"Leaking" disk space on FreeBSD servers

Did you do a detailed du during the supposed problem and after the reboot and make a diff of those
to fimd any invlolved files/dirs?
That said, i think you might consider posting on freebsd-[questions|stable] as well.

On Τετ 20 Μαρ 2013 11:49:07 Dan Thomas wrote:

Hi Guys,

We're seeing a problem with some of our FreeBSD/PostgreSQL servers "leaking" quite significant amounts of disk space:

df -h /usr/local/pgsql/

Filesystem Size Used Avail Capacity Mounted on
/dev/mfid1s1d 1.1T 772G 222G 78% /usr/local/pgsql

du -sh /usr/local/pgsql/

741G /usr/local/pgsql/

Stopping Postgres doesn't fix it, but rebooting does which points at the OS rather than PG to me. However, the leak is only apparent in the dedicated pgsql partition, and only on our database servers, so PostgreSQL seems to at least be involved. The partition itself is a relatively standard UFS partition:

grep /usr/local/pgsql /etc/fstab

/dev/mfid1s1d /usr/local/pgsql ufs rw 2 2

tunefs -p /usr/local/pgsql/

tunefs: POSIX.1e ACLs: (-a) disabled
tunefs: NFSv4 ACLs: (-N) disabled
tunefs: MAC multilabel: (-l) disabled
tunefs: soft updates: (-n) enabled
tunefs: gjournal: (-J) disabled
tunefs: trim: (-t) disabled
tunefs: maximum blocks per file in a cylinder group: (-e) 2048
tunefs: average file size: (-f) 16384
tunefs: average number of files in a directory: (-s) 64
tunefs: minimum percentage of free space: (-m) 8%
tunefs: optimization preference: (-o) time
tunefs: volume label: (-L)

LSOF isn't showing any open files:

lsof +L /usr/local/pgsql/ | awk '{ print $8 }' | grep 0 | wc -l

0

We're not creating filesystem snapshots:

find /usr/local/pgsql/ -flags snapshot

Not all of our servers are leaking space, it's only the more recently-installed systems. Here's a quick breakdown of versions:

FreeBSD PostgreSQL Leaking?
8.0 8.4.4 no
8.2 9.0.4 no
8.3 9.1.4 yes
8.3 9.2.3 yes
9.1 9.2.3 yes

Each of these servers is configured with a warm standby, so we've been switching them over to the standby to reclaim the space (rebooting the primary is too much downtime). The standby does *not* demonstrate this problem while it's being used as a standby, but it starts leaking space once it's been made the primary.

Initially I thought this might be related to WAL files, however the pg_xlog dir is symlinked outside of the /usr/local/pgsql partition that is demonstrating this problem:

ll /usr/local/pgsql/data/pg_xlog

lrwxr-xr-x 25B Oct 19 10:48 pg_xlog -> /usr/local/pglog/pg_xlog/

I've exhausted everything I can think of to try to solve this one. Has anyone got any ideas on how to go about debugging this?

Thanks,

Dan

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IT DEV
IT DEPT
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Did you do a detailed du during the supposed problem and after the reboot and make a diff of those to fimd any invlolved files/dirs?

du doesn't show the space in question (du -s shows the actual usage on
disk, df is showing a much higher number), so I doubt this will show
anything up. However, next reboot I'll certainly do that.

That said, i think you might consider posting on freebsd-[questions|stable] as well.

Yes I think that might be a good plan :)

Dan

On 20 March 2013 12:30, Achilleas Mantzios <achill@matrix.gatewaynet.com> wrote:

Did you do a detailed du during the supposed problem and after the reboot
and make a diff of those

to fimd any invlolved files/dirs?

That said, i think you might consider posting on freebsd-[questions|stable]
as well.

On Τετ 20 Μαρ 2013 11:49:07 Dan Thomas wrote:

Hi Guys,

We're seeing a problem with some of our FreeBSD/PostgreSQL servers "leaking"
quite significant amounts of disk space:

df -h /usr/local/pgsql/

Filesystem Size Used Avail Capacity Mounted on
/dev/mfid1s1d 1.1T 772G 222G 78% /usr/local/pgsql

du -sh /usr/local/pgsql/

741G /usr/local/pgsql/

Stopping Postgres doesn't fix it, but rebooting does which points at the OS
rather than PG to me. However, the leak is only apparent in the dedicated
pgsql partition, and only on our database servers, so PostgreSQL seems to at
least be involved. The partition itself is a relatively standard UFS
partition:

