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  #1 (permalink)  
Old 04-19-2008, 10:43 AM
Jakub Ouhrabka
 
Posts: n/a
Default Linux/PostgreSQL scalability issue - problem with 8 cores

Hi all,

we have a PostgreSQL dedicated Linux server with 8 cores (2xX5355). We
came accross a strange issue: when running with all 8 cores enabled
approximatly once a minute (period differs) the system is very busy for
a few seconds (~5-10s) and we don't know why - this issue don't show up
when we tell Linux to use only 2 cores, with 4 cores the problem is here
but it is still better than with 8 cores - all on the same machine, same
config, same workload. We don't see any apparent reason for these peaks.
We'd like to investigate it further but we don't know what to try next.
Any suggenstions? Any tunning tips for Linux+PostgreSQL on 8-way system?
Can this be connected with our heavy use of listen/notify and hundreds
backends in listen mode?

More details are below.

Thanks,

Kuba

System: HP DL360 2x5355, 8G RAM, P600+MSA50 - internal 2x72GB RAID 10
for OS, 10x72G disks RAID 10 for PostgreSQL data and wal
OS: Linux 2.6 64bit (kernel 2.6.21, 22, 23 makes little difference)
PostgreSQL: 8.2.4 (64bit), shared buffers 1G

Nothing else than PostgreSQL is running on the server. Cca 800
concurrent backends. Majority of backends in LISTEN doing nothing.
Client interface for most backends is ecpg+libpq.

Problem description:

The system is usually running 80-95% idle. Approximatly once a minute
for cca 5-10s there is a peak in activity which looks like this:

vmstat (and top or atop) reports 0% idle, 100% in user mode, very low
iowait, low IO activity, higher number of contex switches than usual but
not exceedingly high (2000-4000cs/s, usually 1500cs/s), few hundreds
waiting processes per second (usually 0-1/s). From looking at top and
running processes we can't see any obvious reason for the peak.
According to PostgreSQL log the long running commands from these moments
are e.g. begin transaction lasting several seconds.

When only 2 cores are enabled (kernel command line) then everything is
running smoothly. 4 cores exibits slightly better behavior than 8 cores
but worse than 2 cores - the peaks are visible.

We've tried kernel versions 2.6.21-23 (latest revisions as of beginning
December from kernel.org) the pattern slightly changed but it may also
be that the workload slightly changed.

pgbench or any other stress testing runs smoothly on the server.

The only strange thing about our usage pattern I can think of is heavy
use of LISTEN/NOTIFY especially hunderds backends in listen mode.

When restarting our connected clients the peaks are not there from time
0, they are visible after a while - seems something gets synchronized
and causing troubles then.

Since the server is PostgreSQL dedicated and no our client applications
are running on it - and there is a difference when 2 and 8 cores are
enabled - we think that the peaks are not caused by our client
applications.

How can we diagnose what is happening during the peaks?
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  #2 (permalink)  
Old 04-19-2008, 10:43 AM
Sven Geisler
 
Posts: n/a
Default Re: Linux/PostgreSQL scalability issue - problem with 8cores

Hi Jakub,

I do have a similar server (from DELL), which performance well with our
PostgreSQL application. I guess the peak in context switches is the only
think you can see.

Anyhow, I think it is you're LISTEN/NOTIFY approach which cause that
behaviour. I guess all backends do listen to the same notification.
I don't know the exact implementation, but I can imagine that all
backends are access the same section in the shared memory which cause
the increase of context switches. More cores means more access at the
same time.

Can you change your implementation?
- split you problem - create multiple notification if possible
- do an UNLISTEN if possible
- use another signalisation technique

