Mysql – High CPU usage by Apache/MySQL

Apache2cpu-usageMySQLperformance

I have a problem with CPU usage on the website that uses WordPress, Apache, and MySQL. During the day, from time to time, CPU usage by MySQL and Apache goes up to 2400% (I have 24 cores in total), the server freezes, the average load goes up to 24.

Recently, there was a little more traffic than usual, but this thing shouldn't be permanent, right? I've updated the kernel, the database, libraries, restarted many times. And still, it freezes. I've looked at the process list of the DB, but there is nothing extraordinary. In the database, there are pretty large amounts of data. Just a couple of weeks ago it worked fine, and now it doesn't. So, it shouldn't be unoptimized queries.

What can be the causes of such behavior?

Update:

the result of A) SHOW GLOBAL STATUS LIKE 'com_%r%_table';

+-----------------------+-------+
| Variable_name         | Value |
+-----------------------+-------+
| Com_alter_table       | 5     |
| Com_create_table      | 34    |
| Com_drop_table        | 0     |
| Com_rename_table      | 0     |
| Com_show_create_table | 0     |
+-----------------------+-------+
5 rows in set (3.04 sec)

B) SHOW GLOBAL STATUS LIKE 'uptime%';

+---------------------------+--------+
| Variable_name             | Value  |
+---------------------------+--------+
| Uptime                    | 455524 |
| Uptime_since_flush_status | 455524 |
+---------------------------+--------+
2 rows in set (0.01 sec)

C) SHOW GLOBAL STATUS LIKE '%dirty%';

+--------------------------------+-------+
| Variable_name                  | Value |
+--------------------------------+-------+
| Innodb_buffer_pool_pages_dirty | 0     |
| Innodb_buffer_pool_bytes_dirty | 0     |
+--------------------------------+-------+
2 rows in set (0.00 sec)

p.s. I still have problems with the server.
I needed to change the character set on one of the databases, and it took a little more than a day to finish, with just 400 000 rows. Before, it used to take some time, but not that much. I was wondering, could it be, that after the DDOS attack, there can be some changes to the database, so that it performs worse?

Update 2:

mysqltuner results:

[--] Skipped version check for MySQLTuner script
[OK] Logged in using credentials from Debian maintenance account.
[OK] Currently running supported MySQL version 8.0.26-0ubuntu0.20.04.2
[OK] Operating on 64-bit architecture
 
-------- Log file Recommendations ------------------------------------------------------------------
[OK] Log file /var/log/mysql/error.log exists
[--] Log file: /var/log/mysql/error.log(0B)
[--] Log file /var/log/mysql/error.log is empty. Assuming log-rotation. Use --server-log={file} for explicit file
 
-------- Storage Engine Statistics -----------------------------------------------------------------
[--] Status: +ARCHIVE +BLACKHOLE +CSV -FEDERATED +InnoDB +MEMORY +MRG_MYISAM +MyISAM +PERFORMANCE_SCHEMA 
[--] Data in InnoDB tables: 262.4G (Tables: 179)
[OK] Total fragmented tables: 0
 
-------- Analysis Performance Metrics --------------------------------------------------------------
[--] innodb_stats_on_metadata: OFF
[OK] No stat updates during querying INFORMATION_SCHEMA.
 
-------- Security Recommendations ------------------------------------------------------------------
[--] Skipped due to unsupported feature for MySQL 8
 
-------- CVE Security Recommendations --------------------------------------------------------------
[OK] NO SECURITY CVE FOUND FOR YOUR VERSION
 