grep /usr/local/pgsql /etc/fstab

/dev/mfid1s1d /usr/local/pgsql ufs rw 2 2

tunefs -p /usr/local/pgsql/

tunefs: POSIX.1e ACLs: (-a) disabled
tunefs: NFSv4 ACLs: (-N) disabled
tunefs: MAC multilabel: (-l) disabled
tunefs: soft updates: (-n) enabled
tunefs: gjournal: (-J) disabled
tunefs: trim: (-t) disabled
tunefs: maximum blocks per file in a cylinder group: (-e) 2048
tunefs: average file size: (-f) 16384
tunefs: average number of files in a directory: (-s) 64
tunefs: minimum percentage of free space: (-m) 8%
tunefs: optimization preference: (-o) time
tunefs: volume label: (-L)

LSOF isn't showing any open files:

lsof +L /usr/local/pgsql/ | awk '{ print $8 }' | grep 0 | wc -l

0

We're not creating filesystem snapshots:

find /usr/local/pgsql/ -flags snapshot

Not all of our servers are leaking space, it's only the more
recently-installed systems. Here's a quick breakdown of versions:

FreeBSD PostgreSQL Leaking?
8.0 8.4.4 no
8.2 9.0.4 no
8.3 9.1.4 yes
8.3 9.2.3 yes
9.1 9.2.3 yes

Each of these servers is configured with a warm standby, so we've been
switching them over to the standby to reclaim the space (rebooting the
primary is too much downtime). The standby does *not* demonstrate this
problem while it's being used as a standby, but it starts leaking space once
it's been made the primary.

Initially I thought this might be related to WAL files, however the pg_xlog
dir is symlinked outside of the /usr/local/pgsql partition that is
demonstrating this problem:

ll /usr/local/pgsql/data/pg_xlog

lrwxr-xr-x 25B Oct 19 10:48 pg_xlog -> /usr/local/pglog/pg_xlog/

I've exhausted everything I can think of to try to solve this one. Has
anyone got any ideas on how to go about debugging this?

Thanks,

Dan

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IT DEV

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On Τετ 20 Μαρ 2013 12:47:39 Dan Thomas wrote:

Did you do a detailed du during the supposed problem and after the reboot and make a diff of those to fimd any invlolved files/dirs?

du doesn't show the space in question (du -s shows the actual usage on
disk, df is showing a much higher number), so I doubt this will show
anything up. However, next reboot I'll certainly do that.

du (without -s) shows the whole hierarchy, du -s behaves like du -d 0,
so at this point diff the output of (plain) su is definitely somth worth doing.

That said, i think you might consider posting on freebsd-[questions|stable] as well.

Yes I think that might be a good plan :)

Dan

On 20 March 2013 12:30, Achilleas Mantzios <achill@matrix.gatewaynet.com> wrote:

Did you do a detailed du during the supposed problem and after the reboot
and make a diff of those

to fimd any invlolved files/dirs?

That said, i think you might consider posting on freebsd-[questions|stable]
as well.

On Τετ 20 Μαρ 2013 11:49:07 Dan Thomas wrote:

Hi Guys,

We're seeing a problem with some of our FreeBSD/PostgreSQL servers "leaking"
quite significant amounts of disk space:

df -h /usr/local/pgsql/

Filesystem Size Used Avail Capacity Mounted on
/dev/mfid1s1d 1.1T 772G 222G 78% /usr/local/pgsql

du -sh /usr/local/pgsql/

741G /usr/local/pgsql/

Stopping Postgres doesn't fix it, but rebooting does which points at the OS
rather than PG to me. However, the leak is only apparent in the dedicated
pgsql partition, and only on our database servers, so PostgreSQL seems to at
least be involved. The partition itself is a relatively standard UFS
partition:

grep /usr/local/pgsql /etc/fstab

/dev/mfid1s1d /usr/local/pgsql ufs rw 2 2

tunefs -p /usr/local/pgsql/

tunefs: POSIX.1e ACLs: (-a) disabled
tunefs: NFSv4 ACLs: (-N) disabled
tunefs: MAC multilabel: (-l) disabled
tunefs: soft updates: (-n) enabled
tunefs: gjournal: (-J) disabled
tunefs: trim: (-t) disabled
tunefs: maximum blocks per file in a cylinder group: (-e) 2048
tunefs: average file size: (-f) 16384
tunefs: average number of files in a directory: (-s) 64
tunefs: minimum percentage of free space: (-m) 8%
tunefs: optimization preference: (-o) time
tunefs: volume label: (-L)

