(2006) MySQL server has gone away - mysql

Question

I've read so many threads as well as the MySQL documentation about this issue and nothing suggested seems to work.
Here's my.cnf
[client]
port = 3306
socket = /var/run/mysqld/mysqld.sock
[mysqld_safe]
socket = /var/run/mysqld/mysqld.sock
nice = 0
[mysqld]
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
default-storage-engine=INNODB
character-set-server=utf8
collation-server=utf8_bin
interactive_timeout = 2880000
wait_timeout = 2880000
net_write_timeout = 6000
net_read_timeout = 6000
delayed_insert_timeout = 6000
key_buffer = 256M
key-buffer-size = 32M
max_allowed_packet = 600M
thread_stack = 256K
thread_cache_size = 8
max-connections = 500
thread-cache-size = 50
open-files-limit = 65535
table-definition-cache = 4096
table-open-cache = 10240
query-cache-type = 0
query_cache_limit = 2M
query_cache_size = 32M
myisam-recover = BACKUP
innodb_buffer_pool_size = 384M
innodb_additional_mem_pool_size = 20M
innodb_log_file_size = 10M
innodb_log_buffer_size = 64M
innodb_flush_log_at_trx_commit = 1
innodb_lock_wait_timeout = 180
log_error = /var/log/mysql/error.log
expire_logs_days = 10
max_binlog_size = 100M
[mysqldump]
quick
quote-names
max_allowed_packet = 64M
[isamchk]
key_buffer = 32M
In addition I ran queries in the MySQL CLI to make sure my settings were sticking, and they appear to be:
mysql> select ##global.wait_timeout, ##session.wait_timeout;
+-----------------------+------------------------+
| ##global.wait_timeout | ##session.wait_timeout |
+-----------------------+------------------------+
| 2880000 | 2880000 |
+-----------------------+------------------------+
mysql> select ##global.max_allowed_packet, ##session.max_allowed_packet;
+-----------------------------+------------------------------+
| ##global.max_allowed_packet | ##session.max_allowed_packet |
+-----------------------------+------------------------------+
| 629145600 | 629145600 |
+-----------------------------+------------------------------+
Server environment: Ubuntu Server 14.04LTS
MySQL version: 5.6
This is a dedicated MySQL server, it has no other apps on it.
I am not running out of memory:
MemTotal: 32948824 kB
MemFree: 31494136 kB
Cached: 281624 kB
SwapCached: 0 kB
SwapTotal: 33550332 kB
SwapFree: 33550332 kB

Answer 1

I was finally able to fix this issue but bypassing the MySQL Workbench Migration Tool and using mysqldup to generate the database .sql file used to restore to the server. Here's what I did:
Deleted all databases from the MySQL server that was timing out
Exported all the data from our backup database via mysqldump
Restored that dump file to the new MySQL server (the one that was
timing out)
Ran mysql_upgrade, all tables OK Executed the query: everything now
works
Here's the strange thing: mysqlcheck and mysql_upgrade, when run on the database that was somehow timing out, were returning status OK and not finding any errors. I do not know why, but I see this is a pretty strange and annoying problem, considering that's exactly what mysqlcheck is for.
Anyway if you're having this problem try to restore the database from an older backup (if you have one) and see if that works.