-------- Performance Metrics -----------------------------------------------------------------------
[--] Up for: 5d 11h 4m 6s (15M q [31.945 qps], 191K conn, TX: 80G, RX: 2G)
[--] Reads / Writes: 99% / 1%
[--] Binary logging is enabled (GTID MODE: OFF)
[--] Physical Memory     : 31.4G
[--] Max MySQL memory    : 9.8G
[--] Other process memory: 0B
[--] Total buffers: 176.0M global + 65.1M per thread (151 max threads)
[--] P_S Max memory usage: 72B
[--] Galera GCache Max memory usage: 0B
[OK] Maximum reached memory usage: 9.8G (31.14% of installed RAM)
[OK] Maximum possible memory usage: 9.8G (31.14% of installed RAM)
[OK] Overall possible memory usage with other process is compatible with memory available
[OK] Slow queries: 0% (0/15M)
[!!] Highest connection usage: 100%  (151/151)
[OK] Aborted connections: 0.09%  (174/191712)
[!!] name resolution is active : a reverse name resolution is made for each new connection and can reduce performance
[--] Query cache have been removed in MySQL 8
[OK] Sorts requiring temporary tables: 0% (0 temp sorts / 5M sorts)
[OK] No joins without indexes
[OK] Temporary tables created on disk: 0% (0 on disk / 2M total)
[OK] Thread cache hit rate: 92% (15K created / 191K connections)
[OK] Table cache hit rate: 99% (21M hits / 21M requests)
[OK] table_definition_cache(2000) is upper than number of tables(506)
[OK] Open file limit used: 0% (6/10K)
[OK] Table locks acquired immediately: 100% (9 immediate / 9 locks)
[OK] Binlog cache memory access: 99.57% (25538 Memory / 25647 Total)
 
-------- Performance schema ------------------------------------------------------------------------
[--] Memory used by P_S: 72B
[--] Sys schema is installed.
 
-------- ThreadPool Metrics ------------------------------------------------------------------------
[--] ThreadPool stat is disabled.
 
-------- MyISAM Metrics ----------------------------------------------------------------------------
[--] MyISAM Metrics are disabled on last MySQL versions.
 
-------- InnoDB Metrics ----------------------------------------------------------------------------
[--] InnoDB is enabled.
[--] InnoDB Thread Concurrency: 0
[OK] InnoDB File per table is activated
[!!] InnoDB buffer pool / data size: 128.0M/262.4G
[!!] Ratio InnoDB log file size / InnoDB Buffer pool size (75 %): 48.0M * 2/128.0M should be equal to 25%
[OK] InnoDB buffer pool instances: 1
[--] Number of InnoDB Buffer Pool Chunk : 1 for 1 Buffer Pool Instance(s)
[OK] Innodb_buffer_pool_size aligned with Innodb_buffer_pool_chunk_size & Innodb_buffer_pool_instances
[OK] InnoDB Read buffer efficiency: 98.29% (925392031 hits/ 941450541 total)
[!!] InnoDB Write Log efficiency: 309.39% (25100125 hits/ 8112662 total)
[!!] InnoDB log waits: 0.00% (65 waits / 33212787 writes)
 
-------- Aria Metrics ------------------------------------------------------------------------------
[--] Aria Storage Engine not available.
 
-------- TokuDB Metrics ----------------------------------------------------------------------------
[--] TokuDB is disabled.
 
-------- XtraDB Metrics ----------------------------------------------------------------------------
[--] XtraDB is disabled.
 
-------- Galera Metrics ----------------------------------------------------------------------------
[--] Galera is disabled.
 
-------- Replication Metrics -----------------------------------------------------------------------
[--] Galera Synchronous replication: NO
[--] No replication slave(s) for this server.
[--] Binlog format: ROW
[--] XA support enabled: ON
[--] Semi synchronous replication Master: Not Activated
[--] Semi synchronous replication Slave: Not Activated
[--] This is a standalone server
 
-------- Recommendations ---------------------------------------------------------------------------
General recommendations:
    Reduce or eliminate persistent connections to reduce connection usage
    Configure your accounts with ip or subnets only, then update your configuration with skip-name-resolve=1
    Before changing innodb_log_file_size and/or innodb_log_files_in_group read this: *link*
Variables to adjust:
    max_connections (> 151)
    wait_timeout (< 28800)
    interactive_timeout (< 28800)
    innodb_buffer_pool_size (>= 262.4G) if possible.
    innodb_log_file_size should be (=16M) if possible, so InnoDB total log files size equals to 25% of buffer pool size.
    innodb_log_buffer_size (>= 16M)

