innobackupex partial backup copies all idb files

During a partial backup idb files from unselected databases are being copied. Only those InnoDB tables that were created after we changed the server to innodb_file_per_table are being copied - those that are not in the shared tablespace.

I run: /usr/bin/innobackupex --databases “rt mysql zzzz_delete_me_zzz” --no-timestamp --use-memory=1G junk2

The resulting backup has the following directory structure:

junk2/├── backup-my.cnf├── drupal_eggiebuzz_dev│ ├── g2_AccessMap.ibd… SNIP …│ └── gallery2_WebDavLockMap.ibd├── emeitner│ └── Users.ibd├── ibdata1├── mysql│ ├── columns_priv.frm│ ├── columns_priv.MYD│ ├── columns_priv.MYI… SNIP …│ ├── user.frm│ ├── user_info.frm│ ├── user_info.MYD│ ├── user_info.MYI│ ├── user.MYD│ └── user.MYI├── rt│ ├── db.opt│ ├── group_rights_map.frm│ ├── group_rights_map.MYD│ ├── group_rights_map.MYI… SNIP …│ ├── rights_sets.frm│ ├── rights_sets.MYD│ └── rights_sets.MYI├── xtrabackup_binary├── xtrabackup_binlog_info├── xtrabackup_checkpoints├── xtrabackup_logfile└── zzzz_delete_me_zzz ├── db.opt ├── zzzzz.frm └── zzzzz.ibd

Notice that the databases I selected for backup contain the frm files as they should. The other unwanted databases,“emeitner” and “drupal_eggiebuzz_dev”, only contain the idb files.

Server is Debian Squeeze
mysql-server-5.1 package version 5.1.61-0+squeeze1
percona-xtrabackup package version 2.0.0-417.squeeze.

Any ideas?

Output of the above command:

InnoDB Backup Utility v1.5.1-xtrabackup; Copyright 2003, 2009 Innobase Oyand Percona Inc 2009-2012. All Rights Reserved.This software is published underthe GNU GENERAL PUBLIC LICENSE Version 2, June 1991.120601 10:31:39 innobackupex: Starting mysql with options: --unbuffered --120601 10:31:39 innobackupex: Connected to database with mysql child process (pid=424)120601 10:31:45 innobackupex: Connection to database server closedIMPORTANT: Please check that the backup run completes successfully. At the end of a successful backup run innobackupex prints “completed OK!”.innobackupex: Using mysql Ver 14.14 Distrib 5.1.61, for debian-linux-gnu (x86_64) using readline 6.1innobackupex: Using mysql server version Copyright © 2000, 2011, Oracle and/or its affiliates. All rights reserved.innobackupex: Created backup directory /var/staged-backups/mysql/staged/test/junk2120601 10:31:45 innobackupex: Starting mysql with options: --unbuffered --120601 10:31:45 innobackupex: Connected to database with mysql child process (pid=513)120601 10:31:47 innobackupex: Connection to database server closed120601 10:31:47 innobackupex: Starting ibbackup with command: xtrabackup_51 --backup --suspend-at-end --target-dir=/var/staged-backups/mysql/staged/test/junk2 --use-memory=1Ginnobackupex: Waiting for ibbackup (pid=539) to suspendinnobackupex: Suspend file '/var/staged-backups/mysql/staged/test/junk2/xtrabackup_suspended’xtrabackup_51 version 2.0.0 for MySQL server 5.1.59 unknown-linux-gnu (x86_64) (revision id: undefined)xtrabackup: uses posix_fadvise().xtrabackup: cd to /var/lib/mysqlxtrabackup: Target instance is assumed as followings.xtrabackup: innodb_data_home_dir = xtrabackup: innodb_data_file_path = ibdata1:100M:autoextendxtrabackup: innodb_log_group_home_dir = ./xtrabackup: innodb_log_files_in_group = 2xtrabackup: innodb_log_file_size = 1073741824>> log scanned up to (0 2162200892)[01] Copying ibdata1 to /var/staged-backups/mysql/staged/test/junk2/ibdata1>> log scanned up to (0 2162200892)>> log scanned up to (0 2162200892)[01] …done[01] Copying ./zzzz_delete_me_zzz/zzzzz.ibd to /var/staged-backups/mysql/staged/test/junk2/./zzzz_delete_me_zzz/zzzzz.ibd[01] …done[01] Copying ./drupal_eggiebuzz_dev/g2_TkOperatnMimeTypeMap.ibd to /var/staged-backups/mysql/staged/test/junk2/./drupal_eggiebuzz_dev/g2_TkOperatnMimeTypeMap.ibd[01] …done… SNIP …[01] Copying ./drupal_eggiebuzz_dev/g2_MovieItem.ibd to /var/staged-backups/mysql/staged/test/junk2/./drupal_eggiebuzz_dev/g2_MovieItem.ibd[01] …done[01] Copying ./emeitner/Users.ibd to /var/staged-backups/mysql/staged/test/junk2/./emeitner/Users.ibd[01] …done120601 10:32:01 innobackupex: Continuing after ibbackup has suspended120601 10:32:01 innobackupex: Starting mysql with options: --unbuffered --120601 10:32:01 innobackupex: Connected to database with mysql child process (pid=1196)>> log scanned up to (0 2162200892)120601 10:32:03 innobackupex: Starting to lock all tables…>> log scanned up to (0 2162200892)>> log scanned up to (0 2162200892)120601 10:32:13 innobackupex: All tables locked and flushed to disk120601 10:32:13 innobackupex: Starting to backup .frm, .MRG, .MYD, .MYI,innobackupex: .TRG, .TRN, .ARM, .ARZ, .CSM, .CSV and .opt files ininnobackupex: subdirectories of '/var/lib/mysql’innobackupex: Backing up file '/var/lib/mysql/zzzz_delete_me_zzz/db.opt’innobackupex: Backing up file '/var/lib/mysql/zzzz_delete_me_zzz/zzzzz.frm’innobackupex: Backing up files ‘/var/lib/mysql/rt/.{frm,MYD,MYI,MRG,TRG,TRN,ARM,ARZ,CSM,CSV,opt,par}’ (10 files)innobackupex: Backing up files '/var/lib/mysql/mysql/.{frm,MYD,MYI,MRG,TRG,TRN,ARM,ARZ,CSM,CSV,opt,par}’ (72 files)120601 10:32:13 innobackupex: Finished backing up .frm, .MRG, .MYD, .MYI, .TRG, .TRN, .ARM, .ARZ, .CSV, .CSM and .opt filesinnobackupex: Resuming ibbackupxtrabackup: The latest check point (for incremental): '0:2162200892’xtrabackup: Stopping log copying thread…>> log scanned up to (0 2162200892)xtrabackup: Transaction log of lsn (0 2162200892) to (0 2162200892) was copied.120601 10:32:15 innobackupex: All tables unlocked120601 10:32:15 innobackupex: Connection to database server closedinnobackupex: Backup created in directory '/var/staged-backups/mysql/staged/test/junk2’innobackupex: MySQL binlog position: filename ‘’, position 120601 10:32:15 innobackupex: completed OK!