Mysql – How to tune MySQL with results from thesqltuner

MySQL

I ran mysqltuner and got this:

-------- General Statistics --------------------------------------------------
[--] Skipped version check for MySQLTuner script
[OK] Currently running supported MySQL version 5.5.35-0ubuntu0.12.04.2
[OK] Operating on 32-bit architecture with less than 2GB RAM

-------- Storage Engine Statistics -------------------------------------------
[--] Status: -Archive -BDB -Federated +InnoDB -ISAM -NDBCluster 
[--] Data in PERFORMANCE_SCHEMA tables: 0B (Tables: 17)
[!!] InnoDB is enabled but isn't being used
[OK] Total fragmented tables: 0

-------- Performance Metrics -------------------------------------------------
[--] Up for: 1m 57s (112 q [0.957 qps], 41 conn, TX: 19K, RX: 7K)
[--] Reads / Writes: 100% / 0%
[--] Total buffers: 192.0M global + 2.7M per thread (151 max threads)
[!!] Maximum possible memory usage: 597.8M (120% of installed RAM)
[OK] Slow queries: 0% (0/112)
[OK] Highest usage of available connections: 1% (2/151)
[OK] Key buffer size / total MyISAM indexes: 16.0M/100.0K
[!!] Query cache efficiency: 0.0% (0 cached / 71 selects)
[OK] Query cache prunes per day: 0
[OK] Temporary tables created on disk: 20% (54 on disk / 267 total)
[OK] Thread cache hit rate: 95% (2 created / 41 connections)
[OK] Table cache hit rate: 23% (41 open / 171 opened)
[OK] Open file limit used: 4% (48/1K)
[OK] Table locks acquired immediately: 100% (62 immediate / 62 locks)

-------- Recommendations -----------------------------------------------------
General recommendations:
    Add skip-innodb to MySQL configuration to disable InnoDB
    MySQL started within last 24 hours - recommendations may be inaccurate
    Reduce your overall MySQL memory footprint for system stability
    Enable the slow query log to troubleshoot bad queries
Variables to adjust:
  *** MySQL's maximum memory usage is dangerously high ***
  *** Add RAM before increasing MySQL buffer variables ***
    query_cache_limit (> 1M, or use smaller result sets)

my.cnf file

#
# The MySQL database server configuration file.
#
# You can copy this to one of:
# - "/etc/mysql/my.cnf" to set global options,
# - "~/.my.cnf" to set user-specific options.
# 
# One can use all long options that the program supports.
# Run program with --help to get a list of available options and with
# --print-defaults to see which it would actually understand and use.
#
# For explanations see
# http://dev.mysql.com/doc/mysql/en/server-system-variables.html

# This will be passed to all mysql clients
# It has been reported that passwords should be enclosed with ticks/quotes
# escpecially if they contain "#" chars...
# Remember to edit /etc/mysql/debian.cnf when changing the socket location.
[client]
port        = 3306
socket      = /var/run/mysqld/mysqld.sock

# Here is entries for some specific programs
# The following values assume you have at least 32M ram

# This was formally known as [safe_mysqld]. Both versions are currently parsed.
[mysqld_safe]
socket      = /var/run/mysqld/mysqld.sock
nice        = 0

