Thread: How to improve: performance of query on postgresql 8.3 takes days

Dear postgresql list,

I have some troubles generating data for a analysis task at hand.

I have a table (table A) containing 5 million records and 28 number of attributes. This table is 461MB big if I copy it to a csv file.

I want to create another table (table B) based on the contents of table A plus some 15 extra attributes (in pl/pgsql written functions which produce those extra attributes)

So my statement looks like this:

create tableB as (

select some attributes, function1(A.attribute1)as attributeX+1, function2(A.attribute1,A.Attribute2,A.attribute3,A.attribute4,A.attribute5) as attribute X+2......function15(A.attribute1,A.attribute9) as attributeX+15 from tableA as A)

This takes almost 60 hours to finish on my database server running debian 5.0 with XFS as filesystem containing 4GB RAM. I'm using postgresql server version 8.3 (but am seeing the same phenomena on my FreeBSD 8.0 database server running postgresql 8.4 as well)

I arrived at 15 functions because I had 7 or 8 joins in the past and saw that my disk was getting hid and I had heard someplace that RAM is faster so I rewrote those 7 or 8 joins as functions in pl/pgsql. They were just simple lookups, although some of the functions are looking stuff up in tables containing 78000 records. However, I thought this wouldn't be a problem because they are simple functions which look up the value of one variable based on a parameter. 3 of the more special functions are shown here:

CREATE OR REPLACE FUNCTION agenttype1(a character)

RETURNS integer AS

$BODY$

DECLARE

i integer;

t1_rij canxagents%ROWTYPE;

BEGIN

select * into t1_rij from canxagents where agent = a;

if NOT FOUND THEN i := 0;

ELSE

if t1_rij.aantal >= 0 and t1_rij.aantal <=499 THEN i := 1;

ELSE

if t1_rij.aantal > 500 and t1_rij.aantal <=1999 THEN i := 2;

ELSE

if t1_rij.aantal >= 2000 THEN i := 3;

END IF;

END IF;

END IF;

END IF;

return i ;

END;

$BODY$

LANGUAGE 'plpgsql' VOLATILE

COST 100;

CREATE OR REPLACE FUNCTION agenttype2(a character)

RETURNS integer AS

$BODY$

DECLARE

i integer;

t1_rij showagents%ROWTYPE;

BEGIN

select * into t1_rij from showagents where agent = a;

if NOT FOUND THEN i := 0;

ELSE

if t1_rij.aantal >= 0 and t1_rij.aantal <=499 THEN i := 1;

ELSE

if t1_rij.aantal > 500 and t1_rij.aantal <=999 THEN i := 2;

ELSE

if t1_rij.aantal >= 1000 THEN i := 3;

END IF;

END IF;

END IF;

END IF;

return i ;

END;

$BODY$

LANGUAGE 'plpgsql' VOLATILE

COST 100;

CREATE OR REPLACE FUNCTION agenttype3(a character)

RETURNS integer AS

$BODY$

DECLARE

i integer;

t1_rij noagents%ROWTYPE;

BEGIN

select * into t1_rij from noagents where agent = a;

if NOT FOUND THEN i := 0;

ELSE

if t1_rij.aantal >= 0 and t1_rij.aantal <=299 THEN i := 1;

ELSE

if t1_rij.aantal > 300 and t1_rij.aantal <=899 THEN i := 2;

ELSE

if t1_rij.aantal >= 900 THEN i := 3;

END IF;

END IF;

END IF;

END IF;

return i ;

END;

$BODY$

LANGUAGE 'plpgsql' VOLATILE

COST 100;

The interesting parts of my postgresql.conf file look like this:

#------------------------------------------------------------------------------

# RESOURCE USAGE (except WAL)

#------------------------------------------------------------------------------

# - Memory -

shared_buffers = 512MB # min 128kB or max_connections*16kB

# (change requires restart)

temp_buffers = 8MB # min 800kB

#max_prepared_transactions = 5 # can be 0 or more

# (change requires restart)

# Note: Increasing max_prepared_transactions costs ~600 bytes of shared memory

# per transaction slot, plus lock space (see max_locks_per_transaction).

work_mem = 50MB # min 64kB

maintenance_work_mem = 256MB # min 1MB

#max_stack_depth = 2MB # min 100kB

# - Free Space Map -

max_fsm_pages = 153600 # min max_fsm_relations*16, 6 bytes each

# (change requires restart)

#max_fsm_relations = 1000 # min 100, ~70 bytes each

# (change requires restart)

# - Kernel Resource Usage -

#max_files_per_process = 1000 # min 25

# (change requires restart)

#shared_preload_libraries = '' # (change requires restart)

