Re: Out of Memory and Configuration Problems (Big Computer)

On 5/28/10 8:43:48 PM, Tom Wilcox wrote:
> I ran this query:
>
> EXPLAIN ANALYZE UPDATE nlpg.match_data SET org = org;
>
> And I got this result:
>
> "Seq Scan on match_data  (cost=0.00..9762191.68 rows=32205168 width=206)
> (actual time=76873.592..357450.519 rows=27777961 loops=1)"
> "Total runtime: 8028212.367 ms"

That would seem to indicate that the problem is in your Python
functions.

Some ideas for next steps:
* Perhaps it's just a few rows that have data in them that the
   function has difficulty with.  Add some debugging/logging to
   the function and see if the row it bombs on has anything unusual
   in it (such as a very large text field)
* While large, that function is fairly simplistic.  You may want
   to consider rewriting it as an SQL function, which should be
   more efficient in any event.

>
>
> On 28 May 2010 19:39, Tom Wilcox <hungrytom@googlemail.com
> <mailto:hungrytom@googlemail.com>> wrote:
>
>     Oops. Sorry about that.
>
>     I am having this problem with multiple queries however I am
>     confident that a fair number may involve the custom plpython
>     "normalise" function which I have made myself. I didn't think it
>     would be complicated enough to produce a memory problem.. here it is:
>
>     -- Normalises common address words (i.e. 'Ground' maps to 'grd')
>     CREATE OR REPLACE FUNCTION normalise(s text) RETURNS text AS $$
>     ADDR_FIELD_DELIM = ' '
>
>     # Returns distinct list without null or empty elements
>     def distinct_str(list):
>          seen = set()
>          return [x for x in list if x not in seen and not seen.add(x)
>     and x!=None and len(x)>0]
>
>     # normalise common words in given address string
>     def normalise(match_data):
>          if match_data==None: return ''
>          import re
>          # Tokenise
>          toks = distinct_str(re.split(r'\s', match_data.lower()))
>          out = ''
>          for tok in toks:
>              ## full word replace
>              if tok == 'house' : out += 'hse'+ADDR_FIELD_DELIM
>              elif tok == 'ground' : out += 'grd'+ADDR_FIELD_DELIM
>              elif tok == 'gnd' : out += 'grd'+ADDR_FIELD_DELIM
>              elif tok == 'front' : out += 'fnt'+ADDR_FIELD_DELIM
>              elif tok == 'floor' : out += 'flr'+ADDR_FIELD_DELIM
>              elif tok == 'floors' : out += 'flr'+ADDR_FIELD_DELIM
>              elif tok == 'flrs' : out += 'flr'+ADDR_FIELD_DELIM
>              elif tok == 'fl' : out += 'flr'+ADDR_FIELD_DELIM
>              elif tok == 'basement' : out += 'bst'+ADDR_FIELD_DELIM
>              elif tok == 'subbasement' : out += 'sbst'+ADDR_FIELD_DELIM
>              elif tok == 'bsmt' : out += 'bst'+ADDR_FIELD_DELIM
>              elif tok == 'lbst' : out += 'lower bst'+ADDR_FIELD_DELIM
>              elif tok == 'street' : out += 'st'+ADDR_FIELD_DELIM
>              elif tok == 'road' : out += 'rd'+ADDR_FIELD_DELIM
>              elif tok == 'lane' : out += 'ln'+ADDR_FIELD_DELIM
>              elif tok == 'rooms' : out += 'rm'+ADDR_FIELD_DELIM
>              elif tok == 'room' : out += 'rm'+ADDR_FIELD_DELIM
>              elif tok == 'no' : pass
>              elif tok == 'number' : pass
>              elif tok == 'and' : out += '&'+ADDR_FIELD_DELIM
>              elif tok == 'rear' : out += 'rr'+ADDR_FIELD_DELIM
>              elif tok == 'part' : out += 'pt'+ADDR_FIELD_DELIM
>              elif tok == 'south' : out += 's'+ADDR_FIELD_DELIM
>              elif tok == 'sth' : out += 's'+ADDR_FIELD_DELIM
>              elif tok == 'north' : out += 'n'+ADDR_FIELD_DELIM
