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  1. Percona Server
  2. PS-992

LP #1598950: ALTER TABLE ... ENGINE = TOKUDB crashes on Ubuntu 12.04

    Details

    • Type: Bug
    • Status: Done
    • Priority: High
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: Packaging

      Description

      **Reported in Launchpad by Sveta Smirnova last update 26-05-2017 00:11:07

      ALTER TABLE ... ENGINE = TOKUDB crashes on Ubuntu 12.04

      How to repeat:

      0. Fresh Ubuntu Precise64 install:

      $ uname -a
      Linux precise64 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:39:51 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

      1. Download latest 5.6 version: Percona-Server-5.6.30-rel76.3-Linux.x86_64.ssl100

      2. Install jemalloc, libaio, libnuma, disable transparent pages:

      vagrant@precise64:~/Percona-Server-5.6.30-rel76.3-Linux.x86_64.ssl100/mysql-test$ sudo su
      root@precise64:/home/vagrant/Percona-Server-5.6.30-rel76.3-Linux.x86_64.ssl100/mysql-test# echo never > /sys/kernel/mm/transparent_hugepage/enabled
      root@precise64:/home/vagrant/Percona-Server-5.6.30-rel76.3-Linux.x86_64.ssl100/mysql-test# echo never > /sys/kernel/mm/transparent_hugepage/defrag
      root@precise64:/home/vagrant/Percona-Server-5.6.30-rel76.3-Linux.x86_64.ssl100/mysql-test# exit

      3. Start MTR:

      LD_PRELOAD=/usr/lib/libjemalloc.so ./mtr -start --suite=tokudb --mysqld=-log-bin=master auto_increment &

      4. Enable TokuDB:

      vagrant@precise64:~/Percona-Server-5.6.30-rel76.3-Linux.x86_64.ssl100/mysql-test$ sudo ../bin/ps_tokudb_admin --enable -uroot -h127.0.0.1 -P13001
      Checking if Percona Server is running with jemalloc enabled...
      INFO: Percona Server is running with jemalloc enabled.

      Checking transparent huge pages status on the system...
      INFO: Transparent huge pages are enabled (should be disabled).

      Checking if thp-setting=never option is already set in config file...
      INFO: Option thp-setting=never is set in the config file.

      Checking TokuDB engine plugin status...
      ERROR: TokuDB engine plugin is partially installed. Please cleanup manually.

      First strange thing: it complains about transparent pages, but they are disabled

      5. Verify TokuDB engine enabled:

      mysql> show engines;
      -------------------------------------------------------------------------------------------------------------------------------+

      Engine Support Comment Transactions XA Savepoints

      -------------------------------------------------------------------------------------------------------------------------------+

      InnoDB YES Percona-XtraDB, Supports transactions, row-level locking, and foreign keys YES YES YES
      MRG_MYISAM YES Collection of identical MyISAM tables NO NO NO
      MyISAM DEFAULT MyISAM storage engine NO NO NO
      BLACKHOLE YES /dev/null storage engine (anything you write to it disappears) NO NO NO
      CSV YES CSV storage engine NO NO NO
      TokuDB YES Percona TokuDB Storage Engine with Fractal Tree(tm) Technology YES YES YES

      ...

      6. create database sbtest;

      7. Create a table (non-TokuDB):

      sysbench --test=oltp --oltp-table-size=1000000 --mysql-user=root --mysql-host=127.0.0.1 --mysql-port=13001 prepare

      8. Alter sbtest table:

      mysql> alter table sbtest engine=tokudb;
      ERROR 2013 (HY000): Lost connection to MySQL server during query
      mysql> worker[1] Server [mysqld.1 - pid: 8200, winpid: 8200, exit: 256] died

      Only 0 of 1 completed.
      mysql-test-run: *** ERROR: Not all tests completed

      Relevant part of the error log file:

      Version: '5.6.30-76.3-log' socket: '/home/vagrant/Percona-Server-5.6.30-rel76.3-Linux.x86_64.ssl100/mysql-test/var/tmp/mysqld.1.sock' port: 13001 Percona Server (GPL), Release 76.3, Revision 3850db5
      21:30:04 UTC - 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.
      Please help us make Percona Server better by reporting any
      bugs at http://bugs.percona.com/

      key_buffer_size=1048576
      read_buffer_size=131072
      max_used_connections=1
      max_threads=153
      thread_count=1
      connection_count=1
      It is possible that mysqld could use up to
      key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 61881 K bytes of memory
      Hope that's ok; if not, decrease some variables in the equation.

