The solution is simple but strange, if you copy your /var/lib/mysql directory to another server and think it will work, be sure to check if you have /var/log/mysql and binary log files.  If you do, the server will not work and will give you errors like below and crash without the proper log files.

UPDATE user SET password=password("newpass") WHERE user='root';
flush privileges;

ERROR 2013 (HY000): Lost connection to MySQL server during query

No connection. Trying to reconnect...
Connection id:    1
Current database: *** NONE ***

Database changed


/var/log/mysqld.log output:

As we can see it is crashing and also looking for non-existent logfiles.

170116  2:31:44  InnoDB: Started; log sequence number 4 1641421037
170116  2:31:44 [Note] /usr/libexec/mysqld: ready for connections.
Version: '5.1.73'  socket: '/var/lib/mysql/mysql.sock'  port: 3306  Source distribution
170116  2:31:45  InnoDB: Assertion failure in thread 140102772668160 in file handler/ha_innodb.cc line 875
InnoDB: Failing assertion: cset == 0
InnoDB: We intentionally generate a memory trap.
InnoDB: Submit a detailed bug report to http://bugs.mysql.com.
InnoDB: If you get repeated assertion failures or crashes, even
InnoDB: immediately after the mysqld startup, there may be
InnoDB: corruption in the InnoDB tablespace. Please refer to
InnoDB: http://dev.mysql.com/doc/refman/5.1/en/forcing-innodb-recovery.html
InnoDB: about forcing recovery.
07:31:45 UTC - mysqld got signal 6 ;
This could be because you hit a bug. It is also possible that this binary
or one of the libraries it was linked against is corrupt, improperly built,
or misconfigured. This error can also be caused by malfunctioning hardware.
We will try our best to scrape up some info that will hopefully help
diagnose the problem, but since we have already crashed,
something is definitely wrong and this may fail.

key_buffer_size=16384
read_buffer_size=262144
max_used_connections=0
max_threads=151
thread_count=0
connection_count=0
It is possible that mysqld could use up to
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 49909 K  bytes of memory
Hope that's ok; if not, decrease some variables in the equation.

Thread pointer: 0x0
Attempting backtrace. You can use the following information to find out
where mysqld died. If you see no messages after this, something went
terribly wrong...
stack_bottom = 0 thread_stack 0x20000
/usr/libexec/mysqld(my_print_stacktrace+0x29) [0x8509f9]
/usr/libexec/mysqld(handle_fatal_signal+0x483) [0x6a3f13]
/lib64/libpthread.so.0(+0xf7e0) [0x7f6c44f1c7e0]
/lib64/libc.so.6(gsignal+0x35) [0x7f6c435505e5]
/lib64/libc.so.6(abort+0x175) [0x7f6c43551dc5]
/usr/libexec/mysqld() [0x72d7ab]
/usr/libexec/mysqld(dict_mem_table_add_col+0x20e) [0x7605de]
/usr/libexec/mysqld(dict_load_table+0x99e) [0x75bf8e]
/usr/libexec/mysqld(dict_load_table_on_id+0x403) [0x75cd13]
/usr/libexec/mysqld(row_purge_step+0x39c) [0x7b360c]
/usr/libexec/mysqld(que_run_threads+0x55b) [0x7a255b]
/usr/libexec/mysqld(trx_purge+0x332) [0x7cc902]
/usr/libexec/mysqld(srv_master_thread+0x708) [0x7c5298]
/lib64/libpthread.so.0(+0x7aa1) [0x7f6c44f14aa1]
/lib64/libc.so.6(clone+0x6d) [0x7f6c43606aad]
The manual page at http://dev.mysql.com/doc/mysql/en/crashing.html contains
information that should help you find out what is causing the crash.
170116 02:31:45 mysqld_safe Number of processes running now: 0
170116 02:31:45 mysqld_safe mysqld restarted
170116  2:31:45 [Warning] '--skip-locking' is deprecated and will be removed in a future release. Please use '--skip-external-locking' instead.
170116  2:31:45  InnoDB: Initializing buffer pool, size = 8.0M
170116  2:31:45  InnoDB: Completed initialization of buffer pool
InnoDB: The log sequence number in ibdata files does not match
InnoDB: the log sequence number in the ib_logfiles!
170116  2:31:45  InnoDB: Database was not shut down normally!
InnoDB: Starting crash recovery.
InnoDB: Reading tablespace information from the .ibd files...
InnoDB: Restoring possible half-written data pages from the doublewrite
InnoDB: buffer...
InnoDB: In a MySQL replication slave the last master binlog file
InnoDB: position 0 6823363, file name bin.000001
InnoDB: Last MySQL binlog file position 0 611287495, file name /var/log/mysql/bin.000118
170116  2:31:45  InnoDB: Started; log sequence number 4 1641421037
170116  2:31:45 [Note] /usr/libexec/mysqld: ready for connections.
Version: '5.1.73'  socket: '/var/lib/mysql/mysql.sock'  port: 3306  Source distribution

The solution

Make sure you copy /var/log/mysql as well.

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