Regards
Sven


Jakub Ouhrabka schrieb:
> Hi all,
>
> we have a PostgreSQL dedicated Linux server with 8 cores (2xX5355). We
> came accross a strange issue: when running with all 8 cores enabled
> approximatly once a minute (period differs) the system is very busy for
> a few seconds (~5-10s) and we don't know why - this issue don't show up
> when we tell Linux to use only 2 cores, with 4 cores the problem is here
> but it is still better than with 8 cores - all on the same machine, same
> config, same workload. We don't see any apparent reason for these peaks.
> We'd like to investigate it further but we don't know what to try next.
> Any suggenstions? Any tunning tips for Linux+PostgreSQL on 8-way system?
> Can this be connected with our heavy use of listen/notify and hundreds
> backends in listen mode?
>
> More details are below.
>
> Thanks,
>
> Kuba
>
> System: HP DL360 2x5355, 8G RAM, P600+MSA50 - internal 2x72GB RAID 10
> for OS, 10x72G disks RAID 10 for PostgreSQL data and wal
> OS: Linux 2.6 64bit (kernel 2.6.21, 22, 23 makes little difference)
> PostgreSQL: 8.2.4 (64bit), shared buffers 1G
>
> Nothing else than PostgreSQL is running on the server. Cca 800
> concurrent backends. Majority of backends in LISTEN doing nothing.
> Client interface for most backends is ecpg+libpq.
>
> Problem description:
>
> The system is usually running 80-95% idle. Approximatly once a minute
> for cca 5-10s there is a peak in activity which looks like this:
>
> vmstat (and top or atop) reports 0% idle, 100% in user mode, very low
> iowait, low IO activity, higher number of contex switches than usual but
> not exceedingly high (2000-4000cs/s, usually 1500cs/s), few hundreds
> waiting processes per second (usually 0-1/s). From looking at top and
> running processes we can't see any obvious reason for the peak.
> According to PostgreSQL log the long running commands from these moments
> are e.g. begin transaction lasting several seconds.
>
> When only 2 cores are enabled (kernel command line) then everything is
> running smoothly. 4 cores exibits slightly better behavior than 8 cores
> but worse than 2 cores - the peaks are visible.
>
> We've tried kernel versions 2.6.21-23 (latest revisions as of beginning
> December from kernel.org) the pattern slightly changed but it may also
> be that the workload slightly changed.
>
> pgbench or any other stress testing runs smoothly on the server.
>
> The o usage panly strange thing about ourttern I can think of is heavy
> use of LISTEN/NOTIFY especially hunderds backends in listen mode.
>
> When restarting our connected clients the peaks are not there from time
> 0, they are visible after a while - seems something gets synchronized
> and causing troubles then.
>
> Since the server is PostgreSQL dedicated and no our client applications
> are running on it - and there is a difference when 2 and 8 cores are
> enabled - we think that the peaks are not caused by our client
> applications.
>
> How can we diagnose what is happening during the peaks?
>
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> TIP 1: if posting/reading through Usenet, please send an appropriate
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> message can get through to the mailing list cleanly


--
Sven Geisler <sgeisler@aeccom.com> Tel +49.30.921017.81 Fax .50
Senior Developer, AEC/communications GmbH & Co. KG Berlin, Germany

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  #3 (permalink)  
Old 04-19-2008, 10:43 AM
Tom Lane
 
Posts: n/a
Default Re: Linux/PostgreSQL scalability issue - problem with 8 cores

Jakub Ouhrabka <kuba@comgate.cz> writes:
> we have a PostgreSQL dedicated Linux server with 8 cores (2xX5355). We
> came accross a strange issue: when running with all 8 cores enabled
> approximatly once a minute (period differs) the system is very busy for
> a few seconds (~5-10s) and we don't know why - this issue don't show up
> when we tell Linux to use only 2 cores, with 4 cores the problem is here
> but it is still better than with 8 cores - all on the same machine, same
> config, same workload. We don't see any apparent reason for these peaks.


Interesting. Maybe you could use oprofile to try to see what's
happening? It sounds a bit like momentary contention for a spinlock,
but exactly what isn't clear.

> Can this be connected with our heavy use of listen/notify and hundreds
> backends in listen mode?


Perhaps. Have you tried logging executions of NOTIFY to see if they are
correlated with the spikes?

regards, tom lane

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  #4 (permalink)  
Old 04-19-2008, 10:43 AM
Jakub Ouhrabka
 
Posts: n/a
Default Re: Linux/PostgreSQL scalability issue - problem with 8cores

Hi Tom,

> Interesting. Maybe you could use oprofile to try to see what's
> happening? It sounds a bit like momentary contention for a spinlock,
> but exactly what isn't clear.


ok, we're going to try oprofile, will let you know...

