LP #1302882: InnoDB: Warning: table 'mysql/innodb_index_stats' in InnoDB data dictionary has unknown flags 50.

**Reported in Launchpad by Mark Casey last update 08-07-2014 07:47:56

I'm seeing this message when running XtraBackup, but others have said they see it in the error logs.

https://mobile.twitter.com/Savagedlight/status/436098380662452224?screen_name=Savagedlight
http://www.percona.com/forums/questions-discussions/mysql-and-percona-server/13799-problems-after-upgrade-to-5-6?_=1396649017509

Below are commands I used to reproduce on a new machine, followed by a very lightly spaced out and commented copy of the full console session.

Steps to reproduce on clean machine:

• I used an EC2 instance ( m1.small - Ubuntu Server 13.10 (PV) - ami-7eaecc4e (64-bit) ) -

ubuntu@ip-172-31-18-97:~$ sudo su
root@ip-172-31-18-97:/home/ubuntu# apt-key adv --keyserver keys.gnupg.net --recv-keys 1C4CBDCDCD2EFD2A
root@ip-172-31-18-97:/home/ubuntu# echo 'deb http://repo.percona.com/apt saucy main'>>/etc/apt/sources.list
root@ip-172-31-18-97:/home/ubuntu# echo 'deb-src http://repo.percona.com/apt saucy main'>>/etc/apt/sources.list
root@ip-172-31-18-97:/home/ubuntu# apt-get update
root@ip-172-31-18-97:/home/ubuntu# apt-get install percona-server-server-5.6 xtrabackup
[[ did not set root password ]]
root@ip-172-31-18-97:/home/ubuntu# mkdir /root/backup
root@ip-172-31-18-97:/home/ubuntu# echo '[mysqld]' > /etc/mysql/my.cnf
root@ip-172-31-18-97:/home/ubuntu# echo 'datadir=/var/lib/mysql' >> /etc/mysql/my.cnf
root@ip-172-31-18-97:/home/ubuntu# innobackupex /root/backup/
root@ip-172-31-18-97:/home/ubuntu# innobackupex --apply-log /root/backup/2014-04-04_22-32-23/
[[ no issue so far ]]
root@ip-172-31-18-97:/home/ubuntu# echo 'SET storage_engine=InnoDB; CREATE DATABASE foo' | mysql
root@ip-172-31-18-97:/home/ubuntu# echo 'SET storage_engine=InnoDB; use foo; CREATE TABLE IF NOT EXISTS bar (bar1 INT);' | mysql
root@ip-172-31-18-97:/home/ubuntu# echo 'use foo; INSERT INTO `bar` (`bar1`) VALUES ('154');' | mysql
root@ip-172-31-18-97:/home/ubuntu# rm /root/backup/2014-04-04_22-32-23/ -rf
root@ip-172-31-18-97:/home/ubuntu# innobackupex /root/backup/
root@ip-172-31-18-97:/home/ubuntu# innobackupex --apply-log /root/backup/2014-04-04_22-40-13/
root@ip-172-31-18-97:/home/ubuntu# echo 'SET storage_engine=InnoDB; use foo; CREATE TABLE IF NOT EXISTS baz (baz1 VARCHAR(20),baz2 DATE);' | mysql
root@ip-172-31-18-97:/home/ubuntu# echo 'use foo; INSERT INTO `baz` (`baz1`,`baz2`) VALUES ("Darlene Koch","1989-11-20"); ' | mysql
root@ip-172-31-18-97:/home/ubuntu# echo 'use foo; INSERT INTO `baz` (`baz1`,`baz2`) VALUES ("Lora Keller","1994-05-31"); ' | mysql
root@ip-172-31-18-97:/home/ubuntu# service mysql restart
root@ip-172-31-18-97:/home/ubuntu# rm /root/backup/2014-04-04_22-40-13/ -rf
root@ip-172-31-18-97:/home/ubuntu# innobackupex /root/backup/
root@ip-172-31-18-97:/home/ubuntu# innobackupex --apply-log /root/backup/2014-04-04_22-47-14/
...

InnoDB: Renaming log file ./ib_logfile101 to ./ib_logfile0
InnoDB: New log files created, LSN=1650086
InnoDB: Highest supported file format is Barracuda.
InnoDB: 128 rollback segment(s) are active.
InnoDB: Waiting for purge to start
2014-04-04 22:47:56 7f5e32d84700 InnoDB: Warning: table 'mysql/innodb_index_stats'
InnoDB: in InnoDB data dictionary has unknown flags 50.
2014-04-04 22:47:56 7f5e32d84700 InnoDB: Warning: table 'mysql/innodb_table_stats'
InnoDB: in InnoDB data dictionary has unknown flags 50.
InnoDB: 5.6.15 started; log sequence number 1650188

...
– Issue reached –

– FULL SESSION BELOW –

login as: ubuntu
Authenticating with public key "foo"

The programs included with the Ubuntu system are free software;
the exact distribution terms for each program are described in the
individual files in /usr/share/doc/*/copyright.

