Disk Image Size Causing MySQL Crash?

I've recently migrated my server to a new Linode with 48GB of disk space. Over the past few days my DB has been crashing intermittently.

I've just noticed my disk storage is at 100% capacity with 256MB used up by Swap and the remaining used by my Ubuntu disk image. Could lowering the amount of memory available to my Ubuntu disk be helpful in preventing these crashes by freeing up RAM?

9 Replies

The storage allocated and the storage free in the Linode manager only indicates how much you have allocated for the Linode to potentially use. To find out how much disk space is actually used in Ubuntu you need to type:

df

Have you checked the MySQL and system logs to see if there are any errors in there indicating why the db server has crashed? Hard disk space and RAM are mutually exclusive (unless you're using a RAM disk or something non-Linode default).

I've been checking the MySQL logs. I'm not very familiar with reading failure logs but after addressing the SQL errors, most of what I've found looks to be reporting errors upon MySQL restart, like "function 'innodb' already exists." There's nothing in regards to what is triggering the shutdowns in the first place.

There is one error that is occasionally logged during restart regarding. It reports my server not being able allocate enough memory to InnoDB buffer pool, which is only set to the default 128.0M

About the quote below:
@The Other Air Force:

The storage allocated and the storage free in the Linode manager only indicates how much you have allocated for the Linode to potentially use.

Does this mean I should continue allocating 100% of my disk space to make full use of my Linode?

I keep all my disk space allocated. That way Ubuntu can use it.

Back to MySQL what are the results of:

> free -m

Is it actually the MySQL server that is having problems or is it the application that is trying to connect with it? Can you tell us exactly what error messages you are getting or what is leading you to believe that there is a problem with the server vs. the application?

I don't think there's anything wrong with the MySQL server, though there is a chance I defined less than optimal configs in the my.cnf config file. I used Percona Config Wizard (https://tools.percona.com/wizard)

The application itself isn't very memory efficient. It's a Wordpress theme that uses some inefficient queries to access a fairly large database. But the site wasn't crashing with nearly as much frequency on my previous Linode, which was much smaller and running only a 32 bit instance of MySQL. This suggests to me that the problem is in my server configs.

Below is what free -m returns. Note I've moved 100MB to Swap since my original post.

                         total       used       free     shared    buffers     cached
Mem:                     1992        917       1075         26         10        200
-/+ buffers/cache:        706       1285
Swap:                    351          0          351

I should also note, DB crashes were exacerbated even more when I switched all my DB tables from MyISAM to InnoDB two days ago. I've since switched back to MyISAM but the DB is still crashing with the same regularity.

What's the contents of /var/log/syslog when it crashes. Is anything else running on the server i.e. apache?

I checks syslog after a fresh crash this afternoon. I see that oom-killer kicked in

Feb 10 15:27:13 mylinode kernel: apache2 invoked oom-killer: gfp_mask=0x200da, order=0, oom_score_adj=0

The previous entry was logged 2 minutes prior

Feb 10 15:25:01 mylinode CRON[5655]: (root) CMD (command -v debian-sa1 > /dev/null && debian-sa1 1 1)

I don't think this is the issue though, because if I'm reading the log file correctly, it looks like I have an absurd amount of Apache2 processes running. Monitoring my server using 'top', I typically only see 1-5 Apache processes running at a time.