> Perhaps. Have you tried logging executions of NOTIFY to see if they
> are correlated with the spikes?


We didn't log the notifies but I think it's not correlated. We'll have a
detailed look next time we try it (with oprofile).

Thanks for suggestions!

Kuba


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  #5 (permalink)  
Old 04-19-2008, 10:43 AM
Jakub Ouhrabka
 
Posts: n/a
Default Re: Linux/PostgreSQL scalability issue - problem with 8 cores

Hi Sven,

> I guess all backends do listen to the same notification.


Unfortunatelly no. The backends are listening to different notifications
in different databases. Usually there are only few listens per database
with only one exception - there are many (hundreds) listens in one
database but all for different notifications.

> Can you change your implementation?
> - split you problem - create multiple notification if possible


Yes, it is like this.

> - do an UNLISTEN if possible


Yes, we're issuing unlistens when appropriate.

> - use another signalisation technique


We're planning to reduce the number of databases/backends/listens but
anyway we'd like to run system on 8 cores if it is running without any
problems on 2 cores...

Thanks for the suggestions!

Kuba

Sven Geisler napsal(a):
> Hi Jakub,
>
> I do have a similar server (from DELL), which performance well with our
> PostgreSQL application. I guess the peak in context switches is the only
> think you can see.
>
> Anyhow, I think it is you're LISTEN/NOTIFY approach which cause that
> behaviour. I guess all backends do listen to the same notification.
> I don't know the exact implementation, but I can imagine that all
> backends are access the same section in the shared memory which cause
> the increase of context switches. More cores means more access at the
> same time.
>
> Can you change your implementation?
> - split you problem - create multiple notification if possible
> - do an UNLISTEN if possible
> - use another signalisation technique
>
> Regards
> Sven
>
>
> Jakub Ouhrabka schrieb:
>> Hi all,
>>
>> we have a PostgreSQL dedicated Linux server with 8 cores (2xX5355). We
>> came accross a strange issue: when running with all 8 cores enabled
>> approximatly once a minute (period differs) the system is very busy for
>> a few seconds (~5-10s) and we don't know why - this issue don't show up
>> when we tell Linux to use only 2 cores, with 4 cores the problem is here
>> but it is still better than with 8 cores - all on the same machine, same
>> config, same workload. We don't see any apparent reason for these peaks.
>> We'd like to investigate it further but we don't know what to try next.
>> Any suggenstions? Any tunning tips for Linux+PostgreSQL on 8-way system?
>> Can this be connected with our heavy use of listen/notify and hundreds
>> backends in listen mode?
>>
>> More details are below.
>>
>> Thanks,
>>
>> Kuba
>>
>> System: HP DL360 2x5355, 8G RAM, P600+MSA50 - internal 2x72GB RAID 10
>> for OS, 10x72G disks RAID 10 for PostgreSQL data and wal
>> OS: Linux 2.6 64bit (kernel 2.6.21, 22, 23 makes little difference)
>> PostgreSQL: 8.2.4 (64bit), shared buffers 1G
>>
>> Nothing else than PostgreSQL is running on the server. Cca 800
>> concurrent backends. Majority of backends in LISTEN doing nothing.
>> Client interface for most backends is ecpg+libpq.
>>
>> Problem description:
>>
>> The system is usually running 80-95% idle. Approximatly once a minute
>> for cca 5-10s there is a peak in activity which looks like this:
>>
>> vmstat (and top or atop) reports 0% idle, 100% in user mode, very low
>> iowait, low IO activity, higher number of contex switches than usual but
>> not exceedingly high (2000-4000cs/s, usually 1500cs/s), few hundreds
>> waiting processes per second (usually 0-1/s). From looking at top and
>> running processes we can't see any obvious reason for the peak.
>> According to PostgreSQL log the long running commands from these moments
>> are e.g. begin transaction lasting several seconds.
>>
>> When only 2 cores are enabled (kernel command line) then everything is
>> running smoothly. 4 cores exibits slightly better behavior than 8 cores
>> but worse than 2 cores - the peaks are visible.
>>
>> We've tried kernel versions 2.6.21-23 (latest revisions as of beginning
>> December from kernel.org) the pattern slightly changed but it may also
>> be that the workload slightly changed.
>>
>> pgbench or any other stress testing runs smoothly on the server.
>>
>> The o usage panly strange thing about ourttern I can think of is heavy
>> use of LISTEN/NOTIFY especially hunderds backends in listen mode.
>>
>> When restarting our connected clients the peaks are not there from time
>> 0, they are visible after a while - seems something gets synchronized
>> and causing troubles then.
>>
>> Since the server is PostgreSQL dedicated and no our client applications
>> are running on it - and there is a difference when 2 and 8 cores are
>> enabled - we think that the peaks are not caused by our client
>> applications.
>>
>> How can we diagnose what is happening during the peaks?
>>
>> ---------------------------(end of broadcast)---------------------------
>> TIP 1: if posting/reading through Usenet, please send an appropriate
>> subscribe-nomail command to majordomo@postgresql.org so that your
>> message can get through to the mailing list cleanly

