I recently loaded a large (~5GB) database from an SQLdump into a local MySQL server database. Loaded fine after a couple of tries, and initially I could query without a problem, although queries took ~1.5 minutes (which is not ideal, but fine).
Now, however, the queries drop out after a couple of seconds with
ERROR 2013 (HY000): Lost connection to MySQL server during query
and I even had a
ERROR 2006 (HY000): MySQL server has gone away No connection. Trying to reconnect...
This is extra weird because it worked fine for the first hour or so (both through
mysql-workbench and through the standard command line interface).
I've already upped my
max_allowed_packet size in
my.conf to 64MB, but that has no impact. Any ideas? I'm on Ubuntu 12.04 (3.3.6-030306-generic kernel).
UGH. So it looks like either a bug or maybe some kind of hardware failure. error.log shows a load of hex, followed by
p c -> y; InnoDB: End of page dump 130509 18:25:51 InnoDB: Page checksum 3880653435, prior-to-4.0.14-form checksum 3737975691 InnoDB: stored checksum 386314462, prior-to-4.0.14-form stored checksum 3737975691 InnoDB: Page lsn 4 759090297, low 4 bytes of lsn at page end 759090297 InnoDB: Page number (if stored to page already) 240815, InnoDB: space id (if created with >= MySQL-4.1.1 and stored already) 0 InnoDB: Page may be an update undo log page InnoDB: Page may be an index page where index id is 208 InnoDB: (index "PRIMARY" of table "chembl_15"."compound_structures") InnoDB: Database page corruption on disk or a failed InnoDB: file read of page 240815. InnoDB: You may have to recover from a backup. InnoDB: It is also possible that your operating InnoDB: system has corrupted its own file cache InnoDB: and rebooting your computer removes the InnoDB: error. InnoDB: If the corrupt page is an index page InnoDB: you can also try to fix the corruption InnoDB: by dumping, dropping, and reimporting InnoDB: the corrupt table. You can use CHECK InnoDB: TABLE to scan your table for corruption. InnoDB: See also http://dev.mysql.com/doc/refman/5.5/en/forcing-innodb-recovery.html InnoDB: about forcing recovery. InnoDB: Ending processing because of a corrupt database page. 130509 18:25:51 InnoDB: Assertion failure in thread 139737190622976 in file buf0buf.c line 3629 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. 23:25:51 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=2 max_threads=151 thread_count=2 connection_count=2 It is possible that mysqld could use up to key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 346682 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 0x30000 /usr/sbin/mysqld(my_print_stacktrace+0x29)[0x7f172cfd87b9] /usr/sbin/mysqld(handle_fatal_signal+0x483)[0x7f172ce9e8f3] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0)[0x7f172bbebcb0] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35)[0x7f172b257425] /lib/x86_64-linux-gnu/libc.so.6(abort+0x17b)[0x7f172b25ab8b] /usr/sbin/mysqld(+0x5f2b81)[0x7f172d075b81] /usr/sbin/mysqld(+0x620cc9)[0x7f172d0a3cc9] /usr/sbin/mysqld(+0x5ad1c0)[0x7f172d0301c0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x7e9a)[0x7f172bbe3e9a] /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7f172b314ccd] 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. 130509 18:25:51 [Note] Plugin 'FEDERATED' is disabled. 130509 18:25:51 InnoDB: The InnoDB memory heap is disabled 130509 18:25:51 InnoDB: Mutexes and rw_locks use GCC atomic builtins 130509 18:25:51 InnoDB: Compressed tables use zlib 18.104.22.168 130509 18:25:51 InnoDB: Initializing buffer pool, size = 128.0M 130509 18:25:52 InnoDB: Completed initialization of buffer pool 130509 18:25:52 InnoDB: highest supported file format is Barracuda. InnoDB: The log sequence number in ibdata files does not match InnoDB: the log sequence number in the ib_logfiles! 130509 18:25:52 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... 130509 18:25:52 InnoDB: Waiting for the background threads to start 130509 18:25:53 InnoDB: 5.5.31 started; log sequence number 21293128389 130509 18:25:53 [Note] Server hostname (bind-address): '127.0.0.1'; port: 3306 130509 18:25:53 [Note] - '127.0.0.1' resolves to '127.0.0.1'; 130509 18:25:53 [Note] Server socket created on IP: '127.0.0.1'. 130509 18:25:53 [Note] Event Scheduler: Loaded 0 events 130509 18:25:53 [Note] /usr/sbin/mysqld: ready for connections. Version: '5.5.31-0ubuntu0.12.04.1' socket: '/var/run/mysqld/mysqld.sock' port: 3306 (Ubuntu) InnoDB: Database page corruption on disk or a failed InnoDB: file read of page 240815. InnoDB: You may have to recover from a backup. 130509 18:27:15 InnoDB: Page dump in ascii and hex (16384 bytes): len 16384; hex
Any thoughts :-(