On Mon, Mar 3, 2014 at 9:17 PM, acanada <acanada@xxxxxxx> wrote:
Hello,Thankyou for your answer.I have made more changes than a simple re-indexing recently. I have moved the sorting field to the table in order to avoid the join clause. Now the schema is very simple. The query only implies one table:x=> \d+ entity_compounddict2document;Table "public.entity_compounddict2document"Column | Type | Modifiers | Storage | Description------------------+--------------------------------+-----------+----------+-------------id | integer | not null | plain |document_id | integer | | plain |name | character varying(255) | | extended |qualifier | character varying(255) | | extended |tagMethod | character varying(255) | | extended |created | timestamp(0) without time zone | | plain |updated | timestamp(0) without time zone | | plain |curation | integer | | plain |hepval | double precision | | 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:"entity_compounddict2document_pkey" PRIMARY KEY, btree (id)"entity_compound2document_cardval" btree (cardval)"entity_compound2document_heptermnormscore" btree ("hepTermNormScore")"entity_compound2document_heptermvarscore" btree ("hepTermVarScore")"entity_compound2document_hepval" btree (hepval)"entity_compound2document_name" btree (name)"entity_compound2document_nephval" btree (nephval)"entity_compound2document_patterncount" btree ("patternCount")"entity_compound2document_phosval" btree (phosval)"entity_compound2document_rulescore" btree ("ruleScore")Has OIDs: notablename | indexname | num_rows | table_size | index_size | unique | number_of_scans | tuples_read | tuples_fetchedentity_compounddict2document | entity_compound2document_cardval | 5.42452e+07 | 6763 MB | 1162 MB | Y | 0 | 0 | 0entity_compounddict2document | entity_compound2document_heptermnormscore | 5.42452e+07 | 6763 MB | 1162 MB | Y | 0 | 0 | 0entity_compounddict2document | entity_compound2document_heptermvarscore | 5.42452e+07 | 6763 MB | 1162 MB | Y | 0 | 0 | 0entity_compounddict2document | entity_compound2document_hepval | 5.42452e+07 | 6763 MB | 1162 MB | Y | 0 | 0 | 0entity_compounddict2document | entity_compound2document_name | 5.42452e+07 | 6763 MB | 1505 MB | Y | 24 | 178680 | 0entity_compounddict2document | entity_compound2document_nephval | 5.42452e+07 | 6763 MB | 1162 MB | Y | 0 | 0 | 0entity_compounddict2document | entity_compound2document_patterncount | 5.42452e+07 | 6763 MB | 1162 MB | Y | 0 | 0 | 0entity_compounddict2document | entity_compound2document_phosval | 5.42452e+07 | 6763 MB | 1162 MB | Y | 0 | 0 | 0entity_compounddict2document | entity_compound2document_rulescore | 5.42452e+07 | 6763 MB | 1162 MB | Y | 0 | 0 | 0entity_compounddict2document | entity_compounddict2document_pkey | 5.42452e+07 | 6763 MB | 1162 MB | Y | 0 | 0 | 0The table has aprox. 54,000,000 rowsThere are no NULLs in hepval field and pg_settings haven't changed. I also have done "analyze" to this table.I have simplified the query and added the last advise that you told me:Query:explain analyze select * from (select * from entity_compounddict2document where name='ranitidine') as a order by a.hepval;QUERY PLAN------------------------------------------------------------------------------------------------------------------------------------------------------Sort (cost=11060.50..11067.55 rows=2822 width=133) (actual time=32715.097..32716.488 rows=13512 loops=1)Sort Key: entity_compounddict2document.hepvalSort Method: quicksort Memory: 2301kB-> Bitmap Heap Scan on entity_compounddict2document (cost=73.82..10898.76 rows=2822 width=133) (actual time=6.034..32695.483 rows=13512 loops=1)Recheck Cond: ((name)::text = 'ranitidine'::text)-> Bitmap Index Scan on entity_compound2document_name (cost=0.00..73.12 rows=2822 width=0) (actual time=3.221..3.221 rows=13512 loops=1)Index Cond: ((name)::text = 'ranitidine'::text)Total runtime: 32717.548 msAnother query:explain analyze select * from (select * from entity_compounddict2document where name='progesterone' ) as a order by a.hepval;QUERY PLAN------------------------------------------------------------------------------------------------------------------------------------------------------------Sort (cost=367879.25..368209.24 rows=131997 width=133) (actual time=9262.887..9287.046 rows=138165 loops=1)Sort Key: entity_compounddict2document.hepvalSort Method: quicksort Memory: 25622kB-> Bitmap Heap Scan on entity_compounddict2document (cost=2906.93..356652.81 rows=131997 width=133) (actual time=76.316..9038.485 rows=138165 loops=1)Recheck Cond: ((name)::text = 'progesterone'::text)-> Bitmap Index Scan on entity_compound2document_name (cost=0.00..2873.93 rows=131997 width=0) (actual time=40.913..40.913 rows=138165 loops=1)Index Cond: ((name)::text = 'progesterone'::text)Total runtime: 9296.815 msIt has improved (I supose because of the lack of the join table) but still taking a lot of time... Anything I can do??Any help would be very appreciated. Thank you very much.
Good to know performance has increased.
Can you help us know if the "helpval" column and "name" column have high duplicate values ? "n_distinct" value from pg_stats table would have that info.
Below could be a possible workaround -
As mentioned earlier in this email, a composite Index on name and hepval column might help. If the table does not go through lot of INSERTS, then consider performing a CLUSTER on the table using the same INDEX.
Other recommendations -
Please drop off all the Non-primary key Indexes which have 0 scans / hits. This would harm the DB and the DB server whilst maintenance and DML operations.
Regards,
Venkata Balaji N
Fujitsu Australia