>

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  #6 (permalink)  
Old 04-19-2008, 10:43 AM
Alvaro Herrera
 
Posts: n/a
Default Re: Linux/PostgreSQL scalability issue - problem with 8cores

Jakub Ouhrabka wrote:

> > - do an UNLISTEN if possible

>
> Yes, we're issuing unlistens when appropriate.


You are vacuuming pg_listener periodically, yes? Not that this seems to
have any relationship to your problem, but ...

--
Alvaro Herrera http://www.CommandPrompt.com/
The PostgreSQL Company - Command Prompt, Inc.

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  #7 (permalink)  
Old 04-19-2008, 10:43 AM
Jakub Ouhrabka
 
Posts: n/a
Default Re: Linux/PostgreSQL scalability issue - problem with 8 cores

Alvaro,

>>> - do an UNLISTEN if possible

>> Yes, we're issuing unlistens when appropriate.

>
> You are vacuuming pg_listener periodically, yes? Not that this seems
> to have any relationship to your problem, but ...


yes, autovacuum should take care of this. But looking forward for
multiple-workers in 8.3 as it should help us during high load periods
(some tables might wait too long for autovacuum now - but it's not that
big problem for us...).

Thanks for great work!

Kuba
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  #8 (permalink)  
Old 04-19-2008, 10:43 AM
James Mansion
 
Posts: n/a
Default Re: Linux/PostgreSQL scalability issue - problem with 8cores

Jakub Ouhrabka wrote:
> How can we diagnose what is happening during the peaks?

Can you try forcing a core from a bunch of the busy processes? (Hmm -
does Linux have an equivalent to the useful Solaris pstacks?)

James

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  #9 (permalink)  
Old 04-19-2008, 10:43 AM
David Boreham
 
Posts: n/a
Default Re: Linux/PostgreSQL scalability issue - problem with 8cores

James Mansion wrote:
> Jakub Ouhrabka wrote:
>> How can we diagnose what is happening during the peaks?

> Can you try forcing a core from a bunch of the busy processes? (Hmm -
> does Linux have an equivalent to the useful Solaris pstacks?)

There's a 'pstack' for Linux, shipped at least in Red Hat distributions
(and possibly others,
I'm not sure). It's a shell script wrapper around gdb, so easily ported
to any Linux.



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  #10 (permalink)  
Old 04-19-2008, 10:43 AM
Jakub Ouhrabka
 
Posts: n/a
Default Re: Linux/PostgreSQL scalability issue - problem with 8cores

Hi Tom & all,

>> It sounds a bit like momentary contention for a spinlock,
>> but exactly what isn't clear.


> ok, we're going to try oprofile, will let you know...


yes, it seems like contention for spinlock if I'm intepreting oprofile
correctly, around 60% of time during spikes is in s_lock. [for details
see below].