[mysqld]
#
# * Basic Settings
#
user        = mysql
pid-file    = /var/run/mysqld/mysqld.pid
socket      = /var/run/mysqld/mysqld.sock
port        = 3306
basedir     = /usr
datadir     = /var/lib/mysql
tmpdir      = /tmp
lc-messages-dir = /usr/share/mysql
skip-external-locking
#
# Instead of skip-networking the default is now to listen only on
# localhost which is more compatible and is not less secure.
bind-address        = 127.0.0.1
#
# * Fine Tuning
#
key_buffer      = 16M
max_allowed_packet  = 16M
thread_stack        = 192K
thread_cache_size       = 8
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched
myisam-recover         = BACKUP
#max_connections        = 100
#table_cache            = 64
#thread_concurrency     = 10
#
# * Query Cache Configuration
#
query_cache_limit   = 1M
query_cache_size        = 16M
#
# * Logging and Replication
#
# Both location gets rotated by the cronjob.
# Be aware that this log type is a performance killer.
# As of 5.1 you can enable the log at runtime!
#general_log_file        = /var/log/mysql/mysql.log
#general_log             = 1
#
# Error log - should be very few entries.
#
log_error = /var/log/mysql/error.log
#
# Here you can see queries with especially long duration
#log_slow_queries   = /var/log/mysql/mysql-slow.log
#long_query_time = 2
#log-queries-not-using-indexes
#
# The following can be used as easy to replay backup logs or for replication.
# note: if you are setting up a replication slave, see README.Debian about
#       other settings you may need to change.
#server-id      = 1
#log_bin            = /var/log/mysql/mysql-bin.log
expire_logs_days    = 10
max_binlog_size         = 100M
#binlog_do_db       = include_database_name
#binlog_ignore_db   = include_database_name
#
# * InnoDB
#
# InnoDB is enabled by default with a 10MB datafile in /var/lib/mysql/.
# Read the manual for more InnoDB related options. There are many!
#
# * Security Features
#
# Read the manual, too, if you want chroot!
# chroot = /var/lib/mysql/
#
# For generating SSL certificates I recommend the OpenSSL GUI "tinyca".
#
# ssl-ca=/etc/mysql/cacert.pem
# ssl-cert=/etc/mysql/server-cert.pem
# ssl-key=/etc/mysql/server-key.pem



[mysqldump]
quick
quote-names
max_allowed_packet  = 16M

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

[isamchk]
key_buffer      = 16M

#
# * IMPORTANT: Additional settings that can override those from this file!
#   The files must end with '.cnf', otherwise they'll be ignored.
#
!includedir /etc/mysql/conf.d/

Best Answer

First of all I would use this recommendation:

MySQL started within last 24 hours - recommendations may be inaccurate

let mysql run for at least 7 days and then do the check.

Then: Enable the slow query log to troubleshoot bad queries

add to your my.cnf: log_slow_queries = /var/log/mysql/mysql-slow.log

It looks like you're MySQL server is able to use more memory than you actually have on your server:

[!!] Maximum possible memory usage: 597.8M (120% of installed RAM)

The rest of recommendations don't have any meaning without your my.cnf config file.

SUGGESTION

Your key_buffer_size is only 16MB, but your MyISAM indexes total 59MB. In a highly-trafficked website, I can see index pages getting kicked out of and pushed into the MyISAM keycache frequently. This could have an affect on indexes being updated and overall write performance on the MyISAM tables.

You could just bump up key_buffer_size to 64 MB.

You must add this to /etc/my.cnf

[mysqld]
key_buffer_size=64M

You don't even need to restart mysql. Just run this:

SET @MB = 1024 * 1024;
SET GLOBAL key_buffer_size = @MB * 64;

You can also convert the row format of all your MyISAM tables. This will just about double the disk space used by will increase read performance 20-25%. I wrote about this before as well:

Here is a script to convert all your MyISAM tables to Fixed Row Format

SQLSTMT="SELECT CONCAT('ALTER TABLE ',table_schema,'.',table_name,' ROW_FORMAT=Fixed;')"
SQLSTMT="${SQLSTMT} FROM information_schema.tables WHERE engine='MyISAM' AND"
SQLSTMT="${SQLSTMT} table_schema NOT IN ('information_schema','mysql','performance_schema')"
mysql -uroot -p -A --skip-column-names -e"${SQLSTMT}" > /root/MakeFixedRows.sql
mysql -uroot -p < /root/MakeFixedRows.sql

ALTERNATE SUGGESTION

Given you have a total of 488 MB of of MyISAM data and indexes, I would like to suggest the following: Switch Everything to InnoDB. I have two reasons:

REASON # 1

MyISAM only caches indexes. InnoDB caches data and indexes. See my post : What are the main differences between InnoDB and MyISAM?

This will reduce disk I/O for reading data and indexes. In your particular case, you can easily handle an InnoDB Buffer Pool of 512M and basically fit everything into RAM.

REASON # 2

The MyISAM storage engine cannot access multiple CPUs. InnoDB can. In fact, I have many posts on tweeking InnoDB for this:

Jul 23, 2012 : How to get the most out of MySQL on a QuadCore machine with 16 GB of RAM?
Sep 20, 2011 : Multi cores and MySQL Performance
Sep 12, 2011 : Possible to make MySQL use more than one core?
May 26, 2011 : About single threaded versus multithreaded databases performance

EPILOGUE

I would like you really consider the conversion from MyISAM to InnoDB

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.