      Thread pointer: 0x7f1914b5f000
      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 = 7f19218bae10 thread_stack 0x40000
      /home/vagrant/Percona-Server-5.6.30-rel76.3-Linux.x86_64.ssl100/bin/mysqld(my_print_stacktrace+0x2e)[0x8e087e]
      /home/vagrant/Percona-Server-5.6.30-rel76.3-Linux.x86_64.ssl100/bin/mysqld(handle_fatal_signal+0x491)[0x6a7881]
      /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0)[0x7f19212d7cb0]
      /usr/lib/libjemalloc.so(free+0x6b)[0x7f19214e8e1b]
      /lib/x86_64-linux-gnu/libpthread.so.0(pthread_create+0x279)[0x7f19212d03b9]
      /home/vagrant/Percona-Server-5.6.30-rel76.3-Linux.x86_64.ssl100/lib/mysql/plugin/ha_tokudb.so(Z20toku_ft_loader_closeP11ft_loader_sPFvP9toku_dbiiP10toku_dbtS4_PvES5_PFiS5_fES5+0x3a2)[0x7f191957d982]
      /home/vagrant/Percona-Server-5.6.30-rel76.3-Linux.x86_64.ssl100/lib/mysql/plugin/ha_tokudb.so(Z17toku_loader_closeP13_toku_loader+0x157)[0x7f191957e8f7]
      /home/vagrant/Percona-Server-5.6.30-rel76.3-Linux.x86_64.ssl100/lib/mysql/plugin/ha_tokudb.so(_ZN9ha_tokudb15end_bulk_insertEb+0x4be)[0x7f19194abd1e]
      /home/vagrant/Percona-Server-5.6.30-rel76.3-Linux.x86_64.ssl100/bin/mysqld(_Z17mysql_alter_tableP3THDPcS1_P24st_ha_create_informationP10TABLE_LISTP10Alter_infojP8st_orderb+0x2c4e)[0x769c6e]
      /home/vagrant/Percona-Server-5.6.30-rel76.3-Linux.x86_64.ssl100/bin/mysqld(_ZN19Sql_cmd_alter_table7executeEP3THD+0x43c)[0x83445c]
      /home/vagrant/Percona-Server-5.6.30-rel76.3-Linux.x86_64.ssl100/bin/mysqld(_Z21mysql_execute_commandP3THD+0xd9a)[0x71a95a]
      /home/vagrant/Percona-Server-5.6.30-rel76.3-Linux.x86_64.ssl100/bin/mysqld(_Z11mysql_parseP3THDPcjP12Parser_state+0x598)[0x71ef58]
      /home/vagrant/Percona-Server-5.6.30-rel76.3-Linux.x86_64.ssl100/bin/mysqld(_Z16dispatch_command19enum_server_commandP3THDPcj+0xef8)[0x71fee8]
      /home/vagrant/Percona-Server-5.6.30-rel76.3-Linux.x86_64.ssl100/bin/mysqld(_Z24do_handle_one_connectionP3THD+0x15f)[0x6f392f]
      /home/vagrant/Percona-Server-5.6.30-rel76.3-Linux.x86_64.ssl100/bin/mysqld(handle_one_connection+0x47)[0x6f3a17]
      /home/vagrant/Percona-Server-5.6.30-rel76.3-Linux.x86_64.ssl100/bin/mysqld(pfs_spawn_thread+0x143)[0xb3be23]
      /lib/x86_64-linux-gnu/libpthread.so.0(+0x7e9a)[0x7f19212cfe9a]
      /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7f191f5604bd]

      Trying to get some variables.
      Some pointers may be invalid and cause the dump to abort.
      Query (7f18fb01b010): alter table sbtest engine=tokudb
      Connection ID (thread ID): 5
      Status: NOT_KILLED

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                Reporter:
                lpjirasync lpjirasync (Inactive)
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                  Updated:
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