Re: Query taking long time

Il 05/mar/2014 00:36 "Venkata Balaji Nagothi" <vbnpgc(at)gmail(dot)com> ha scritto:
>
> After looking at the distinct values, yes the composite Index on "name"
and "hepval" is not recommended. That would worsen - its expected.
>
> We need to look for other possible work around. Please drop off the above
Index. Let me see if i can drill further into this.
>
> Meanwhile - can you help us know the memory parameters (work_mem,
temp_buffers etc) set ?
>
> Do you have any other processes effecting this query's performance ?
>
> Any info about your Disk, RAM, CPU would also help.
>
> Regards,
> Venkata Balaji N
>
> Fujitsu Australia
>
>
>
>
> Venkata Balaji N
>
> Sr. Database Administrator
> Fujitsu Australia
>
>
> On Tue, Mar 4, 2014 at 10:23 PM, acanada <acanada(at)cnio(dot)es> wrote:
>>
>> 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(at)cnio(dot)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
>>
>>
>>
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>

Hi I think the problem is th heap scan of the table , that the backend have
to do because the btree to bitmap conversion becomes lossy. Try to disable
the enable_bitmapscan for the current session and rerun the query.

Mat Dba