Re: [PERFORM] trouble with a join on OS X

2007-02-05 Thread Shane Ambler

Kirk Wythers wrote:

The 4G (32bit) limit may be where you hit the out of memory errors (or 
is postgres get around that with it's caching?).


Any idea if postgres on OS X can truely access more that 4 gigs if the 
64 bit version is built? I have tried building the 64 bit version of 
some other apps on OS X, and I have never been convinced that they 
behaved as true 64 bit.




I haven't tried myself



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Re: [PERFORM] trouble with a join on OS X

2007-02-04 Thread Kirk Wythers


On Feb 3, 2007, at 9:59 AM, Shane Ambler wrote:



just so you can look into it for your own curiosity ;-) - Mac OS X  
uses the startup disk for VM storage. You can find the files in - / 
var/vm


You will find the swapfiles there, the size of the swapfiles  
progressively get larger - swapfile0 and 1 are 64M then 2 is 128M,  
3 is 256M, 4 is 512M, 5 is 1G each is preallocated so it only  
gives you a rough idea of how much vm is being used. You would run  
out when your startup disk is full, though most apps probably hit  
the wall at 4G of vm unless you have built a 64bit version.


The 4G (32bit) limit may be where you hit the out of memory errors  
(or is postgres get around that with it's caching?).


Any idea if postgres on OS X can truely access more that 4 gigs if  
the 64 bit version is built? I have tried building the 64 bit version  
of some other apps on OS X, and I have never been convinced that they  
behaved as true 64 bit.






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[PERFORM] trouble with a join on OS X

2007-02-02 Thread Kirk Wythers
I am trying to do fairly simple joins on climate databases that  
should return ~ 7 million rows of data. However, I'm getting an error  
message on a OS X (10.4 tiger server) machine that seems to imply  
that I am running out of memory. The errors are:


psql(15811) malloc: *** vm_allocate(size=8421376) failed (error code=3)
psql(15811) malloc: *** error: can't allocate region
psql(15811) malloc: *** set a breakpoint in szone_error to debug

The query should return all data from all climate stations. In order  
to test the query I tried narrowing the SELECT statement to a return  
data for a single station. This query worked (ie did not cause the  
malloc errors) and returned the expected 200,000 or so rows. Since  
this worked I don't think there is a problem with the join syntax.


This a a dual G5 box with 6 gigs of ram running postgresql 8.1. I  
have not tired altering kernel resources (as described in http:// 
www.postgresql.org/docs/8.1/interactive/kernel-resources.html#SHARED- 
MEMORY-PARAMETERS), or compiling for 64 bit. I'm just not sure what  
to try next. Does anyone have any suggestions?


Best Regards,

Kirk


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Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Steinar H. Gunderson
On Fri, Feb 02, 2007 at 07:52:48AM -0600, Kirk Wythers wrote:
 psql(15811) malloc: *** vm_allocate(size=8421376) failed (error code=3)
 psql(15811) malloc: *** error: can't allocate region
 psql(15811) malloc: *** set a breakpoint in szone_error to debug

It sounds like you are out of memory. Have you tried reducing work_mem?
Actually, what does your postgresql.conf look like with regard to memory
settings?

 This a a dual G5 box with 6 gigs of ram running postgresql 8.1. I  
 have not tired altering kernel resources (as described in http:// 
 www.postgresql.org/docs/8.1/interactive/kernel-resources.html#SHARED- 
 MEMORY-PARAMETERS), or compiling for 64 bit. I'm just not sure what  
 to try next. Does anyone have any suggestions?

Compiling for 64 bit might very well help you, but it sounds odd to use
several gigabytes of RAM for a sort.

Could you post EXPLAIN ANALYZE for the query with only one row, as well
as your table schema?

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Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Gábriel Ákos

Richard Huxton wrote:

Kirk Wythers wrote:
I am trying to do fairly simple joins on climate databases that should 
return ~ 7 million rows of data. However, I'm getting an error message 
on a OS X (10.4 tiger server) machine that seems to imply that I am 
running out of memory. The errors are:


psql(15811) malloc: *** vm_allocate(size=8421376) failed (error code=3)

Is this actually in psql - the client code rather than the backend?

Could it be that its allocating memory for its 7million result rows and 
running out of space for your user account?




