Poorly configurated mysql server

Question

Recently I took all MySQL servers that we had over a few servers and put in a single VPS dedicated to MySQL. As a source of information, I used Aurimas Mikalauskas ebook "Speedemy - MySQL Configuration Tuning Handbook" to configure the server. It all looked great until I realize that it was eating away the swap (and probably going slow). Then I went to the config file and reduced the suggested memory to store innodb_buffer_pool_size to value even lower than the suggested 80%.

Today I went there to check how the server was doing, and notice it had eaten a bunch of my swap again, and since I don't trust myself, I decided to ask here what I may be doing wrong.

The server is a VPS with 16GB of RAM and 6 cores.

This is my free output:

              total        used        free      shared  buff/cache   available
Mem:       16393988    13286624     2009964         876     1097400     2798976
Swap:        975868      610360      365508

This is my configuration file (ignore the Portuguese comments):

#   Arquivo de configuração do mysql
#   Criado por Guilherme Richter, 19/05/2020

[client]
#   Usado apenas para casos especificos
port        = 3306
socket      = /var/run/mysqld/mysqld.sock

[mysql]
#   Configurações do cliente
auto-rehash                     # Auto completar        (DEFAULT: FALSE)

[mysqld]
#   Configuração do servidor
pid_file            = /var/run/mysqld/mysqld.pid
socket              = /var/run/mysqld/mysqld.sock
datadir             = /var/lib/mysql
log_error           = /var/log/mysql/error.log
user                = mysql
bind_address        = 0.0.0.0       # Ouve todos os endereços

#   Configurações genericas do servidor
max_allowed_packet          = 32M       # Tamanho maximo do pacote. (DEFAULT: 64M)
max_connections             = 2000      # Maximo de coneções        (DEFAULT: 151)
open_files_limit            = 10000     # Maximo de arquivos abertos    (DEFAULT: 10000)
tmp_table_size              = 64M       # Limite tamanho tabela em mem  (DEFAULT: 16M)
max_heap_table_size         = 64M       # Limite tamanho tabela em mem  (DEFAULT: 16M)
tmpdir                      = /tmp      # Diretorio /tmp/       (DEFAULT: /tmp/)
default_storage_engine      = InnoDB    # Engine default        (DEFAULT: InnoDB)
skip_name_resolve                       # Desabilita resolução DNS  (DEFAULT: FALSE)

#   Configurações de log binario
log_bin                         # Log binario ativo     (DEFAULT: TRUE)
server_id                   = 1     # Identifica servidor para log  (DEFAULT: 1)
max_binlog_size             = 256M      # Tamanho maximo log binario    (DEFAULT: 1G)
binlog_expire_logs_seconds  = 604800    # Max tempo log binario     (DEFAULT: 2592000)
sync_binlog                 = 0     # Somente pra replicação    (DEFAULT: TRUE)

#   Configurações especificas do InnoDB
innodb_buffer_pool_size         = 10000M    # Tamanho do buffer (<80% mem)  (DEFAULT: 128M)
#http://www.speedemy.com/mysql/17-key-mysql-config-file-settings/innodb_log_file_size/ (Verificar a melhor configuração quando o servidor estiver no ar.
innodb_log_file_size                = 256M      # Tamanho do log de recovery    (DEFAULT: 48M)
innodb_log_buffer_size              = 16M       # Tamanho do buffer     (DEFAULT: 16M)
innodb_flush_log_at_trx_commit      = 0     # Commita o banco a cada evento (DEFAULT: 1)
innodb_flush_method                 = O_DIRECT  # Evita double buffer       (DEFAULT: fsync)
innodb_buffer_pool_instances        = 8     # Regioes que dividem o buffer  (DEFAULT: 8)
innodb_thread_concurrency           = 12        # Limita o numero de threads    (DEFAULT: 0)
innodb_io_capacity                  = 800       # Quantas escritas por segundo  (DEFAULT: 200)
innodb_io_capacity_max              = 3000      # Quantas escritas/s stress (DEFAULT: 2000)
innodb_stats_on_metadata            = 0     # Estatisticas redundantes  (DEFAULT: 0)
innodb_buffer_pool_dump_at_shutdown = 1     # Restart mais rapido       (DEFAULT: 1)
innodb_buffer_pool_load_at_startup  = 1     # Restart mais rápdio       (DEFAULT: 1)
innodb_buffer_pool_dump_pct         = 75        # Restart mais rápido       (DEFAULT: 25)
innodb_adaptive_hash_index_parts    = 16        # Partições de Index        (DEFAULT: 8)
innodb_checksum_algorithm           = crc32         # Aceleração de hardware    (DEFAULT: crc32)
innodb_read_io_threads              = 16        # Threads de leitura        (DEFAULT: 4)
innodb_write_io_threads             = 8     # Threads de escrita        (DEFAULT: 4)
innodb_file_per_table                       # Arquivo por tabelas       (DEFAULT: True)

#   Slow query log 
slow_query_log              = 1     # Guarda queries lentas     (DEFAULT: False)
long_query_time             = 1.0       # Tempo lite da query       (DEFAULT: 10s)

#   Função
log_bin_trust_function_creators     = 1;

I have a bunch of metrics from zabbix too, but I don't understand how to interpreat it.

Any ideas of what I am doing wrong, and how I could fix it?

Answer 1

The default for swappiness is 60; change it to 1: http://mysql.rjweb.org/doc.php/memory#swappiness

Answer 2

Swapping is normal, it doesn't necessarily indicate a problem.

You can, however, make sure the buffer pool never gets swapped out. Allocate 10GB of huge pages at boot time, and instruct MySQL to allocate it's innodb_buffer_pool from there (large-pages=1 in my.cnf). Huge pages are unswappable, so this will ensure your buffer pool never gets swapped out.