Ubuntu comes with ABSOLUTELY NO WARRANTY, to the extent permitted by
applicable law.

ubuntu@ip-172-31-18-97:~$ sudo su
root@ip-172-31-18-97:/home/ubuntu# apt-key adv --keyserver keys.gnupg.net --recv-keys 1C4CBDCDCD2EFD2A
Executing: gpg --ignore-time-conflict --no-options --no-default-keyring --secret-keyring /tmp/tmp.bLAmNjOphc --trustdb-name /etc/apt//trustdb.gpg --keyring /etc/apt/trusted.gpg --primary-keyring /etc/apt/trusted.gpg --keyserver keys.gnupg.net --recv-keys 1C4CBDCDCD2EFD2A
gpg: requesting key CD2EFD2A from hkp server keys.gnupg.net
gpg: key CD2EFD2A: public key "Percona MySQL Development Team <[email protected]>" imported
gpg: Total number processed: 1
gpg: imported: 1
root@ip-172-31-18-97:/home/ubuntu# echo 'deb http://repo.percona.com/apt saucy main'>>/etc/apt/sources.list
root@ip-172-31-18-97:/home/ubuntu# echo 'deb-src http://repo.percona.com/apt saucy main'>>/etc/apt/sources.list
root@ip-172-31-18-97:/home/ubuntu# apt-get update
Ign http://us-west-2.ec2.archive.ubuntu.com saucy InRelease
Ign http://us-west-2.ec2.archive.ubuntu.com saucy-updates InRelease
Get:1 http://us-west-2.ec2.archive.ubuntu.com saucy Release.gpg [933 B]
Get:2 http://us-west-2.ec2.archive.ubuntu.com saucy-updates Release.gpg [933 B]
Get:3 http://us-west-2.ec2.archive.ubuntu.com saucy Release [49.6 kB]
Get:4 http://repo.percona.com saucy InRelease [11.5 kB]
Get:5 http://us-west-2.ec2.archive.ubuntu.com saucy-updates Release [49.6 kB]
Ign http://security.ubuntu.com saucy-security InRelease
Get:6 http://us-west-2.ec2.archive.ubuntu.com saucy/main Sources [1,009 kB]
Get:7 http://repo.percona.com saucy/main Sources [2,806 B]
Get:8 http://security.ubuntu.com saucy-security Release.gpg [933 B]
Get:9 http://us-west-2.ec2.archive.ubuntu.com saucy/universe Sources [6,108 kB]
Get:10 http://repo.percona.com saucy/main amd64 Packages [10.3 kB]
Get:11 http://security.ubuntu.com saucy-security Release [49.6 kB]
Get:12 http://security.ubuntu.com saucy-security/main Sources [40.2 kB]
Get:13 http://security.ubuntu.com saucy-security/universe Sources [8,837 B]
Ign http://repo.percona.com saucy/main Translation-en_US
Get:14 http://security.ubuntu.com saucy-security/main amd64 Packages [107 kB]
Ign http://repo.percona.com saucy/main Translation-en
Get:15 http://us-west-2.ec2.archive.ubuntu.com saucy/main amd64 Packages [1,239 kB]
Get:16 http://security.ubuntu.com saucy-security/universe amd64 Packages [37.0 kB]
Get:17 http://us-west-2.ec2.archive.ubuntu.com saucy/universe amd64 Packages [5,643 kB]
Get:18 http://security.ubuntu.com saucy-security/main Translation-en [59.3 kB]
Get:19 http://security.ubuntu.com saucy-security/universe Translation-en [21.7 kB]
Get:20 http://us-west-2.ec2.archive.ubuntu.com saucy-updates/main Sources [81.4 kB]
Get:21 http://us-west-2.ec2.archive.ubuntu.com saucy-updates/universe Sources [68.6 kB]
Get:22 http://us-west-2.ec2.archive.ubuntu.com saucy-updates/main amd64 Packages [224 kB]
Get:23 http://us-west-2.ec2.archive.ubuntu.com saucy-updates/universe amd64 Packages [159 kB]
Ign http://us-west-2.ec2.archive.ubuntu.com saucy/main Translation-en_US
Ign http://us-west-2.ec2.archive.ubuntu.com saucy/main Translation-en
Ign http://us-west-2.ec2.archive.ubuntu.com saucy/universe Translation-en_US
Ign http://us-west-2.ec2.archive.ubuntu.com saucy/universe Translation-en
Ign http://us-west-2.ec2.archive.ubuntu.com saucy-updates/main Translation-en_US
Ign http://us-west-2.ec2.archive.ubuntu.com saucy-updates/main Translation-en
Ign http://us-west-2.ec2.archive.ubuntu.com saucy-updates/universe Translation-en_US
Ign http://us-west-2.ec2.archive.ubuntu.com saucy-updates/universe Translation-en
Ign http://security.ubuntu.com saucy-security/main Translation-en_US
Ign http://security.ubuntu.com saucy-security/universe Translation-en_US
Fetched 15.0 MB in 18s (810 kB/s)
Reading package lists... Done

