./configure --prefix=/usr/local/php-5.6.4 --with-config-file-path=/usr/local/php-5.6.4/etc --with-mysql=/usr --with-mysqli=/usr/bin/mysql_config --enable-fpm

提示：configure: error: Cannot find MySQL header files under /usr.

去除 /usr

重新运行编译命令

./configure --prefix=/usr/local/php-5.6.4 --with-config-file-path=/usr/local/php-5.6.4/etc --with-mysql --with-mysqli=/usr/bin/mysql_config --enable-fpm