MySQL 5.1 High Cpu usage on CentOS 6

centosMySQLmysql-5.1

I am running MySQL 5.1 on a CentOS 6 server with 16G ram. I got also apache on it.

MySQL is constantly using too much cpu.

top - 17:40:36 up 112 days, 12:13,  1 user,  load average: 1.24, 1.72, 1.82
Tasks: 222 total,   1 running, 221 sleeping,   0 stopped,   0 zombie
Cpu(s): 12.3%us, 11.6%sy,  0.4%ni, 72.9%id,  2.8%wa,  0.0%hi,  0.1%si,  0.0%st
Mem:  16329040k total, 12946136k used,  3382904k free,   587252k buffers
Swap:  1051832k total,  1050988k used,      844k free,  4986272k cached

  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND                                                                                                                                 
25368 mysql     20   0 8854m 5.3g 5064 S 295.4 33.9  11912:37 mysqld                                                                                                                                 
 1757 apache    20   0  982m  80m  28m S  2.0  0.5   0:03.04 httpd                                                                                                                                   
 2494 apache    20   0  878m  68m  27m S  2.0  0.4   0:00.92 httpd

my.cnf

[client]
default-character-set=utf8

[mysqld]
local-infile=0
datadir=/var/lib/mysql
socket=/var/lib/mysql/mysql.sock
user=mysql
symbolic-links=0
bind-address=127.0.0.1

key_buffer        = 800M
max_allowed_packet    = 32M
thread_stack        = 256K
thread_cache        = 8
thread_cache_size    = 20
thread_concurrency = 4
max_connections        = 510
table_cache            = 9000
interactive_timeout = 80
tmp_table_size = 540M
max_heap_table_size = 540M
max_connect_errors = 150
wait_timeout = 20
read_rnd_buffer_size = 1024K
connect_timeout = 10
query_cache_type = 1
query_cache_limit   = 40M
query_cache_size        = 128M
innodb_buffer_pool_size = 256M

join_buffer_size = 14M
sort_buffer_size = 14M

[mysqld_safe]
log-error=/var/log/mysqld.log
pid-file=/var/run/mysqld/mysqld.pid

SHOW FULL PROCESSLIST; is returning me on average 2-5 queries.

Here is the output of SHOW VARIABLES; command.

We got MyISAM and InnoDB tables in this system.

Thank you for any suggestions.

EDIT 1

Here is the vmstat output.

EDIT 2

SHOW GLOBAL STATUS output is available below in the comments.

Best Answer

Let's see the slowest query in the system. Quite likely, fixing it (adding an index, reformulating the SELECT, etc) is the best solution. You mentioned SHOW FULL PROCESSLIST -- That is likely to show the naughty queries; let's see them, plus the associated SHOW CREATE TABLEs.

query_cache_size = 128M -- too big; no more than 50M. A big value slows down the system with pruning.

innodb_buffer_pool_size = 256M and key_buffer = 800M -- What ENGINE are you using? Neither of these values is likely to be 'good'. See http://mysql.rjweb.org/doc.php/memory for further advice. A poorly-sized cache could lead to extra I/O, which would be seen as slow queries.

table_cache = 9000 -- Yikes! How many tables do you have? (Thousands of tables is an OS problem.)

Related Solutions

MySQL – Differences Between mysqld_safe and mysqld

As we all know, mysqld_safe and mysqld are very different

mysqld : The database server instance daemon

mysqld_safe : Control program that examines and sets the environment for mysqld to execute. The mysqld executable is actually launched in a loop. When mysqld terminates, the mysqld_safe program will examine the return results and decide whether

mysqld terminated normally (intentional shutdown), leaves mysqld_safe
mysqld terminated abnormally (crash or kill -9 of mysqld)
- Loop back, mysqld fails on retry, leaves mysqld_safe
- Loop back, mysqld starts up, stays in the mysqld_safe loop

Why is it important to have mysqld and mysqld_safe using the same MySQL version?