root@ip-172-31-18-97:/home/ubuntu# apt-get install percona-server-server-5.6 xtrabackup
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following extra packages will be installed:
libaio1 libdbd-mysql-perl libdbi-perl libmysqlclient18 libperconaserverclient18.1 percona-server-client-5.6 percona-server-common-5.6 percona-xtrabackup
Suggested packages:
libclone-perl libmldbm-perl libnet-daemon-perl libplrpc-perl libsql-statement-perl tinyca
The following NEW packages will be installed:
libaio1 libdbd-mysql-perl libdbi-perl libmysqlclient18 libperconaserverclient18.1 percona-server-client-5.6 percona-server-common-5.6 percona-server-server-5.6 percona-xtrabackup
xtrabackup
0 upgraded, 10 newly installed, 0 to remove and 34 not upgraded.
Need to get 40.3 MB of archives.
After this operation, 138 MB of additional disk space will be used.
Do you want to continue [Y/n]?
Get:1 http://us-west-2.ec2.archive.ubuntu.com/ubuntu/ saucy/main libaio1 amd64 0.3.109-4 [6,364 B]
Get:2 http://us-west-2.ec2.archive.ubuntu.com/ubuntu/ saucy/main libdbi-perl amd64 1.627-1 [874 kB]
Get:3 http://repo.percona.com/apt/ saucy/main percona-server-common-5.6 amd64 5.6.16-64.2-569.saucy [11.0 kB]
Get:4 http://us-west-2.ec2.archive.ubuntu.com/ubuntu/ saucy/main libdbd-mysql-perl amd64 4.023-1 [97.3 kB]
Get:5 http://us-west-2.ec2.archive.ubuntu.com/ubuntu/ saucy/universe xtrabackup all 2.1.3-618-1 [12.8 kB]
Get:6 http://repo.percona.com/apt/ saucy/main libperconaserverclient18.1 amd64 5.6.16-64.2-569.saucy [18.5 kB]
Get:7 http://repo.percona.com/apt/ saucy/main percona-server-client-5.6 amd64 5.6.16-64.2-569.saucy [10.2 MB]
Get:8 http://repo.percona.com/apt/ saucy/main libmysqlclient18 amd64 5.5.35-rel33.0-611.saucy [858 kB]
Get:9 http://repo.percona.com/apt/ saucy/main percona-server-server-5.6 amd64 5.6.16-64.2-569.saucy [19.6 MB]
Get:10 http://repo.percona.com/apt/ saucy/main percona-xtrabackup amd64 2.1.8-733-1.saucy [8,608 kB]
Fetched 40.3 MB in 9s (4,334 kB/s)
Preconfiguring packages ...
Selecting previously unselected package libaio1:amd64.
(Reading database ... 53343 files and directories currently installed.)
Unpacking libaio1:amd64 (from .../libaio1_0.3.109-4_amd64.deb) ...
Selecting previously unselected package percona-server-common-5.6.
Unpacking percona-server-common-5.6 (from .../percona-server-common-5.6_5.6.16-64.2-569.saucy_amd64.deb) ...
Selecting previously unselected package libdbi-perl.
Unpacking libdbi-perl (from .../libdbi-perl_1.627-1_amd64.deb) ...
Selecting previously unselected package libperconaserverclient18.1.
Unpacking libperconaserverclient18.1 (from .../libperconaserverclient18.1_5.6.16-64.2-569.saucy_amd64.deb) ...
Selecting previously unselected package percona-server-client-5.6.
Unpacking percona-server-client-5.6 (from .../percona-server-client-5.6_5.6.16-64.2-569.saucy_amd64.deb) ...
Selecting previously unselected package libmysqlclient18.
Unpacking libmysqlclient18 (from .../libmysqlclient18_5.5.35-rel33.0-611.saucy_amd64.deb) ...
Selecting previously unselected package libdbd-mysql-perl.
Unpacking libdbd-mysql-perl (from .../libdbd-mysql-perl_4.023-1_amd64.deb) ...
Processing triggers for man-db ...
Setting up percona-server-common-5.6 (5.6.16-64.2-569.saucy) ...
Selecting previously unselected package percona-server-server-5.6.
(Reading database ... 53585 files and directories currently installed.)
Unpacking percona-server-server-5.6 (from .../percona-server-server-5.6_5.6.16-64.2-569.saucy_amd64.deb) ...
Selecting previously unselected package percona-xtrabackup.
Unpacking percona-xtrabackup (from .../percona-xtrabackup_2.1.8-733-1.saucy_amd64.deb) ...
Selecting previously unselected package xtrabackup.
Unpacking xtrabackup (from .../xtrabackup_2.1.3-618-1_all.deb) ...
Processing triggers for ureadahead ...
Processing triggers for man-db ...
Setting up libaio1:amd64 (0.3.109-4) ...
Setting up libdbi-perl (1.627-1) ...
Setting up libperconaserverclient18.1 (5.6.16-64.2-569.saucy) ...
Setting up percona-server-client-5.6 (5.6.16-64.2-569.saucy) ...
Setting up libmysqlclient18 (5.5.35-rel33.0-611.saucy) ...
Setting up libdbd-mysql-perl (4.023-1) ...
Setting up percona-server-server-5.6 (5.6.16-64.2-569.saucy) ...