We've tried several times to get stacktrace from some of the running
backends during spikes, we got always this:

0x00002b005d00a9a9 in semop () from /lib/libc.so.6
#0 0x00002b005d00a9a9 in semop () from /lib/libc.so.6
#1 0x000000000054fe53 in PGSemaphoreLock (sema=0x2b00a04e5090,
interruptOK=0 '\0') at pg_sema.c:411
#2 0x0000000000575d95 in LWLockAcquire (lockid=SInvalLock,
mode=LW_EXCLUSIVE) at lwlock.c:455
#3 0x000000000056fbfe in ReceiveSharedInvalidMessages
(invalFunction=0x5e9a30 <LocalExecuteInvalidationMessage>,
resetFunction=0x5e9df0 <InvalidateSystemCaches>) at sinval.c:159
#4 0x0000000000463505 in StartTransactionCommand () at xact.c:1439
#5 0x000000000056fa4b in ProcessCatchupEvent () at sinval.c:347
#6 0x000000000056fb20 in CatchupInterruptHandler
(postgres_signal_arg=<value optimized out>) at sinval.c:221
#7 0x00002b005cf6f110 in killpg () from /lib/libc.so.6
#8 0x0000000000000000 in ?? ()

Is this enough info to guess what's happening? What should we try next?

Thanks,

Kuba

oprofile results:

[I've shortened path from /usr/local/pg... to just pg for better
readilibity]

# opreport --long-filenames
CPU: Core 2, speed 2666.76 MHz (estimated)
Counted CPU_CLK_UNHALTED events (Clock cycles when not halted) with a
unit mask of 0x00 (Unhalted core cycles) count 100000
CPU_CLK_UNHALT...|
samples| %|
------------------
125577 90.7584 pg-8.2.4/bin/postgres
3792 2.7406 /lib/libc-2.3.6.so
3220 2.3272 /usr/src/linux-2.6.22.15/vmlinux
2145 1.5503 /usr/bin/oprofiled
1540 1.1130 /xfs
521 0.3765 pg-8.2.4/lib/plpgsql.so
441 0.3187 /cciss
374 0.2703 /oprofile

....

