DBD::mysql error

Reported by Jeremy Bowers on 2013-05-16
6
This bug affects 1 person
Affects Status Importance Assigned to Milestone
Percona XtraBackup
Medium
Alexey Kopytov
2.1
Medium
Alexey Kopytov

Bug Description

I upgraded from xtrabackup-2.0.7 to xtrabackup-2.1.1 yesterday. I'm using Ubuntu 12.04 LTS and percona-server5.5. Backups worked great until after the upgrade. Here's what happens:

<email address hidden>:/backups# innobackupex /backups/backup_dir/

InnoDB Backup Utility v1.5.1-xtrabackup; Copyright 2003, 2009 Innobase Oy
and Percona Ireland Ltd 2009-2012. All Rights Reserved.

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

130516 16:34:30 innobackupex: Connecting to MySQL server with DSN 'dbi:mysql:;mysql_read_default_group=xtrabackup' (using password: NO).
130516 16:34:30 innobackupex: Connected to MySQL server
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 5.5.30-30.2-log

innobackupex: Created backup directory /backups/backup_dir/2013-05-16_16-34-30
WARNING : A left over instance of xtrabackup pid file '/tmp/xtrabackup_pid' was found.

130516 16:34:30 innobackupex: Starting ibbackup with command: xtrabackup_55 --defaults-group="mysqld" --backup --suspend-at-end --target-dir=/backups/backup_dir/2013-05-16_16-34-30 --tmpdir=/tmp
innobackupex: Waiting for ibbackup (pid=7562) to suspend
innobackupex: Suspend file '/backups/backup_dir/2013-05-16_16-34-30/xtrabackup_suspended_2'

xtrabackup_55 version 2.1.1 for Percona Server 5.5.16 Linux (x86_64) (revision id: 600)
xtrabackup: uses posix_fadvise().
xtrabackup: cd to /var/lib/mysql
xtrabackup: Target instance is assumed as followings.
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 = 52428800
xtrabackup: using O_DIRECT
>> log scanned up to (65109353)
[01] Copying ./ibdata1 to /backups/backup_dir/2013-05-16_16-34-30/ibdata1
>> log scanned up to (65109353)
[01] ...done
>> log scanned up to (65109353)

130516 16:34:33 innobackupex: Continuing after ibbackup has suspended
130516 16:34:33 innobackupex: Starting to lock all tables...
130516 16:34:33 innobackupex: All tables locked and flushed to disk

130516 16:34:33 innobackupex: Starting to backup non-InnoDB tables and files
innobackupex: in subdirectories of '/var/lib/mysql'
innobackupex: Backing up file '/var/lib/mysql/percona/db.opt'
innobackupex: Backing up file '/var/lib/mysql/percona/checksums.frm'
innobackupex: Backing up files '/var/lib/mysql/mysql/*.{frm,isl,MYD,MYI,MAD,MAI,MRG,TRG,TRN,ARM,ARZ,CSM,CSV,opt,par}' (72 files)
>> log scanned up to (65109353)
innobackupex: Backing up file '/var/lib/mysql/change_tracking_data/web_hooks.frm'
innobackupex: Backing up file '/var/lib/mysql/change_tracking_data/fields_changed.frm'
innobackupex: Backing up file '/var/lib/mysql/change_tracking_data/js_phrases.frm'
innobackupex: Backing up file '/var/lib/mysql/change_tracking_data/db.opt'
innobackupex: Backing up file '/var/lib/mysql/change_tracking_data/js_plural_phrases.frm'
innobackupex: Backing up files '/var/lib/mysql/performance_schema/*.{frm,isl,MYD,MYI,MAD,MAI,MRG,TRG,TRN,ARM,ARZ,CSM,CSV,opt,par}' (18 files)
>> log scanned up to (65109353)
innobackupex: Backing up files '/var/lib/mysql/company_stuff1/*.{frm,isl,MYD,MYI,MAD,MAI,MRG,TRG,TRN,ARM,ARZ,CSM,CSV,opt,par}' (256 files)
>> log scanned up to (65109353)
>> log scanned up to (65109353)
>> log scanned up to (65109353)
innobackupex: Backing up files '/var/lib/mysql/company_stuff2/*.{frm,isl,MYD,MYI,MAD,MAI,MRG,TRG,TRN,ARM,ARZ,CSM,CSV,opt,par}' (256 files)
>> log scanned up to (65109353)
>> log scanned up to (65109353)
>> log scanned up to (65109353)
innobackupex: Backing up files '/var/lib/mysql/company_stuff3/*.{frm,isl,MYD,MYI,MAD,MAI,MRG,TRG,TRN,ARM,ARZ,CSM,CSV,opt,par}' (256 files)
>> log scanned up to (65109353)
>> log scanned up to (65109353)
>> log scanned up to (65109353)
innobackupex: Backing up files '/var/lib/mysql/company_stuff4/*.{frm,isl,MYD,MYI,MAD,MAI,MRG,TRG,TRN,ARM,ARZ,CSM,CSV,opt,par}' (256 files)
>> log scanned up to (65109353)
>> log scanned up to (65109353)
>> log scanned up to (65109353)
130516 16:34:47 innobackupex: Finished backing up non-InnoDB tables and files