# - Cost-Based Vacuum Delay -

#vacuum_cost_delay = 0 # 0-1000 milliseconds

#vacuum_cost_page_hit = 1 # 0-10000 credits

#vacuum_cost_page_miss = 10 # 0-10000 credits

#vacuum_cost_page_dirty = 20 # 0-10000 credits

#vacuum_cost_limit = 200 # 1-10000 credits

# - Background Writer -

#bgwriter_delay = 200ms # 10-10000ms between rounds

#bgwriter_lru_maxpages = 100 # 0-1000 max buffers written/round

#bgwriter_lru_multiplier = 2.0 # 0-10.0 multipler on buffers scanned/round

#------------------------------------------------------------------------------

# WRITE AHEAD LOG

#------------------------------------------------------------------------------

# - Settings -

#fsync = on # turns forced synchronization on or off

#synchronous_commit = on # immediate fsync at commit

#wal_sync_method = fsync # the default is the first option

# supported by the operating system:

# open_datasync

# fdatasync

# fsync

# fsync_writethrough

# open_sync

#full_page_writes = on # recover from partial page writes

#wal_buffers = 64kB # min 32kB

# (change requires restart)

#wal_writer_delay = 200ms # 1-10000 milliseconds

#commit_delay = 0 # range 0-100000, in microseconds

#commit_siblings = 5 # range 1-1000

# - Checkpoints -

#checkpoint_segments = 3 # in logfile segments, min 1, 16MB each

#checkpoint_timeout = 5min # range 30s-1h

#checkpoint_completion_target = 0.5 # checkpoint target duration, 0.0 - 1.0

#checkpoint_warning = 30s # 0 is off

# - Archiving -

#archive_mode = off # allows archiving to be done

# (change requires restart)

#archive_command = '' # command to use to archive a logfile segment

#archive_timeout = 0 # force a logfile segment switch after this

# time; 0 is off

#------------------------------------------------------------------------------

# QUERY TUNING

#------------------------------------------------------------------------------

# - Planner Method Configuration -

#enable_bitmapscan = on

#enable_hashagg = on

#enable_hashjoin = on

#enable_indexscan = on

#enable_mergejoin = on

#enable_nestloop = on

#enable_seqscan = on

#enable_sort = on

#enable_tidscan = on

# - Planner Cost Constants -

#seq_page_cost = 1.0 # measured on an arbitrary scale

#random_page_cost = 4.0 # same scale as above

#cpu_tuple_cost = 0.01 # same scale as above

#cpu_index_tuple_cost = 0.005 # same scale as above

#cpu_operator_cost = 0.0025 # same scale as above

effective_cache_size = 256MB # was 128

# - Genetic Query Optimizer -

#geqo = on

#geqo_threshold = 12

#geqo_effort = 5 # range 1-10

#geqo_pool_size = 0 # selects default based on effort

#geqo_generations = 0 # selects default based on effort

#geqo_selection_bias = 2.0 # range 1.5-2.0

# - Other Planner Options -

#default_statistics_target = 10 # range 1-1000

#constraint_exclusion = off

#from_collapse_limit = 8

#join_collapse_limit = 8 # 1 disables collapsing of explicit

# JOIN clauses

Questions

1. What can I do to let the creation of table B go faster?

2. Do you think the use of indices (but where) would help me? I didn't go that route because in fact I don't have a where clause in the create table B statement. I could put indices on the little tables I'm using in the functions.

