Huge latency to connect webapp to docker mysql container via Hibernate - mysql

Question

I'm trying to port my web-app created on Windows, using Hibernate, XAMPP for Apache tomcat and mysql server, to Linux, using Docker.
After i've done the following steps, The first feature of my web.app is login/register form: On Windows all works perfectly, but with container there is latency about tens of minutes.. and sometime there is also 500 http error!!
docker run -d --name mysql-phpmyadmin -p 127.0.0.1:8686:80 -p 127.0.0.1:3306:3306 grzesiekb/mysql-phpmyadmin
docker run -d -p 8484:8080 -p 8007:8009 --name tomcat8-linked --link mysql-phpmyadmin:mysqlphp tomcat:8.0-jre8 and then deploy under webapps/ folder my warfile
In my hibernate.cfg.xml, you can see it here (i have problems to paste it in a viewable way) :)
in my mysql container my.cnf there is:
[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
#
# Instead of skip-networking the default is now to listen only on
# localhost which is more compatible and is not less secure.
bind-address = 0.0.0.0
#
# * Fine Tuning
#
key_buffer = 16M
max_allowed_packet = 16M
thread_stack = 192K
thread_cache_size = 8
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched
myisam-recover = BACKUP
#max_connections = 100
#table_cache = 64
#thread_concurrency = 10
#
# * 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
[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/
By default, this mysql container only allows connection from localhost: for allowing connections from everywhere, i've done:
GRANT ALL PRIVILEGES ON . TO 'root'#'%' IDENTIFIED BY 'password' WITH GRANT OPTION;
FLUSH PRIVILEGES;
Then i've imported my dql dump via phpmyadmin
Describe the results you received:
Huge latency, related to i don't know which problem, and in a random way there is no way to connect to mysql. No logs. My teacher said that probably it's a DNS problem related to Docker network.
Describe the results you expected:
Connection to the db immediately, like in Windows using XAMPP

Answer 1

You should try to make your setup as standard as possible to avoid bugs due to non-standard practices.
Use official or at least popular images (with millions of pulls) instead of your mysql-phpmyadmin with a hundred pulls :
https://hub.docker.com/search/?isAutomated=0&isOfficial=1&page=1&pullCount=0&q=mysql
https://hub.docker.com/search/?isAutomated=0&isOfficial=0&page=1&pullCount=0&q=phpmyadmin
I'm not sure why you declare ip with host port and container port, maybe don't do this if it's not necessary, publish only host port and container port, not ip.
Don't use --link since it's deprecated, create a bridge network and run each container with --network my-bridge-network.
Upgrade your Ubuntu to the latest LTS version (16.04.2) with the latest available "HWE" kernel for this LTS version (you have to upgrade kernel with a seperate command as explained here : sudo apt-get install --install-recommends xserver-xorg-hwe-16.04