Let me illustrate it this way: Percona Server sometimes has additional features in mysqld_safe for manipulating the OS. For example, I have seen numactl --interleave=all in a Percona Server mysqld_safe. If that line was not there, the mysqld for Percona Server may run into issues with memory and swapping.

The same scenario could possibly be the case for Oracle's (ugh, still hate saying that) mysqld and mysqld_safe. There could be improvements from one major release to another that would be removed if the mysqld_safe was older.

Rather than exploring the possibilities of using a old mysqld_safe and a new mysqld (or vica versa), please make your life simple and reinstall MySQL 5.5.30 from scratch.

Before doing so, please run

updatedb
locate mysqld_safe

in Linux and see if there are two lingering. If there are, get the paths straightened out. Otherwise, you may have to reinstall MySQL 5.5.30.

Mysql – How to debug a db memory-leak causing thesql to go before it’s own limits

...even surpassing it's theorically maximum possible allocation.

[OK] Maximum possible memory usage: 7.3G (46% of installed RAM)

There is not actually a way to calculate maximum possible memory usage for MySQL, because there is no cap on the memory it can request from the system.

The calculation done by mysqltuner.pl is only an estimate, based on a formula that doesn't take into account all possible variables, because if all possible variables were taken into account, the answer would always be "infinite." It's unfortunate that it's labeled this way.

Here is my theory on what's contributing to your excessive memory usage:

thread_cache_size       = 128

Given that your max_connections is set to 200, the value of 128 for thread_cache_size seems far too high. Here's what makes me think this might be contributing to your problem:

When a thread is no longer needed, the memory allocated to it is released and returned to the system unless the thread goes back into the thread cache. In that case, the memory remains allocated.

^{http://dev.mysql.com/doc/refman/5.6/en/memory-use.html}

If your workload causes even an occasional client thread to require a large amount of memory, those threads may be holding onto that memory, then going back to the pool and sitting around, continuing to hold on to memory they don't technically "need" any more, on the premise that holding on to the memory is less costly than releasing it if you're likely to need it again.

I think it's worth a try to do the following, after first making a note of how much memory MySQL is using at the moment.

Note how many threads are currently cached:

mysql> show status like 'Threads_cached';
+----------------+-------+
| Variable_name  | Value |
+----------------+-------+
| Threads_cached | 9     |
+----------------+-------+
1 row in set (0.00 sec)

Next, disable the thread cache.

mysql> SET GLOBAL thread_cache_size = 0;

This disables the thread cache, but the cached threads will stay in the pool until they're used one more time. Disconnect from the server, then reconnect and repeat.

mysql> show status like 'Threads_cached';

Continue disconnecting, reconnecting, and checking until the counter reaches 0.

Then, see how much memory MySQL is holding.

You may see a decrease, possibly significant, and then again you may not. I tested this on one of my systems, which had 9 threads in the cache. Once those threads had all been cleared out of the cache, the total memory held by MySQL did decrease... not by much, but it does illustrate that threads in the cache do release at least some memory when they are destroyed.

If you see a significant decrease, you may have found your problem. If you don't, then there's one more thing that needs to happen, and how quickly it can happen depends on your environment.

If the theory holds that the other threads -- the ones currently servicing active client connections -- have significant memory allocated to them, either because of recent work in their current client session or because of work requiring a lot of memory that was done by another connection prior to them languishing in the pool, then you won't see all of the potential reduction in memory consumption until those threads are allowed to die and be destroyed. Presumably your application doesn't hold them forever, but how long it will take to know for sure whether there's a difference will depend on whether you have the option of cycling your application (dropping and reconnecting the client threads) or if you'll have to just wait for them to be dropped and reconnected over time on their own.

But... it seems like a worthwhile test. You should not see a substantial performance penalty by setting thread_cache_size to 0. Fortunately, thread_cache_size is a dynamic variable, so you can freely change it with the server running.