mysql using 80% cpu usage

Question

my mysql is using about 70-80% every time of cpu and about 5% memory, and many times when high traffic, websites takes too long to load

could someone help me?

my server is 8 core with 32gb ram, im using centos 6.9 with cpanel/cloudlinux

here is my my.cnf and mysqltuner log

[mysqld]

innodb_file_per_table=1

local-infile=0

tmpdir =/dev/shm

max_connections = 1024

max_user_connections=650

key_buffer_size = 1024M

myisam_sort_buffer_size = 64M

#default-storage-engine=MyISAM

join_buffer_size = 1M

read_buffer_size = 1M

sort_buffer_size = 256K

thread_cache_size = 384

wait_timeout = 20

connect_timeout = 10

tmp_table_size = 64M

max_heap_table_size = 64M

max_allowed_packet = 64M

net_buffer_length = 16384

max_connect_errors = 10

thread_concurrency = 16

concurrent_insert = 2

read_rnd_buffer_size = 786432

bulk_insert_buffer_size = 8M

query_cache_limit = 7M

query_cache_size = 64M

query_cache_type = 1

query_prealloc_size = 262144

query_alloc_block_size = 65536

transaction_alloc_block_size = 8192

transaction_prealloc_size = 4096

max_write_lock_count = 16

innodb_buffer_pool_size=8G #75 % of RAM

innodb_flush_log_at_trx_commit=2

innodb_thread_concurrency=8 # of cpus

innodb_flush_method=O_DIRECT


[mysqld_safe]

open_files_limit = 8192


[mysqldump]

quick

max_allowed_packet = 16M


[myisamchk]

key_buffer = 384M

sort_buffer = 384M

read_buffer = 256M

/////////////////////////////

and here is mysqltuner output

-------- Performance Metrics -----------------------------------------------------------------------

[--] Up for: 2d 3h 25m 54s (23M q [127.290 qps], 468K conn, TX: 138G, RX: 7G)

[--] Reads / Writes: 89% / 11%

[--] Binary logging is disabled

[--] Physical Memory : 31.3G

[--] Max MySQL memory : 12.9G

[--] Other process memory: 3.9G

[--] Total buffers: 9.1G global + 3.2M per thread (1024 max threads)

[--] P_S Max memory usage: 555M

[--] Galera GCache Max memory usage: 0B

[OK] Maximum reached memory usage: 10.0G (31.77% of installed RAM)

[OK] Maximum possible memory usage: 12.9G (41.28% of installed RAM)

[OK] Overall possible memory usage with other process is compatible with memory available

[OK] Slow queries: 0% (5K/23M)

[OK] Highest usage of available connections: 8% (85/1024)

[OK] Aborted connections: 0.55% (2598/468725)

[!!] name resolution is active : a reverse name resolution is made for each new connection and can reduce performance

[!!] Query cache may be disabled by default due to mutex contention.

[OK] Query cache efficiency: 61.7% (12M cached / 19M selects)

[!!] Query cache prunes per day: 1008253

[OK] Sorts requiring temporary tables: 0% (2K temp sorts / 34M sorts)

[!!] Joins performed without indexes: 150075

[!!] Temporary tables created on disk: 52% (577K on disk / 1M total)

[OK] Thread cache hit rate: 99% (85 created / 468K connections)

[!!] Table cache hit rate: 1% (2K open / 102K opened)

[OK] Open file limit used: 24% (1K/8K)

[OK] Table locks acquired immediately: 99% (38M immediate / 38M locks)


-------- Performance schema ------------------------------------------------------------------------

[--] Memory used by P_S: 555.4M

[--] Sys schema isn't installed.


-------- ThreadPool Metrics ------------------------------------------------------------------------

[--] ThreadPool stat is disabled.


-------- MyISAM Metrics ----------------------------------------------------------------------------

[!!] Key buffer used: 26.8% (287M used / 1B cache)

[OK] Key buffer size / total MyISAM indexes: 1.0G/1.5G

[OK] Read Key buffer hit rate: 100.0% (2B cached / 572K reads)

[!!] Write Key buffer hit rate: 30.1% (2M cached / 899K writes)


-------- InnoDB Metrics ----------------------------------------------------------------------------

[--] InnoDB is enabled.

[--] InnoDB Thread Concurrency: 8

[OK] InnoDB File per table is activated

[OK] InnoDB buffer pool / data size: 8.0G/1.2G

[!!] Ratio InnoDB log file size / InnoDB Buffer pool size (1.171875 %): 48.0M * 2/8.0G should be equal 25%

[OK] InnoDB buffer pool instances: 8

[--] InnoDB Buffer Pool Chunk Size not used or defined in your version

[OK] InnoDB Read buffer efficiency: 100.00% (786635092 hits/ 786673138 total)

[!!] InnoDB Write Log efficiency: 51.42% (236640 hits/ 460226 total)

[OK] InnoDB log waits: 0.00% (0 waits / 223586 writes)


-------- AriaDB Metrics ----------------------------------------------------------------------------

[--] AriaDB is disabled.