130516 16:34:47 innobackupex: Waiting for log copying to finish

xtrabackup: The latest check point (for incremental): '65109353'
xtrabackup: Stopping log copying thread.
.>> log scanned up to (65109353)

xtrabackup: Transaction log of lsn (65109353) to (65109353) was copied.
DBD::mysql::db do failed: Lost connection to MySQL server during query at /usr/bin/innobackupex line 1438.
innobackupex: Error:
Error executing 'UNLOCK TABLES': DBD::mysql::db do failed: Lost connection to MySQL server during query at /usr/bin/innobackupex line 1438.

The errors at the end indicate it probably relates to the change to use perl dbd::mysql instead of the mysql client directly, but I'm not sure where to go from here.

Alexey Kopytov (akopytov) wrote :

Jeremy,

It looks like wait_timeout on the server is set to some very small value. Can you confirm this? Thanks.

Jeremy Bowers (cubiclelord) wrote :

mysql> show variables like "wait_timeout";
+---------------+-------+
| Variable_name | Value |
+---------------+-------+
| wait_timeout | 28800 |
+---------------+-------+
1 row in set (0.00 sec)

Thanx for the help Alexey

Jeremy Bowers (cubiclelord) wrote :
Download full text (3.2 KiB)

I just tried xtrabackup-2.1.2 and it looks like it does fix the error I had listed. I now have a separate, but I believe to be a related bug. If you'd prefer I can open a new ticket, but in the meantime I'll post it here:

I'm using percona-server-5.5 and Ubuntu 12.04 with xtrabackup-2.1.2. If I run xtrabackup --stream=tar ./ > backup.tar, I get the appropriate backup file, with no errors, but if I then pipe that command into gzip like the documentation says I can (and which worked fine in xtrabackup-2.0.7) the backup appears to go on forever and doesn't ever finish:

<email address hidden>:~# innobackupex --stream=tar ./ | gzip - > backup.tar.gz

InnoDB Backup Utility v1.5.1-xtrabackup; Copyright 2003, 2009 Innobase Oy
and Percona Ireland Ltd 2009-2012. All Rights Reserved.

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

130521 15:22:39 innobackupex: Connecting to MySQL server with DSN 'dbi:mysql:;mysql_read_default_group=xtrabackup' (using password: NO).
130521 15:22:39 innobackupex: Connected to MySQL server
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 5.5.30-30.2-log

innobackupex: Created backup directory /root

130521 15:22:39 innobackupex: Starting ibbackup with command: xtrabackup_55 --defaults-group="mysqld" --backup --suspend-at-end --target-dir=/tmp --tmpdir=/tmp --stream=tar
innobackupex: Waiting for ibbackup (pid=1855) to suspend
innobackupex: Suspend file '/tmp/xtrabackup_suspended_2'

xtrabackup_55 version 2.1.2 for Percona Server 5.5.16 Linux (x86_64) (revision id: 611)
xtrabackup: uses posix_fadvise().
xtrabackup: cd to /var/lib/mysql
xtrabackup: Target instance is assumed as followings.
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 = 5242880
xtrabackup: using O_DIRECT
>> log scanned up to (1204575598)
[01] Streaming ./ibdata1
>> log scanned up to (1204576025)
>> log scanned up to (1204576025)
>> log scanned up to (1204576025)
>> log scanned up to (1204576025)
>> log scanned up to (1204576025)
>> log scanned up to (1204576025)
[01] ...done
>> log scanned up to (1204576025)

130521 15:22:47 innobackupex: Continuing after ibbackup has suspended
130521 15:22:47 innobackupex: Starting to lock all tables...
DBD::mysql::db do failed: Lost connection to MySQL server during query at /usr/bin/innobackupex line 1441.
innobackupex: Error:
Error executing 'FLUSH TABLES WITH READ LOCK': DBD::mysql::db do failed: Lost connection to MySQL server during query at /usr/bin/innobackupex line 1441.

>> log scanned up to (1204576452)
>> log scanned up to (1204576452)
>> log scanned up to (1204576452)
>> log scanned up to (1204576452)
>> log scanned up to (1204576452)
>> log scanned up to (1204576452)
>> log scanned up to (1204576452)
>> log scanned up to (1204576452)
>> log scanned up to (1204576452)
...

The log scanning, as far as I can tell just continues to g...

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