Hi,

If you look at the message carefully, it looks like (for me) that the 
client is running out of memory. Can't allocate that 8,4MB :)


Regards,
Akos



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Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Tom Lane
=?ISO-8859-1?Q?G=E1briel_=C1kos?= [EMAIL PROTECTED] writes:
 Richard Huxton wrote:
 Kirk Wythers wrote:
 I am trying to do fairly simple joins on climate databases that should 
 return ~ 7 million rows of data.

 If you look at the message carefully, it looks like (for me) that the 
 client is running out of memory. Can't allocate that 8,4MB :)

Right, the join result doesn't fit in the client's memory limit.
This is not too surprising, as the out-of-the-box ulimit settings
on Tiger appear to be

$ ulimit -a
core file size(blocks, -c) 0
data seg size (kbytes, -d) 6144
file size (blocks, -f) unlimited
max locked memory (kbytes, -l) unlimited
max memory size   (kbytes, -m) unlimited
open files(-n) 256
pipe size  (512 bytes, -p) 1
stack size(kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes(-u) 266
virtual memory(kbytes, -v) unlimited
$

6 meg of memory isn't gonna hold 7 million rows ... so either raise
ulimit -d (quite a lot) or else use a cursor to fetch the result
in segments.

regards, tom lane

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Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Kirk Wythers

Thanks for the reply Steiner,

On Feb 2, 2007, at 8:41 AM, Steinar H. Gunderson wrote:


On Fri, Feb 02, 2007 at 07:52:48AM -0600, Kirk Wythers wrote:
psql(15811) malloc: *** vm_allocate(size=8421376) failed (error  
code=3)

psql(15811) malloc: *** error: can't allocate region
psql(15811) malloc: *** set a breakpoint in szone_error to debug


It sounds like you are out of memory. Have you tried reducing  
work_mem?
Actually, what does your postgresql.conf look like with regard to  
memory

settings?


I have not altered postgresql.conf. I assume these are the defaults:

# - Memory -

shared_buffers = 300# min 16 or  
max_connections*2, 8KB each

#temp_buffers = 1000# min 100, 8KB each
#max_prepared_transactions = 5  # can be 0 or more
# note: increasing max_prepared_transactions costs ~600 bytes of  
shared memory

# per transaction slot, plus lock space (see max_locks_per_transaction).
#work_mem = 1024# min 64, size in KB
#maintenance_work_mem = 16384   # min 1024, size in KB
#max_stack_depth = 2048 # min 100, size in KB

What about altering the sysctl values in /etc/rc to:
sysctl -w kern.sysv.shmmax=167772160
sysctl -w kern.sysv.shmmin=1
sysctl -w kern.sysv.shmmni=32
sysctl -w kern.sysv.shmseg=8
sysctl -w kern.sysv.shmall=65536

RIght now they are:
sysctl -w kern.sysv.shmmax=4194304 kern.sysv.shmmin=1  
kern.sysv.shmmni=32 kern.s

ysv.shmseg=8 kern.sysv.shmall=1024





This a a dual G5 box with 6 gigs of ram running postgresql 8.1. I
have not tired altering kernel resources (as described in http://
www.postgresql.org/docs/8.1/interactive/kernel-resources.html#SHARED-
MEMORY-PARAMETERS), or compiling for 64 bit. I'm just not sure what
to try next. Does anyone have any suggestions?


Compiling for 64 bit might very well help you, but it sounds odd to  
use

several gigabytes of RAM for a sort.

Could you post EXPLAIN ANALYZE for the query with only one row, as  
well

as your table schema?


met_data=# EXPLAIN ANALYSE SELECT sites.station_id, sites.longname,  
sites.lat, sites.lon, sites.thepoint_meter, weather.date,  
weather.year, weather.month, weather.day, weather.doy,  
weather.precip, weather.tmin, weather.tmax, weather.snowfall,  
weather.snowdepth, weather.tmean FROM sites LEFT OUTER JOIN weather  
ON sites.station_id = weather.station_id WHERE weather.station_id =  
210018 AND weather.year = 1893 AND weather.doy = 365;

QUERY PLAN
 
---
Nested Loop  (cost=0.00..33426.63 rows=1 width=96) (actual  
time=2.140..101.122 rows=1 loops=1)
   -  Index Scan using sites_pkey on sites  (cost=0.00..5.25 rows=1  
width=60) (actual time=0.106..0.111 rows=1 loops=1)

 Index Cond: (210018 = station_id)
   -  Index Scan using weather_pkey on weather   
(cost=0.00..33421.37 rows=1 width=40) (actual time=2.011..100.983  
rows=1 loops=1)

 Index Cond: (station_id = 210018)
 Filter: ((year = 1893) AND (doy = 365))
Total runtime: 101.389 ms
(7 rows)

The schema is public, but I'm not sure how to do an EXPAIN ANALYSE on  
a schema.




