Re: Query taking long time

Hello,

I don't know if this helps to figure out what is the problem but after adding the multicolumn index on name and hepval, the performance is even worse (¿?).  Ten times worse...

explain analyze select * from (select * from entity_compounddict2document  where name='progesterone') as a order by a.hepval;

                                                                         QUERY PLAN                                                                          

-------------------------------------------------------------------------------------------------------------------------------------------------------------

 Sort  (cost=422746.18..423143.94 rows=159104 width=133) (actual time=95769.674..95797.943 rows=138165 loops=1)

   Sort Key: entity_compounddict2document.hepval

   Sort Method:  quicksort  Memory: 25622kB

   ->  Bitmap Heap Scan on entity_compounddict2document  (cost=3501.01..408999.90 rows=159104 width=133) (actual time=70.789..95519.258 rows=138165 loops=1)

         Recheck Cond: ((name)::text = 'progesterone'::text)

         ->  Bitmap Index Scan on entity_compound2document_name  (cost=0.00..3461.23 rows=159104 width=0) (actual time=35.174..35.174 rows=138165 loops=1)

               Index Cond: ((name)::text = 'progesterone'::text)

 Total runtime: 95811.838 ms

(8 rows)

Any ideas please?

Thank you 

Andrés.

El Mar 4, 2014, a las 12:28 AM, Venkata Balaji Nagothi escribió:

On Mon, Mar 3, 2014 at 9:17 PM, acanada <acanada@cnio.es> 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: no

           tablename            |                   indexname                                              |  num_rows    | table_size  | index_size | unique | number_of_scans | tuples_read | tuples_fetched 

 entity_compounddict2document   | entity_compound2document_cardval               | 5.42452e+07 | 6763 MB    | 1162 MB    | Y      |               0 |           0 |              0

 entity_compounddict2document   | entity_compound2document_heptermnormscore      | 5.42452e+07 | 6763 MB    | 1162 MB    | Y      |               0 |           0 |              0

 entity_compounddict2document   | entity_compound2document_heptermvarscore       | 5.42452e+07 | 6763 MB    | 1162 MB    | Y      |               0 |           0 |              0

 entity_compounddict2document   | entity_compound2document_hepval                | 5.42452e+07 | 6763 MB    | 1162 MB    | Y      |               0 |           0 |              0

 entity_compounddict2document   | entity_compound2document_name                  | 5.42452e+07 | 6763 MB    | 1505 MB    | Y      |              24 |      178680 |              0

 entity_compounddict2document   | entity_compound2document_nephval               | 5.42452e+07 | 6763 MB    | 1162 MB    | Y      |               0 |           0 |              0

 entity_compounddict2document   | entity_compound2document_patterncount          | 5.42452e+07 | 6763 MB    | 1162 MB    | Y      |               0 |           0 |              0

 entity_compounddict2document   | entity_compound2document_phosval               | 5.42452e+07 | 6763 MB    | 1162 MB    | Y      |               0 |           0 |              0

 entity_compounddict2document   | entity_compound2document_rulescore             | 5.42452e+07 | 6763 MB    | 1162 MB    | Y      |               0 |           0 |              0

 entity_compounddict2document   | entity_compounddict2document_pkey              | 5.42452e+07 | 6763 MB    | 1162 MB    | Y      |               0 |           0 |              0

The table has aprox. 54,000,000 rows

There 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.hepval

   Sort 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 ms

Another 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.hepval

   Sort 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 ms

It 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.

"entity_compounddict2document" table goes through high INSERTS ?

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

**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.

**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.