Feb 10 15:27:13 mylinode kernel: 16126 pages reserved
Feb 10 15:27:13 mylinode kernel: [ pid ]   uid  tgid total_vm      rss nr_ptes swapents oom_score_adj name
Feb 10 15:27:13 mylinode kernel: [ 1456]     0  1456     5071        1      14      273             0 upstart-udev-br
Feb 10 15:27:13 mylinode kernel: [ 1461]     0  1461    12325        1      27      145         -1000 systemd-udevd
Feb 10 15:27:13 mylinode kernel: [ 2444]     0  2444     2560        0       6      573             0 dhclient
Feb 10 15:27:13 mylinode kernel: [ 2649]   102  2649     9781        1      23       88             0 dbus-daemon
Feb 10 15:27:13 mylinode kernel: [ 2727]     0  2727    10865       13      27       69             0 systemd-logind
Feb 10 15:27:13 mylinode kernel: [ 2736]     0  2736    15343       28      32      142         -1000 sshd
Feb 10 15:27:13 mylinode kernel: [ 2738]     0  2738     4787        0      13       43             0 atd
Feb 10 15:27:13 mylinode kernel: [ 2739]     0  2739     5916       23      16       43             0 cron
Feb 10 15:27:13 mylinode kernel: [ 2753]   101  2753    63963       77      27       89             0 rsyslogd
Feb 10 15:27:13 mylinode kernel: [ 2817]     0  2817     3920        1      13      146             0 upstart-file-br
Feb 10 15:27:13 mylinode kernel: [ 2819]     0  2819     4015        0      13      263             0 upstart-socket-
Feb 10 15:27:13 mylinode kernel: [ 2821]   105  2821   472444    47076     358    87305             0 mysqld
Feb 10 15:27:13 mylinode kernel: [ 2867]     0  2867    24659       53      47      390             0 sendmail-mta
Feb 10 15:27:13 mylinode kernel: [ 3158]     0  3158    78253     2750      90        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 3187]     0  3187    66396     1780      31        0             0 fail2ban-server
Feb 10 15:27:13 mylinode kernel: [ 3229]     0  3229     3199       40      11        0             0 getty
Feb 10 15:27:13 mylinode kernel: [ 3345]   103  3345     7863      150      20        0             0 ntpd
Feb 10 15:27:13 mylinode kernel: [ 3368]     0  3368    26446      273      53        0             0 sshd
Feb 10 15:27:13 mylinode kernel: [ 3404]  1000  3404    26446      271      52        0             0 sshd
Feb 10 15:27:13 mylinode kernel: [ 3405]  1000  3405     5563      420      16        0             0 bash
Feb 10 15:27:13 mylinode kernel: [ 4307]    33  4307    80672    12282     109        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 4343]    33  4343   116884    48398     180        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 4433]    33  4433    84282    16034     117        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 4440]    33  4440    83661    16264     116        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 4457]    33  4457    81064    12773     110        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 4458]    33  4458    83032    14720     114        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 4466]    33  4466    87206    18817     121        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 4503]    33  4503   113967    46300     178        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 4505]    33  4505    85272    16833     118        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 4512]    33  4512    85312    17147     120        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 4565]    33  4565    95000    26641     136        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 4566]    33  4566    84041    15744     117        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 4626]    33  4626    84444    16130     117        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 4732]    33  4732    95024    27384     139        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 5056]    33  5056    79887    11825     108        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 5283]    33  5283    81158    12768     109        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 5284]    33  5284    79773     8968     103        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 5285]    33  5285    81363    10349     106        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 5286]    33  5286    81152    12778     109        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 5330]    33  5330    81157    12702     109        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 5331]    33  5331    82528    14922     114        0             0 apache2
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Feb 10 15:27:13 mylinode kernel: [ 5373]    33  5373    81144    12785     109        0             0 apache2
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Feb 10 15:27:13 mylinode kernel: [ 5864]    33  5864    79600     8081     100        0             0 apache2
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Feb 10 15:27:13 mylinode kernel: [ 5899]    33  5899    78308     1476      84        0             0 apache2
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Feb 10 15:27:13 mylinode kernel: [ 5902]    33  5902    78533     2140      87        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 5905]    33  5905    78308     1538      84        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 5908]    33  5908    78308     1470      84        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 5909]    33  5909    78308     1470      84        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 5910]    33  5910    78267     1453      81        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 5912]     0  5912    78255     1444      78        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 5913]    33  5913    78259     1446      80        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 5914]    33  5914    78259     1446      80        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 5915]    33  5915    78271     1462      84        0             0 apache2
Feb 10 15:27:13 mylinode kernel: [ 5916]    33  5916    78265     1451      80        0             0 apache2
Feb 10 15:27:13 mylinode kernel: Out of memory: Kill process 2821 (mysqld) score 224 or sacrifice child

Yep apache's the problem the Ubuntu defaults are insane. Search the forums for MaxClients. For a 2GB node you'll want no more than 10 MaxClients, you'll also want to set KeepAlives < 3 seconds or even turn them off.

Thanks obs. I've began sizing down my maxclients as suggested, though not yet to only 10. I remember now setting apache2.conf according to the specs suggested in this article ~~[https://www.linode.com/docs/websites/hosting-a-website#optimizing-apache-for-a-linode-1gb" target="_blank">](https://www.linode.com/docs/websites/ho … linode-1gb">https://www.linode.com/docs/websites/hosting-a-website#optimizing-apache-for-a-linode-1gb](

I have also taken your suggestion and turned keepAlive off. Though does this now mean that every CSS file and every image request will now need to spawn a new Apache thread?

Also, about my previous syslog excerpt. My previous MaxKeepAliveTimeout was 5 sec which is fairly generous, so does the number of Apache processes typically suggest bot activity or a DNS type of attack? For my site to get that many new HTTP requests simultaneously doesn't seem normal.

Thanks obs and Other Air Force for your time so far!

That doc says 80 MaxClients which is very high for a 2GB node if you could allocate every bit of ram to apache that would be 25.6MB per process. If you're using mod_php then that's no where near enough, especially if you're running MySQL along side it. If you set it to 10 and say you can allocate 1GB to apache then you'd get a little over 100MB per process, which may not be enough depending on your site, although looking at your ps output 10 should be fine.

When someone requests a resource from your site keep alives keep the connection open for x number of seconds so that subsequent requests can use the same connection, however this means the process can't serve someone else. With keep alives off each resource uses a new connection. The best settings will depend on what you're serving, if your pages have a lot of files then keep alives can be useful if you're serving downloads then there's not much point.

The number of processes just means you had a traffic burst, could simply be google crawling your site, you'd have to check your access logs.

I created a pull request to update the docs.

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