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Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Kirk Wythers


On Feb 2, 2007, at 9:46 AM, Tom Lane wrote:


=?ISO-8859-1?Q?G=E1briel_=C1kos?= [EMAIL PROTECTED] writes:

Richard Huxton wrote:

Kirk Wythers wrote:
I am trying to do fairly simple joins on climate databases that  
should

return ~ 7 million rows of data.



If you look at the message carefully, it looks like (for me) that the
client is running out of memory. Can't allocate that 8,4MB :)


Right, the join result doesn't fit in the client's memory limit.
This is not too surprising, as the out-of-the-box ulimit settings
on Tiger appear to be

$ ulimit -a
core file size(blocks, -c) 0
data seg size (kbytes, -d) 6144
file size (blocks, -f) unlimited
max locked memory (kbytes, -l) unlimited
max memory size   (kbytes, -m) unlimited
open files(-n) 256
pipe size  (512 bytes, -p) 1
stack size(kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes(-u) 266
virtual memory(kbytes, -v) unlimited
$

6 meg of memory isn't gonna hold 7 million rows ... so either raise
ulimit -d (quite a lot) or else use a cursor to fetch the result
in segments.



Thanks Tom... Any suggestions as to how much to raise ulimit -d? And  
how to raise ulimit -d?


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Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Steinar H. Gunderson
On Fri, Feb 02, 2007 at 10:05:29AM -0600, Kirk Wythers wrote:
 Thanks Tom... Any suggestions as to how much to raise ulimit -d? And  
 how to raise ulimit -d?

Try multiplying it by 100 for a start:

  ulimit -d 614400

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Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Tom Lane
Steinar H. Gunderson [EMAIL PROTECTED] writes:
 On Fri, Feb 02, 2007 at 10:05:29AM -0600, Kirk Wythers wrote:
 Thanks Tom... Any suggestions as to how much to raise ulimit -d? And  
 how to raise ulimit -d?

 Try multiplying it by 100 for a start:
   ulimit -d 614400

Or just ulimit -d unlimited

regards, tom lane

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Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Kirk Wythers

Tom,

I tried ulimit -d 614400, but the query ended with the same error. I  
thought then that the message:

psql(21522) malloc: *** vm_allocate(size=8421376) failed (error code=3)
psql(21522) malloc: *** error: can't allocate region
psql(21522) malloc: *** set a breakpoint in szone_error to debug
out of memory for query result

was telling me that I needed 841376 for the querry, so I tied bumping  
ulimit -d up another 10 to 6244000. However, that attempt gave the  
error:

truffula:~ kwythers$ ulimit -d 6144000
-bash: ulimit: data seg size: cannot modify limit: Operation not  
permitted


So I tried re-setting ulimit -d back to 6144, which worked, but now I  
can not seem to get ulimit -d to change again. It will not even allow  
ulimit -d 614400 (even though that worked a second ago). This seems  
very odd.




On Feb 2, 2007, at 10:11 AM, Tom Lane wrote:



Steinar H. Gunderson [EMAIL PROTECTED] writes:


On Fri, Feb 02, 2007 at 10:05:29AM -0600, Kirk Wythers wrote:


Thanks Tom... Any suggestions as to how much to raise ulimit -d? And
how to raise ulimit -d?





Try multiplying it by 100 for a start:
  ulimit -d 614400



Or just ulimit -d unlimited

regards, tom lane

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Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Tom Lane
Kirk Wythers [EMAIL PROTECTED] writes:
 However, setting ulimit to unlimited does not seem to solve the  
 issue. Output from ulimit -a is:

Possibly a silly question, but you are running the client code under the
shell session that you adjusted ulimit for, yes?

regards, tom lane

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Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Kirk Wythers
At this point there are no silly questions. But I am running the  
query under the shell session that I adjusted. I did discover that  
ulimit -d only changes the shell session that you issue the command  
in. So I changed ulimit -d to unlimited, connected to the db with  
psql db_name, then ran the select command (all in the same shell).



