Hi there,

First of all, let me say that I'm a web developer and have very limited knowledge on server management but am a fast learner, so I've done a lot of research on what needs to be done to fix this issue, but I can't for the life of me figure it out.

So I started noticing that every 2 hours or so, the server "reboots" itself for a few minutes to the point where even linode graphs are showing the gap. There is an actual gap and not that the statistics have dropped to zero. Here's the screenshot - notice the two hour gaps between 5am onwards:



Before this, as you can see in the IO rate, I thought that, that was the cause of the issue. Disk thrashing - but even after fixing that issue (I was accidentally saving cache to disk instead of APC), the restarts were still persistent.

Now thinking this was a memory issue, I had our server migrated to Dallas so that we could upgrade to 1GB from 512MB. Now let me add here that this is a server that is only running a single wordpress site. It's nothing too fancy, but seems to be taking up a lot for some reason.

I setup the server using https://github.com/okor/LEMPress - LEMPress as suggested by one of the users on the Linode IRC channel.

Now I'm thinking that the server is running out of memory, but I don't see any errors that would suggest so.

Here is my my.cnf config - http://p.linode.com/7571
I've run mysqltuner and go the following results:

-------- General Statistics --------------------------------------------------
[--] Skipped version check for MySQLTuner script
[OK] Currently running supported MySQL version 5.5.29-0ubuntu0.12.04.2
[OK] Operating on 64-bit architecture

-------- Storage Engine Statistics -------------------------------------------
[--] Status: -Archive -BDB -Federated +InnoDB -ISAM -NDBCluster
[--] Data in MyISAM tables: 357K (Tables: 18)
[--] Data in InnoDB tables: 18M (Tables: 25)
[--] Data in PERFORMANCE_SCHEMA tables: 0B (Tables: 17)
[!!] Total fragmented tables: 26

-------- Performance Metrics -------------------------------------------------
[--] Up for: 29m 48s (1K q [0.582 qps], 106 conn, TX: 3M, RX: 106K)
[--] Reads / Writes: 100% / 0%
[--] Total buffers: 192.0M global + 2.7M per thread (40 max threads)
[OK] Maximum possible memory usage: 299.5M (30% of installed RAM)
[OK] Slow queries: 0% (0/1K)
[OK] Highest usage of available connections: 5% (2/40)
[OK] Key buffer size / total MyISAM indexes: 16.0M/217.0K
[OK] Query cache efficiency: 28.6% (247 cached / 863 selects)
[OK] Query cache prunes per day: 0
[OK] Sorts requiring temporary tables: 0% (0 temp sorts / 105 sorts)
[!!] Temporary tables created on disk: 30% (136 on disk / 449 total)
[OK] Thread cache hit rate: 98% (2 created / 106 connections)
[OK] Table cache hit rate: 24% (85 open / 344 opened)
[OK] Open file limit used: 8% (84/1K)
[OK] Table locks acquired immediately: 100% (756 immediate / 756 locks)
[OK] InnoDB data size / buffer pool: 18.5M/128.0M

-------- Recommendations -----------------------------------------------------
General recommendations:
    Run OPTIMIZE TABLE to defragment tables for better performance
    MySQL started within last 24 hours - recommendations may be inaccurate
    Enable the slow query log to troubleshoot bad queries
    When making adjustments, make tmp_table_size/max_heap_table_size equal
    Reduce your SELECT DISTINCT queries without LIMIT clauses
Variables to adjust:
    tmp_table_size (> 16M)
    max_heap_table_size (> 16M)

It just seems a bit weird that it happens every two hours consistently. I've run the script crontab -l and it said there were no cronjobs for the root user - so I'm at a loss. I was hoping that someone would be able to point me in the right direction?

Thank you in advance for any help you can provide.

cron jobs can also be specified in the directory /etc/cron.d/
(and /etc/cron.hourly/, /etc/cron.daily/, ...)

maybe check the logs in /var/log/, syslog should show if cron is running anything

Thanks Bryan for the response.

It seems that there are quite a few CRON jobs running in the syslog as you said: http://p.linode.com/7573

I've pasted the last 30 minutes or so as that's when the issue reoccured again. However, I'm not too sure what I should be looking for in here to identify the culprit behind it?