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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