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Thread: query with pg_trgm sometimes very slow

query with pg_trgm sometimes very slow

From
Volker Böhm
Date:
Hi,
I have a table for addresses:

CREATE TABLE adressen.adresse
(
    pool_pk      integer         NOT NULL,
    adressnr_pk  integer         NOT NULL,
    anrede       varchar(8),
    vorname      varchar(50)     DEFAULT ''::character varying NOT NULL,
    name1        varchar(100)    NOT NULL,
    name2        varchar(80)     DEFAULT ''::character varying NOT NULL,
    name3        varchar(80)     DEFAULT ''::character varying NOT NULL,
    strasse      varchar(80)     DEFAULT ''::character varying NOT NULL,
    plz          varchar(8)      DEFAULT ''::character varying NOT NULL,
    ort          varchar(80)     DEFAULT ''::character varying NOT NULL,
    changed      timestamptz,
    id2          integer
);

The primary key is on 'pool_pk' and 'adressnr_pk' and amongst some other
indexes there is an index

CREATE INDEX trgm_adresse ON adressen.adresse USING gist
(normalize_string((btrim((((((((normalize_string((((COALESCE((vorname)::text,
''::text) || ' '::text) ||   (name1)::text))::character varying,
(-1)))::text || ' '::text) ||
(normalize_string((COALESCE((strasse)::text, ''::text))::character
varying, (-2)))::text) || ' '::text) || (plz)::text) || ' '::text) ||
(normalize_string((COALESCE((ort)::text, ''::text))::character varying,
(-3)))::text)))::character varying) gist_trgm_ops);

When I try to retrieve some addresses similar to a new address, I use
the following query

SELECT pool_pk AS pool, adressnr_pk AS adrnr, vorname, name1,
     strasse, plz, ort, ratio_ld_adresse($1, $2, $3, $4, name1,
     strasse, plz, ort)::double precision AS ratio
FROM adressen.adresse
WHERE normalize_string(trim(normalize_string(coalesce(vorname::text, '')
     || ' ' || name1::text, -1) ||  ' ' ||
     normalize_string(coalesce(strasse::text, ''), -2) || ' ' ||
plz::text ||
     ' ' || normalize_string(coalesce(ort::text, ''), -3))) %
     normalize_string(trim(normalize_string($1::text) ||  ' ' ||
     normalize_string(coalesce($2::text, ''), -2) || ' ' || $3::text ||
     ' ' || normalize_string(coalesce($4::text, ''), -3)))
     ORDER BY 1, 8 DESC, 2;

which means: take the normalized (lower case, no accents ...) parts of
the address, concatinate them to
     <name> <street> <zip> <city>
and search for a similar address in the existing addresses. The
described index 'trgm_adresse' is built on the same expression.

The function 'normalize_string' is written in plpythonu and doesn't use
any database calls. The same with the function 'ratio_ld_adresse', which
calculates the levenshtein distance for two entire addresses.

Most the time everything works fine and one search (in about 500,000
addresses) lasts about 2 to 5 seconds. But sometimes the search takes 50
or even 300 seconds.

We have two machines which have the same software installation (Ubuntu
14.10 server, Postgres 9.4.4) the production server has 4 GB memory and
2 processors and the test server 2 GB memory and 1 processor. Both are
virtual machines on two different ESX-servers.

On both machines postgres was installed out of the box (apt-get ...)
without configuration modifications (except network interfaces in
pg_hba.conf). The test machine is a little bit slower but the very slow
searches occur much more (~ 35 %) than on the production machine (~10 %).

An explain tells

QUERY PLAN
Sort  (cost=2227.31..2228.53 rows=489 width=65)
   Sort Key: pool_pk, ((ratio_ld_adresse('Test 2'::character varying,
'Am Hang 12'::character varying, '12345'::character varying,
'Irgendwo'::character varying, name1, strasse, plz, ort))::double
precision), adressnr_pk
   ->  Index Scan using trgm_adresse on adresse (cost=1.43..2205.46
rows=489 width=65)
         Index Cond:
((normalize_string((btrim((((((((normalize_string((((COALESCE((vorname)::text,
''::text) || ' '::text) || (name1)::text))::character varying,
(-1)))::text || ' '::text) ||
(normalize_string((COALESCE((strasse)::text, ''::text))::character
varying, (-2)))::text) || ' '::text) || (plz)::text) || ' '::text) ||
(normalize_string((COALESCE((ort)::text, ''::text))::character varying,
(-3)))::text)))::character varying, 0))::text % 'test 2 am hang 12 12345
irgendwo'::text)

which shows that the index is used and the result should arrive within
some seconds (2228 is not very expensive).

