Reduce MySQL Core Dump Size by Excluding the InnoDB Buffer Pool

When things go horrible wrong and a process crashes, one of the most powerful things to investigate the cause of the crash is a core dump. As the amount of memory allocated to processes such as MySQL has increased – in some cases approaching 1TiB of memory – enabling core dumps can cause problems of their own. MySQL Server 8.0.14 and later supports an option to reduce the size of the core dump which will be discussed in this blog.

Typically the largest single user of memory for MySQL is the InnoDB buffer pool. This is used to cache the data and indexes for tables using the InnoDB storage engine (the default). It is rarely important to know what is stored in the InnoDB buffer pool when investigating a crash, so a good way to reduce the core dump size is to exclude the buffer pool. In MySQL 8.0.14 innodb_buffer_pool_in_core_file configuration option was added for this purpose. It defaults to ON which means the buffer pool is included in the core dumps (same behaviour as in older releases).

Contribution

Thanks for Facebook for the contribution that implemented the innodb_buffer_pool_in_core_file option.

Let’s look a bit more into core dumps, how to enable them, why you may want to exclude the InnoDB buffer pool, and an example.

Information

The innodb_buffer_pool_in_core_file option only applies on Linux with kernel 3.4 and later. For this reason the rest of the blog assumes Linux is used.

Enabling Core Dumps

Core dumps can be enabled by including the core-file option in the MySQL configuration. It is disabled by default. However, on Linux/Unix it is in general not enough to enable core-file to get a core dump in case of a crash as the system will also limit the size of a core dump. Typically this limit is 0 by default.

The details of the steps required to enable core dumps depends on the Linux distribution used. The following will discuss the core-file option and the limit on the core size. However, the exact steps required may differ for your system and possibly include additional steps.

Enabling Core Dumps in MySQL

As mentioned, the option in MySQL to enable core dumps is core-file. This can only be set using the MySQL configuration file (my.cnf or my.ini). For example:

[mysqld]
core-file

After you have updated the configuration file, the change will take effect the next time MySQL is restarted.

Core Size Limit

Linux includes various limitations on the resources a process can use. This helps improve the stability of the system as a whole, but the default limits may be too restrictive for something like a database host where one process uses most of the resources. One of the limitations is the size of the core dump and typically the default limit is 0.

You can verify the current limits for your process using the proc file system, for example (assuming only a single mysqld process on the system):

shell$ sudo cat /proc/$(pidof mysqld)/limits
Limit                     Soft Limit           Hard Limit           Units     
Max cpu time              unlimited            unlimited            seconds   
Max file size             unlimited            unlimited            bytes     
Max data size             unlimited            unlimited            bytes     
Max stack size            8388608              unlimited            bytes     
Max core file size        0                    unlimited            bytes     
Max resident set          unlimited            unlimited            bytes     
Max processes             10240                12288                processes 
Max open files            10240                65536                files     
Max locked memory         65536                65536                bytes     
Max address space         unlimited            unlimited            bytes     
Max file locks            unlimited            unlimited            locks     
Max pending signals       15611                15611                signals   
Max msgqueue size         819200               819200               bytes     
Max nice priority         0                    0                    
Max realtime priority     0                    0                    
Max realtime timeout      unlimited            unlimited            us

There are various ways to change the limits for MySQL and which one to use depends on how you start MySQL. If you start MySQL from the command-line, you can simply use the ulimit command first:

shell$ ulimit -c unlimited                                                                                                                                                                                                        

# Start MySQL
                                                                                                                                               
shell$ sudo cat /proc/$(pidof mysqld)/limits | grep 'core file size'
Max core file size        unlimited            unlimited            bytes

This has set the limit for the core file size to unlimited.

Warning

Do not blindly set the size to unlimited. If you configure the limit too high, you may run out of disk space preventing MySQL from restarting.