LSOF isn't showing any open files:

lsof +L /usr/local/pgsql/ | awk '{ print $8 }' | grep 0 | wc -l

0

We're not creating filesystem snapshots:

find /usr/local/pgsql/ -flags snapshot

Not all of our servers are leaking space, it's only the more
recently-installed systems. Here's a quick breakdown of versions:

FreeBSD PostgreSQL Leaking?
8.0 8.4.4 no
8.2 9.0.4 no
8.3 9.1.4 yes
8.3 9.2.3 yes
9.1 9.2.3 yes

Each of these servers is configured with a warm standby, so we've been
switching them over to the standby to reclaim the space (rebooting the
primary is too much downtime). The standby does *not* demonstrate this
problem while it's being used as a standby, but it starts leaking space once
it's been made the primary.

Initially I thought this might be related to WAL files, however the pg_xlog
dir is symlinked outside of the /usr/local/pgsql partition that is
demonstrating this problem:

ll /usr/local/pgsql/data/pg_xlog

lrwxr-xr-x 25B Oct 19 10:48 pg_xlog -> /usr/local/pglog/pg_xlog/

I've exhausted everything I can think of to try to solve this one. Has
anyone got any ideas on how to go about debugging this?

Thanks,

Dan

-

Achilleas Mantzios

IT DEV

IT DEPT

Dynacom Tankers Mgmt

-
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IT DEV
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On Wed, Mar 20, 2013 at 7:49 AM, Dan Thomas <godders@gmail.com> wrote:

Not all of our servers are leaking space, it's only the more
recently-installed systems. Here's a quick breakdown of versions:

FWIW, I do not observe this behavior. My database has very heavy write
load, and old data is purged after it is aged about 7 months, so I do get
lots of fragmentation. However, I do not have any disk space "phantom" loss.

How long does it take for you to accumulate this "leak"? My first instinct
is that you have unlinked files still referenced by some application. That
is really the only way you get these discrepancies. lsof *should* have
showed them to you. Try fstat in case there's some bug in lsof.

Also, your tunefs output seems to be not from FreeBSD 9.1. Specifically, it
is not emitting this line:

tunefs: soft update journaling: (-j) disabled

It is a very useful option to turn on for large file systems. I can recover
a 6TB file system in about 5 seconds on a crash reboot with that on.

[root@d04]# ps axuw34214
USER PID %CPU %MEM VSZ RSS TT STAT STARTED TIME COMMAND
pgsql 34214 0.0 0.5 5426964 154484 0- S 28Feb13 1:30.66
/usr/local/bin/postgres -D /u/data/postgres
[root@d04]# df -h /u/data
Filesystem Size Used Avail Capacity Mounted on
/dev/ufs/ramdisk 707G 137G 513G 21% /u/data
[root@d04]# du -sh /u/data
137G /u/data
[root@d04]# uname -a
FreeBSD d04.m1e.net 9.1-RELEASE FreeBSD 9.1-RELEASE #1 r243808: Mon Dec 3
09:56:27 EST 2012
vivek@lorax.kcilink.com:/usr/obj/u/lorax1/usr9/src/sys/KCI64
amd64
[root@d04]# uptime
9:50AM up 74 days, 17:36, 1 user, load averages: 0.21, 0.18, 0.17
[root@d04]# psql --version
psql (PostgreSQL) 9.2.3
[root@d04]#

regarding journaling, there is the counter argument that you do not need to do the same job twice,
in the sense that we already spend a considerable amount of time retaining the WAL in postgresql,
no need to redo the same on FS level.
"Crush"-intensive systems (for lack of a better word) might benefit from FS journaling, but the
best option here is try and find the cause. FreeBSD systems are supposed to not crush,
that's why ppl use them in the first place.

On Τετ 20 Μαρ 2013 10:11:58 Vick Khera wrote:

On Wed, Mar 20, 2013 at 7:49 AM, Dan Thomas <godders@gmail.com> wrote:

Not all of our servers are leaking space, it's only the more recently-installed systems. Here's a quick breakdown of versions:

FWIW, I do not observe this behavior. My database has very heavy write load, and old data is purged after it is aged about 7 months, so I do get lots of fragmentation. However, I do not have any disk space "phantom" loss.

How long does it take for you to accumulate this "leak"? My first instinct is that you have unlinked files still referenced by some application. That is really the only way you get these discrepancies. lsof *should* have showed them to you. Try fstat in case there's some bug in lsof.

Also, your tunefs output seems to be not from FreeBSD 9.1. Specifically, it is not emitting this line:

tunefs: soft update journaling: (-j) disabled

It is a very useful option to turn on for large file systems. I can recover a 6TB file system in about 5 seconds on a crash reboot with that on.

