InnoDB Internals

A high level overview

Presented by Peter Sylvester

About the presenter

● Joined Pythian team in January 2015

● Internal Principal Consultant at Pythian since June 2016
● Worked with MySQL since 2008 (5.0) in both DBA and DBD roles
● Originally worked as SQL Server DBA
● Is originally from Detroit, but currently lives in the Greater Toronto Area.
● Social media
● Twitter = @PeterTheDBA
● Linkedin = https://www.linkedin.com/in/petertsylvester

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Basis of presentation

● Re-read the MySQL 5.6 reference guide on InnoDB and found it to be very vague.
● Reached out to other SMEs and performed my own lab work to help fill in the gaps.
● Turned my notes into a 5-part blog post series covering InnoDB Mechanics (MySQL
5.6) related to…
● Memory
● I/O (file structure and logs)
● I/O (table data)
● Concurrency
● Consistency / Statistics Handlings
● 55 Variables covered

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Presentation outline

● What is InnoDB?
● Importance of InnoDB
● InnoDB: A brief history
● InnoDB High Level Mechanics
● Memory
● IO

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What is InnoDB?

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Why is it important to understand InnoDB mechanics?

● InnoDB is the ACID compliant solution for MySQL, making it the most attractive and
most commonly used storage engine for modern installations of MySQL today.
● MySQL 8.0 is starting to phase out MYISAM engine
● No transportable MYISAM tablespaces
● mysql schema is now INNODB
● AWS RDS platforms either discourage use of MYISAM (MySQL / RDS backup
consistency issues) or just don’t allow it at all (Aurora)
● InnoDB = MySQL (OLTP) : MySQL (OLTP) = InnoDB

Having a high level understanding of InnoDB mechanics allows for ease of configuration
and ease of troubleshooting

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InnoDB: A brief History

● 1995: Originally developed by Innobase (Heikki Turri. Finland)

● 2001: MySQL 3.23, InnoDB support is added
● 2003: MySQL 4.0, InnoDB is enabled by default
● 2010: MySQL 5.1, InnoDB plugin 1.0.7 is released as a plugin, allowed for
Barracuda file format (eventually rolled into later minor versions of MySQL 5.5)
● 2010: MySQL 5.5, InnoDB is default storage engine, fast index creation added
● 2013: MySQL 5.6, InnoDB memcached plugin, fulltext index, and Online DDL are
added
● 2015: MySQL 5.7, InnoDB specific table partitioning is added
● ???: MySQL 8.0, the beginning of MYISAM phase out

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InnoDB Mechanics

● Memory
● I/O
● Other considerations

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InnoDB Mechanics: Memory

● InnoDB Buffer Pool

● Old blocks percentage / Old blocks time
● Buffer pool instances
● Adaptive Hash indexing

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InnoDB Mechanics: Memory: Buffer Pool

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InnoDB Mechanics: Memory: Buffer Pool

innodb_buffer_pool_size

● Default: 128M
● Should be approximately 75% of system memory
● Note that global memory is also shared with MYISAM key cache

Metric:

● SHOW ENGINE INNODB STATUS

● BUFFER POOL AND MEMORY
■ Free Buffers
■ Buffer pool hit rate

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InnoDB Mechanics: Memory: Buffer Pool

innodb_old_blocks_pct

● Default: 37%
● Consider increasing under high eviction (not made young) scenarios where a page
is being evicted before it is considered ‘hot’
● Consider decreasing if you have largely stagnant data

Metric

● SHOW ENGINE INNODB STATUS

● BUFFER POOL AND MEMORY
■ Pages not made young

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InnoDB Mechanics: Memory: Buffer Pool

innodb_old_blocks_time

● Default: 1 second
● Prevent hot pages from being removed from the buffer pool by full table scans,
commonly occurring with logical backups like mysqldump

Metric

● SHOW ENGINE INNODB STATUS

● BUFFER POOL AND MEMORY
■ Pages not made young

Experimentation with old blocks pct and old blocks time may be required to find the best
configuration for your use case.

