Re: postgresql.conf recommendations

[David Whittaker <dave@xxxxxxxxxx>]

Hi Josh,

On Wed, Feb 6, 2013 at 1:20 PM, Josh Krupka <jkrupka@xxxxxxxxx> wrote:

David,

Interesting observations.  I had not been tracking the interrupts but perhaps I should take a look.  How are you measuring them over a period of time, or are you just getting them real time? 

I initially saw it happen with vmstat, but now I'm collecting them every 5 minutes over SNMP with Cacti.

 

Did you turn off THP all together or just the THP defrag?

We disabled THP all together, with the thought that we might re-enable without defrag if we got positive results.  At this point I don't think THP is the root cause though, so I'm curious to see if anyone else gets positive results from disabling it.  We definitely haven't seen any performance hit from turning it off.

 

On Wed, Feb 6, 2013 at 10:42 AM, David Whittaker <dave@xxxxxxxxxx> wrote:

Josh/Johnny,

We've been seeing a similar problem as well, and had also figured THP was involved.  We found this in syslog: https://gist.github.com/davewhittaker/4723285, which led us to disable THP 2 days ago.  At first the results seemed good.  In particular, our issues always seemed interrupt related and the average interrupts/sec immediately dropped from 7k to around 3k after restarting.  The good news is that we didn't see any spike in system CPU time yesterday.  The bad news is that we did see a spike in app latency that originated from the DB, but now the spike is in user CPU time and seems to be spread across all of the running postgres processes.  Interrupts still blew up to 21k/sec when it happened.  We are still diagnosing, but I'd be curious to see if either of you get similar results from turning THP off.

On Tue, Feb 5, 2013 at 11:23 PM, Josh Krupka <jkrupka@xxxxxxxxx> wrote:

I've been looking into something on our system that sounds similar to what you're seeing.  I'm still researching it, but I'm suspecting the memory compaction that runs as part of transparent huge pages when memory is allocated... yet to be proven.  The tunable you mentioned controls the compaction process that runs at allocation time so it can try to allocate large pages, there's a separate one that controls if the compaction is done in khugepaged, and a separate one that controls whether THP is used at all or not (/sys/kernel/mm/transparent_hugepage/enabled, or perhaps different in your distro)

What's the output of this command?
egrep 'trans|thp|compact_' /proc/vmstat
compact_stall represents the number of processes that were stalled to do a compaction, the other metrics have to do with other parts of THP.  If you see compact_stall climbing, from what I can tell those might be causing your spikes.  I haven't found a way of telling how long the processes have been stalled. You could probably get a little more insight into the processes with some tracing assuming you can catch it quickly enough.  Running perf top will also show the compaction happening but that doesn't necessarily mean it's impacting your running processes.

On Tue, Feb 5, 2013 at 6:46 PM, Johnny Tan <johnnydtan@xxxxxxxxx> wrote:

# cat /sys/kernel/mm/redhat_transparent_hugepage/defrag 

[always] never

On Tue, Feb 5, 2013 at 5:37 PM, Josh Krupka <jkrupka@xxxxxxxxx> wrote:

Just out of curiosity, are you using transparent huge pages?

On Feb 5, 2013 5:03 PM, "Johnny Tan" <johnnydtan@xxxxxxxxx> wrote:

Server specs:

Dell R610

dual E5645 hex-core 2.4GHz

192GB RAM

RAID 1: 2x400GB SSD (OS + WAL logs)

RAID 10: 4x400GB SSD (/var/lib/pgsql)

/etc/sysctl.conf:

kernel.msgmnb = 65536

kernel.msgmax = 65536

kernel.shmmax = 68719476736

kernel.shmall = 4294967296

vm.overcommit_memory = 0

vm.swappiness = 0

vm.dirty_background_bytes = 536870912

vm.dirty_bytes = 536870912

postgresql.conf:

listen_addresses = '*' # what IP address(es) to listen on;

max_connections = 150 # (change requires restart)