Update 3:

Today my server froze again. The process that overloaded the CPU was the apache2. I've managed to stop the service. And suddenly everything started working smoothly. I've tried to do the backup of the database, the one with a lot of rows, and it worked just fine. But, after some time it all froze again: CPU usage by some processes was at 2400%, the load average exceeded 24. So, my suggestion, that it's not the apache, that loads the CPU, not the MySQL either. Some of the processes, like htop or gzip, which I'm using for the backup, also have high CPU usage, from time to time. What could it be then? Could this be the result of a DDOS attack, and if so, how can I fix it?

Best Answer

Rate Per Second = RPS

Suggestions to consider for your my.cnf [mysqld] section

innodb_buffer_pool_size=22G  # from 128M to better accomodate your 262G of data
max_connections=256  # from 151 since you have had all connections used
thread_cache_size=150  # from 9 to reduce threads_created RPhr of 111
innodb_log_file_size=4G  # from 50M to support more than and hour before rotation
innodb_log_buffer_size=1G  # from 16M to support ~ 30 min before write to media

Performance should be significantly improved. There are many more opportunities to improve performance. View profile for contact info and free downloadable Utility Scripts to improve performance.

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Ubuntu – MySQL: How to get the “Maximum possible memory usage” down

You have a server with 256M, but you can't use all of that -- remember there's some OS overhead. Add to that with the fact you're over committing as other folks have mentioned and you'll definitely thrash here. 256M is only enough for a small DB, 20 connections is a lot with what you've got configured.

1) reduce your max connections to 4 (you're using 3 out of 20)

2) optimize your query cache better; 8M is really large, and 64M total is a lot based on your hits/prunes; try a 4/32 combo and see how it goes. Really I think a 2/24 combo would work for you.

3) you have no sorts requiring temp tables, why is that max_heap_table_size verb in there? Comment that out, use the defaults

4) do you actually have 128 tables? Try cutting that table_cache in half to 64 or 48

5) reduce thread_cache_size to 4

6) optimize those tables to reduce fragmenting

Those are some things to start with. It looks like you threw a bunch of numbers in a config without any actual profiling to know what you needed and have created a mess; if all else fails go back to the defaults and get rid of your custom settings and start over using some performance tuning guides you can find on Google. Get the output of SHOW VARIABLES and SHOW STATUS, find any one of a bajillion tuning guides and plug in your actual, real numbers into their equations and that'll tell you the exact-ish numbers you need to put in your config file.

MySQL DB causing high IO running Zabbix server

innodb_buffer_pool_size > 1G, because your dataset size is 1,8GB.

To decrease number of reads you need to increase innodb_buffer_pool_size. To decrease number of writes you need to edit your zabbix templates (disabling some unnecessary items like free inodes, increase intervals between checks).

You have Reads / Writes ratio at 57% / 43%, so enabling Query Cache will not help (it may make things worse, because writes to tables invalidates cache).

Think about increasing tmp_table_size and max_heap_table_size to avoid creating tmp tables on disk (13% of tmp tables). Temporary tables are in MB? it is count? If it is counter, its too high.

Decrease number of connection to 50 (your highest number was 33).

innodb_support_xa = false
innodb_buffer_pool_size = 256M # It depends how many memory is available to MySQL, more is better.
innodb_flush_log_at_trx_commit = 0 # disable writing to logs on every commit and disable fsync on each write
innodb_max_dirty_pages_pct = 90 # avoid flushing dirty pages to disk
innodb_flush_method = O_DIRECT # direct access to disk without OS cache
thread_cache_size = 4
query_cache_size = 0
table_cache = 80? # a little more than number_of_tables_in_zabbix_database

Usefull link about InnoDB optimization.

Best Answer

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Ubuntu – MySQL: How to get the “Maximum possible memory usage” down

MySQL DB causing high IO running Zabbix server

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