Bug #38573 Mysql 5.1.26 restarts showing a mysql.err possible bug report
Submitted: 5 Aug 2008 13:42 Modified: 8 Oct 2008 11:24
Reporter: David Fuller Email Updates:
Status: No Feedback Impact on me:
None 
Category:MySQL Server: Errors Severity:S3 (Non-critical)
Version:5.1.26-rc OS:Linux
Assigned to: CPU Architecture:Any

[5 Aug 2008 13:42] David Fuller
Description:
We have seen this error off and on since running 5.1.26-rc.  We have not seen this error before up to version 5.1.25-rc.

080805  6:04:58 - mysqld got signal 11 ;
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=262144
max_used_connections=60
max_threads=500
threads_connected=18
It is possible that mysqld could use up to
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 405551 K
bytes of memory
Hope that's ok; if not, decrease some variables in the equation.

thd: 0x7f83e8b56b90
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...
/usr/local/mysql/sbin/mysqld(print_stacktrace+0x1e) [0x6f96ce]
/usr/local/mysql/sbin/mysqld(handle_segfault+0x327) [0x5c0727]
/lib/libpthread.so.0 [0x7f8b742307d0]
/usr/local/mysql/sbin/mysqld [0x61b380]
/usr/local/mysql/sbin/mysqld [0x62f5b2]
/usr/local/mysql/sbin/mysqld [0x62f2cd]
/usr/local/mysql/sbin/mysqld [0x63323c]
/usr/local/mysql/sbin/mysqld(JOIN::optimize()+0x527) [0x6339f7]
/usr/local/mysql/sbin/mysqld(mysql_select(THD*, Item***, TABLE_LIST*, unsigned int, List<Item>&, Item*, unsigned int, st_order*, st_order*, Item*, st_order*, unsigned long long, select_result*, st_select_lex_unit*, st_select_lex*)+0xa5) [0x63c9b5]
/usr/local/mysql/sbin/mysqld(mysql_explain_union(THD*, st_select_lex_unit*, select_result*)+0x179) [0x63d219]
/usr/local/mysql/sbin/mysqld [0x5cb6f2]
/usr/local/mysql/sbin/mysqld(mysql_execute_command(THD*)+0x442f) [0x5d3c1f]
/usr/local/mysql/sbin/mysqld(mysql_parse(THD*, char const*, unsigned int, char const**)+0x2dd) [0x5d729d]
/usr/local/mysql/sbin/mysqld(dispatch_command(enum_server_command, THD*, char*, unsigned int)+0xb4d) [0x5d7dfd]
/usr/local/mysql/sbin/mysqld(do_command(THD*)+0xca) [0x5d873a]
/usr/local/mysql/sbin/mysqld(handle_one_connection+0x7dd) [0x5c8d1d]
/lib/libpthread.so.0 [0x7f8b742283f7]
/lib/libc.so.6(clone+0x6d) [0x7f8b729c7b2d]
Trying to get some variables.
Some pointers may be invalid and cause the dump to abort...
thd->query at 0x7f83f01db780  is invalid pointer
thd->thread_id=1593256
thd->killed=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.

It then happened again here:

080805  6:27:37 - mysqld got signal 11 ;
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=262144
max_used_connections=19
max_threads=500
threads_connected=16
It is possible that mysqld could use up to
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 405551 K
bytes of memory
Hope that's ok; if not, decrease some variables in the equation.