3. What about the functions? Should I code them differently?

4. What about my server configuration. What could be done over there?

Thanks in advanced

  On 07/29/10 2:58 PM, Dino Vliet wrote:
>
> Dear postgresql list,
>
>
> I have some troubles generating data for a analysis task at hand.
>
>
> I have a table (table A) containing 5 million records and 28 number of
> attributes. This table is 461MB big if I copy it to a csv file.
>
>
> I want to create another table (table B) based on the contents of
> table A plus some 15 extra attributes (in pl/pgsql written functions
> which produce those extra attributes)
>
>
> So my statement looks like this:
>
>
> create tableB as (
>
> select some attributes, function1(A.attribute1)as attributeX+1,
> function2(A.attribute1,A.Attribute2,A.attribute3,A.attribute4,A.attribute5)
> as attribute X+2......function15(A.attribute1,A.attribute9) as
> attributeX+15 from tableA as A)
>
>
> This takes almost 60 hours to finish on my database server running
> debian 5.0 with XFS as filesystem containing 4GB RAM. I'm using
> postgresql server version 8.3 (but am seeing the same phenomena on my
> FreeBSD 8.0 database server running postgresql 8.4 as well)
>
>
> I arrived at 15 functions because I had 7 or 8 joins in the past and
> saw that my disk was getting hid and I had heard someplace that RAM is
> faster so I rewrote those 7 or 8 joins as functions in pl/pgsql. They
> were just simple lookups, although some of the functions are looking
> stuff up in tables containing 78000 records. However, I thought this
> wouldn't be a problem because they are simple functions which look up
> the value of one variable based on a parameter. 3 of the more special
> functions are shown here:
>
> ...
>
>   1.
>
>       What can I do to let the creation of table B go faster?
>
>   2.
>
>       Do you think the use of indices (but where) would help me? I
>       didn't go that route because in fact I don't have a where clause
>       in the create table B statement. I could put indices on the
>       little tables I'm using in the functions.
>
>   3.
>
>       What about the functions? Should I code them differently?
>
>   4.
>
>       What about my server configuration. What could be done over there?
>
>
> Thanks in advanced
>
>

certainly your lookup tables should have a index on the key you're using
to look up values.   without said index, that 78000 row 'little' table
will have to be sequentially scanned for every one of your several
million rows.

with said indexes, you may find that just doing JOINs when you actually
use this data rather than creating a new table will work quite nicely.
you could use a VIEW to do the joins transparently on the fly.

In response to Dino Vliet :
> I arrived at 15 functions because I had 7 or 8 joins in the past and saw that
> my disk was getting hid and I had heard someplace that RAM is faster so I
> rewrote those 7 or 8 joins as functions in pl/pgsql. They were just simple
> lookups, although some of the functions are looking stuff up in tables
> containing 78000 records. However, I thought this wouldn't be a problem because
> they are simple functions which look up the value of one variable based on a
> parameter. 3 of the more special functions are shown here:

I disaagree with you. The database has to do the same job, wherever with
7 or 8 joins or with functions, but functions (in this case) are slower.

You should run EXPLAIN <your statement with 7 or 8 joins> and show us
the result, i believe there are missing indexes.


> # - Memory -
>
>
> shared_buffers = 512MB # min 128kB or max_connections*16kB

How much RAM contains your server? You should set this to approx. 25% of RAM.


> work_mem = 50MB # min 64kB

That's maybe too much, but it depends on your workload. If you have a
lot of simultaneous and complex queries you run out of RAM, but if there
only one user (only one connection) it's okay.


> effective_cache_size = 256MB # was 128

That's too tow, effective_cache_size = shared_buffers + OS-cache


> Questions
>
>
>  1. What can I do to let the creation of table B go faster?

Use JOINs for table-joining, not functions.


>
>  2. Do you think the use of indices (but where) would help me? I didn't go that
>     route because in fact I don't have a where clause in the create table B
>     statement. I could put indices on the little tables I'm using in the
>     functions.

Yes! Create indexes on the joining columns.


>
>  3. What about the functions? Should I code them differently?

Don't use functions for that kind of table-joining.


>
>  4. What about my server configuration. What could be done over there?

see above.


Regards, Andreas
--
Andreas Kretschmer
Kontakt:  Heynitz: 035242/47150,   D1: 0160/7141639 (mehr: -> Header)
GnuPG: 0x31720C99, 1006 CCB4 A326 1D42 6431  2EB0 389D 1DC2 3172 0C99

On 29 Jul 2010, at 23:58, Dino Vliet wrote:

> CREATE OR REPLACE FUNCTION agenttype1(a character)
> RETURNS integer AS

> LANGUAGE 'plpgsql' VOLATILE
> COST 100;
>
>
> CREATE OR REPLACE FUNCTION agenttype2(a character)
> RETURNS integer AS

> LANGUAGE 'plpgsql' VOLATILE
> COST 100;
>
>
> CREATE OR REPLACE FUNCTION agenttype3(a character)
> RETURNS integer AS

> LANGUAGE 'plpgsql' VOLATILE
> COST 100;

As others have already said, using these functions will be less efficient than using joins.

Regardless of that though, you should at least declare these functions as STABLE instead of VOLATILE, see:

http://www.postgresql.org/docs/8.4/interactive/xfunc-volatility.html

Alban Hertroys

--
Screwing up is an excellent way to attach something to the ceiling.


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