Installing MySQL 5.6 from Source on Linux: A Complete Configuration Guide

System Preparation and Configuration

Building MySQL 5.6 from source requires careful system tuning to ensure optimal database performance. This guide covers the essential configuration steps needed before installation.

Storage Configuration

For production environments, RAID 10 provides the best balance between read performance, write performance, and data redundancy. Physical servers with SSD storage are strongly recommended for database workloads.

Recommended RAID controller settings:

  • Write Policy: WriteBack (WB)
  • Read Policy: ReadAdaptive or normal — avoid ReadAhead on database servers
  • IO Policy: Direct

File and Process Limits

Database servers require high file descriptor limits to handle numerous concurrent connections. Add the following entries to the system security configuration:


# vim /etc/security/limits.conf
*  soft  nofile    65535
*  hard  nofile   65535
*  soft        nproc         65535
*  hard        nproc         65535

NUMA Optimization

Non-Uniform Memory Access (NUMA) can cause memory allocation issues on database servers. Disable it through one of these methods:

  • BIOS settings (recommended for physical servers)
  • Kernel parameter: Add numa=off to the kernel line in /etc/grub.conf

Kernel Parameters

Tune the kernel for database workloads by modifying the system control configuration:


# vim  /etc/sysctl.conf
fs.file-max = 65536
vm.min_free_kbytes = 1048576
vm.swappiness = 10
vm.dirty_ratio = 10
vm.vfs_cache_pressure=150
vm.dirty_ratio = 10
vm.overcommit_memory = 1
vm.drop_caches = 1
kernel.panic = 60
net.core.somaxconn = 8192
net.ipv4.tcp_max_syn_backlog = 8192
vm.zone_reclaim_mode = 0

IO Scheduler Configuration

The deadline or noop scheduler algorithms perform best for database workloads. Apply the settings temporarily and persistently:


# Apply immediately (replace sda with your device name)
echo {SCHEDULER-NAME} > /sys/block/{DEVICE-NAME}/queue/scheduler

# Make permanent via /etc/rc.local
echo {SCHEDULER-NAME} > /sys/block/{DEVICE-NAME}/queue/scheduler

Transparent Huge Pages

Disable transparent huge pages (THP) to prevent potential memory allocation issues:


# Disable THP immediately
echo never > /sys/kernel/mm/transparent_hugepage/enabled
echo never > /sys/kernel/mm/transparent_hugepage/defrag

# Disable THP persistently via /etc/rc.local
echo never > /sys/kernel/mm/transparent_hugepage/enabled
echo never > /sys/kernel/mm/transparent_hugepage/defrag

MySQL Installation

Installing Dependencies

Install all required compilation tools and libraries:


# yum install -y nc rsync screen lrzsz expect cmake make gcc gcc-c++ \
perl bison bc thread libaio libaio-devel zlib zlib-devel nc \
python python-devel cmake ncurses-devel sysstat \
perl-ExtUtils-CBuilder perl-CPAN perl-Log-Dispatch \
perl-Config-Tiny perl-Parallel-ForkManager perl-Config-IniFiles

Creating System User

Create a dedicated system user for MySQL operations:


# groupadd mysql
# useradd -g mysql mysql

Directory Structure

Plan and create the directory structure for MySQL data, logs, and runtime files:


# mkdir -p /data/my3306
# mkdir -p /u02/my3306/data
# mkdir -p /u02/my3306/log/iblog
# mkdir -p /u02/my3306/log/binlog
# mkdir -p  /u02/my3306/tmp
# mkdir -p /u02/my3306/run
# chown -R mysql:mysql /u02/my3306

Compiling from Source

Extract the source archive and compile with configuration options tailored to your requirements:


# tar zxvf mysql-5.6.35.tar.gz
# cd mysql-5.6.35/
# cmake . \
-DCMAKE_INSTALL_PREFIX=/usr/local/mysql5.6 \
-DDEFAULT_CHARSET=utf8mb4 \
-DEXTRA_CHARSETS=all \
-DWITH_MYISAM_STORAGE_ENGINE=1 \
-DWITH_INNOBASE_STORAGE_ENGINE=1 \
-DWITH_ARCHIVE_STORAGE_ENGINE=1 \
-DWITH_PARTITION_STORAGE_ENGINE=1 \
-DWITH_PERFSCHEMA_STORAGE_ENGINE=1 \
-DWITH_FEDERATED_STORAGE_ENGINE=1

# make
# make install

Configuration File

Create the MySQL configuration file with production-appropriate settings:


