Re: Issue with WAL logs temporary not replaying

Tomas,

Indeed, I haven't put enough detail in the original post. That is a fair
point, thank you. Let me follow up on each of your comments.

unfortunately your message is missing some pretty important information,
> like for example which OS you're running, what PostgreSQL version are you
> using (and if you built it on your own or installed from some package
> repository).

We are using Docker container based on Alpine 3.5. It has a custom-built
PostgreSQL 9.6.3 installation. The customization is negligible, e.g. we did
not alter configure and make process in any way. We only included pglogical
extension. Here are the very sources for our image –
https://github.com/edenlabllc/alpine-postgre/blob/master/
pglogical/Dockerfile
. The Dockerfile is based on the "official" postgres image 9.6.3 from
docker library, e.g. https://github.com/docker-library/postgres/tree/
a554d043a3b77937120d325b30fefaad2e3be12d/9.6/alpine
.

Also, you mention replicas. What type of replication are you using? The
> built-in streaming replication, or something else?

We use logical replication. We are interested in replicating selected
columns from tables across several databases in our kubernetes cluster. For
this we are using pglogical REL2.0.1, built with patch that allows it to
compile under Alpine. Here's the patch: https://github.com/
alpinelinux/aports/commit/f4f856564dfb2589c1800bd51322f4eadfc67cf1

> Firstly, I very much doubt using pg_resetxlog is a good idea, especially
> when it's rather unclear what was the actual root cause.

Noted. In hindsight I think our best course of action would have been to
make a copy of PG_DATA table.

Secondly, I don't quite understand what you mean by "recovery" here. The
> regular recovery process (say, after a crash) makes it impossible to
> connect to the database, so I'm not sure what you mean by running vacuum
> analyze (not to mention how it could have improved the recovery speed).

By recovery I mean a sort of self-healing of a running database. Let me
make a little step back and explain this.

After several restart attempts, the DB would still not get up. Instead it
was complaining about inability to "locate a valid checkpoint record".
After we ran pg_resetxlog and tried to start the database again, the
"locate a valid checkpoint record" error was gone, and we ended up with a
100% working database.

From this point onwards we began issuing SELECT statements, once in several
minutes, to see if the database sees the missing records. The records
indeed began to slowly appear in our tables. I _think_ this was happening
because the database began reading them from WAL, in the background. Again
– at this point the database was (or seemed to be) fully operational. It
was just catching up on data (this is my impression).

It seems as if pg_resetxlog removed some WAL segment (hence the
mentioned "PANIC:
could not locate a valid checkpoint record" log), which initially caused
the database to stuck and not read further WAL segments.

Well, considering you did pg_resetxlog ... I'm surprised you only lost two
> records, but it's a question what state are the indexes in etc.

I never considered indexes to play part in the issue. Noted on that, thank
you.

Man, that's an extremely noisy log file. There are errors caused by broken
> pg_hba.conf entries and so on, which makes it extremely difficult to look
> for possible other errors ... I'm not going to waste time by doing that.

Ugh, sorry about that. I wanted to provide a vanilla version of the log,
e.g. "as is". Below is an updated variant. I removed duplicate lines. The
log file went down from 14794 to 329 lines:
https://gist.githubusercontent.com/gmile/6df9ce393b11fb369856b84c4e9f75
5a/raw/7779c8341482d8df39257ab033e809b187227389/postgresql-short.log

The most interesting stuff, in my opinion, is around PANIC lines. Also,
there are a lot of the following lines:

ERROR: requested WAL segment 000000010000000300000089 has already been
removed

I'm yet to find out why these happened and what they mean.