On Feb 2, 2007, at 11:59 AM, Tom Lane wrote:


Kirk Wythers [EMAIL PROTECTED] writes:

However, setting ulimit to unlimited does not seem to solve the
issue. Output from ulimit -a is:


Possibly a silly question, but you are running the client code  
under the

shell session that you adjusted ulimit for, yes?

regards, tom lane

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Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Kirk Wythers


On Feb 2, 2007, at 10:11 AM, Tom Lane wrote:


Steinar H. Gunderson [EMAIL PROTECTED] writes:

On Fri, Feb 02, 2007 at 10:05:29AM -0600, Kirk Wythers wrote:

Thanks Tom... Any suggestions as to how much to raise ulimit -d? And
how to raise ulimit -d?



Try multiplying it by 100 for a start:
  ulimit -d 614400


Or just ulimit -d unlimited


Thanks to everyone so far.

However, setting ulimit to unlimited does not seem to solve the  
issue. Output from ulimit -a is:


truffula:~ kwythers$ ulimit -a
core file size(blocks, -c) 0
data seg size (kbytes, -d) unlimited
file size (blocks, -f) unlimited
max locked memory (kbytes, -l) unlimited
max memory size   (kbytes, -m) unlimited
open files(-n) 256
pipe size  (512 bytes, -p) 1
stack size(kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes(-u) 100
virtual memory(kbytes, -v) unlimited

Also, changes to kernel settings in /etc/rc include:
sysctl -w kern.sysv.shmmax=167772160
sysctl -w kern.sysv.shmmin=1
sysctl -w kern.sysv.shmmni=32
sysctl -w kern.sysv.shmseg=8
sysctl -w kern.sysv.shmall=65536

However, I'm still getting the memory error:

met_data=# SELECT sites.station_id, sites.longname, sites.lat,  
sites.lon, sites.thepoint_meter, weather.date, weather.year,  
weather.month, weather.day, weather.doy, weather.precip,  
weather.tmin, weather.tmax, weather.snowfall, weather.snowdepth,  
weather.tmean FROM sites LEFT OUTER JOIN weather ON sites.station_id  
= weather.station_id;

psql(532) malloc: *** vm_allocate(size=8421376) failed (error code=3)
psql(532) malloc: *** error: can't allocate region
psql(532) malloc: *** set a breakpoint in szone_error to debug
out of memory for query result


Any other ideas out there?





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Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Tom Lane
Kirk Wythers [EMAIL PROTECTED] writes:
 However, setting ulimit to unlimited does not seem to solve the  
 issue.

After some experimentation I'm left wondering exactly what ulimit's -d
option is for on OS X, because it sure doesn't seem to be limiting
process data size.  (I should have been suspicious of a value as small
as 6 meg, anyway.)  I tried selecting a large unconstrained join on my own
OS X machine, and what I saw (watching with top) was that the psql
process VSIZE went up to 1.75Gb before it failed with the same error as
Kirk got:

regression=# select * from tenk1 a , tenk1 b;
psql(16572) malloc: *** vm_allocate(size=8421376) failed (error code=3)
psql(16572) malloc: *** error: can't allocate region
psql(16572) malloc: *** set a breakpoint in szone_error to debug

Since this is just a bog-standard Mini with 512M memory, it was pretty
thoroughly on its knees by this point :-(.  I'm not sure how to find out
about allocated swap space in OS X, but my bet is that the above message
should be understood as totally out of virtual memory.

My suggestion is to use a cursor to retrieve the data in more
manageably-sized chunks than 7M rows.  (If you don't want to mess with
managing a cursor explicitly, as of 8.2 there's a psql variable
FETCH_COUNT that can be set to make it happen behind the scenes.)

regards, tom lane

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Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Luke Lonergan
Tom,

On 2/2/07 2:18 PM, Tom Lane [EMAIL PROTECTED] wrote:

 as of 8.2 there's a psql variable
 FETCH_COUNT that can be set to make it happen behind the scenes.)

FETCH_COUNT is a godsend and works beautifully for exactly this purpose.

Now he's got to worry about how to page through 8GB of results in something
less than geological time with the space bar ;-)

- Luke



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Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Joshua D. Drake
Luke Lonergan wrote:
 Tom,
 
 On 2/2/07 2:18 PM, Tom Lane [EMAIL PROTECTED] wrote:
 
 as of 8.2 there's a psql variable
 FETCH_COUNT that can be set to make it happen behind the scenes.)
 
 FETCH_COUNT is a godsend and works beautifully for exactly this purpose.
 