[root@d04]# ps axuw34214
USER PID %CPU %MEM VSZ RSS TT STAT STARTED TIME COMMAND
pgsql 34214 0.0 0.5 5426964 154484 0- S 28Feb13 1:30.66 /usr/local/bin/postgres -D /u/data/postgres
[root@d04]# df -h /u/data
Filesystem Size Used Avail Capacity Mounted on
/dev/ufs/ramdisk 707G 137G 513G 21% /u/data
[root@d04]# du -sh /u/data
137G /u/data
[root@d04]# uname -a
FreeBSD d04.m1e.net 9.1-RELEASE FreeBSD 9.1-RELEASE #1 r243808: Mon Dec 3 09:56:27 EST 2012 vivek@lorax.kcilink.com:/usr/obj/u/lorax1/usr9/src/sys/KCI64 amd64
[root@d04]# uptime
9:50AM up 74 days, 17:36, 1 user, load averages: 0.21, 0.18, 0.17
[root@d04]# psql --version
psql (PostgreSQL) 9.2.3
[root@d04]#

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On Wed, Mar 20, 2013 at 10:34 AM, Achilleas Mantzios <
achill@matrix.gatewaynet.com> wrote:

regarding journaling, there is the counter argument that you do not need
to do the same job twice,

in the sense that we already spend a considerable amount of time retaining
the WAL in postgresql,

no need to redo the same on FS level.

There's a difference in the file system integrity and the DB integrity. PG
will keep the DB integrity just fine without the file system journaling.
The journaling just makes recovery from crash that much faster. ie,
running fsck on 6TB of disk storage takes a LONG time, sometimes hours, but
with the journal enabled, it takes a few seconds.

Of course, but does it make sense for you to pay the ~ 5%/day performance penalty for the ~0.5%/year chance of having your system crush?
Unless your FreeBSD server is stuffed with exotic gamer hardware, i don't see the likehood of crush getting larger than that.

On Τετ 20 Μαρ 2013 10:39:58 Vick Khera wrote:

On Wed, Mar 20, 2013 at 10:34 AM, Achilleas Mantzios <achill@matrix.gatewaynet.com> wrote:

regarding journaling, there is the counter argument that you do not need to do the same job twice,
in the sense that we already spend a considerable amount of time retaining the WAL in postgresql,
no need to redo the same on FS level.

There's a difference in the file system integrity and the DB integrity. PG will keep the DB integrity just fine without the file system journaling. The journaling just makes recovery from crash that much faster. ie, running fsck on 6TB of disk storage takes a LONG time, sometimes hours, but with the journal enabled, it takes a few seconds.

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IT DEV
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How long does it take for you to accumulate this "leak"?

It grows at between 2 and 4 gigabytes per day on average. It seems to
be related to load on the database, as it grows slower over the
weekends when the servers are under less load. Here's a graph that
shows growth of one server (from reboot to about ~30gb difference)
over the last couple of weeks:
http://i.imgur.com/AwzQ46j.png

The flatter parts are the weekends, but otherwise it's reasonably constant.

That is really the only way you get these discrepancies. lsof *should* have showed them to you.
Try fstat in case here's some bug in lsof.

After a bit of messing around with fstat and find (it doesn't make it
easy!) I've confirmed all the inodes fstat is reporting exist on disk,
which backs up lsof. I also confirmed both lsof and fstat were
detecting unlinked files by manually holding a file open and unlinking
it. Can't see much evidence that it's an open file.

Also, your tunefs output seems to be not from FreeBSD 9.1

That example was from an 8.3 machine (it's the one I'm testing with as
it's got the biggest disk usage deficit). The 9.1 box has this:

tunefs: soft update journaling: (-j) enabled

..but is still exhibiting this behaviour.

FWIW, I do not observe this behaviour

We actually have another FreeBSD8.3/PG9.1 machine under different (but
similar) load that *doesn't* demonstrate this behaviour. There's
nothing obvious in the differences in usage patterns that we can see
(we're not using any exotic features or anything), but it certainly
suggests that it's *something* related to PG or our usage of it.

On 20 March 2013 14:11, Vick Khera <vivek@khera.org> wrote:

On Wed, Mar 20, 2013 at 7:49 AM, Dan Thomas <godders@gmail.com> wrote:

Not all of our servers are leaking space, it's only the more
recently-installed systems. Here's a quick breakdown of versions:

FWIW, I do not observe this behavior. My database has very heavy write load,
and old data is purged after it is aged about 7 months, so I do get lots of
fragmentation. However, I do not have any disk space "phantom" loss.