• Stopping MySQL (Percona Server) mysqld [ OK ]

• Percona Server is distributed with several useful UDF (User Defined Function) from Percona Toolkit.
• Run the following commands to create these functions:

mysql -e "CREATE FUNCTION fnv1a_64 RETURNS INTEGER SONAME 'libfnv1a_udf.so'"
mysql -e "CREATE FUNCTION fnv_64 RETURNS INTEGER SONAME 'libfnv_udf.so'"
mysql -e "CREATE FUNCTION murmur_hash RETURNS INTEGER SONAME 'libmurmur_udf.so'"

• See http://www.percona.com/doc/percona-server/5.6/management/udf_percona_toolkit.html for more details

• Starting MySQL (Percona Server) database server mysqld [ OK ]
• Checking for corrupt, not cleanly closed and upgrade needing tables.
  Setting up percona-xtrabackup (2.1.8-733-1.saucy) ...
  Setting up xtrabackup (2.1.3-618-1) ...
  Processing triggers for libc-bin ...
  Processing triggers for ureadahead ...

[[ did not set root password ]]

root@ip-172-31-18-97:/home/ubuntu# mkdir /root/backup

root@ip-172-31-18-97:/home/ubuntu# echo '[mysqld]' > /etc/mysql/my.cnf
root@ip-172-31-18-97:/home/ubuntu# echo 'datadir=/var/lib/mysql' >> /etc/mysql/my.cnf

root@ip-172-31-18-97:/home/ubuntu# innobackupex /root/backup/

InnoDB Backup Utility v1.5.1-xtrabackup; Copyright 2003, 2009 Innobase Oy
and Percona LLC and/or its affiliates 2009-2013. All Rights Reserved.

This software is published under
the GNU GENERAL PUBLIC LICENSE Version 2, June 1991.

Get the latest version of Percona XtraBackup, documentation, and help resources:
http://www.percona.com/xb/p

140404 22:32:23 innobackupex: Connecting to MySQL server with DSN 'dbi:mysql:;mysql_read_default_group=xtrabackup' (using password: NO).
140404 22:32:23 innobackupex: Connected to MySQL server
140404 22:32:23 innobackupex: Executing a version check against the server...
140404 22:32:23 innobackupex: Done.
IMPORTANT: Please check that the backup run completes successfully.
At the end of a successful backup run innobackupex
prints "completed OK!".

innobackupex: Using mysql server version 5.6.16-64.2-569.saucy

innobackupex: Created backup directory /root/backup/2014-04-04_22-32-23

140404 22:32:23 innobackupex: Starting ibbackup with command: xtrabackup_56 --defaults-group="mysqld" --backup --suspend-at-end --target-dir=/root/backup/2014-04-04_22-32-23 --tmpdir=/tmp
innobackupex: Waiting for ibbackup (pid=3084) to suspend
innobackupex: Suspend file '/root/backup/2014-04-04_22-32-23/xtrabackup_suspended_2'

xtrabackup_56 version 2.1.8 for MySQL server 5.6.15 Linux (x86_64) (revision id: undefined)
xtrabackup: uses posix_fadvise().
xtrabackup: cd to /var/lib/mysql
xtrabackup: using the following InnoDB configuration:
xtrabackup: innodb_data_home_dir = ./
xtrabackup: innodb_data_file_path = ibdata1:10M:autoextend
xtrabackup: innodb_log_group_home_dir = ./
xtrabackup: innodb_log_files_in_group = 2
xtrabackup: innodb_log_file_size = 50331648
>> log scanned up to (1626007)
[01] Copying ./ibdata1 to /root/backup/2014-04-04_22-32-23/ibdata1
[01] ...done
[01] Copying ./mysql/innodb_index_stats.ibd to /root/backup/2014-04-04_22-32-23/mysql/innodb_index_stats.ibd
[01] ...done
[01] Copying ./mysql/innodb_table_stats.ibd to /root/backup/2014-04-04_22-32-23/mysql/innodb_table_stats.ibd
[01] ...done
[01] Copying ./mysql/slave_relay_log_info.ibd to /root/backup/2014-04-04_22-32-23/mysql/slave_relay_log_info.ibd
[01] ...done
>> log scanned up to (1626007)
[01] Copying ./mysql/slave_worker_info.ibd to /root/backup/2014-04-04_22-32-23/mysql/slave_worker_info.ibd
[01] ...done
[01] Copying ./mysql/slave_master_info.ibd to /root/backup/2014-04-04_22-32-23/mysql/slave_master_info.ibd
[01] ...done
xtrabackup: Creating suspend file '/root/backup/2014-04-04_22-32-23/xtrabackup_suspended_2' with pid '3085'

140404 22:32:25 innobackupex: Continuing after ibbackup has suspended
140404 22:32:25 innobackupex: Starting to lock all tables...
>> log scanned up to (1626007)
140404 22:32:25 innobackupex: All tables locked and flushed to disk

140404 22:32:25 innobackupex: Starting to backup non-InnoDB tables and files
innobackupex: in subdirectories of '/var/lib/mysql'
innobackupex: Backing up files '/var/lib/mysql/mysql/*.