>              elif tok == 'nth' : out += 'n'+ADDR_FIELD_DELIM
>              elif tok == 'west' : out += 'w'+ADDR_FIELD_DELIM
>              elif tok == 'wst' : out += 'w'+ADDR_FIELD_DELIM
>              elif tok == 'east' : out += 'e'+ADDR_FIELD_DELIM
>              elif tok == 'est' : out += 'e'+ADDR_FIELD_DELIM
>              elif tok == 'first' : out += '1st'+ADDR_FIELD_DELIM
>              elif tok == 'second' : out += '2nd'+ADDR_FIELD_DELIM
>              elif tok == 'third' : out += '3rd'+ADDR_FIELD_DELIM
>              elif tok == 'fourth' : out += '4th'+ADDR_FIELD_DELIM
>              elif tok == 'fifth' : out += '5th'+ADDR_FIELD_DELIM
>              elif tok == 'sixth' : out += '6th'+ADDR_FIELD_DELIM
>              elif tok == 'seventh' : out += '7th'+ADDR_FIELD_DELIM
>              elif tok == 'eighth' : out += '8th'+ADDR_FIELD_DELIM
>              elif tok == 'ninth' : out += '9th'+ADDR_FIELD_DELIM
>              elif tok == 'tenth' : out += '10th'+ADDR_FIELD_DELIM
>              elif tok == 'eleventh' : out += '11th'+ADDR_FIELD_DELIM
>              elif tok == 'twelfth' : out += '12th'+ADDR_FIELD_DELIM
>              elif tok == 'thirteenth' : out += '13th'+ADDR_FIELD_DELIM
>              elif tok == 'fourteenth' : out += '14th'+ADDR_FIELD_DELIM
>              elif tok == 'fifteenth' : out += '15th'+ADDR_FIELD_DELIM
>              elif tok == 'sixteenth' : out += '16th'+ADDR_FIELD_DELIM
>              elif tok == 'seventeenth' : out += '17th'+ADDR_FIELD_DELIM
>              elif tok == 'eighteenth' : out += '18th'+ADDR_FIELD_DELIM
>              elif tok == 'nineteenth' : out += '19th'+ADDR_FIELD_DELIM
>              elif tok == 'twentieth' : out += '20th'+ADDR_FIELD_DELIM
>              # numbers 0 - 20
>              elif tok == 'one' : out += '1'+ADDR_FIELD_DELIM
>              elif tok == 'two' : out += '2'+ADDR_FIELD_DELIM
>              elif tok == 'three' : out += '3'+ADDR_FIELD_DELIM
>              elif tok == 'four' : out += '4'+ADDR_FIELD_DELIM
>              elif tok == 'five' : out += '5'+ADDR_FIELD_DELIM
>              elif tok == 'six' : out += '6'+ADDR_FIELD_DELIM
>              elif tok == 'seven' : out += '7'+ADDR_FIELD_DELIM
>              elif tok == 'eight' : out += '8'+ADDR_FIELD_DELIM
>              elif tok == 'nine' : out += '9'+ADDR_FIELD_DELIM
>              elif tok == 'ten' : out += '10'+ADDR_FIELD_DELIM
>              elif tok == 'eleven' : out += '11'+ADDR_FIELD_DELIM
>              elif tok == 'twelve' : out += '12'+ADDR_FIELD_DELIM
>              elif tok == 'thirteen' : out += '13'+ADDR_FIELD_DELIM
>              elif tok == 'fourteen' : out += '14'+ADDR_FIELD_DELIM
>              elif tok == 'fifteen' : out += '15'+ADDR_FIELD_DELIM
>              elif tok == 'sixteen' : out += '16'+ADDR_FIELD_DELIM
>              elif tok == 'seventeen' : out += '17'+ADDR_FIELD_DELIM
>              elif tok == 'eighteen' : out += '18'+ADDR_FIELD_DELIM
>              elif tok == 'nineteen' : out += '19'+ADDR_FIELD_DELIM
>              elif tok == 'twenty' : out += '20'+ADDR_FIELD_DELIM
>              # town dictionary items
>              elif tok == 'borough' : pass
>              elif tok == 'city' : pass
>              elif tok == 'of' : pass
>              elif tok == 'the' : pass
>              # a few extras (from looking at voa)
>              elif tok == 'at' : pass
>              elif tok == 'incl' : pass
>              elif tok == 'inc' : pass
>              else: out += tok+ADDR_FIELD_DELIM
>          return out
>
>     return normalise(s)
>     $$ LANGUAGE plpythonu;
>
>
>     Here's the create script for the table from pgAdmin (I hope that