-------- TokuDB Metrics ----------------------------------------------------------------------------

[--] TokuDB is disabled.


-------- XtraDB Metrics ----------------------------------------------------------------------------

[--] XtraDB is disabled.


-------- RocksDB Metrics ---------------------------------------------------------------------------

[--] RocksDB is disabled.


-------- Spider Metrics ----------------------------------------------------------------------------

[--] Spider is disabled.


-------- Connect Metrics ---------------------------------------------------------------------------

[--] Connect is disabled.


-------- Galera Metrics ----------------------------------------------------------------------------

[--] Galera is disabled.


-------- Replication Metrics -----------------------------------------------------------------------

[--] Galera Synchronous replication: NO

[--] No replication slave(s) for this server.

[--] This is a standalone server.


-------- Recommendations ---------------------------------------------------------------------------

General recommendations:

Run OPTIMIZE TABLE to defragment tables for better performance

OPTIMIZE TABLE `modsec`.`hits`; -- can free 382.777297973633 MB

Total freed space after theses OPTIMIZE TABLE : 382.777297973633 Mb

Set up a Secure Password for user@host ( SET PASSWORD FOR 'user'@'SpecificDNSorIp' = PASSWORD('secure_password'); )
 Restrict Host for user@% to user@SpecificDNSorIp

Configure your accounts with IP or subnets only, then update your configuration with skip-name-resolve=1

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 which have no LIMIT clause

Increase table_open_cache gradually to avoid file descriptor limits

Read this before increasing table_open_cache over 64: table_cache negative scalability

Beware that open_files_limit (8192) variable

should be greater than table_open_cache (2000)

Consider installing Sys schema from GitHub - mysql/mysql-sys: The MySQL sys schema

Read this before changing innodb_log_file_size and/or innodb_log_files_in_group: MySQL :: MySQL 5.7 Reference Manual :: 14.7.2 Changing the Number or Size of InnoDB Redo Log Files

Variables to adjust:

query_cache_size (=0)

query_cache_type (=0)

query_cache_size (> 64M)

join_buffer_size (> 1.0M, or always use indexes with joins)

tmp_table_size (> 64M)

max_heap_table_size (> 64M)

table_open_cache (> 2000)

innodb_log_file_size should be (=1G) if possible, so InnoDB total log files size equals to 25% of buffer pool size.

Answer 1

"You can't tune your way out of a performance problem."

The Query Cache may be part of the problem. It is running moderately efficiently, but there are a lot of prunes -- 12/second. Prunes are costly.

MyISAM may be part of the problem. You should convert to InnoDB.

While some of mysqltuner's and Wilson's suggestions will help some, the real problem with high CPU is almost always poor indexes or poorly formatted queries.

Turn on the slowlog with long_query_time 1; wait a day; run pt-query-digest or mysqldumpslow -s t to find the 'worst' queries. Then has for help in speeding them up. More.

This may be the most important tuner comment in your case:

[!!] Temporary tables created on disk: 52% (577K on disk / 1M total)

That's about 6/second, about the 90th percentile compared to other servers. Are you running on Windows? What version of MySQL?

Do you use TEXT for columns that could be suitably sized VARCHAR(...)? Do you use SELECT * when you need only smaller list of columns? Both of these can lead to tmp tables on disk.

Efficiency in many:many schema.

Answer 2

Suggestions for your my.cnf/ini [mysqld] section

#sort_buffer_size=256k  # disable to allow default to work for you
#read_buffer_size=1M  # disable to allow default to work for you
#read_rnd_buffer_size  # disable to allow default to work for you
#join_buffer_size  # disable to allow default to work for you

key_buffer_size=384M  # from 1024M only 287M used today
max_connections=164  # from 1024 because max_used_connections 85 today
wait_timeout=40  # from 20 seconds - does not allow much think time
#max_allowed_packet=64M  # to disable and allow 1M default if you need more,

in your SESSION< SET @max_allowed_packet=nnnnnn; up to 1G THAT IS THE LIMIT

#query_cache_limit=7M  # disable to allow default of 1M  only 9 would fit
query_cache_min_res_unit=512  #from def 4096 to increase capacity of QC
query_prealloc_size=32768  # 262144  to minimize RAM malloc
query_alloc_block_size=32768  # from 65535 to be same as p_a_s

Please spend 2 minutes at www.mysqlcalculator.com and you will find with the first 4 variables to be disabled, your RAM footprint is much larger than necessary for improved response time.

Answer 3

The query cache was implemented in a non-optimal way. It has contention problems and way too frequent data invalidation which could be the cause of your high CPU usage.

What is the value of innodb_log_file_size? If it is not at least 1G (I tend to prefer 2G anyway) you should actually increase it. Otherwise you will have flushing problems and, yes, this affects the CPU.

Per-session buffers can also affect the CPU usage negatively. The effect of choosing a too high or too low value is usually relevant. Just use the defaults.

I don't think that MyISAM can increase your CPU usage. Usually there are other reasons to get rid of it. But it is much less complex than InnoDB, that is why it should not be your CPU's enemy.