Thread: Vacuum of newly activated 8.3.12 standby receives warnings page xxx is uninitialized --- fixing

We have been seeing these warnings recently whenever a standby is
brought up (typically to check it is ok). Sometimes they are coupled
with corrupted indexes which require a REINDEX to fix. Initially I
thought these uninitialized pages were due to primary crashes or
hardware issues, however I've now managed to come up with a recipe to
generate them on demand on my workstation.

Pitrtools appears to be an essential part of the recipe - at this stage
I'm not sure if it is actually doing something directly to cause this or
merely tickling some Postgres recovery bug.

The essential triggering element seems to be performing a base backup
while the system is busy. Here's the description:

1/ Patch 8.3's pgbench using the attached diff, and initialize scale 100
dataset
2/ Get Pitrtools primary and standby config's setup (examples attached)
3/ Start pgbench with at least 4 clients and 200000 transactions
4/ After history has approx 10000 rows initiate backup from the standby
5/ After history has approx 140000 rows bring up the standby and perform
a VACUUM

Typically I'm seeing a large number of consecutive uninitialized pages
in the accounts table. What is also very interesting is that if I setup
the standby in a more "bare bones" manner (i.e manually running
pg_start_backup and rsync + pg_standby) then I can *never* elicit any
uninitialized pages.

I'm frankly puzzled about what Pitrtools is doing that is different - I
only noticed it using rsync compression (-z) and doing rsync backups via
pulling from the standby rather than pushing from the primary (I'm in
the process of trying these variations out in the bare bones case). Just
as I'm writing this I see Pitrtools rsync's pg_xlog - I wonder if there
is/are timing issues which mean that recovery might use some (corrupted)
logs from there before the (clean) archived ones arrive (will check).

Some more detail about the system:

Postgres 8.3.12 on Ubuntu Lucid x86_64 and Debian Lenny (lxc guests),
rsync 3, Pitrtools 1.2-1

Postgres config changes:

autovacuum = off          # prevent any relation truncation
max_fsm_pages = 20000     # encourage new page creation

Pitrtools Steps:

primary:
$ grep archive_command postgresql.conf
archive_command = 'cmd_archiver -C /etc/pitrtools/cmd_archiver.ini -F %p'

standby:
$ cmd_standby -C /etc/pitrtools/cmd_standby.ini -B
$ cmd_standby -C /etc/pitrtools/cmd_standby.ini -Astop_basebackup
$ cp /etc/postgresql/8.3/main/pg_hba.conf \
      /var/lib/postgresql/8.3/main/pg_hba.conf
$ cp /etc/postgresql/8.3/main/postgresql.conf \
      /var/lib/postgresql/8.3/main/postgresql.conf
$ cmd_standby -C /etc/pitrtools/cmd_standby.ini -S
$ cmd_standby -C /etc/pitrtools/cmd_standby.ini -F999

Bare Bones Steps:

primary:
$ grep archive_command postgresql.conf
  archive_command = 'rsync %p standby:/var/lib/postgresql/archive'

$ psql -c "SELECT pg_start_backup('backup');"
$ rsync --exclude pg_xlog/\* --exclude postmaster.pid -a * \
         standby:/var/lib/postgresql/8.3/main
$ psql -c "SELECT pg_stop_backup();

standby:
$ grep restore_command recovery.conf
restore_command = '/usr/lib/postgresql/8.3/bin/pg_standby -t
/tmp/trigger.5432 /var/lib/postgresql/archive %f %p %r'
$ /etc/init.d/postgresql-8.3 start
$ touch /tmp/trigger.5432



regards

Mark

P.s: cc'ing Pg Hackers as variation of this topic has come up there
several times.

Well, it is none of the things I considered.

The problem seems to be due to use of "--delete" in the base backup
rsync (see diff attached).  In fact I can now reproduce the
uninitialized pages using the "bare bones" method:

primary:
$ grep archive_command postgresql.conf
  archive_command = 'rsync %p standby:/var/lib/postgresql/archive'
$ pgbench -c 4 -t 200000 bench
(wait for approx 10000 transactions)

standby:
$ psql -h primary -c "SELECT pg_start_backup('backup');"
$ rsync --exclude pg_xlog/\* --exclude postmaster.pid --delete
--exclude=backup_label \
         primary:/var/lib/postgresql/8.3/main/* \
         /var/lib/postgresql/8.3/main
$ psql -h primary -c "SELECT pg_stop_backup();

$ grep restore_command recovery.conf
restore_command = '/usr/lib/postgresql/8.3/bin/pg_standby -t
/tmp/trigger.5432 /var/lib/postgresql/archive %f %p %r'
$ /etc/init.d/postgresql-8.3 start
(wait for approx 140000 transactions)
$ touch /tmp/trigger.5432

Removing the offending

--delete --exclude=backup_label

options from the base backup step makes everything work properly again.