For the record, these are the lines that I removed from the log:

sed -i '' '/LOG: incomplete startup packet/d' postgres.log
sed -i '' '/FATAL: password authentication failed for user "db"/d
postgres.log
sed -i '' '/DETAIL: Password does not match for user "db"./d postgres.log
sed -i '' '/Connection matched pg_hba.conf line 95: "host all all all
md5"/d' postgres.log
sed -i '' '/DETAIL: Password does not match for user "pghoard"/d'
postgres.log
sed -i '' '/FATAL: password authentication failed for user "pghoard"/d'
postgres.log
sed -i '' '/WARNING: concurrent insert in progress within table
"declarations_status_hstr"/d' postgres.log
sed -i '' '/WARNING: concurrent insert in progress within table
"audit_log"/d' postgres.log

I don't know. You have not provided any information about the storage
> system, and we don't have access to system logs that might show if
> something happened at this level. But in general yes, a storage issue might
> cause this.

We use volumes provided by Kubernetes which, in turn, are disks from Google
Compute Engine. I don't know the exact characteristics of SSDs. Would it
make sense to try and get to the bottom of the SSDs stats?

The file system used by PG_DATA folder is ext4.

It wouldn't. But it's unclear how you came to that conclusion.

My logic is the following:

1. db is up and responding to write requests,
2. the data is not actually seen in the tables,
3. the data is actually seen in a logical replica,
4. we restart db, it refuses to start and raises an error,
5. we mitigate the error,
6. db restarts successfully,
7. data slowly restores "by itself".

Given replica had good data and since by design replica takes its data from
original DB's WAL... we concluded that all inserted data made it to the WAL
but not further, e.g. not in the actual tables. Again: since the records
were missing from tables in the original database, somehow PostgreSQL was
not applying data from WAL to tables.

It all looked as if some code in postgresql that does "now, move data from
WAL to table" action would get stuck or something. While at the same time
worker processes that deal with DB connections and queries would continue
to operate normally. Ultimately pg_resetxlog would unstuck the "now, move
data from WAL to table" code.

I'm totally may be making things up here. This is only my impression based
on observation. I'd very much like to be corrected.

There's only one log for PostgreSQL, so it would have to be in that file
> depending on the log level.

Got it.

Please inspect the core dumps using gdb and share the backtraces. There are
> instructions how to do that on the wiki

I'm going to try and extract backtraces from the core dumps. I don't
usually do this on a daily basis, so it will take some time. I will come
back with results when I have something.

On Wed, Jan 31, 2018 at 8:18 PM, Tomas Vondra <tomas(dot)vondra(at)2ndquadrant(dot)com>
wrote:

