1. Fix this issue via WHM
In Tweak Settings, enable “Calculate the disk usage of account MySQL and PostgreSQL databases.”

The default setting is “disabled”, or unchecked.

1b. Fix this issue via SSH
Or you can enable MySQL database calculation via SSH by editing /var/cpanel/cpanel.config

You’ll want to search for

disk_usage_include_sqldbs=0

and change it to

disk_usage_include_sqldbs=1

If the parameter is not present, you’ll want to add it.

2. Run the update script to perform the initial calculations:
Finally, to calculate your MySQL and PostgreSQL database sizes, run the following:

# /scripts/update_db_cache

# touch /var/log/mysql-indexes.log
#chown mysql:mysql var/log/mysql-indexes.log

Edit /etc/my.cnf, and insert:

log-queries-not-using-indexes = /var/log/mysql-indexes.log

Insert the following into /etc/my.cnf:

log-slow-queries = /var/log/mysql/mysql-slow.log
long_query_time = 5

Save my.cnf and do the following when you return to a shell:

#touch /var/log/mysql/mysql-slow.log
#chown mysql:mysql /var/log/mysql/mysql-slow.log
#service mysql restart

From Day32.com:

http://www.day32.com/MySQL/tuning-primer.sh


# wget http://www.day32.com/MySQL/tuning-primer.sh
# sh tuning-primer.sh


Sample output:

-- MYSQL PERFORMANCE TUNING PRIMER --
- By: Matthew Montgomery -

MySQL Version 5.0.81-community i686

Uptime = 14 days 0 hrs 20 min 44 sec
Avg. qps = 10
Total Questions = 12160398
Threads Connected = 3

Server has been running for over 48hrs.
It should be safe to follow these recommendations

To find out more information on how each of these
runtime variables effects performance visit:

http://dev.mysql.com/doc/refman/5.0/en/server-system-variables.html

Visit http://www.mysql.com/products/enterprise/advisors.html
for info about MySQL’s Enterprise Monitoring and Advisory Service

SLOW QUERIES
The slow query log is NOT enabled.
Current long_query_time = 10 sec.
You have 90 out of 12160419 that take longer than 10 sec. to complete
Your long_query_time may be too high, I typically set this under 5 sec.

BINARY UPDATE LOG
The binary update log is NOT enabled.
You will not be able to do point in time recovery
See http://dev.mysql.com/doc/refman/5.0/en/point-in-time-recovery.html

WORKER THREADS
Current thread_cache_size = 8
Current threads_cached = 5
Current threads_per_sec = 0
Historic threads_per_sec = 0
Your thread_cache_size is fine

MAX CONNECTIONS
Current max_connections = 100
Current threads_connected = 3
Historic max_used_connections = 101
The number of used connections is 101% of the configured maximum.
You should raise max_connections

MEMORY USAGE
Max Memory Ever Allocated : 1.63 G
Configured Max Per-thread Buffers : 1.20 G
Configured Max Global Buffers : 426 M
Configured Max Memory Limit : 1.61 G
Physical Memory : 3.96 G
Max memory limit seem to be within acceptable norms

KEY BUFFER
Current MyISAM index space = 108 M
Current key_buffer_size = 384 M
Key cache miss rate is 1 : 3157
Key buffer free ratio = 85 %
Your key_buffer_size seems to be fine

QUERY CACHE
Query cache is enabled
Current query_cache_size = 32 M
Current query_cache_used = 18 M
Current query_cache_limit = 1 M
Current Query cache Memory fill ratio = 59.10 %
Current query_cache_min_res_unit = 4 K
MySQL won’t cache query results that are larger than query_cache_limit in size

SORT OPERATIONS
Current sort_buffer_size = 2 M
Current read_rnd_buffer_size = 8 M
Sort buffer seems to be fine

JOINS
Current join_buffer_size = 132.00 K
You have had 53627 queries where a join could not use an index properly
You should enable “log-queries-not-using-indexes”
Then look for non indexed joins in the slow query log.
If you are unable to optimize your queries you may want to increase your
join_buffer_size to accommodate larger joins in one pass.

Note! This script will still suggest raising the join_buffer_size when
ANY joins not using indexes are found.