You can also configure the limit in the /etc/security/limits.conf file or in a new file in /etc/security/limits.d/. This is a better way to persist a setting and allows you for example to configure the limits for a given user. For example to set the core dump file size to unlimited for the mysql user:

mysql    soft    core    unlimited
mysql    hard    core    unlimited

However, on distributions using systemd (including Oracle Linux 7, Red Hat Enterprise Linux (RHEL) 7, and CentOS 7), systemd completely ignores /etc/security/limits.conf. Instead you need to use the service file for the process. For MySQL this is the /usr/lib/systemd/system/mysqld.service file, or if you have multiple instances on one host, /usr/lib/systemd/system/mysqld@.service. If you use Debian, replace mysqld with mysql. The option to set in the service file is LimitCore, for example:

[Service]
LimitCore = infinity

If you use mysqld_safe to start MySQL, you can use the core-file-size option (in the [mysqld_safe] group in the MySQL configuration file or on the command-line) to change the limit. This requires that the hard limit is high enough for the requested limit.

Problems with Core Dumps

Over time the amount of memory allocated to MySQL has grown. This particularly applies to the InnoDB buffer pool – as databases handle more data, there is also a greater need to cache the most used data and indexes in memory. Today, some MySQL instances have total memory allocations approaching 1TiB.

When a core dump happens, the memory allocated to the process is written out to disk. For processes using a large amount of memory, this may take some time. Furthermore, there is a possibility that the system may run out of disk, particularly if repeated crashes occur. The disk space usage can particularly be an issue when MySQL is running as a service as it is likely the core file in that case is written to the data directory. From a support perspective, it is also less than trivial to share a core dump that is several hundred gigabytes large.

Warning

Remember that the core dump is a snapshot of the process memory. This means that any data loaded into memory will be present in the core dump. This is particularly something to consider if you store sensitive data in your database. Even if you have transparent data encryption (TDE) enabled, the data in memory will be decrypted!

Excluding the InnoDB buffer pool from the core dump does reduce the amount of data in the core dump, but some data will still be included, for example because it is stored in memory for sorting or as part of a query result.

The InnoDB buffer pool is in most cases the largest contributor – it can easily contribute 75% or more of the total core dump size. So, excluding the buffer pool can significantly reduce the size of the core dump. I will give an example at the end of the blog.

Example

To finish off this blog, let’s look at an example. In this case, MySQL has been configured with innodb_buffer_pool_size = 2G and data has been loaded, so most of the buffer is in use:

mysql> SELECT SUM(FREE_BUFFERS)
         FROM information_schema.INNODB_BUFFER_POOL_STATS;
+-------------------+
| SUM(FREE_BUFFERS) |
+-------------------+
|                 0 |
+-------------------+
1 row in set (0.02 sec)

And from the output of top

  PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND
11142 mysql     20   0 4121468 2.261g      0 S   4.0 58.6   2:38.50 mysqld 

When MySQL is killed with signal 11 (segmentation fault), a core dump is created. Without innodb_buffer_pool_in_core_file, the core dump is almost 3 gigabytes (see output at the end of the blog).

If the new feature is enabled by adding innodb_buffer_pool_in_core_file to the configuration file or by persisting it

mysql> SET PERSIST innodb_buffer_pool_in_core_file = OFF;
Query OK, 0 rows affected (0.02 sec)

The change takes effect immediately. The core dump will now be much smaller – around the size of the buffer pool smaller:

shell$ ls -lh /var/lib/mysql/core.*
-rw-------. 1 mysql mysql 2.8G Feb 11 20:30 /var/lib/mysql/core.11142
-rw-------. 1 mysql mysql 759M Feb 11 20:47 /var/lib/mysql/core.14456

Here core.11142 is with innodb_buffer_pool_in_core_file enabled and core.14456 with the option disabled.

Tip

Want to know more? There are more details in the reference manual at Excluding Buffer Pool Pages from Core Files and in the blog from the server team: MySQL 8.0: Excluding the Buffer Pool from a Core File.

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