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Problema Mysql - Demorando muito pra responder e ás vezes nem responde

Roberto Monteiro
   - 05 out 2016

Será que alguém pode me ajudar? Eu administro um sistema que funciona via intranet em uma rede institucional que abrange um estado inteiro, ele roda virtualizado em uma blade no ambiente linux Debian Jessie 8, seguem as configurações do servidor:

Processador Intel Xeon X5650 2.67 GHz com 8 núcleos,
16 GB de memória ram,
600 GB de espaço de disco
servidor Apache 2.4.10,
MySQL 5.5.50-0+deb8u1
PHP 5.6.24-0+deb8u1

O problema é que o sistema funcionava corretamente na versão 7 do Debian, porém, após atualizar a versão para o Jessie 8, ele tem apresentado algumas inconsistências no quesito conexão de clientes, alguns clientes se conectam normalmente, enquanto outros ficam bastante tempo esperando resposta do servidor ou aguardando conexão e acaba dando tempo limite esgotado. Já modifiquei de várias formas o arquivo my.cnf a fim de tentar solucionar o problema, entretanto não obtive nenhum sucesso, rodei também o tuning-primer.sh e o mysqltuner.pl, segui as instruções de otimização de ambos e nenhum resultado satisfatório. Segue o arquivo my.cnf para que alguém possa verificar e talvez viabilizar uma solução cabível.
#Código

# 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
skip-innodb_checksums
skip-name-resolve
#
# 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		= 512M
max_allowed_packet	= 64M
thread_stack		= 16M
thread_cache_size       = 10
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched
myisam-recover         = BACKUP
max_connections        = 500
table_cache            = 2048
thread_concurrency     = 10000
wait_timeout	       = 15
#
# * 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
#slow_query_log_file = /var/log/mysql/mysql-slow.log
#slow_query_log      = 1
#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
#innodb_thread_concurrency	= 10000
#innodb_thread_sleepy_delay	= 15


[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/