OPEN FILES LIMIT
Current open_files_limit = 4096 files
The open_files_limit should typically be set to at least 2x-3x
that of table_cache if you have heavy MyISAM usage.
Your open_files_limit value seems to be fine

TABLE CACHE
Current table_cache value = 512 tables
You have a total of 4104 tables
You have 512 open tables.
Current table_cache hit rate is 1%, while 100% of your table cache is in use
You should probably increase your table_cache

TEMP TABLES
Current max_heap_table_size = 16 M
Current tmp_table_size = 32 M
Of 1081722 temp tables, 35% were created on disk
Effective in-memory tmp_table_size is limited to max_heap_table_size.
Perhaps you should increase your tmp_table_size and/or max_heap_table_size
to reduce the number of disk-based temporary tables
Note! BLOB and TEXT columns are not allow in memory tables.
If you are using these columns raising these values might not impact your
ratio of on disk temp tables.

TABLE SCANS
Current read_buffer_size = 2 M
Current table scan ratio = 1537 : 1
read_buffer_size seems to be fine

TABLE LOCKING
Current Lock Wait ratio = 1 : 1545
You may benefit from selective use of InnoDB.
If you have long running SELECT’s against MyISAM tables and perform
frequent updates consider setting ‘low_priority_updates=1′
If you have a high concurrency of inserts

One more:

http://www.mysqltuner.pl

# wget http://www.mysqltuner.pl
# perl mysqltuner.pl


Sample Output:

>> MySQLTuner 1.0.0 – Major Hayden
>> Bug reports, feature requests, and downloads at http://mysqltuner.com/
>> Run with ‘–help’ for additional options and output filtering

——– General Statistics ————————————————–
[--] Skipped version check for MySQLTuner script
[OK] Currently running supported MySQL version 5.0.81-community
[!!] Switch to 64-bit OS – MySQL cannot currently use all of your RAM

——– Storage Engine Statistics ——————————————-
[--] Status: +Archive -BDB -Federated +InnoDB -ISAM -NDBCluster
[--] Data in MyISAM tables: 374M (Tables: 3987)
[--] Data in InnoDB tables: 3M (Tables: 98)
[--] Data in MEMORY tables: 0B (Tables: 2)
[!!] Total fragmented tables: 201

——– Performance Metrics ————————————————-
[--] Up for: 14d 0h 24m 52s (12M q [10.043 qps], 491K conn, TX: 3B, RX: 1B)
[--] Reads / Writes: 86% / 14%
[--] Total buffers: 442.0M global + 12.3M per thread (100 max threads)
[OK] Maximum possible memory usage: 1.6G (41% of installed RAM)
[OK] Slow queries: 0% (91/12M)
[!!] Highest connection usage: 100% (101/100)
[OK] Key buffer size / total MyISAM indexes: 384.0M/111.0M
[OK] Key buffer hit rate: 100.0% (3B cached / 1M reads)
[OK] Query cache efficiency: 75.8% (7M cached / 9M selects)
[!!] Query cache prunes per day: 33741
[OK] Sorts requiring temporary tables: 0% (1 temp sorts / 1M sorts)
[!!] Joins performed without indexes: 53627
[!!] Temporary tables created on disk: 35% (587K on disk / 1M total)
[OK] Thread cache hit rate: 99% (2K created / 491K connections)
[!!] Table cache hit rate: 1% (512 open / 38K opened)
[OK] Open file limit used: 24% (1K/4K)
[OK] Table locks acquired immediately: 99% (3M immediate / 3M locks)
[OK] InnoDB data size / buffer pool: 3.7M/8.0M

——– Recommendations —————————————————–
General recommendations:
Run OPTIMIZE TABLE to defragment tables for better performance
Enable the slow query log to troubleshoot bad queries
Reduce or eliminate persistent connections to reduce connection usage
Adjust your join queries to always utilize indexes
When making adjustments, make tmp_table_size/max_heap_table_size equal
Reduce your SELECT DISTINCT queries without LIMIT clauses
Increase table_cache gradually to avoid file descriptor limits
Variables to adjust:
max_connections (> 100)
wait_timeout (< 28800)
interactive_timeout (< 28800) query_cache_size (> 32M)
join_buffer_size (> 128.0K, or always use indexes with joins)
tmp_table_size (> 32M)
max_heap_table_size (> 16M)
table_cache (> 512)