I'd be interested to know if the other folks getting these warnings were
using unusual rsync options either during backup or for archiving.

regards

Mark

On 30/12/10 13:32, Mark Kirkwood wrote:
>
> I'm frankly puzzled about what Pitrtools is doing that is different -
> I only noticed it using rsync compression (-z) and doing rsync backups
> via pulling from the standby rather than pushing from the primary (I'm
> in the process of trying these variations out in the bare bones case).
> Just as I'm writing this I see Pitrtools rsync's pg_xlog - I wonder if
> there is/are timing issues which mean that recovery might use some
> (corrupted) logs from there before the (clean) archived ones arrive
> (will check).
>

On Thu, Dec 30, 2010 at 3:55 AM, Mark Kirkwood
<mark.kirkwood@catalyst.net.nz> wrote:
> Well, it is none of the things I considered.
>
> The problem seems to be due to use of "--delete" in the base backup rsync
> (see diff attached).  In fact I can now reproduce the uninitialized pages
> using the "bare bones" method:

Any time a relation is extended, we end up with a page of all zeros at
the end until the updated page is written out, which often doesn't
happen until the next checkpoint.  So it doesn't seem too mysterious
that you could end up with all zeroes pages on the standby initially,
but WAL replay ought to fix that.  I suppose the reason it isn't is
because you've excluded the backup label, so recovery will begin from
the wrong place.  Unless I'm missing something, that seems like a
really bad idea.

--
Robert Haas
EnterpriseDB: http://www.enterprisedb.com
The Enterprise PostgreSQL Company

On 30.12.2010 10:55, Mark Kirkwood wrote:
> Removing the offending
>
> --delete --exclude=backup_label
>
> options from the base backup step makes everything work properly again.

I don't see why --delete would make any difference, but you shouldn't 
exclude backup_label from the base backup. The backup label file is an 
important part of the online backup, it cannot be recovered safely 
without it.

--   Heikki Linnakangas  EnterpriseDB   http://www.enterprisedb.com

On 31/12/10 11:01, Heikki Linnakangas wrote: <blockquote cite="mid:4D1D0122.6090802@enterprisedb.com" type="cite">On
30.12.201010:55, Mark Kirkwood wrote: <br /><blockquote type="cite">Removing the offending <br /><br /> --delete
--exclude=backup_label<br /><br /> options from the base backup step makes everything work properly again. <br
/></blockquote><br/> I don't see why --delete would make any difference, but you shouldn't exclude backup_label from
thebase backup. The backup label file is an important part of the online backup, it cannot be recovered safely without
it.<br /><br /></blockquote><font size="-1"><font face="Helvetica"><br /> Yes, you (and Robert) are entirely correct, I
wasconfused in my understanding of the "--delete --exclude=backup_label" and thought it to mean "exclude the backup
labelfrom the delete". Yeah the --delete is harmless, it is the exclude backup_label that is causing the problem.<br
/><br/> Note to all current Pitrtools users, this impacts you! We need to get a corrected version out soon I would
think.<br/><br /> I note that this uninitialized pages with standbys has cropped up from time to time - I wonder if in
most/allthe cases folk were using Pitrtools?<br /><br /> regards<br /><br /> Mark<br /><br /><br /><br /></font></font> 

On 31/12/10 11:11, Mark Kirkwood wrote:
>
> Yes, you (and Robert) are entirely correct, I was confused in my 
> understanding of the "--delete --exclude=backup_label" and thought it 
> to mean "exclude the backup label from the delete". Yeah the --delete 
> is harmless, it is the exclude backup_label that is causing the problem.
>
> Note to all current Pitrtools users, this impacts you! We need to get 
> a corrected version out soon I would think.
>

Also (not surprisingly) I can confirm that data corruption is possible:

1/ Perform approx 140000 transactions against the primary
2/ Cancel Pgbench
3/ Issue "SELECT pg_switch_xlog()" on primary
4/ Bring up standby after checking it has applied last log

The resulting primary and standby should be identical, but:

primary:

bench=# SELECT count(*) FROM branches; count
-------   100

bench=# SELECT count(*) FROM accounts;  count
---------- 10000000

standby:

bench=# SELECT count(*) FROM branches; count
-------   132

bench=# SELECT count(*) FROM accounts;  count
--------- 9998269

The other counts are the same. We have lost some accounts records, but 
have gained duplicates in branches:

bench=# REINDEX TABLE branches;
ERROR:  could not create unique index "branches_pkey"
DETAIL:  Table contains duplicated values.

regards

Mark

On Fri, 2010-12-31 at 11:11 +1300, Mark Kirkwood wrote:
>
> I note that this uninitialized pages with standbys has cropped up from
> time to time - I wonder if in most/all the cases folk were using
> Pitrtools?

I deployed Pitrtools a lot when I was working for CMD, and I haven't
seen any issues with that. It is just a wrapper, nothing else...

Regards,
--
Devrim GÜNDÜZ
PostgreSQL Danışmanı/Consultant, Red Hat Certified Engineer
PostgreSQL RPM Repository: http://yum.pgrpms.org
Community: devrim~PostgreSQL.org, devrim.gunduz~linux.org.tr
http://www.gunduz.org  Twitter: http://twitter.com/devrimgunduz

On 05/01/11 04:43, Devrim GÜNDÜZ wrote:
> On Fri, 2010-12-31 at 11:11 +1300, Mark Kirkwood wrote:
>> I note that this uninitialized pages with standbys has cropped up from
>> time to time - I wonder if in most/all the cases folk were using
>> Pitrtools?
> I deployed Pitrtools a lot when I was working for CMD, and I haven't
> seen any issues with that. It is just a wrapper, nothing else...
>
>

Note that if you perform the backup step when the system is quiet then 
there is typically no problem with the standby - it is only when the 
backup coincides with any level of activity that you can elicit the 
previously mentioned problems.

Obviously the case I have included in the first mail shows up the 
problem immediately, but in fact it is reasonably hard to trigger and I 
spent quite a while getting to the state of being able to trigger the 
uninitialized pages on demand.

While Pitrtools it is a wrapper,  the use of "--exclude=backup_label" is 
incorrect and needs to be removed.

regards

Mark