{frm,isl,MYD,MYI,MAD,MAI,MRG,TRG,TRN,ARM,ARZ,CSM,CSV,opt,par}' (74 files)
>> log scanned up to (1626007)
innobackupex: Backing up files '/var/lib/mysql/performance_schema/*.{frm,isl,MYD,MYI,MAD,MAI,MRG,TRG,TRN,ARM,ARZ,CSM,CSV,opt,par}

' (53 files)
>> log scanned up to (1626007)
140404 22:32:27 innobackupex: Finished backing up non-InnoDB tables and files

140404 22:32:27 innobackupex: Waiting for log copying to finish

xtrabackup: The latest check point (for incremental): '1626007'
xtrabackup: Stopping log copying thread.
.>> log scanned up to (1626007)

xtrabackup: Creating suspend file '/root/backup/2014-04-04_22-32-23/xtrabackup_log_copied' with pid '3085'
xtrabackup: Transaction log of lsn (1626007) to (1626007) was copied.
140404 22:32:28 innobackupex: All tables unlocked

innobackupex: Backup created in directory '/root/backup/2014-04-04_22-32-23'
140404 22:32:28 innobackupex: Connection to database server closed
140404 22:32:28 innobackupex: completed OK!

root@ip-172-31-18-97:/home/ubuntu# innobackupex --apply-log /root/backup/2014-04-04_22-32-23/

InnoDB Backup Utility v1.5.1-xtrabackup; Copyright 2003, 2009 Innobase Oy
and Percona LLC and/or its affiliates 2009-2013. All Rights Reserved.

This software is published under
the GNU GENERAL PUBLIC LICENSE Version 2, June 1991.

Get the latest version of Percona XtraBackup, documentation, and help resources:
http://www.percona.com/xb/p

IMPORTANT: Please check that the apply-log run completes successfully.
At the end of a successful apply-log run innobackupex
prints "completed OK!".

140404 22:32:58 innobackupex: Starting ibbackup with command: xtrabackup_56 --defaults-file="/root/backup/2014-04-04_22-32-23/backup-my.cnf" --defaults-group="mysqld" --prepare --target-dir=/root/backup/2014-04-04_22-32-23 --tmpdir=/tmp

xtrabackup_56 version 2.1.8 for MySQL server 5.6.15 Linux (x86_64) (revision id: undefined)
xtrabackup: cd to /root/backup/2014-04-04_22-32-23
xtrabackup: This target seems to be not prepared yet.
xtrabackup: xtrabackup_logfile detected: size=2097152, start_lsn=(1626007)
xtrabackup: using the following InnoDB configuration for recovery:
xtrabackup: innodb_data_home_dir = ./
xtrabackup: innodb_data_file_path = ibdata1:10M:autoextend
xtrabackup: innodb_log_group_home_dir = ./
xtrabackup: innodb_log_files_in_group = 1
xtrabackup: innodb_log_file_size = 2097152
xtrabackup: using the following InnoDB configuration for recovery:
xtrabackup: innodb_data_home_dir = ./
xtrabackup: innodb_data_file_path = ibdata1:10M:autoextend
xtrabackup: innodb_log_group_home_dir = ./
xtrabackup: innodb_log_files_in_group = 1
xtrabackup: innodb_log_file_size = 2097152
xtrabackup: Starting InnoDB instance for recovery.
xtrabackup: Using 104857600 bytes for buffer pool (set by --use-memory parameter)
InnoDB: The InnoDB memory heap is disabled
InnoDB: Mutexes and rw_locks use GCC atomic builtins
InnoDB: Compressed tables use zlib 1.2.3
InnoDB: Using CPU crc32 instructions
InnoDB: Initializing buffer pool, size = 100.0M
InnoDB: Completed initialization of buffer pool
InnoDB: Highest supported file format is Barracuda.
InnoDB: The log sequence numbers 1625997 and 1625997 in ibdata files do not match the log sequence number 1626007 in the ib_logfiles!
InnoDB: Database was not shutdown normally!
InnoDB: Starting crash recovery.
InnoDB: Reading tablespace information from the .ibd files...
InnoDB: Restoring possible half-written data pages
InnoDB: from the doublewrite buffer...
InnoDB: 128 rollback segment(s) are active.
InnoDB: Waiting for purge to start
InnoDB: 5.6.15 started; log sequence number 1626007

[notice (again)]
If you use binary log and don't use any hack of group commit,
the binary log position seems to be:

xtrabackup: starting shutdown with innodb_fast_shutdown = 1
InnoDB: FTS optimize thread exiting.
InnoDB: Starting shutdown...
InnoDB: Shutdown completed; log sequence number 1626017

