The FreeBSD Diary

set /kernel: pid 801 (mysqld), uid 88 on /var: file system full

Hmmm, mysqld ran out of space on /var.  That's not nice.

Over a 36 hour period, the FreshPorts webserver ran out of space on /var four times.  This effectively ground the server to a halt.  Incoming http requests could not be answered and the database queries were failing.  To say the least, I was not amused.  Once is annoying, twice is frustrating, etc.

This little article documents that incident and shows the solution I came up with.

/var: file system full

I also noticed that logcheck was giving me messages such as this:

set /kernel: pid 801 (mysqld), uid 88 on /var: file system full
set sendmail[89053]: NOQUEUE: low on space (have 89, SMTP-DAEMON 
                                 needs 101 in /var/spool/mqueue)

Hmmm, /var?  Why is that full?

I had a look around /var, first checking /var/log.  Nothing unusual there.  Then I did this:

# cd /var
# ls -lt | head

The resulting listing had /var/tmp at the top of the list.  That said to me that /var/tmp was the last directory written to.  So I inspected that directory:

# cd /var/tmp
# ls
SQL1b07_0.ISD   SQL1b0d_0.ISM   SQL1b11_0.ISD   SQL1b15_0.ISM
SQL1b07_0.ISM   SQL1b0f_0.ISD   SQL1b11_0.ISM
SQL1b0d_0.ISD   SQL1b0f_0.ISM   SQL1b15_0.ISD

That's odd.  Why are those files there?  By this time, I was convinced it was mysqld which was having trouble.  But I didn't know why.  I knew I had to free up space.  So I stopped apache and then mysqld:

# /usr/local/sbin/apachectl stop
# mysqladmin -u root -p shutdown
Enter password:

After that, the /var/tmp files, mentioned above, disappeared.  Good.   That's that fixed.  Famous last words.

I restarted mysqld and then apache:

# /usr/local/etc/rc.d/mysqld.sh
# /usr/local/sbin/apachectl start

I noted that /var utilization was still down at 15%. Good.

Have a look at /var/log and you'll also find the following files:

• messages - system messages
• maillog - mail log

As I mentioned above, your apache logs are also stored in /var/log, but I've changed that default. My apache logs are stored on another volume, for convenience.

Also note, log files can be rotated; see man newsyslog and Apache - rotating log files.

What are the implications if /var fills up?  It means the system was unable to do anything.  It had no space to write logs, no where to spool incoming mail.  Effectively, it was halted.

About 20 minutes later, I noticed /var was back up to 50%.  I checked the logs to see what was happening.  Again, nothing jumped out at me.  I shoved the probable cause of this problem into the background and went on to answer email.

Eventually, the more complex database queries came to mind.  I started playing with some of the web pages while keeping an eye on /var/tmp.  Eventually I found a web page which would caused files to be created in /var/tmp.  One of my those queries quickly took /var to 50%.  I started to wonder what would happen if a couple of these queries were launched concurrently or coincided with an incoming port commit.  I'll bet that would be enough to fill up /var/tmp.   There and then I decided I needed more /var.

Filesystem   1K-blocks     Used    Avail Capacity  Mounted on
/dev/ad0s1e      19815     2778    15452    15%    /var

That's not a great deal of space. Only about 15MB free.  So I decided to give it some more space.  Luckily, I had lots of spare disk, some of which was extremely underutilized.  The plan was to change the mount point for /var to another drive. This must be done with care as a running system actually needs and uses /var dynamically. You shouldn't just umount /var and mount it somewhere else.

Here are my before and after images of /etc/fstab:

/dev/ad0s1e  /var        ufs     rw              2       2
/dev/da1s1   /usr3       ufs     rw              2       2

I changed this to:

/dev/ad0s1e  /var-old    ufs     rw              2       2
/dev/da1s1   /var        ufs     rw              2       2

This means that the new /var will be where /usr3 once was. The original /var will available under /var-old, just in case I need to view it.

But I did not reboot, nor did I mount or umount anything yet.   The above could have been done in single user mode, but I decided to do it from my nice GUI client where I could easily cut and paste.

These changes ensure that on the next reboot, the system will mount the proper volumes in the right places.

In the next step, we'll get the old /var over to the new location.  And we'll do that from single user mode.

shutdown now

to do this:

# cp -Rp /var /usr3

I did a copy because I wanted to keep the original files in the old location, just in case.  I could have done a mv instead of a cp, but I chose not to.  The above command copied everything from the existing /var to the new location.  Then I umounted the existing mount points:

# umount /var
# umount /usr3

and umounted the new ones:

# mount /var
# mount /var-old

I verified that the mounts had succeeded by viewing the output of mount.

This showed that the /dev/da1s1 was mounted as /var and that /dev/ad0s1e was mounted as /var-old.  Which is exactly what I needed.

# exit

An exit (a CONTROL-D will also work) from single user mode will take you back to multi-user mode.

Side note: the next day, I checked my uptime:

# uptime
10:32PM  up 33 days, 12 mins, 2 users, load averages: 0.18, 0.20, 
                                                             0.15

The moral: dropping to single user mode does not affect your uptime.

A side effect is that the box seems to be a faster. Mind you, this may just be my perception and there has been no actual improvement. But, theoretically, by putting /var on its own SCSI disk, speed can be increased.  One disk can be writing data to /var while the other is reading the database files on /usr.

My theory is that I've always had those SQL files created in /var/tmp, but they've never gotten to such a large size. Perhaps as more and more new ports have been added to the FreshPorts database, a larger temp file is needed for particular types of updates.  And it is merely coincidence that these /var peaks have just started reaching the capacity of the disk.

As always, should you or any of your IM force be caught or killed with more information about the above, your comments will be appreciated.

They all mentioned setting TMPDIR to a different location, say /usr4/tmp and restarting mysqld.