Обсуждение: Huge shared hit for small table

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Hi,

On 2019-11-04 19:38:40 +0000, Scott Rankin wrote:
> In the staging environment, we get this:
> 
> Index Scan using "programPK" on public.program prog  (cost=0.29..0.35 rows=1 width=16) (actual time=0.002..0.003
rows=1loops=21965)
 
>       Output: prog.id, prog.version, prog.active, prog.created_date, prog.last_modified_date, prog.created_by,
prog.last_modified_by,prog.client_id, prog.scheme_id, prog.name, prog.legacy_group_id, prog.custom_fields,
prog.setup_complete,prog.setup_messages, prog.legacy_program_type
 
>       Index Cond: (prog.id = per.program)
>       Buffers: shared hit=87860
> 
> In the production environment, we get this:
> 
> Index Scan using "programPK" on public.program prog  (cost=0.29..0.36 rows=1 width=16) (actual time=0.017..4.251
rows=1loops=21956)
 
>        Output: prog.id, prog.version, prog.active, prog.created_date, prog.last_modified_date, prog.created_by,
prog.last_modified_by,prog.client_id, prog.scheme_id, prog.name, prog.legacy_group_id, prog.custom_fields,
prog.setup_complete,prog.setup_messages, prog.legacy_program_type
 
>        Index Cond: (prog.id = per.program)
>        Buffers: shared hit=25437716
> 
> The tables in both environments are about the same size (18MB) and the indexes are about the same size (360kb/410kb)
–and the shared hits are pretty much the same on the other nodes of the query between the two environments.
 

It'd be worthwhile to look at the index stats using pgstatindex. Also,
could you show the definition of those indexes?


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> 
> Internal Revenue Service regulations require that certain types of written advice include a disclaimer. To the extent
thepreceding message contains advice relating to a Federal tax issue, unless expressly stated otherwise the advice is
notintended or written to be used, and it cannot be used by the recipient or any other taxpayer, for the purpose of
avoidingFederal tax penalties, and was not written to support the promotion or marketing of any transaction or matter
discussedherein.
 

GNGNGGRR.

Greetings,

Andres Freund

On Mon, Nov 04, 2019 at 07:38:40PM +0000, Scott Rankin wrote:
> In the staging environment, we get this:
> 
> Index Scan using "programPK" on public.program prog  (cost=0.29..0.35 rows=1 width=16) (actual time=0.002..0.003
rows=1loops=21965)
 
>       Output: prog.id, prog.version, prog.active, prog.created_date, prog.last_modified_date, prog.created_by,
prog.last_modified_by,prog.client_id, prog.scheme_id, prog.name, prog.legacy_group_id, prog.custom_fields,
prog.setup_complete,prog.setup_messages, prog.legacy_program_type
 
>       Index Cond: (prog.id = per.program)
>       Buffers: shared hit=87860
> 
> In the production environment, we get this:
> 
> Index Scan using "programPK" on public.program prog  (cost=0.29..0.36 rows=1 width=16) (actual time=0.017..4.251
rows=1loops=21956)
 
>        Output: prog.id, prog.version, prog.active, prog.created_date, prog.last_modified_date, prog.created_by,
prog.last_modified_by,prog.client_id, prog.scheme_id, prog.name, prog.legacy_group_id, prog.custom_fields,
prog.setup_complete,prog.setup_messages, prog.legacy_program_type
 
>        Index Cond: (prog.id = per.program)
>        Buffers: shared hit=25437716
> 
> The tables in both environments are about the same size (18MB) and the indexes are about the same size (360kb/410kb)
–and the shared hits are pretty much the same on the other nodes of the query between the two environments.
 

I think it's because some heap pages are being visited many times, due to the
index tuples being badly "fragmented".  Note, I'm not talking about
fragmentation of index *pages*, which is what pgstattuple reports (which
wouldn't have nearly so detrimental effect).  I could probably say that the
index tuples are badly "correlated" with the heap.

I'm guessing there are perhaps 25437716/87860 = 290 index tuples per page, and
they rarely point to same heap page as their siblings.  "Hit" means that this
affects you even though it's cached (by postgres).  So this is apparently slow
due to reading each page ~300 times rather than once to get its tuples all at
once.

> This has happened one time before, and we did a “REINDEX” on the program table – and that made the problem mostly go
away. Now it seems to be back, and I’m not sure what to make of it.
 

..which is consistent with my hypothesis.

You can use pg_repack or CREATE INDEX+DROP+RENAME hack (which is what pg_repack
-i does).  In a fresh index, its tuples are sorted by heap TID.  You could
CLUSTER the table itself (or pg_repack -t) on that index column.

In PG v12 you can use REINDEX CONCURRENTLY (but beware there's a crash
affecting its progress reporting, fix to be included in v12.1).