140404 22:33:00 innobackupex: Restarting xtrabackup with command: xtrabackup_56 --defaults-file="/root/backup/2014-04-04_22-32-23/backup-my.cnf" --defaults-group="mysqld" --prepare --target-dir=/root/backup/2014-04-04_22-32-23 --tmpdir=/tmp
for creating ib_logfile*

xtrabackup_56 version 2.1.8 for MySQL server 5.6.15 Linux (x86_64) (revision id: undefined)
xtrabackup: cd to /root/backup/2014-04-04_22-32-23
xtrabackup: This target seems to be already prepared.
xtrabackup: notice: xtrabackup_logfile was already used to '--prepare'.
xtrabackup: using the following InnoDB configuration for recovery:
xtrabackup: innodb_data_home_dir = ./
xtrabackup: innodb_data_file_path = ibdata1:10M:autoextend
xtrabackup: innodb_log_group_home_dir = ./
xtrabackup: innodb_log_files_in_group = 2
xtrabackup: innodb_log_file_size = 50331648
xtrabackup: using the following InnoDB configuration for recovery:
xtrabackup: innodb_data_home_dir = ./
xtrabackup: innodb_data_file_path = ibdata1:10M:autoextend
xtrabackup: innodb_log_group_home_dir = ./
xtrabackup: innodb_log_files_in_group = 2
xtrabackup: innodb_log_file_size = 50331648
xtrabackup: Starting InnoDB instance for recovery.
xtrabackup: Using 104857600 bytes for buffer pool (set by --use-memory parameter)
InnoDB: The InnoDB memory heap is disabled
InnoDB: Mutexes and rw_locks use GCC atomic builtins
InnoDB: Compressed tables use zlib 1.2.3
InnoDB: Using CPU crc32 instructions
InnoDB: Initializing buffer pool, size = 100.0M
InnoDB: Completed initialization of buffer pool
InnoDB: Setting log file ./ib_logfile101 size to 48 MB
InnoDB: Setting log file ./ib_logfile1 size to 48 MB
InnoDB: Renaming log file ./ib_logfile101 to ./ib_logfile0
InnoDB: New log files created, LSN=1626017
InnoDB: Highest supported file format is Barracuda.
InnoDB: 128 rollback segment(s) are active.
InnoDB: Waiting for purge to start
InnoDB: 5.6.15 started; log sequence number 1626124

[notice (again)]
If you use binary log and don't use any hack of group commit,
the binary log position seems to be:

xtrabackup: starting shutdown with innodb_fast_shutdown = 1
InnoDB: FTS optimize thread exiting.
InnoDB: Starting shutdown...
InnoDB: Shutdown completed; log sequence number 1626134
140404 22:33:08 innobackupex: completed OK!

[[ no issue so far ]]

root@ip-172-31-18-97:/home/ubuntu# echo 'SET storage_engine=InnoDB; CREATE DATABASE foo' | mysql
root@ip-172-31-18-97:/home/ubuntu# echo 'SET storage_engine=InnoDB; use foo; CREATE TABLE IF NOT EXISTS bar (bar1 INT);' | mysql
root@ip-172-31-18-97:/home/ubuntu# echo 'use foo; INSERT INTO `bar` (`bar1`) VALUES ('154');' | mysql

root@ip-172-31-18-97:/home/ubuntu# rm /root/backup/2014-04-04_22-32-23/ -rf
root@ip-172-31-18-97:/home/ubuntu# innobackupex /root/backup/

InnoDB Backup Utility v1.5.1-xtrabackup; Copyright 2003, 2009 Innobase Oy
and Percona LLC and/or its affiliates 2009-2013. All Rights Reserved.

This software is published under
the GNU GENERAL PUBLIC LICENSE Version 2, June 1991.

Get the latest version of Percona XtraBackup, documentation, and help resources:
http://www.percona.com/xb/p

140404 22:40:13 innobackupex: Connecting to MySQL server with DSN 'dbi:mysql:;mysql_read_default_group=xtrabackup' (using password: NO).
140404 22:40:13 innobackupex: Connected to MySQL server
140404 22:40:13 innobackupex: Executing a version check against the server...
140404 22:40:13 innobackupex: Done.
IMPORTANT: Please check that the backup run completes successfully.
At the end of a successful backup run innobackupex
prints "completed OK!".