shared_buffers = 48GB # min 128kB

work_mem = 1310MB # min 64kB

maintenance_work_mem = 24GB # min 1MB

wal_level = hot_standby # minimal, archive, or hot_standby

checkpoint_segments = 64 # in logfile segments, min 1, 16MB each

checkpoint_timeout = 30min # range 30s-1h

checkpoint_completion_target = 0.5 # checkpoint target duration, 0.0 - 1.0

max_wal_senders = 5 # max number of walsender processes

wal_keep_segments = 2000 # in logfile segments, 16MB each; 0 disables

hot_standby = on # "on" allows queries during recovery

max_standby_archive_delay = 120s # max delay before canceling queries

max_standby_streaming_delay = 120s # max delay before canceling queries

effective_cache_size = 120GB

constraint_exclusion = partition # on, off, or partition

log_destination = 'syslog' # Valid values are combinations of

logging_collector = on # Enable capturing of stderr and csvlog

log_directory = 'pg_log' # directory where log files are written,

log_filename = 'postgresql-%a.log' # log file name pattern,

log_truncate_on_rotation = on # If on, an existing log file with the

log_rotation_age = 1d # Automatic rotation of logfiles will

log_rotation_size = 0 # Automatic rotation of logfiles will

log_min_duration_statement = 500 # -1 is disabled, 0 logs all statements

log_checkpoints = on

log_line_prefix = 'user=%u db=%d remote=%r ' # special values:

log_lock_waits = on # log lock waits >= deadlock_timeout

autovacuum = on # Enable autovacuum subprocess?  'on'

log_autovacuum_min_duration = 0 # -1 disables, 0 logs all actions and

autovacuum_max_workers = 5 # max number of autovacuum subprocesses

datestyle = 'iso, mdy'

lc_messages = 'en_US.UTF-8' # locale for system error message

lc_monetary = 'en_US.UTF-8' # locale for monetary formatting

lc_numeric = 'en_US.UTF-8' # locale for number formatting

lc_time = 'en_US.UTF-8' # locale for time formatting

default_text_search_config = 'pg_catalog.english'

deadlock_timeout = 300ms

per pgtune:

#------------------------------------------------------------------------------

# pgtune wizard run on 2013-02-05

# Based on 198333224 KB RAM in the server

#------------------------------------------------------------------------------

default_statistics_target = 100

maintenance_work_mem = 1GB

checkpoint_completion_target = 0.9

effective_cache_size = 128GB

work_mem = 1152MB

wal_buffers = 8MB

checkpoint_segments = 16

shared_buffers = 44GB

max_connections = 80

We use pgbouncer (set to 140 connections) in transaction pooling mode in front of our db.

The problem:

For the most part, the server hums along. No other applications run on this server other than postgres. Load averages rarely break 2.0, it never swaps, and %iowait is usually not more than 0.12

But periodically, there are spikes in our app's db response time. Normally, the app's db response time hovers in the 100ms range for most of the day. During the spike times, it can go up to 1000ms or 1500ms, and the number of pg connections goes to 140 (maxed out to pgbouncer's limit, where normally it's only about 20-40 connections). Also, during these times, which usually last less than 2 minutes, we will see several thousand queries in the pg log (this is with log_min_duration_statement = 500), compared to maybe one or two dozen 500ms+ queries in non-spike times.

Inbetween spikes could be an hour, two hours, sometimes half a day. There doesn't appear to be any pattern that we can see:

* there are no obvious queries that are locking the db

* it doesn't necessarily happen during high-traffic times, though it can

* it doesn't happen during any known system, db, or app regularly-scheduled job, including crons

* in general, there's no discernible regularity to it at all

* it doesn't coincide with checkpoint starts or completions

* it doesn't coincide with autovacuums

* there are no messages in any system logs that might indicate any system or hardware-related issue

Besides spikes in our graphs, the only other visible effect is that %system in sar goes from average of 0.7 to as high as 10.0 or so (%iowait and all other sar variables remain the same).

And according to our monitoring system, web requests get queued up, and our alerting system sometimes either says there's a timeout or that it had multiple web response times greater than 300ms, and so we suspect (but have no proof) that some users will see either a long hang or possibly a timeout. But since it's almost always less than two minutes, and sometimes less than one, we don't really hear any complaints (guessing that most people hit reload, and things work again, so they continue on), and we haven't been able to see any negative effect ourselves.

But we want to get in front of the problem, in case it is something that will get worse as traffic continues to grow. We've tweaked various configs on the OS side as well as the postgresql.conf side. What's posted above is our current setup, and the problem persists.

Any ideas as to where we could even look?

Also, whether related or unrelated to the spikes, are there any recommendations for our postgresql.conf or sysctl.conf based on our hardware? From pgtune's output, I am lowering maintenance_work_mem from 24GB down to maybe 2GB, but I keep reading conflicting things about other settings, such as checkpoints or max_connections.

johnny