When such a slow query is running, 'top' shows nearly '100 % wait' and
'iotop' shows 3 - 8 MB/sec disk read by a process
     postgres: vb vb 10.128.96.25(60435) FETCH

Also the postgres log, which was told to log every task longer than 5000
ms, shows

     2015-09-02 13:44:48 CEST [25237-1] vb@vb LOG:  duration: 55817.191
ms  execute <unnamed>: FETCH FORWARD 4096 IN "py:0xa2d61f6c"

Since I never used a FETCH command in my life, this must be used by
pg_trgm or something inside it (gin, gist etc.)

If during a slow Query one (or several) more instance(s) of the same
query are started, all of them hang and return at the _same second_ some
minutes later. Even if the other queries are on different addresses.

2015-08-31 09:09:00 GMT LOG:  duration: 98630.958 ms  execute <unnamed>:
FETCH FORWARD 4096 IN "py:0x7fb780a07e10"
2015-08-31 09:09:00 GMT LOG:  duration: 266887.136 ms  execute
<unnamed>: FETCH FORWARD 4096 IN "py:0x7fb780a95dd8"
2015-08-31 09:09:00 GMT LOG:  duration: 170311.627 ms  execute
<unnamed>: FETCH FORWARD 4096 IN "py:0x7fb780a77e10"
2015-08-31 09:09:00 GMT LOG:  duration: 72614.474 ms  execute <unnamed>:
FETCH FORWARD 4096 IN "py:0x7fb780a0ce10"
2015-08-31 09:09:00 GMT LOG:  duration: 78561.131 ms  execute <unnamed>:
FETCH FORWARD 4096 IN "py:0x7fb780a08da0"
2015-08-31 09:09:00 GMT LOG:  duration: 182392.792 ms  execute
<unnamed>: FETCH FORWARD 4096 IN "py:0x7fb78170c2b0"
2015-08-31 09:09:00 GMT LOG:  duration: 245632.530 ms  execute
<unnamed>: FETCH FORWARD 4096 IN "py:0x7fb7809ddc50"
2015-08-31 09:09:00 GMT LOG:  duration: 84760.400 ms  execute <unnamed>:
FETCH FORWARD 4096 IN "py:0x7fb7809f7dd8"
2015-08-31 09:09:00 GMT LOG:  duration: 176402.352 ms  execute
<unnamed>: FETCH FORWARD 4096 IN "py:0x7fb7809fc668"

Does anyone have an idea, how to solve this problem?

regards Volker

--
Volker Böhm     Tel.: +49 4141 981155      www.vboehm.de
Voßkuhl 5       Fax:  +49 4141 981154
21682 Stade     mailto:volker@vboehm.de

Re: query with pg_trgm sometimes very slow

From
Jeff Janes
Date:
On Wed, Sep 2, 2015 at 7:00 AM, Volker Böhm <volker@vboehm.de> wrote:


CREATE INDEX trgm_adresse ON adressen.adresse USING gist (normalize_string((btrim((((((((normalize_string((((COALESCE((vorname)::text, ''::text) || ' '::text) ||   (name1)::text))::character varying, (-1)))::text || ' '::text) || (normalize_string((COALESCE((strasse)::text, ''::text))::character varying, (-2)))::text) || ' '::text) || (plz)::text) || ' '::text) || (normalize_string((COALESCE((ort)::text, ''::text))::character varying, (-3)))::text)))::character varying) gist_trgm_ops);


You might have better luck with gin_trgm_ops than gist_trgm_ops.  Have you tried that?

...


When such a slow query is running, 'top' shows nearly '100 % wait' and 'iotop' shows 3 - 8 MB/sec disk read by a process
    postgres: vb vb 10.128.96.25(60435) FETCH

Also the postgres log, which was told to log every task longer than 5000 ms, shows

    2015-09-02 13:44:48 CEST [25237-1] vb@vb LOG:  duration: 55817.191 ms  execute <unnamed>: FETCH FORWARD 4096 IN "py:0xa2d61f6c"

Since I never used a FETCH command in my life, this must be used by pg_trgm or something inside it (gin, gist etc.)


The FETCH is probably being automatically added by whatever python library you are use to talk to PostgreSQL.  Are you using a named cursor in python?  In any event, that is not the cause of the problem.

Can you get the result of the indexed expression for a query that is slow?