innobackupex: Using mysql server version 5.6.16-64.2-569.saucy

innobackupex: Created backup directory /root/backup/2014-04-04_22-40-13

140404 22:40:13 innobackupex: Starting ibbackup with command: xtrabackup_56 --defaults-group="mysqld" --backup --suspend-at-end --target-dir=/root/backup/2014-04-04_22-40-13 --tmpdir=/tmp
innobackupex: Waiting for ibbackup (pid=3418) to suspend
innobackupex: Suspend file '/root/backup/2014-04-04_22-40-13/xtrabackup_suspended_2'

xtrabackup_56 version 2.1.8 for MySQL server 5.6.15 Linux (x86_64) (revision id: undefined)
xtrabackup: uses posix_fadvise().
xtrabackup: cd to /var/lib/mysql
xtrabackup: using the following InnoDB configuration:
xtrabackup: innodb_data_home_dir = ./
xtrabackup: innodb_data_file_path = ibdata1:10M:autoextend
xtrabackup: innodb_log_group_home_dir = ./
xtrabackup: innodb_log_files_in_group = 2
xtrabackup: innodb_log_file_size = 50331648
>> log scanned up to (1634528)
[01] Copying ./ibdata1 to /root/backup/2014-04-04_22-40-13/ibdata1
>> log scanned up to (1634528)
>> log scanned up to (1634528)
[01] ...done
[01] Copying ./mysql/innodb_index_stats.ibd to /root/backup/2014-04-04_22-40-13/mysql/innodb_index_stats.ibd
[01] ...done
[01] Copying ./mysql/innodb_table_stats.ibd to /root/backup/2014-04-04_22-40-13/mysql/innodb_table_stats.ibd
[01] ...done
[01] Copying ./mysql/slave_relay_log_info.ibd to /root/backup/2014-04-04_22-40-13/mysql/slave_relay_log_info.ibd
[01] ...done
[01] Copying ./mysql/slave_worker_info.ibd to /root/backup/2014-04-04_22-40-13/mysql/slave_worker_info.ibd
[01] ...done
[01] Copying ./mysql/slave_master_info.ibd to /root/backup/2014-04-04_22-40-13/mysql/slave_master_info.ibd
[01] ...done
[01] Copying ./foo/bar.ibd to /root/backup/2014-04-04_22-40-13/foo/bar.ibd
[01] ...done
>> log scanned up to (1634528)
xtrabackup: Creating suspend file '/root/backup/2014-04-04_22-40-13/xtrabackup_suspended_2' with pid '3419'

140404 22:40:17 innobackupex: Continuing after ibbackup has suspended
140404 22:40:17 innobackupex: Starting to lock all tables...
140404 22:40:17 innobackupex: All tables locked and flushed to disk

140404 22:40:17 innobackupex: Starting to backup non-InnoDB tables and files
innobackupex: in subdirectories of '/var/lib/mysql'
innobackupex: Backing up files '/var/lib/mysql/mysql/*.

{frm,isl,MYD,MYI,MAD,MAI,MRG,TRG,TRN,ARM,ARZ,CSM,CSV,opt,par}' (74 files)
>> log scanned up to (1634528)
>> log scanned up to (1634528)
innobackupex: Backing up files '/var/lib/mysql/performance_schema/*.{frm,isl,MYD,MYI,MAD,MAI,MRG,TRG,TRN,ARM,ARZ,CSM,CSV,opt,par}

' (53 files)
>> log scanned up to (1634528)
innobackupex: Backing up file '/var/lib/mysql/foo/db.opt'
innobackupex: Backing up file '/var/lib/mysql/foo/bar.frm'
140404 22:40:20 innobackupex: Finished backing up non-InnoDB tables and files

140404 22:40:20 innobackupex: Waiting for log copying to finish

xtrabackup: The latest check point (for incremental): '1634528'
xtrabackup: Stopping log copying thread.
.>> log scanned up to (1634528)

xtrabackup: Creating suspend file '/root/backup/2014-04-04_22-40-13/xtrabackup_log_copied' with pid '3419'
xtrabackup: Transaction log of lsn (1634528) to (1634528) was copied.
140404 22:40:21 innobackupex: All tables unlocked

innobackupex: Backup created in directory '/root/backup/2014-04-04_22-40-13'
140404 22:40:21 innobackupex: Connection to database server closed
140404 22:40:21 innobackupex: completed OK!

root@ip-172-31-18-97:/home/ubuntu# innobackupex --apply-log /root/backup/2014-04-04_22-40-13/

InnoDB Backup Utility v1.5.1-xtrabackup; Copyright 2003, 2009 Innobase Oy
and Percona LLC and/or its affiliates 2009-2013. All Rights Reserved.

This software is published under
the GNU GENERAL PUBLIC LICENSE Version 2, June 1991.

Get the latest version of Percona XtraBackup, documentation, and help resources:
http://www.percona.com/xb/p

IMPORTANT: Please check that the apply-log run completes successfully.
At the end of a successful apply-log run innobackupex
prints "completed OK!".