thd: 0x371d9790
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...
/usr/local/mysql/sbin/mysqld(print_stacktrace+0x1e) [0x6f96ce]
/usr/local/mysql/sbin/mysqld(handle_segfault+0x327) [0x5c0727]
/lib/libpthread.so.0 [0x7f8c4727c7d0]
/usr/local/mysql/sbin/mysqld [0x61b380]
/usr/local/mysql/sbin/mysqld [0x62f5b2]
/usr/local/mysql/sbin/mysqld [0x62f2cd]
/usr/local/mysql/sbin/mysqld [0x63323c]
/usr/local/mysql/sbin/mysqld(JOIN::optimize()+0x527) [0x6339f7]
/usr/local/mysql/sbin/mysqld(mysql_select(THD*, Item***, TABLE_LIST*, unsigned int, List<Item>&, Item*, unsigned int, st_order*, st_order*, Item*, st_order*, unsigned long long, select_result*, st_select_lex_unit*, st_select_lex*)+0xa5) [0x63c9b5]
/usr/local/mysql/sbin/mysqld(mysql_explain_union(THD*, st_select_lex_unit*, select_result*)+0x179) [0x63d219]
/usr/local/mysql/sbin/mysqld [0x5cb6f2]
/usr/local/mysql/sbin/mysqld(mysql_execute_command(THD*)+0x442f) [0x5d3c1f]
/usr/local/mysql/sbin/mysqld(mysql_parse(THD*, char const*, unsigned int, char const**)+0x2dd) [0x5d729d]
/usr/local/mysql/sbin/mysqld(dispatch_command(enum_server_command, THD*, char*, unsigned int)+0xb4d) [0x5d7dfd]
/usr/local/mysql/sbin/mysqld(do_command(THD*)+0xca) [0x5d873a]
/usr/local/mysql/sbin/mysqld(handle_one_connection+0x7dd) [0x5c8d1d]
/lib/libpthread.so.0 [0x7f8c472743f7]
/lib/libc.so.6(clone+0x6d) [0x7f8c45a13b2d]
Trying to get some variables.
Some pointers may be invalid and cause the dump to abort...
thd->query at 0x7f84c4ba5790  is invalid pointer
thd->thread_id=1995
thd->killed=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.
080805 06:27:37 mysqld_safe Number of processes running now: 0
080805 06:27:37 mysqld_safe mysqld restarted
080805  6:27:37 [Warning] The syntax 'for replication startup options' is deprecated and will be removed in MySQL 5.2. Please use 'CHANGE MASTER' instead.
InnoDB: Log scan progressed past the checkpoint lsn 302 913573923
080805  6:27:43  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: Doing recovery: scanned up to log sequence number 302 918816768
InnoDB: Doing recovery: scanned up to log sequence number 302 924059648
InnoDB: Doing recovery: scanned up to log sequence number 302 929302528
InnoDB: Doing recovery: scanned up to log sequence number 302 934545408
InnoDB: Doing recovery: scanned up to log sequence number 302 939788288
InnoDB: Doing recovery: scanned up to log sequence number 302 942515691
InnoDB: Transaction 0 1663209138 was in the XA prepared state.
InnoDB: 1 transaction(s) which must be rolled back or cleaned up
InnoDB: in total 0 row operations to undo
InnoDB: Trx id counter is 0 1663209472

The machine has 32GB of RAM, 28GB used for innodb.

How to repeat:
This happens with normal slaving. The machine only handles select queries from our users.  The inserts/updates are received from master.  Master is running 5.1.25-rc.
[5 Aug 2008 13:47] MySQL Verification Team
Thank you for the bug report. Looks this a server crash, could you run the query which provoked that crash and provide the dump of the table (create and data statements)?. That test case will help a lot. Thanks in advance.
[5 Sep 2008 23:00] Bugs System
No feedback was provided for this bug for over a month, so it is
being suspended automatically. If you are able to provide the
information that was originally requested, please do so and change
the status of the bug back to "Open".
[6 Sep 2008 16:25] David Fuller
Sorry for the late response but I have been out most of August very ill.

We have seen that the statement which causes the slaving to stop is an update query on one specific table.
[8 Sep 2008 11:24] Susanne Ebrecht
Many thanks for your feedback. Anyway, we need the update statement and the construction of your database ....
or better, we need a short test with which we can reproduce this behaviour.
[8 Oct 2008 23:00] Bugs System
No feedback was provided for this bug for over a month, so it is
being suspended automatically. If you are able to provide the
information that was originally requested, please do so and change
the status of the bug back to "Open".