time  ("acanada", )
           Re: Query taking long time  (Evgeniy Shishkin, )
            Re: Query taking long time  ("acanada", )
             Re: Query taking long time  (Venkata Balaji Nagothi, )
       Re: Query taking long time  (desmodemone, )
        Re: Query taking long time  ("acanada", )
         Re: Query taking long time  (Evgeny Shishkin, )
          Re: Query taking long time  ("acanada", )
           Re: Query taking long time  (Venkata Balaji Nagothi, )
            Re: Query taking long time  ("acanada", )
             Re: Query taking long time  (Venkata Balaji Nagothi, )
 Re: Query taking long time  ("acanada", )
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=15020width=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..21.764rows=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
inforequired 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
tothe 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_.curationAS curation4, e0_.created AS created5, e0_.updated AS updated6, d1_.id AS id7, d1_.kind AS kind8, d1_.uid
ASuid9, d1_."sentenceId" AS sentenceid10, d1_.text AS text11, d1_.hepval AS hepval12, d1_.cardval AS cardval13,
d1_.nephvalAS 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
NULLORDER 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..8452.592rows=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..17.129rows=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
newto 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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