 Now he's got to worry about how to page through 8GB of results in something
 less than geological time with the space bar ;-)

\o /tmp/really_big_cursor_return

;)

Joshua D. Drake

 
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Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Luke Lonergan
 \o /tmp/really_big_cursor_return
 
 ;)

Tough crowd :-D

- Luke



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Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Kirk Wythers


On Feb 2, 2007, at 7:53 PM, Luke Lonergan wrote:


Tough crowd :-D


No kidding ;-)



Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Joshua D. Drake
Luke Lonergan wrote:
 \o /tmp/really_big_cursor_return

 ;)
 
 Tough crowd :-D

Yeah well Andrew probably would have said use sed and pipe it through
awk to get the data you want.

Joshua D. Drake

 
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Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Kirk Wythers


On Feb 2, 2007, at 7:39 PM, Luke Lonergan wrote:


Tom,

On 2/2/07 2:18 PM, Tom Lane [EMAIL PROTECTED] wrote:


as of 8.2 there's a psql variable
FETCH_COUNT that can be set to make it happen behind the scenes.)


FETCH_COUNT is a godsend and works beautifully for exactly this  
purpose.


Now he's got to worry about how to page through 8GB of results in  
something

less than geological time with the space bar ;-)


I actually have no intention of paging through the results, but  
rather need to use the query to get the results into a new table with  
UPDATE, so that a GIS system can do some interpolations with subsets  
of the results.




- Luke





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Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Geoffrey

Joshua D. Drake wrote:

Luke Lonergan wrote:

\o /tmp/really_big_cursor_return

;)

Tough crowd :-D


Yeah well Andrew probably would have said use sed and pipe it through
awk to get the data you want.


Chances are, if you're using awk, you shouldn't need sed. :)

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Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Joshua D. Drake
Geoffrey wrote:
 Joshua D. Drake wrote:
 Luke Lonergan wrote:
 \o /tmp/really_big_cursor_return

 ;)
 Tough crowd :-D

 Yeah well Andrew probably would have said use sed and pipe it through
 awk to get the data you want.
 
 Chances are, if you're using awk, you shouldn't need sed. :)

Chances are.. if you are using awk or sed, you should use perl ;)

Joshua D. Drake



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Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Tom Lane
Kirk Wythers [EMAIL PROTECTED] writes:
 On Feb 2, 2007, at 7:39 PM, Luke Lonergan wrote:
 Now he's got to worry about how to page through 8GB of results in  
 something less than geological time with the space bar ;-)

 I actually have no intention of paging through the results, but  
 rather need to use the query to get the results into a new table with  
 UPDATE, so that a GIS system can do some interpolations with subsets  
 of the results.

Er ... then why are you SELECTing the data at all?  You can most likely
get it done much faster if the data stays inside the database engine.

regards, tom lane

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Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Kirk Wythers


On Feb 2, 2007, at 8:32 PM, Tom Lane wrote:


Kirk Wythers [EMAIL PROTECTED] writes:

On Feb 2, 2007, at 7:39 PM, Luke Lonergan wrote:

Now he's got to worry about how to page through 8GB of results in
something less than geological time with the space bar ;-)



I actually have no intention of paging through the results, but
rather need to use the query to get the results into a new table with
UPDATE, so that a GIS system can do some interpolations with subsets
of the results.


Er ... then why are you SELECTing the data at all?  You can most  
likely

get it done much faster if the data stays inside the database engine.




The new table needs to be filled with the results of the join. If  
there is a way to do this without a SELECT, please share.


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Re: [PERFORM] trouble with a join on OS X

2007-02-02 Thread Joshua D. Drake
Kirk Wythers wrote:
 
 On Feb 2, 2007, at 8:32 PM, Tom Lane wrote:
 
 Kirk Wythers [EMAIL PROTECTED] writes:
 On Feb 2, 2007, at 7:39 PM, Luke Lonergan wrote:
 Now he's got to worry about how to page through 8GB of results in
 something less than geological time with the space bar ;-)

 I actually have no intention of paging through the results, but
 rather need to use the query to get the results into a new table with
 UPDATE, so that a GIS system can do some interpolations with subsets
 of the results.

 Er ... then why are you SELECTing the data at all?  You can most likely
 get it done much faster if the data stays inside the database engine.


 
 The new table needs to be filled with the results of the join. If there
 is a way to do this without a SELECT, please share.


INSERT INTO foo SELECT * FROM BAR JOIN baz USING (id)

Joshua D. Drake

 
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