CPU: Core 2, speed 2666.76 MHz (estimated)
Counted CPU_CLK_UNHALTED events (Clock cycles when not halted) with a
unit mask of 0x00 (Unhalted core cycles) count 100000
samples % app name symbol name
85355 61.6887 pg-8.2.4/bin/postgres s_lock
9803 7.0849 pg-8.2.4/bin/postgres LWLockRelease
5535 4.0003 pg-8.2.4/bin/postgres LWLockAcquire
3792 2.7406 /lib/libc-2.3.6.so (no symbols)
3724 2.6915 pg-8.2.4/bin/postgres DropRelFileNodeBuffers
2145 1.5503 /usr/bin/oprofiled (no symbols)
2069 1.4953 pg-8.2.4/bin/postgres GetSnapshotData
1540 1.1130 /xfs (no symbols)
1246 0.9005 pg-8.2.4/bin/postgres hash_search_with_hash_value
1052 0.7603 pg-8.2.4/bin/postgres AllocSetAlloc
1015 0.7336 pg-8.2.4/bin/postgres heapgettup
879 0.6353 pg-8.2.4/bin/postgres hash_any
862 0.6230 /usr/src/linux-2.6.22.15/vmlinux mwait_idle
740 0.5348 pg-8.2.4/bin/postgres hash_seq_search
674 0.4871 pg-8.2.4/bin/postgres HeapTupleSatisfiesNow
557 0.4026 pg-8.2.4/bin/postgres SIGetDataEntry
552 0.3989 pg-8.2.4/bin/postgres equal
469 0.3390 pg-8.2.4/bin/postgres SearchCatCache
441 0.3187 /cciss (no symbols)
433 0.3129 /usr/src/linux-2.6.22.15/vmlinux find_busiest_group
413 0.2985 pg-8.2.4/bin/postgres PinBuffer
393 0.2840 pg-8.2.4/bin/postgres MemoryContextAllocZeroAligned
374 0.2703 /oprofile (no symbols)
275 0.1988 pg-8.2.4/bin/postgres ExecInitExpr
253 0.1829 pg-8.2.4/bin/postgres base_yyparse
206 0.1489 pg-8.2.4/bin/postgres CatalogCacheFlushRelation
201 0.1453 pg-8.2.4/bin/postgres MemoryContextAlloc
194 0.1402 pg-8.2.4/bin/postgres _bt_compare
188 0.1359 /nf_conntrack (no symbols)
158 0.1142 /bnx2 (no symbols)
147 0.1062 pg-8.2.4/bin/postgres pgstat_initstats
139 0.1005 pg-8.2.4/bin/postgres fmgr_info_cxt_security
132 0.0954 /usr/src/linux-2.6.22.15/vmlinux task_rq_lock
131 0.0947 /bin/bash (no symbols)
129 0.0932 pg-8.2.4/bin/postgres AllocSetFree
125 0.0903 pg-8.2.4/bin/postgres ReadBuffer
124 0.0896 pg-8.2.4/bin/postgres MemoryContextCreate
124 0.0896 pg-8.2.4/bin/postgres SyncOneBuffer
124 0.0896 pg-8.2.4/bin/postgres XLogInsert
123 0.0889 pg-8.2.4/bin/postgres _equalAggref
122 0.0882 pg-8.2.4/bin/postgres HeapTupleSatisfiesSnapshot
112 0.0809 pg-8.2.4/bin/postgres copyObject
102 0.0737 pg-8.2.4/bin/postgres UnpinBuffer
99 0.0716 pg-8.2.4/bin/postgres _SPI_execute_plan
99 0.0716 pg-8.2.4/bin/postgres nocachegetattr
98 0.0708 /usr/src/linux-2.6.22.15/vmlinux __wake_up_bit
97 0.0701 pg-8.2.4/bin/postgres TransactionIdIsInProgress
94 0.0679 pg-8.2.4/bin/postgres check_stack_depth
93 0.0672 pg-8.2.4/bin/postgres base_yylex
91 0.0658 pg-8.2.4/bin/postgres pfree
89 0.0643 pg-8.2.4/lib/plpgsql.so exec_stmts
86 0.0622 /usr/src/linux-2.6.22.15/vmlinux __switch_to
85 0.0614 pg-8.2.4/bin/postgres LockAcquire
83 0.0600 pg-8.2.4/bin/postgres FunctionCall2
82 0.0593 pg-8.2.4/bin/postgres ExecInitAgg
82 0.0593 /usr/src/linux-2.6.22.15/vmlinux system_call
79 0.0571 pg-8.2.4/bin/postgres pgstat_write_statsfile
77 0.0557 pg-8.2.4/bin/postgres heap_getsysattr
73 0.0528 pg-8.2.4/bin/postgres .plt
72 0.0520 /lib/ld-2.3.6.so (no symbols)
71 0.0513 pg-8.2.4/bin/postgres SearchSysCache
71 0.0513 pg-8.2.4/bin/postgres _bt_checkkeys
68 0.0491 /usr/src/linux-2.6.22.15/vmlinux apic_timer_interrupt
67 0.0484 pg-8.2.4/bin/postgres slot_deform_tuple
64 0.0463 pg-8.2.4/bin/postgres TupleDescInitEntry
64 0.0463 pg-8.2.4/bin/postgres newarc
63 0.0455 /usr/src/linux-2.6.22.15/vmlinux __wake_up
62 0.0448 pg-8.2.4/bin/postgres LocalExecuteInvalidationMessage
61 0.0441 /usr/src/linux-2.6.22.15/vmlinux try_to_wake_up
60 0.0434 pg-8.2.4/bin/postgres ReceiveSharedInvalidMessages
59 0.0426 pg-8.2.4/bin/postgres ExecutorStart
58 0.0419 pg-8.2.4/bin/postgres DirectFunctionCall1
58 0.0419 pg-8.2.4/bin/postgres ScanKeywordLookup
57 0.0412 pg-8.2.4/bin/postgres hash_search
56 0.0405 pg-8.2.4/bin/postgres CatalogCacheComputeHashValue
56 0.0405 pg-8.2.4/bin/postgres ExecProject
55 0.0398 pg-8.2.4/bin/postgres _bt_first
54 0.0390 pg-8.2.4/lib/plpgsql.so exec_eval_simple_expr
53 0.0383 pg-8.2.4/bin/postgres AllocSetDelete
53 0.0383 pg-8.2.4/bin/postgres CleanupTempFiles
52 0.0376 pg-8.2.4/bin/postgres ExecCreateTupleTable
52 0.0376 pg-8.2.4/lib/plpgsql.so copy_plpgsql_datum
49 0.0354 pg-8.2.4/bin/postgres MemoryContextAllocZero
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