[debian-mysql] Bug#870433: mysql-server: crash during upgrade to mariadb

Tue Aug 1 22:26:41 UTC 2017

Package: mysql-server
Version: 5.5.9999+default
Severity: important

Dear Maintainer,

the post install step fails with:

```
Setting up mariadb-server-10.1 (10.1.23-9+deb9u1) ...
/var/lib/dpkg/info/mariadb-server-10.1.postinst: line 17:  8957 Done                    echo "$password_column_fix_query"
      8958 Aborted                 | $MYSQL_BOOTSTRAP 2>&1
      8959                       | $ERR_LOGGER
dpkg: error processing package mariadb-server-10.1 (--configure):
 subprocess installed post-installation script returned error exit status 134
dpkg: dependency problems prevent configuration of default-mysql-server:
 default-mysql-server depends on mariadb-server-10.1; however:
  Package mariadb-server-10.1 is not configured yet.

dpkg: error processing package default-mysql-server (--configure):
 dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of mysql-server:
 mysql-server depends on default-mysql-server; however:
  Package default-mysql-server is not configured yet.

dpkg: error processing package mysql-server (--configure):
 dependency problems - leaving unconfigured
Errors were encountered while processing:
 mariadb-server-10.1
 default-mysql-server
 mysql-server
E: Sub-process /usr/bin/dpkg returned an error code (1)
```

Probably caused by:

```
» /usr/bin/mysql_install_db --skip-auth-anonymous-user --auth-root-authentication-method=socket --rpm --cross-bootstrap --user=mysql --disable-log-bin
2017-08-02  0:20:17 139707596689984 [Note] /usr/sbin/mysqld (mysqld 10.1.23-MariaDB-9+deb9u1) starting as process 8381 ...
Aborted

Installation of system tables failed!  Examine the logs in
/var/lib/mysql for more information.

The problem could be conflicting information in an external
my.cnf files. You can ignore these by doing:

    shell> /usr/scripts/scripts/mysql_install_db --defaults-file=~/.my.cnf

You can also try to start the mysqld daemon with:

    shell> /usr/sbin/mysqld --skip-grant --general-log &

and use the command line tool /usr/bin/mysql
to connect to the mysql database and look at the grant tables:

    shell> /usr/bin/mysql -u root mysql
    mysql> show tables;

Try 'mysqld --help' if you have problems with paths.  Using
--general-log gives you a log in /var/lib/mysql that may be helpful.

The latest information about mysql_install_db is available at
https://mariadb.com/kb/en/installing-system-tables-mysql_install_db
MariaDB is hosted on launchpad; You can find the latest source and
email lists at http://launchpad.net/maria

Please check all of the above before submitting a bug report
at http://mariadb.org/jira
```

The following error can be found in the logs:

```
2017-08-02  0:12:02 139668228993600 [Note] InnoDB: Using mutexes to ref count buffer pool pages
2017-08-02  0:12:02 139668228993600 [Note] InnoDB: The InnoDB memory heap is disabled
2017-08-02  0:12:02 139668228993600 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2017-08-02  0:12:02 139668228993600 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
2017-08-02  0:12:02 139668228993600 [Note] InnoDB: Compressed tables use zlib 1.2.8
2017-08-02  0:12:02 139668228993600 [Note] InnoDB: Using Linux native AIO
2017-08-02  0:12:02 139668228993600 [Note] InnoDB: Using generic crc32 instructions
2017-08-02  0:12:02 139668228993600 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2017-08-02  0:12:02 139668228993600 [Note] InnoDB: Completed initialization of buffer pool
2017-08-02  0:12:02 139668228993600 [Note] InnoDB: Highest supported file format is Barracuda.
2017-08-02  0:12:02 139668228993600 [Note] InnoDB: Starting crash recovery from checkpoint LSN=625800204
2017-08-02  0:12:02 139668228993600 [Note] InnoDB: Restoring possible half-written data pages from the do
ublewrite buffer...
2017-08-02  0:12:03 139668228993600 [Note] InnoDB: 128 rollback segment(s) are active.
2017-08-02  0:12:03 139668228993600 [Note] InnoDB: Waiting for purge to start
2017-08-02 00:12:03 7f06e87fa700  InnoDB: Assertion failure in thread 139667647211264 in file trx0purge.cc line 692
InnoDB: Failing assertion: purge_sys->iter.trx_no <= purge_sys->rseg->last_trx_no
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/5.6/en/forcing-innodb-recovery.html
InnoDB: about forcing recovery.
170802  0:12:03 [ERROR] 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.

To report this bug, see https://mariadb.com/kb/en/reporting-bugs

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.

Server version: 10.1.23-MariaDB-9+deb9u1
key_buffer_size=16777216
read_buffer_size=131072
max_used_connections=0
max_threads=153
thread_count=0
It is possible that mysqld could use up to 
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 352433 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 = 0x0 thread_stack 0x30000
/usr/sbin/mysqld(my_print_stacktrace+0x2e)[0x55e2acee09ce]
/usr/sbin/mysqld(handle_fatal_signal+0x3bd)[0x55e2aca28d1d]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x110c0)[0x7f070af3f0c0]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0xcf)[0x7f0709839fcf]
2017-08-02  0:12:03 139668228993600 [Note] InnoDB:  Percona XtraDB (http://www.percona.com) 5.6.35-80.0 started; log sequence number 625800314
/lib/x86_64-linux-gnu/libc.so.6(abort+0x16a)[0x7f070983b3fa]
/usr/sbin/mysqld(+0x909ab7)[0x55e2acd98ab7]
/usr/sbin/mysqld(+0x909f74)[0x55e2acd98f74]
/usr/sbin/mysqld(+0x90ac49)[0x55e2acd99c49]
/usr/sbin/mysqld(+0x8f947e)[0x55e2acd8847e]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x7494)[0x7f070af35494]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x3f)[0x7f07098efaff]
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.
```

Please let me know if you need further information

Regards

Jan

-- System Information:
Debian Release: 9.1
  APT prefers stable
  APT policy: (600, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 4.9.0-3-amd64 (SMP w/1 CPU core)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages mysql-server depends on:
iu  default-mysql-server  1.0.2

mysql-server recommends no packages.

mysql-server suggests no packages.

-- no debconf information