How to migrate MySQL data directory in docker container?
<p>I have a docker container running MySQL-5.5 with host data volume. I am upgrading my container to MySQL-5.6. I am starting a new container with the same host volume. MySQL was crashing in the container due to the crash of <code>mysql.user</code> table.</p>

<pre><code>[ERROR] Fatal error: Can't open and lock privilege tables: 
Incorrect key file for table 'user'; try to repair it
160523 12:04:13 mysqld_safe mysqld from pid file  /var/run/mysqld/mysqld.pid ended
</code></pre>

<p>I tried the following to fix that:</p>

<pre><code>root@container# mysqld --skip-grant-tables;
root@container# mysql -uroot -ppassword
mysql&gt; repair table user USE_FRM;
+------------+--------+----------+--------------------------------------------------+
| Table      | Op     | Msg_type | Msg_text                                         |
+------------+--------+----------+--------------------------------------------------+
| mysql.user | repair | info     | Key 1 - Found wrong stored record at 0           |
| mysql.user | repair | info     | Found block that points outside data file at 184 |
| mysql.user | repair | info     | Found block that points outside data file at 292 |
| mysql.user | repair | info     | Found block that points outside data file at 296 |
| mysql.user | repair | info     | Found block that points outside data file at 300 |
| mysql.user | repair | info     | Found block that points outside data file at 304 |
| mysql.user | repair | info     | Found block that points outside data file at 308 |
| mysql.user | repair | info     | Found block that points outside data file at 312 |
| mysql.user | repair | info     | Found block that points outside data file at 316 |
| mysql.user | repair | info     | Found block that points outside data file at 340 |
| mysql.user | repair | info     | Found block that points outside data file at 392 |
| mysql.user | repair | info     | Found block that points outside data file at 396 |
| mysql.user | repair | info     | Found block that points outside data file at 400 |
| mysql.user | repair | info     | Found block that points outside data file at 404 |
| mysql.user | repair | info     | Found block that points outside data file at 408 |
| mysql.user | repair | info     | Found block that points outside data file at 412 |
| mysql.user | repair | info     | Found block that points outside data file at 416 |
| mysql.user | repair | info     | Found block that points outside data file at 420 |
| mysql.user | repair | info     | Found block that points outside data file at 448 |
| mysql.user | repair | info     | Found block that points outside data file at 452 |
| mysql.user | repair | info     | Found block that points outside data file at 456 |
| mysql.user | repair | info     | Found block that points outside data file at 460 |
| mysql.user | repair | info     | Found block that points outside data file at 464 |
| mysql.user | repair | info     | Found block that points outside data file at 468 |
| mysql.user | repair | info     | Found block that points outside data file at 472 |
| mysql.user | repair | info     | Found block that points outside data file at 500 |
| mysql.user | repair | info     | Found block that points outside data file at 504 |
| mysql.user | repair | info     | Found block that points outside data file at 508 |
| mysql.user | repair | info     | Found block that points outside data file at 512 |
| mysql.user | repair | info     | Found block that points outside data file at 516 |
| mysql.user | repair | info     | Found block that points outside data file at 520 |
| mysql.user | repair | info     | Found block that points outside data file at 524 |
| mysql.user | repair | info     | Found block that points outside data file at 528 |
| mysql.user | repair | info     | Found block that points outside data file at 556 |
| mysql.user | repair | info     | Found block that points outside data file at 560 |
| mysql.user | repair | info     | Found block that points outside data file at 564 |
| mysql.user | repair | info     | Found block that points outside data file at 568 |
| mysql.user | repair | info     | Found block that points outside data file at 572 |
| mysql.user | repair | info     | Found block that points outside data file at 576 |
| mysql.user | repair | info     | Found block that points outside data file at 580 |
| mysql.user | repair | info     | Found block that points outside data file at 604 |
| mysql.user | repair | info     | Found block that points outside data file at 608 |
| mysql.user | repair | info     | Found block that points outside data file at 612 |
| mysql.user | repair | info     | Found block that points outside data file at 616 |
| mysql.user | repair | info     | Found block that points outside data file at 620 |
| mysql.user | repair | info     | Found block that points outside data file at 624 |
| mysql.user | repair | info     | Found block that points outside data file at 628 |
| mysql.user | repair | info     | Found block that points outside data file at 632 |
| mysql.user | repair | status   | OK                                               |
+------------+--------+----------+--------------------------------------------------+
49 rows in set (0.00 sec)
</code></pre>

<p><strong>Error:</strong>
I cannot log in into MySQL server using my username/password. Any idea on how should I upgrade my MySQL data?</p>

<pre><code>root@container# mysql -uroot -ppassword
Warning: Using a password on the command line interface can be insecure.
Welcome to the MySQL monitor.  Commands end with; or \g.
Your MySQL connection id is 2
Server version: 5.6.30-0ubuntu0.14.04.1 (Ubuntu)

Copyright (c) 2000, 2016, Oracle and/or its affiliates. All rights reserved.

Oracle is a registered trademark of Oracle Corporation and/or its affiliates. Other names may be trademarks of their respective owners.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

mysql&gt; exit;
Bye
root@container# ps -ef|grep mysql              
root      1509 31492  0 12:15 ?        00:00:00 grep --color=auto mysql
mysql    31281  4823  0 12:06 ?        00:00:01 mysqld --skip-grant-tables --user=mysql
root@container# kill -9 31281
root@container# ps -ef|grep mysql
root      1698 31492  0 12:16 ?        00:00:00 grep --color=auto mysql
root@container# mysqld_safe &amp;
[1] 1700
root@container# 160523 12:16:34 mysqld_safe Can't log to error log and syslog at the same time.  Remove all --log-error configuration     options for --syslog to take effect.
160523 12:16:34 mysqld_safe Logging to '/var/log/mysql/error.log'.
160523 12:16:34 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
^C
root@container# mysql -uroot -ppassword
Warning: Using a password on the command line interface can be insecure.
ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES)
root@container# 
</code></pre>

<p>Reference:</p>

<p><a href="https://stackoverflow.com/questions/28521530/mysql-fatal-error-cant-open-and-lock-privilege-tables-incorrect-file-format">MySQL Fatal error: Can&#39;t open and lock privilege tables: Incorrect file format &#39;user&#39;</a>
<a href="https://bugs.mysql.com/bug.php?id=68385" rel="nofollow noreferrer">https://bugs.mysql.com/bug.php?id=68385</a></p>