MySQL takes huge memory by ignoring buffer pool size

MySQLmysql-5.6Ubuntu

I am facing a very strange problem, looks like on mysql startup, mysql is taking so much memory than 4x of buffer pool size.

I am using Ubuntu VM (4 Core 8 GB) with MySQL 5.6.33. /etc/mysql/my.cnf is as below:

[client]
port        = 3306
socket      = /var/run/mysqld/mysqld.sock

[mysqld_safe]
socket      = /var/run/mysqld/mysqld.sock
nice        = 0

[mysqld]
user        = mysql
pid-file    = /var/run/mysqld/mysqld.pid
socket      = /var/run/mysqld/mysqld.sock
port        = 3306
basedir     = /usr
datadir     = /datafiles/mysql
tmpdir      = /tmp
lc-messages-dir = /usr/share/mysql
skip-external-locking
bind-address        = 0.0.0.0
key_buffer      = 128M
max_allowed_packet  = 128M
thread_stack        = 192K
thread_cache_size       = 8
wait_timeout        = 300
interactive_timeout = 600
max_connect_errors = 1000000
open-files-limit = 1024000
transaction-isolation   = READ-COMMITTED
myisam-recover-options  = BACKUP
max_connections        = 25000
query_cache_limit   = 1M
query_cache_size        = 4M
general_log_file        = /dblogs/audit/general_log.log
general_log             = OFF
log_error = /dblogs/error.log
slow_query_log = ON
slow_query_log_file = /dblogs/SLOW.log
long_query_time =2 
min_examined_row_limit = 5000
server-id       = 1
log_bin         = /dblogs/binarylogs/mysql-bin.log
expire_logs_days    = 10
max_binlog_size   = 10M
binlog_format       = MIXED
innodb_strict_mode = OFF
sql_mode = NO_ENGINE_SUBSTITUTION
innodb_file_format = barracuda
innodb_file_format_max = barracuda
innodb_file_per_table = 1
innodb_data_home_dir        = /datafiles/mysql
innodb_buffer_pool_size = 300M
innodb_buffer_pool_instances = 1
innodb_open_files = 6000
innodb_log_file_size = 512M
innodb_log_buffer_size = 64M
innodb_lock_wait_timeout    = 600
innodb_io_capacity  = 400
innodb_flush_method = O_DSYNC
innodb_flush_log_at_trx_commit = 2
innodb_write_io_threads = 2
innodb_read_io_threads = 2
innodb_log_files_in_group = 2
innodb_monitor_enable = all
join_buffer_size=256K
sort_buffer_size=256K

[mysqldump]
quick
quote-names
max_allowed_packet  = 16M

[mysql]
#no-auto-rehash # faster start of mysql but no tab completition

[isamchk]
key_buffer      = 16M

!includedir /etc/mysql/conf.d/

As, per config file innodb_buffer_pool_size is set 300M and innodb_buffer_pool_instances is set to 1 (no need, as buffer pool is < 1G). error log file also confirms that buffer pool is set to 300.0M

ERROR.log

2020-09-24 01:50:06 4886 [Note] Plugin 'FEDERATED' is disabled.
2020-09-24 01:50:06 4886 [Note] InnoDB: Using atomics to ref count buffer pool pages
2020-09-24 01:50:06 4886 [Note] InnoDB: The InnoDB memory heap is disabled
2020-09-24 01:50:06 4886 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2020-09-24 01:50:06 4886 [Note] InnoDB: Memory barrier is not used
2020-09-24 01:50:06 4886 [Note] InnoDB: Compressed tables use zlib 1.2.8
2020-09-24 01:50:06 4886 [Note] InnoDB: Using Linux native AIO
2020-09-24 01:50:06 4886 [Note] InnoDB: Using CPU crc32 instructions
2020-09-24 01:50:06 4886 [Note] InnoDB: Initializing buffer pool, size = 300.0M
2020-09-24 01:50:06 4886 [Note] InnoDB: Completed initialization of buffer pool
2020-09-24 01:50:06 4886 [Note] InnoDB: Highest supported file format is Barracuda.
2020-09-24 01:50:06 4886 [Note] InnoDB: 128 rollback segment(s) are active.
2020-09-24 01:50:06 4886 [Note] InnoDB: Waiting for purge to start
2020-09-24 01:50:06 4886 [Note] InnoDB: 5.6.33 started; log sequence number 4529735
2020-09-24 01:50:06 4886 [Note] Server hostname (bind-address): '0.0.0.0'; port: 3306
2020-09-24 01:50:06 4886 [Note]   - '0.0.0.0' resolves to '0.0.0.0';
2020-09-24 01:50:06 4886 [Note] Server socket created on IP: '0.0.0.0'.
2020-09-24 01:50:06 4886 [Note] Event Scheduler: Loaded 0 events
2020-09-24 01:50:06 4886 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.6.33-0ubuntu0.14.04.1-log'  socket: '/var/run/mysqld/mysqld.sock'  port: 3306  (Ubuntu)

even more show global variables like '%pool%'; also show that buffer pool is set properly:

+-------------------------------------+----------------+
| Variable_name                       | Value          |
+-------------------------------------+----------------+
| innodb_additional_mem_pool_size     | 8388608        |
| innodb_buffer_pool_dump_at_shutdown | OFF            |
| innodb_buffer_pool_dump_now         | OFF            |
| innodb_buffer_pool_filename         | ib_buffer_pool |
| innodb_buffer_pool_instances        | 1              |
| innodb_buffer_pool_load_abort       | OFF            |
| innodb_buffer_pool_load_at_startup  | OFF            |
| innodb_buffer_pool_load_now         | OFF            |
| innodb_buffer_pool_size             | 314572800      |
+-------------------------------------+----------------+

But after service start if I check using free -h or in top mysql is taking more than 75% of RAM

             total       used       free     shared    buffers     cached
Mem:          7.5G       5.3G       2.1G        28K       2.8M        77M
-/+ buffers/cache:       5.3G       2.2G
Swap:           9G       1.2G       8.8G

top command output:

PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND
 8071 mysql     20   0 6982340 5.741g   9260 S   0.3 77.0   0:02.19 mysqld

I checked by changing innodb_buffer_pool_size to 1G,2G,3G and innodb_buffer_pool_instances to 1,8,10, but irrespective of all these when I start MySQL service 5-6 GB of total RAM (7GB) is taken by Mysql and as soon as I stop the service RAM usages reduced to 224M.

What is this behaviour?
Did I misconfigured the MySQL?
Why Mysql service is taking more than (4x or 8x) of buffer pool size?

Best Answer

These are much too high:

open-files-limit = 1024000      -- 10K is probably plenty big
max_connections        = 25000  -- 151 is probably plenty big
innodb_log_buffer_size = 64M    -- Most DBA find the 8M default OK.
innodb_write_io_threads = 2     -- leave at 4
innodb_read_io_threads  = 2     -- leave at 4

Don't raise settings (except for innodb_buffer_pool_size) before you have some concrete reason for doing so. In general, MySQL and MariaDB are adequately well-tuned "out of the box".

I glanced at the other items you changed; I did not see any that are likely to cause trouble.

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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.

Best Answer

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MySQL – Differences Between mysqld_safe and mysqld

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

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