140404 22:40:51 innobackupex: Starting ibbackup with command: xtrabackup_56 --defaults-file="/root/backup/2014-04-04_22-40-13/backup-my.cnf" --defaults-group="mysqld" --prepare --target-dir=/root/backup/2014-04-04_22-40-13 --tmpdir=/tmp

xtrabackup_56 version 2.1.8 for MySQL server 5.6.15 Linux (x86_64) (revision id: undefined)
xtrabackup: cd to /root/backup/2014-04-04_22-40-13
xtrabackup: This target seems to be not prepared yet.
xtrabackup: xtrabackup_logfile detected: size=2097152, start_lsn=(1634528)
xtrabackup: using the following InnoDB configuration for recovery:
xtrabackup: innodb_data_home_dir = ./
xtrabackup: innodb_data_file_path = ibdata1:10M:autoextend
xtrabackup: innodb_log_group_home_dir = ./
xtrabackup: innodb_log_files_in_group = 1
xtrabackup: innodb_log_file_size = 2097152
xtrabackup: using the following InnoDB configuration for recovery:
xtrabackup: innodb_data_home_dir = ./
xtrabackup: innodb_data_file_path = ibdata1:10M:autoextend
xtrabackup: innodb_log_group_home_dir = ./
xtrabackup: innodb_log_files_in_group = 1
xtrabackup: innodb_log_file_size = 2097152
xtrabackup: Starting InnoDB instance for recovery.
xtrabackup: Using 104857600 bytes for buffer pool (set by --use-memory parameter)
InnoDB: The InnoDB memory heap is disabled
InnoDB: Mutexes and rw_locks use GCC atomic builtins
InnoDB: Compressed tables use zlib 1.2.3
InnoDB: Using CPU crc32 instructions
InnoDB: Initializing buffer pool, size = 100.0M
InnoDB: Completed initialization of buffer pool
InnoDB: Highest supported file format is Barracuda.
InnoDB: The log sequence numbers 1625997 and 1625997 in ibdata files do not match the log sequence number 1634528 in the ib_logfiles!
InnoDB: Database was not shutdown normally!
InnoDB: Starting crash recovery.
InnoDB: Reading tablespace information from the .ibd files...
InnoDB: Restoring possible half-written data pages
InnoDB: from the doublewrite buffer...
InnoDB: 128 rollback segment(s) are active.
InnoDB: Waiting for purge to start
InnoDB: 5.6.15 started; log sequence number 1634528

[notice (again)]
If you use binary log and don't use any hack of group commit,
the binary log position seems to be:

xtrabackup: starting shutdown with innodb_fast_shutdown = 1
InnoDB: FTS optimize thread exiting.
InnoDB: Starting shutdown...
InnoDB: Shutdown completed; log sequence number 1634538

140404 22:40:53 innobackupex: Restarting xtrabackup with command: xtrabackup_56 --defaults-file="/root/backup/2014-04-04_22-40-13/backup-my.cnf" --defaults-group="mysqld" --prepare --target-dir=/root/backup/2014-04-04_22-40-13 --tmpdir=/tmp
for creating ib_logfile*

xtrabackup_56 version 2.1.8 for MySQL server 5.6.15 Linux (x86_64) (revision id: undefined)
xtrabackup: cd to /root/backup/2014-04-04_22-40-13
xtrabackup: This target seems to be already prepared.
xtrabackup: notice: xtrabackup_logfile was already used to '--prepare'.
xtrabackup: using the following InnoDB configuration for recovery:
xtrabackup: innodb_data_home_dir = ./
xtrabackup: innodb_data_file_path = ibdata1:10M:autoextend
xtrabackup: innodb_log_group_home_dir = ./
xtrabackup: innodb_log_files_in_group = 2
xtrabackup: innodb_log_file_size = 50331648
xtrabackup: using the following InnoDB configuration for recovery:
xtrabackup: innodb_data_home_dir = ./
xtrabackup: innodb_data_file_path = ibdata1:10M:autoextend
xtrabackup: innodb_log_group_home_dir = ./
xtrabackup: innodb_log_files_in_group = 2
xtrabackup: innodb_log_file_size = 50331648
xtrabackup: Starting InnoDB instance for recovery.
xtrabackup: Using 104857600 bytes for buffer pool (set by --use-memory parameter)
InnoDB: The InnoDB memory heap is disabled
InnoDB: Mutexes and rw_locks use GCC atomic builtins
InnoDB: Compressed tables use zlib 1.2.3
InnoDB: Using CPU crc32 instructions
InnoDB: Initializing buffer pool, size = 100.0M
InnoDB: Completed initialization of buffer pool
InnoDB: Setting log file ./ib_logfile101 size to 48 MB
InnoDB: Setting log file ./ib_logfile1 size to 48 MB
InnoDB: Renaming log file ./ib_logfile101 to ./ib_logfile0
InnoDB: New log files created, LSN=1634538
InnoDB: Highest supported file format is Barracuda.
InnoDB: 128 rollback segment(s) are active.
InnoDB: Waiting for purge to start
InnoDB: 5.6.15 started; log sequence number 1634828

[notice (again)]
If you use binary log and don't use any hack of group commit,
the binary log position seems to be:

xtrabackup: starting shutdown with innodb_fast_shutdown = 1
InnoDB: FTS optimize thread exiting.
InnoDB: Starting shutdown...
InnoDB: Shutdown completed; log sequence number 1634838
140404 22:41:07 innobackupex: completed OK!

root@ip-172-31