Justin

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On Mon, Nov 4, 2019 at 11:56 AM Justin Pryzby <pryzby@telsasoft.com> wrote:
> I think it's because some heap pages are being visited many times, due to the
> index tuples being badly "fragmented".  Note, I'm not talking about
> fragmentation of index *pages*, which is what pgstattuple reports (which
> wouldn't have nearly so detrimental effect).  I could probably say that the
> index tuples are badly "correlated" with the heap.

But this is a unique index, and Scott indicates that the problem seems
to go away for a while following a REINDEX.

> In PG v12 you can use REINDEX CONCURRENTLY (but beware there's a crash
> affecting its progress reporting, fix to be included in v12.1).

PG v12 will store B-Tree duplicates in heap TID order, so if that's
the problem then upgrading to v12 (and REINDEXing if the upgrade was
performed using pg_upgrade) will fix it for good.

-- 
Peter Geoghegan

Hi,

On 2019-11-04 19:56:57 +0000, Scott Rankin wrote:
> The index is exceedingly simple:
>
>
> CREATE UNIQUE INDEX "programPK" ON program(id int8_ops);
>
> From pg_stat_user_indexes:
>
> Staging:
>
> idx_scan: 5826745
> idx_tup_read: 52715470
> idx_tup_fetch: 52644465
>
> Production:
>
> idx_scan : 7277919087
> idx_tup_read: 90612605047
> idx_tup_fetch: 5207807880

I was basically asking for SELECT * FROM pgstatindex('pgstatindex');
with pgstatindex being from the pgstattuple extension
https://www.postgresql.org/docs/current/pgstattuple.html
not the pg_stat_user_indexes entry...

Greetings,

Andres Freund

Thanks to Justin for the clarification around pgstatindex:

Staging:

version2
tree_level1
index_size425984
root_block_no3
internal_pages1
leaf_pages50
empty_pages0
deleted_pages0
avg_leaf_density70.86
leaf_fragmentation16

Production:

version2
tree_level1
index_size360448
root_block_no3
internal_pages1
leaf_pages41
empty_pages0
deleted_pages1
avg_leaf_density60.44
leaf_fragmentation39.02

On 11/4/19, 3:07 PM, "Peter Geoghegan" <pg@bowt.ie> wrote:

    On Mon, Nov 4, 2019 at 11:56 AM Justin Pryzby <pryzby@telsasoft.com> wrote:
    > I think it's because some heap pages are being visited many times, due to the
    > index tuples being badly "fragmented".  Note, I'm not talking about
    > fragmentation of index *pages*, which is what pgstattuple reports (which
    > wouldn't have nearly so detrimental effect).  I could probably say that the
    > index tuples are badly "correlated" with the heap.

    But this is a unique index, and Scott indicates that the problem seems
    to go away for a while following a REINDEX.

    > In PG v12 you can use REINDEX CONCURRENTLY (but beware there's a crash
    > affecting its progress reporting, fix to be included in v12.1).

    PG v12 will store B-Tree duplicates in heap TID order, so if that's
    the problem then upgrading to v12 (and REINDEXing if the upgrade was
    performed using pg_upgrade) will fix it for good.

    --
    Peter Geoghegan



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On Mon, Nov 4, 2019 at 12:32 PM Jeff Janes <jeff.janes@gmail.com> wrote:
> Could there be a long-open transaction, which is preventing hint-bits from getting on set on the table rows, as well
onthe index rows? 

Contention on a small number of rows may also be a factor.

> A reindex would not by itself fix the problem if it were the long open transaction.  But  if the long open
transactionheld a sufficient lock on the table, then the reindex would block until the transaction went away on its
own,at which point the problem would go away on its own, so it might **appear** to have fixed the problem. 

That seems like the simplest and most likely explanation to me, even
though it isn't particularly simple.

--
Peter Geoghegan

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On Mon, Nov 4, 2019 at 12:38 PM Scott Rankin <srankin@motus.com> wrote:
> Definitely no long-running transactions on this table; in fact, this table is pretty infrequently updated – on the
orderof a few tens of rows updated per day. 

But a long running transaction will have an impact on all tables --
not just the tables that happen to have been accessed so far in the
long running transaction. This is necessary because nothing stops the
long running transaction from SELECTing data from any table at any
time -- we need to pessimistically keep around the data required to
make that work.

--
Peter Geoghegan

I think we have a winner.  I looked in and found a process that was 'idle in transaction' for a couple days - and once
Ikilled it, query performance went back to normal.
 

Thank you all for the very quick responses on this.

On 11/4/19, 3:41 PM, "Peter Geoghegan" <pg@bowt.ie> wrote:

    On Mon, Nov 4, 2019 at 12:38 PM Scott Rankin <srankin@motus.com> wrote:
    > Definitely no long-running transactions on this table; in fact, this table is pretty infrequently updated – on
theorder of a few tens of rows updated per day.
 

    But a long running transaction will have an impact on all tables --
    not just the tables that happen to have been accessed so far in the
    long running transaction. This is necessary because nothing stops the
    long running transaction from SELECTing data from any table at any
    time -- we need to pessimistically keep around the data required to
    make that work.

    --
    Peter Geoghegan



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