>     will be good enough instead of \d as I can't do that right now)..
>
>     -- Table: nlpg.match_data
>
>     -- DROP TABLE nlpg.match_data;
>
>     CREATE TABLE nlpg.match_data
>     (
>        premise_id integer,
>        usrn bigint,
>        org text,
>        sao text,
>     "level" text,
>        pao text,
>     "name" text,
>        street text,
>        town text,
>        pc postcode,
>        postcode text,
>        match_data_id integer NOT NULL DEFAULT
>     nextval('nlpg.match_data_match_data_id_seq1'::regclass),
>        addr_str text,
>        tssearch_name tsvector,
>
>        CONSTRAINT match_data_pkey1 PRIMARY KEY (match_data_id)
>     )
>     WITH (
>        OIDS=FALSE
>     );
>     ALTER TABLE nlpg.match_data OWNER TO postgres;
>     ALTER TABLE nlpg.match_data ALTER COLUMN "name" SET STATISTICS 10000;
>
>
>     -- Index: nlpg.index_match_data_mid
>
>     -- DROP INDEX nlpg.index_match_data_mid;
>
>     CREATE INDEX index_match_data_mid
>        ON nlpg.match_data
>        USING btree
>        (match_data_id);
>
>     -- Index: nlpg.index_match_data_pc
>
>     -- DROP INDEX nlpg.index_match_data_pc;
>
>     CREATE INDEX index_match_data_pc
>        ON nlpg.match_data
>        USING btree
>        (pc);
>
>     -- Index: nlpg.index_match_data_pid
>
>     -- DROP INDEX nlpg.index_match_data_pid;
>
>     CREATE INDEX index_match_data_pid
>        ON nlpg.match_data
>        USING btree
>        (premise_id);
>
>     -- Index: nlpg.index_match_data_tssearch_name
>
>     -- DROP INDEX nlpg.index_match_data_tssearch_name;
>
>     CREATE INDEX index_match_data_tssearch_name
>        ON nlpg.match_data
>        USING gin
>        (tssearch_name);
>
>     -- Index: nlpg.index_match_data_usrn
>
>     -- DROP INDEX nlpg.index_match_data_usrn;
>
>     CREATE INDEX index_match_data_usrn
>        ON nlpg.match_data
>        USING btree
>        (usrn);
>
>     As you can see, no FKs or triggers..
>
>     I am running: EXPLAIN ANALYZE UPDATE nlpg.match_data SET org = org;
>
>     However, as it should take around 90mins (if it is linear) then I
>     thought I would send this now and follow up with the results once it
>     finishes. (Has taken 2hours so far..)
>
>     Thanks very much for your help.
>
>     Tom
>
>
>     On 28 May 2010 17:54, "Bill Moran" <wmoran@potentialtech.com
>     <mailto:wmoran@potentialtech.com>> wrote:
>>
>>     In response to Tom Wilcox <hungrytom@googlemail.com
>>     <mailto:hungrytom@googlemail.com>>:
>>
>>     > In addition, I have discovered that the update query that runs
>>     on each row
>>     > of a 27million row ta...
>>
>>     You're not liable to get shit for answers if you omit the mailing
>>     list from
>>     the conversation, especially since I know almost nothing about tuning
>>     PostgreSQL installed on Windows.
>>
>>     Are there multiple queries having this problem?  The original
>>     query didn't
>>     have normalise() in it, and I would be highly suspicious that a custom
>>     function may have a memory leak or other memory-intensive
>>     side-effects.
>>     What is the code for that function?
>>
>>     For example, does:
>>     UPDATE nlpg.match_data SET org = org WHERE match_data_id;
>>     finish in a reasonable amount of time or exhibit the same out of
>>     memory
>>     problem?
>>
>>     It'd be nice to see a \d on that table ... does it have any
>>     triggers or
>>     cascading foreign keys?
>>
>>     And stop
>>
>>     --
>>
>>     Bill Moran
>>     http://www.potentialtech.com
>>     http://people.collaborativefusion.com/~wmoran/
>>     <http://people.collaborativefusion.com/%7Ewmoran/>
>>
>


--
Bill Moran