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InnoDB Mechanics: Memory: Buffer Pool

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InnoDB Mechanics: Memory: Buffer Pool

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InnoDB Mechanics: Memory: Buffer Pool

innodb_buffer_pool_instances

● Default: 8, unless you have a buffer pool less than 1G, then default will be 1. In
earlier versions of 5.6 the default was 1 regardless.

Metric

● Performance Schema
● Instrument: wait/synch/mutex/innodb/buf_pool_mutex

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InnoDB Mechanics: Memory: Adaptive Hash Index

● Adds dynamic hash indexing to innodb data pages referencing a prefix of frequently
accessed b-tree index pages / leaf nodes
● Is enabled by default
● No control of the algorithm

Metric:

● SHOW ENGINE INNODB STATUS

● INSERT BUFFER AND ADAPTIVE HASH INDEX
■ Adaptive hash searches vs non-hash searches

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InnoDB Mechanics: Memory: Adaptive Hash Index

● Single resource
● Partitioning supported in Percona 5.6 and added in Oracle MySQL 5.7 and
MariaDB 10.2
● If you see semaphore issues that relate to source file btr0sea.c, you need to add
partitions or disable adaptive hash indexing entirely. You may also see
improvement by adjusting innodb_thread_concurrency.
● Mutex latches are directly tied to individual indexes, so contention issues may not
be resolved by adding partitioning if you have one hot index

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InnoDB Mechanics: Memory: Considerations

● Ensure that your memory configuration doesn’t put you in a position where OOM is
a possibility
● Remember that there are other global memory caches like the MYISAM key buffer
as well as session memory caches like the sort, join, read, and read_rnd buffer
● Mysqlcalculator.com is a good baseline

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InnoDB Mechanics: Memory

Q&A

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InnoDB Mechanics: I/O

● Transaction Processes / Redo logs

● Flush processes
● Other considerations

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InnoDB Mechanics: I/O: Complicated, eh?

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InnoDB Mechanics: I/O: Redo Logs

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InnoDB Mechanics: I/O: Redo Logs: Flush log at trx commit 1

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InnoDB Mechanics: I/O: Redo Logs: Flush log at trx commit 2

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InnoDB Mechanics: I/O: Redo Logs: Flush log at trx commit 0

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InnoDB Mechanics: Redo Logs

innodb_log_file_size / innodb_log_files_in_group

● Size of redo log = Innodb_log_file_size * innodb_log_files_in_group

● Default = 48M * 2 = 96M
● Should be able to support 1 hour DML traffic

Metric

● SHOW ENGINE INNODB STATUS

● LOG
■ Log sequence number
● ((LSN position) - (LSN position 1 hour ago)) / 1024^2 = Desired log size in M

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InnoDB Mechanics: Redo Logs

innodb_log_buffer_size

● Default = 8M

Metric

● SHOW ENGINE INNODB STATUS

● LOG
■ Log Sequence Number - Log flushed up to = Used log buffer (bytes)
● Aim to go no higher than 30% consumption with normal traffic. Even when you are
flushing as part of the transaction commit process.

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InnoDB Mechanics: Redo Logs

innodb_flush_log_at_trx_commit

● Default = 1
● Setting to anything other than 1 forces sacrifices ACID compliance for performance
gain

Metric

● Performance schema
● Instrument: wait/io/file/innodb/innodb_log_file

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InnoDB Mechanics: Sync Binlog

sync_binlog

● Unlike redo logs, binary logs are meant to drive PITR and replication and is not a
part of InnoDB data consistency
● Synchronizes the flushing of commit groups to binary log at transaction commit
● Default = 0
● Set to 1 when you want the binary log to stay in sync with InnoDB. This will have a
performance impact. Setting to 0 is still ACID compliant, but the binary logs are not
considered to be consistent to the rest of the RDBMS.