Re: query with pg_trgm sometimes very slow

From
Claudio Freire
Date:
On Wed, Sep 2, 2015 at 4:29 PM, Jeff Janes <jeff.janes@gmail.com> wrote:
> On Wed, Sep 2, 2015 at 7:00 AM, Volker Böhm <volker@vboehm.de> wrote:
>>
>>
>>
>> CREATE INDEX trgm_adresse ON adressen.adresse USING gist
>> (normalize_string((btrim((((((((normalize_string((((COALESCE((vorname)::text,
>> ''::text) || ' '::text) ||   (name1)::text))::character varying,
>> (-1)))::text || ' '::text) || (normalize_string((COALESCE((strasse)::text,
>> ''::text))::character varying, (-2)))::text) || ' '::text) || (plz)::text)
>> || ' '::text) || (normalize_string((COALESCE((ort)::text,
>> ''::text))::character varying, (-3)))::text)))::character varying)
>> gist_trgm_ops);
>
>
>
> You might have better luck with gin_trgm_ops than gist_trgm_ops.  Have you
> tried that?


I just had the exact same problem, and indeed gin fares much better.

Re: query with pg_trgm sometimes very slow

From
Merlin Moncure
Date:
On Thu, Sep 3, 2015 at 6:19 PM, Claudio Freire <klaussfreire@gmail.com> wrote:
> On Wed, Sep 2, 2015 at 4:29 PM, Jeff Janes <jeff.janes@gmail.com> wrote:
>> On Wed, Sep 2, 2015 at 7:00 AM, Volker Böhm <volker@vboehm.de> wrote:
>>>
>>>
>>>
>>> CREATE INDEX trgm_adresse ON adressen.adresse USING gist
>>> (normalize_string((btrim((((((((normalize_string((((COALESCE((vorname)::text,
>>> ''::text) || ' '::text) ||   (name1)::text))::character varying,
>>> (-1)))::text || ' '::text) || (normalize_string((COALESCE((strasse)::text,
>>> ''::text))::character varying, (-2)))::text) || ' '::text) || (plz)::text)
>>> || ' '::text) || (normalize_string((COALESCE((ort)::text,
>>> ''::text))::character varying, (-3)))::text)))::character varying)
>>> gist_trgm_ops);
>>
>>
>>
>> You might have better luck with gin_trgm_ops than gist_trgm_ops.  Have you
>> tried that?
>
>
> I just had the exact same problem, and indeed gin fares much better.

Also, with 9.5 we will see much better worst case performance from gin
via Jeff's patch:
http://git.postgresql.org/gitweb/?p=postgresql.git;a=commitdiff;h=97f3014647a5bd570032abd2b809d3233003f13f

(I had to previously abandon pg_tgrm for a previous project and go
with solr; had this patch been in place that would not have happened)

merlin

Re: query with pg_trgm sometimes very slow

From
Tomas Vondra
Date:

On 09/08/2015 09:15 PM, Merlin Moncure wrote:
...
>> I just had the exact same problem, and indeed gin fares much better.
>
> Also, with 9.5 we will see much better worst case performance from gin
> via Jeff's patch:
> http://git.postgresql.org/gitweb/?p=postgresql.git;a=commitdiff;h=97f3014647a5bd570032abd2b809d3233003f13f
>
> (I had to previously abandon pg_tgrm for a previous project and go
> with solr; had this patch been in place that would not have happened)

Except that pg_tgrm-1.2 is not included in 9.5, because it was committed
in July (i.e. long after 9.5 was branched).


--
Tomas Vondra                   http://www.2ndQuadrant.com/
PostgreSQL Development, 24x7 Support, Remote DBA, Training & Services

Re: query with pg_trgm sometimes very slow

From
Merlin Moncure
Date:
On Tue, Sep 8, 2015 at 4:21 PM, Tomas Vondra
<tomas.vondra@2ndquadrant.com> wrote:
> On 09/08/2015 09:15 PM, Merlin Moncure wrote:
> ...
>>>
>>> I just had the exact same problem, and indeed gin fares much better.
>>
>>
>> Also, with 9.5 we will see much better worst case performance from gin
>> via Jeff's patch:
>>
>> http://git.postgresql.org/gitweb/?p=postgresql.git;a=commitdiff;h=97f3014647a5bd570032abd2b809d3233003f13f
>>
>> (I had to previously abandon pg_tgrm for a previous project and go
>> with solr; had this patch been in place that would not have happened)
>
> Except that pg_tgrm-1.2 is not included in 9.5, because it was committed in
> July (i.e. long after 9.5 was branched).

oops!  thinko.   it shouldn't be too difficult to back patch though if
you're so inclined?

merlin