"ERROR 2013 (HY000): Lost connection to MySQL server during query" while dropping database

Question

I have an empty database that I cannot drop. Initially, it contained a table that I couldn't SELECT from. So I DROP'ed all tables from that database and tried to DROP the database without success :

mysql> drop database my_database;
ERROR 2013 (HY000): Lost connection to MySQL server during query

Now I have an empty database that I cannot remove in my server.

I check the mysql error.log, here is the output :

130812 10:02:45  InnoDB: Assertion failure in thread 140409656780544 in file row0mysql.c line 3682
InnoDB: Failing assertion: table
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/5.5/en/forcing-innodb-recovery.html
InnoDB: about forcing recovery.
14:02:45 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=16777216
read_buffer_size=131072
max_used_connections=3
max_threads=151
thread_count=3
connection_count=3
It is possible that mysqld could use up to
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 346685 K  bytes of memory
Hope that's ok; if not, decrease some variables in the equation.

Thread pointer: 0x7fb3ad55d030
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 = 7fb3abb71e60 thread_stack 0x30000
/usr/sbin/mysqld(my_print_stacktrace+0x29)[0x7fb3ac1516b9]
/usr/sbin/mysqld(handle_fatal_signal+0x3d8)[0x7fb3ac039318]
/lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0)[0x7fb3aab96cb0]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35)[0x7fb3aa1ff425]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x17b)[0x7fb3aa202b8b]
/usr/sbin/mysqld(+0x561acd)[0x7fb3ac192acd]
/usr/sbin/mysqld(+0x542c63)[0x7fb3ac173c63]
/usr/sbin/mysqld(+0x40837f)[0x7fb3ac03937f]
/usr/sbin/mysqld(_Z24plugin_foreach_with_maskP3THDPFcS0_P13st_plugin_intPvEijS3_+0x165)[0x7fb3abf4daa5]
/usr/sbin/mysqld(_Z11mysql_rm_dbP3THDPcbb+0x300)[0x7fb3abf23580]
/usr/sbin/mysqld(_Z21mysql_execute_commandP3THD+0x203c)[0x7fb3abf418ac]
/usr/sbin/mysqld(+0x31301e)[0x7fb3abf4401e]
/usr/sbin/mysqld(_Z16dispatch_command19enum_server_commandP3THDPcj+0x19e7)[0x7fb3abf46247]
/usr/sbin/mysqld(_Z24do_handle_one_connectionP3THD+0x105)[0x7fb3abfe0405]
/usr/sbin/mysqld(handle_one_connection+0x50)[0x7fb3abfe0520]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x7e9a)[0x7fb3aab8ee9a]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7fb3aa2bcccd]

Trying to get some variables.
Some pointers may be invalid and cause the dump to abort.
Query (7fb388004b90): is an invalid pointer
Connection ID (thread ID): 59
Status: NOT_KILLED

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.
130812 10:02:45 [Note] Plugin 'FEDERATED' is disabled.
130812 10:02:45 InnoDB: The InnoDB memory heap is disabled
130812 10:02:45 InnoDB: Mutexes and rw_locks use GCC atomic builtins
130812 10:02:45 InnoDB: Compressed tables use zlib 1.2.7
130812 10:02:45 InnoDB: Using Linux native AIO
130812 10:02:45 InnoDB: Initializing buffer pool, size = 128.0M
130812 10:02:45 InnoDB: Completed initialization of buffer pool
130812 10:02:45 InnoDB: highest supported file format is Barracuda.
130812 10:02:45  InnoDB: Waiting for the background threads to start
130812 10:02:46 InnoDB: 5.5.32 started; log sequence number 25852489043
130812 10:02:46 InnoDB: !!! innodb_force_recovery is set to 4 !!!
130812 10:02:46 [Note] Server hostname (bind-address): '127.0.0.1'; port: 3306
130812 10:02:46 [Note]   - '127.0.0.1' resolves to '127.0.0.1';
130812 10:02:46 [Note] Server socket created on IP: '127.0.0.1'.
130812 10:02:46 [Note] Event Scheduler: Loaded 0 events
130812 10:02:46 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.5.32-0ubuntu0.12.10.1'  socket: '/var/run/mysqld/mysqld.sock'  port: 3306  (Ubuntu)

I tried to put the configuration innodb_force_recovery = 4 and restart MySQL but it had no effect at all.

Reinstalling the server is not an option here. It happened on many machines (2 Ubuntu and 2 CentOS), but I cannot reproduce the problem right now.

Answer 1

I believe it has to do with InnoDB table corruption. I too had a similar issue and was able to pinpoint it to a single table. I'm still in the process of correcting the issue through duplicating the table and removing the single record that is bad in my case.

This link helped me significantly:

Recovering InnoDB Table Corruption

Sorry for incomplete answer, but this helped me quite a bit once I found it.