Metric

● Performance schema
● Instrument: wait/io/file/sql/binlog

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InnoDB Mechanics: I/O: Flush / Checkpoint

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InnoDB Mechanics: I/O: Adaptive Flushing

● innodb_adaptive_flushing
● innodb_adaptive_flushing_lwm
● innodb_max_dirty_pages_pct
● innodb_max_dirty_pages_pct_lwm
● innodb_flushing_avg_loops
● innodb_lru_scan_depth
● innodb_flush_neighbors
● innodb_flush_method
● innodb_write_io_threads
● innodb_io_capacity
● innodb_io_capacity_max

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InnoDB Mechanics: I/O: Flush / Checkpoint

innodb_checksum_algorithm

● Write a checksum to the suffix of a flushed persistent data page

● Used to detect bit rot or partially written pages
● Default = INNODB (proprietary)
● Preferred = crc32, scans 32 bits at a time (vs 8), much faster
● Beware strict mode
● No downgrade option apart from logical restore

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InnoDB Mechanics: I/O: Flush / Checkpoint

innodb_doublewrite

● Protects against partial page writes

● Recovery process scans pages in tables, if inconsistent with checksum, pull from
double write. If Double write is inconsistent with checksum, discard and refer back
to redo log.
● Default: 1 (on)
● Only disable if you have an atomic writing filesystem like ZFS or FusionIO,
journalling is not enough.

Metric

● Performance schema
● Instrument: wait/synch/mutex/InnoDB/buf_dblwr_mutex

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InnoDB Mechanics: I/O: Other considerations

innodb_file_per_table

● Moves data into one ‘table space’ per table

● Speeds up table truncation
● Allows ease of data management, reclaiming space on disk, transportable
tablespaces

Metric

● Performance schema
● Instrument: wait/io/file/innodb/innodb_data_file
● Table: file_summary_by_event_name
● Table: file_summary_by_instance

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InnoDB Mechanics: I/O: Other considerations

innodb_file_format

● Barracuda added as part of the InnoDB Plugin

● Adds dynamic and compressed row formats
● Supports all row formats in the previous version (Antelope)
● It was anticipated that there would be several formats developed, but Barracuda
simply expanded on Antelope. Option to pick a file format is expected to be
removed in 8.0
● Only disable if you believe you may have to downgrade to an older version of
MySQL

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InnoDB Mechanics: I/O

Q&A

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InnoDB variables to consider for a new environment

● Innodb_buffer_pool_size
● Approx 75% of system memory
● Innodb_file_per_table
● On
● Innodb_file_format
● Barracuda
● Innodb_checksum_algorithm
● crc32 (strict if this is brand new with no data)
● Innodb_log_file_size / files in group
● Start with at least 512MB, adjust to make sure you have 1 hour of DML covered

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InnoDB variables to consider for a new environment

● sync_binlog
● 1, keep it that way unless you need to move past an issue
● Innodb_flush_method
● Direct_io is best for most modern use cases. You should still consider fsync if you are not
using innodb file per table
● Innodb_io_capacity
● Set to 60% of IOPS capacity, especially if you’re using EC2 or RDS
● Default is 200, most disk systems are considerably faster
● Innodb_io_capacity_max
● Set to 99% of IOPS capacity

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InnoDB monitoring

● Regardless of issue, always start by looking at the processlist

● Command: Show processlist
● InnoDB engine status
● Command: SHOW ENGINE INNODB STATUS
■ Semaphores / Mutexes (contention saturation)
■ Transaction info (can also get from information_schema.innodb_trx)
■ Background I/O thread status
■ Change buffer status
■ Adaptive hash index status
■ Redo log status
■ Buffer pool status
■ Row operations

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InnoDB monitoring

● Performance_schema
● Key tables
■ Events_waits_summary_global_by_event_name
■ Events_statements_summary_by_digest
● 5.5: Consider enabling when you’re having issues
● 5.6: Consider enabling unless you have a highly concurrent workload
● 5.7: Enable it
● Historical graphing
● Percona Monitoring and Management Platform
● Vivid Cortex

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Q&A

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THANK YOU
Peter Sylvester
linkedin.com/in/petertsylvester
@PeterTheDBA

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