How long does it take for you to accumulate this "leak"? My first instinct
is that you have unlinked files still referenced by some application. That
is really the only way you get these discrepancies. lsof *should* have
showed them to you. Try fstat in case there's some bug in lsof.

Also, your tunefs output seems to be not from FreeBSD 9.1. Specifically, it
is not emitting this line:

tunefs: soft update journaling: (-j) disabled

It is a very useful option to turn on for large file systems. I can recover
a 6TB file system in about 5 seconds on a crash reboot with that on.

[root@d04]# ps axuw34214
USER PID %CPU %MEM VSZ RSS TT STAT STARTED TIME COMMAND
pgsql 34214 0.0 0.5 5426964 154484 0- S 28Feb13 1:30.66
/usr/local/bin/postgres -D /u/data/postgres
[root@d04]# df -h /u/data
Filesystem Size Used Avail Capacity Mounted on
/dev/ufs/ramdisk 707G 137G 513G 21% /u/data
[root@d04]# du -sh /u/data
137G /u/data
[root@d04]# uname -a
FreeBSD d04.m1e.net 9.1-RELEASE FreeBSD 9.1-RELEASE #1 r243808: Mon Dec 3
09:56:27 EST 2012
vivek@lorax.kcilink.com:/usr/obj/u/lorax1/usr9/src/sys/KCI64 amd64
[root@d04]# uptime
9:50AM up 74 days, 17:36, 1 user, load averages: 0.21, 0.18, 0.17
[root@d04]# psql --version
psql (PostgreSQL) 9.2.3
[root@d04]#

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On Ôåô 20 Ìáñ 2013 15:15:23 Dan Thomas wrote:

We actually have another FreeBSD8.3/PG9.1 machine under different (but
similar) load that *doesn't* demonstrate this behaviour. There's
nothing obvious in the differences in usage patterns that we can see
(we're not using any exotic features or anything), but it certainly
suggests that it's *something* related to PG or our usage of it.

Any difference in the architecture of the two systems? (x86, amd64, etc..)
Any difference in the respective output of
% pg_config
?

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Any difference in the architecture of the two systems? (x86, amd64, etc..)
Any difference in the respective output of
% pg_config

Alas, no. Both identical machines running identical versions of
FreeBSD and PG. pg_config on the two machines matches exactly.

On 20 March 2013 15:37, Achilleas Mantzios <achill@matrix.gatewaynet.com> wrote:

On Ôåô 20 Ìáñ 2013 15:15:23 Dan Thomas wrote:

We actually have another FreeBSD8.3/PG9.1 machine under different (but
similar) load that *doesn't* demonstrate this behaviour. There's
nothing obvious in the differences in usage patterns that we can see
(we're not using any exotic features or anything), but it certainly
suggests that it's *something* related to PG or our usage of it.

Any difference in the architecture of the two systems? (x86, amd64, etc..)
Any difference in the respective output of
% pg_config
?

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Dan Thomas <godders@gmail.com> wrote:

We're seeing a problem with some of our FreeBSD/PostgreSQL
servers "leaking" quite significant amounts of disk space:

Stopping Postgres doesn't fix it, but rebooting does which points
at the OS rather than PG to me. However, the leak is only
apparent in the dedicated pgsql partition, and only on our
database servers, so PostgreSQL seems to at least be involved.
The partition itself is a relatively standard UFS partition:

I saw something once which *might* be related.  I don't recall the
OS of FS involved, but in an attempt to reduce the fragmentation of
files which started small and eventually grew large, a large
allocation of contiguous space was made on file creation, and that
space was not release as long as any page for the file remained in
the OS cache.  In the instance where I saw the problem, autovacuum
had been turned off and the instance was just coming up on the
point where wraparound prevention runs were about to be triggered.
pg_clog was where most of the wasted space was.

No guarantees that this is the issue, but it sounded similar....

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On 03/20/2013 01:25 PM, Kevin Grittner wrote:

I saw something once which *might* be related. I don't recall the
OS of FS involved, but in an attempt to reduce the fragmentation of
files which started small and eventually grew large, a large
allocation of contiguous space was made on file creation, and that
space was not release as long as any page for the file remained in
the OS cache.

That was an optimization decision made for XFS in recent kernels, and
the chunks it grabs are very, very large. We had to reduce the default
allocation size to 1MB to disable the elastic allocation system. In the
end, we regained about 50GB of "phantom" space after a re-mount, and
it's stayed that way since.

But that's what du --apparent-size is for. :)

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