> Hi,
>
> unfortunately your message is missing some pretty important information,
> like for example which OS you're running, what PostgreSQL version are
> you using (and if you built it on your own or installed from some
> package repository).
>
> Also, you mention replicas. What type of replication are you using? The
> built-in streaming replication, or something else?
>
> On 01/31/2018 06:56 PM, Eugene Pirogov wrote:
> > Hi,
> >
> > We've experienced a DB incident related to WAL. The issue is now
> > somewhat resolved, and I'm trying to understand what could have caused
> > the problem to occur in the first place. Below is a full chronicle of an
> > incident we've ran into.
> >
> > At some point we realized almost no new data was coming in the DB during
> > the day. We quickly looked and realized the following:
> >
> > * our application was still writing data, unaware that there any
> > issues on the DB end, like if nothing happened at all,
> > * the database was accepting connections (we were able to connect and
> > query),
> > * the database was writing regular text logs,
> > * the database was not writing new data to the tables,
> > * the logical DB replica actually had the expected records replicated
> > and present in the replica tables,
> > * so we made assumption original source WAL data existed and was
> > correct (given the fact logical DB is relying on WAL).
> >
> > We tried to restart the DB, but it would not come up. Instead, a few
> > core dumps in the postgres data folder were generated during our
> attempts.
> >
>
> Please inspect the core dumps using gdb and share the backtraces. There
> are instructions how to do that on the wiki:
>
> https://wiki.postgresql.org/wiki/Getting_a_stack_trace_of_
> a_running_PostgreSQL_backend_on_Linux/BSD
>
> > This is what we saw in the postgres logs:
> >
> > LOG: invalid resource manager ID 112 at 3/89005B10
> > LOG: invalid primary checkpoint record
> > LOG: invalid resource manager ID 138 at 3/89005208
> > LOG: invalid secondary checkpoint record
> > PANIC: could not locate a valid checkpoint record
> >
> >
> > To aid this we used pg_resetxlog. After running the pg_resetxlog
> > command, the DB successfully started and slowly began recovering the
> > data from WAL, automatically. During the recovery process, we ran VACUUM
> > ANALYSE couple of time, which seems to have somehow aided the speed of
> > recovery process (though I could have been a confirmation bias).
> >
>
> Firstly, I very much doubt using pg_resetxlog is a good idea, especially
> when it's rather unclear what was the actual root cause.
>
> Secondly, I don't quite understand what you mean by "recovery" here. The
> regular recovery process (say, after a crash) makes it impossible to
> connect to the database, so I'm not sure what you mean by running vacuum
> analyze (not to mention how it could have improved the recovery speed).
>
> > The DB was fully recovered in 30 minutes.
> >
> > Upon closer inspection, however, we realized we've lost two records from
> > a particular table. The records were replicated to logical replica
> > though, and further inspection showed their insertion timestamp sometime
> > during the day, long after the database supposedly stopped applying new
> > data from WAL to tables.
> >
> > We don't know the reason why these two records were gone (no DELETE
> > statements ever happen in the table in question). The records in
> > question existed in replica table, luckly.
> >
>
> Well, considering you did pg_resetxlog ... I'm surprised you only lost
> two records, but it's a question what state are the indexes in etc.
>
> > The logs for the entire day when the incident happened are available
> > here
> > <https://gist.githubusercontent.com/gmile/6df9ce393b11fb369856b84c4e9f75
> 5a/raw/5ab86c10332f9aef01abf16cb4989334bc7b02a2/postgresql.log> (1.6
> > Mb). Each log line was prepended with a timestamp. Also, we have the
> > core dumps that were generated during attempts to restart the database.
> >
>
> Man, that's an extremely noisy log file. There are errors caused by
> broken pg_hba.conf entries and so on, which makes it extremely difficult
> to look for possible other errors ... I'm not going to waste time by
> doing that.
>
> > My questions are:
> >
> > * what would be some typical reasons for primary/secondary WAL
> > checkpoints to fail? Disk issues? File system issues? OS issues? I'm
> > running out of ideas here.
> >
> > Is there any way I could separate primary and secondary checkpoints
> > in space, so to increase postgres's chances to restore one of them?
>
> I don't know. You have not provided any information about the storage
> system, and we don't have access to system logs that might show if
> something happened at this level. But in general yes, a storage issue
> might cause this.
>
> >
> > * how come postgresql would stop applying WAL logs to tables, and yet
> > keep silence? There was no indication WAL is not being applied,
> > postgres log would be silent (even though it kept writing other
> > commodity messages, such as "incomplete startup packet" and
> > malformed query attempts).
> >
> > Due to this, we noticed the issue only hours after postgres
> > supposedly stopped applying the WAL logs to tables.
> >
>
> It wouldn't. But it's unclear how you came to that conclusion.
>
> > * Is there any other log (like some lower level system log?) where I
> > could see the status of writing / reading / applying WAL segments?
> >
>
> There's only one log for PostgreSQL, so it would have to be in that file
> depending on the log level.
>
> > * What measures could be done to prevent this in future, or at least
> > make the situation easier to recover from (e.g. without data loss)?
> >
>
> The jury is still out on the root cause, so it's too soon to say.
>
>
> regards
>
> --
> Tomas Vondra http://www.2ndQuadrant.com
> PostgreSQL Development, 24x7 Support, Remote DBA, Training & Services
>

--
http://www.gmile.me