# vim /u02/my3306/my.cnf
[client]
port=3306
default-character-set=utf8mb4
socket=/u02/my3306/mysql.sock

[mysql]
pid_file=/u02/my3306/run/mysqld.pid
default-character-set=utf8mb4
no-auto-rehash

[mysqld]
default-time-zone = '+8:00'
character-set-server = utf8mb4
collation-server = utf8mb4_general_ci
autocommit=1
general_log=off
explicit_defaults_for_timestamp=true

# GTID Configuration
gtid-mode                = ON
enforce_gtid_consistency = 1
log_slave_updates        = 1

# System Settings
basedir=/usr/local/mysql5.6
datadir=/u02/my3306/data
max_allowed_packet=1g
max_connections=3000
max_user_connections=2800
open_files_limit=65535
pid_file=/u02/my3306/run/mysqld.pid
port=3306
server_id=20633306
skip_name_resolve=ON
socket=/u02/my3306/run/mysql.sock
tmpdir=/u02/my3306/tmp
query_cache_type = 0
query_cache_size = 0
read-buffer-size = 32M

# Binary Log Settings
log_bin=/u02/my3306/log/binlog/binlog
binlog_cache_size=32768
binlog_format=row
expire_logs_days=7
log_slave_updates=ON
max_binlog_cache_size=2147483648
max_binlog_size=524288000
sync_binlog=100

# Logging Configuration
log_error=/u02/my3306/log/error.log
slow_query_log_file=/u02/my3306/log/slow.log
log_queries_not_using_indexes=0
slow_query_log=1
log_slave_updates=ON
log_slow_admin_statements=1
long_query_time=1
log-queries-not-using-indexes = 0

# Relay Log Settings
relay_log=/u02/my3306/log/relaylog
relay_log_index=/u02/my3306/log/relay.index
relay_log_info_file=/u02/my3306/log/relay-log.info

# Replication Settings
slave_load_tmpdir=/u02/my3306/tmp
slave_skip_errors=OFF

# InnoDB Settings
innodb_data_home_dir=/u02/my3306/log/iblog
innodb_log_group_home_dir=/u02/my3306/log/iblog
innodb_adaptive_flushing=ON
innodb_adaptive_hash_index=ON
innodb_autoinc_lock_mode=1
innodb_buffer_pool_instances=8
innodb_change_buffering=inserts
innodb_checksums=ON
innodb_buffer_pool_size= 4G
innodb_data_file_path=ibdata1:1024M:autoextend
innodb_doublewrite=ON
innodb_file_format=Barracuda
innodb_file_per_table=ON
innodb_flush_log_at_trx_commit=1
innodb_flush_method=O_DIRECT
innodb_io_capacity=1000
innodb_lock_wait_timeout=10
innodb_log_buffer_size=67108864
innodb_log_file_size=1048576000
innodb_log_files_in_group=4
innodb_max_dirty_pages_pct=75
innodb_open_files=60000
innodb_purge_threads=1
innodb_read_io_threads=4
innodb_stats_on_metadata=OFF
innodb_support_xa=ON
innodb_use_native_aio=OFF
innodb_write_io_threads=10

[mysqld_safe]
datadir=/u02/my3306/data

# chown -R mysql.mysql /u02

Database Initialization

Initialize the MySQL data directory with the specified configuration:


# cd /usr/local/mysql5.6
# ./scripts/mysql_install_db --defaults-file=/u02/my3306/my.cnf \
--datadir=/u02/my3306/data --user=mysql

Starting the Database

Launch the MySQL server process:


su - mysql -c "/usr/local/mysql5.6/bin/mysqld_safe --defaults-file=/u02/my3306/my.cnf &"

Post-Installation Security

Secure the installation by removing anonymous accounts, setting the root password, and removing the test database:


# /usr/local/mysql5.6/bin/mysql -uroot -p -S /u02/my3306/run/mysql.sock

# Execute these commands in MySQL client:
delete from mysql.user where user='';
set password=password('xxxxxxx');
drop database test;

Accessing the Database


/usr/local/mysql5.6/bin/mysql -uroot -p -S /u02/my3306/run/mysql.sock

Shutting Down the Daatbase


/usr/local/mysql5.6/bin/mysqladmin -uroot -p -S /u02/my3306/run/mysql.sock shutdown

Tags: MySQL Linux mysql-5.6 source-installation CMake

Posted on Sat, 13 Jun 2026 16:47:42 +0000 by jmandas

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