When your MySQL server accepts local connections but rejects JDBC connections (whether from Tomcat or external clients), you're typically facing one of these fundamental issues:

jdbc:mysql://host:port/db
// Common error pattern:
// CommunicationsException: The last packet sent successfully to the server was 0ms ago

First, eliminate basic network issues:

# From client machine:
telnet mysql_server 3306
nc -zv mysql_server 3306
# On MySQL server:
netstat -tuln | grep 3306

Check these critical settings in /etc/mysql/my.cnf or /etc/my.cnf:

[mysqld]
bind-address = 0.0.0.0  # Instead of 127.0.0.1
skip-name-resolve       # Prevent DNS lookup delays
wait_timeout = 28800    # Default might be too low
interactive_timeout = 28800
max_allowed_packet = 64M

For CentOS/RHEL:

sudo firewall-cmd --permanent --add-port=3306/tcp
sudo firewall-cmd --reload

For Ubuntu/Debian:

sudo ufw allow 3306

The most common pitfall - your user needs remote access rights:

CREATE USER 'appuser'@'%' IDENTIFIED BY 'password';
GRANT ALL PRIVILEGES ON mydb.* TO 'appuser'@'%';
FLUSH PRIVILEGES;

Enhance your connection URL with these parameters:

jdbc:mysql://host:3306/db?autoReconnect=true&useSSL=false&
serverTimezone=UTC&useLegacyDatetimeCode=false&
connectTimeout=5000&socketTimeout=30000

For context.xml (Tomcat 9+):

<Resource name="jdbc/MySQLDB" auth="Container"
          type="javax.sql.DataSource" 
          driverClassName="com.mysql.jdbc.Driver"
          url="jdbc:mysql://host:3306/db?useSSL=false"
          username="user" password="pass" 
          maxTotal="20" maxIdle="10" 
          validationQuery="SELECT 1" />

When using HikariCP in Spring Boot:

spring.datasource.hikari.connection-timeout=30000
spring.datasource.hikari.maximum-pool-size=10
spring.datasource.hikari.idle-timeout=600000
spring.datasource.hikari.max-lifetime=1800000

If enforcing SSL (recommended for production):

jdbc:mysql://host:3306/db?useSSL=true&
requireSSL=true&verifyServerCertificate=false&
clientCertificateKeyStoreUrl=file:/path/to/keystore&
clientCertificateKeyStorePassword=password&
trustCertificateKeyStoreUrl=file:/path/to/truststore&
trustCertificateKeyStorePassword=password

application.properties configuration:

spring.datasource.url=jdbc:mysql://host:3306/db?useSSL=false&serverTimezone=UTC
spring.datasource.username=user
spring.datasource.password=pass
spring.datasource.driver-class-name=com.mysql.cj.jdbc.Driver
spring.jpa.hibernate.ddl-auto=update
spring.jpa.properties.hibernate.dialect=org.hibernate.dialect.MySQL5Dialect

---

When working with MySQL 5.5 and Java applications, the "Communications link failure" error typically indicates one of these fundamental issues:

// Typical error pattern you might see
try {
    Connection conn = DriverManager.getConnection(
        "jdbc:mysql://myserver.com:3306/mydb", 
        "username", 
        "password");
} catch (SQLException e) {
    // This catches our problematic error
    System.out.println("Connection failed: " + e.getMessage());
}

Before diving into configuration, let's verify basic connectivity:

# From your application server terminal:
telnet myserver.com 3306
# Should return "Connected to myserver.com"

# Check MySQL user privileges:
mysql> SELECT Host, User FROM mysql.user;
mysql> SHOW GRANTS FOR 'youruser'@'%';

MySQL 5.5 has several security defaults that often block remote connections:

# In my.cnf or my.ini:
[mysqld]
bind-address = 0.0.0.0  # Instead of 127.0.0.1
skip-name-resolve       # Helps with connection speed
max_allowed_packet=64M  # Prevents packet size issues

# Critical for JDBC:
wait_timeout = 28800
interactive_timeout = 28800

The basic connection string often needs additional parameters:

String url = "jdbc:mysql://myserver.com:3306/mydb" +
    "?useSSL=false" +               // For local/dev environments
    "&autoReconnect=true" +         // Helps with dropped connections
    "&failOverReadOnly=false" +     // Important for write operations
    "&maxReconnects=10" +           // Reconnection attempts
    "&connectTimeout=5000" +        // 5 second timeout
    "&socketTimeout=30000";         // 30 second socket timeout

For Tomcat's context.xml or server.xml:

<Resource name="jdbc/MyDB" 
    auth="Container"
    type="javax.sql.DataSource"
    factory="org.apache.tomcat.jdbc.pool.DataSourceFactory"
    driverClassName="com.mysql.jdbc.Driver"
    url="jdbc:mysql://myserver.com:3306/mydb?useSSL=false"
    username="dbuser"
    password="dbpass"
    maxActive="100"
    maxIdle="30"
    maxWait="10000"
    validationQuery="SELECT 1"
    testOnBorrow="true"/>

MySQL 5.5 works best with specific JDBC driver versions:

// Maven dependency for MySQL Connector/J
<dependency>
    <groupId>mysql</groupId>
    <artifactId>mysql-connector-java</artifactId>
    <version>5.1.47</version>  // Stable for MySQL 5.5
</dependency>

Linux administrators often overlook these:

# Check firewall rules:
sudo iptables -L -n | grep 3306

# For CentOS/RHEL:
sudo semanage port -a -t mysqld_port_t -p tcp 3306
sudo setsebool -P httpd_can_network_connect_db 1

When standard approaches fail, enable MySQL's connection logging:

# Temporary logging (remove after debugging!)
mysql> SET GLOBAL general_log = 'ON';
mysql> SET GLOBAL log_output = 'TABLE';
mysql> SELECT * FROM mysql.general_log ORDER BY event_time DESC LIMIT 20;