Use the --rsync parameter.
Surprisingly, it IS available on xtrabackup, despite it not appearing anywhere on the Percona XtraBackup 2.4 Documentation as of this writting. The documentation that is wrong. =/
If you pass the parameter to the xtrabackup command, it works just like it would with innobackupex. And it make sense that it does, since innobackupex is just a 'caller' symlink now.
I saw in your self-answer that you 'fell-back' to using innobackupex.
I would recommend against it, since, according to documentation:
From Percona XtraBackup version 2.3 innobackupex is has been rewritten in C and set up as a symlink to the
xtrabackup. innobackupex supports all features and syntax as 2.2 version did, but it is now deprecated and
will be removed in next major release. Syntax for new features will not be added to the innobackupex, only to the
It is already outdated and lacking new functionalities that are available in xtrabackup.
In my scenario, backups used to waste 6 minutes in LOCK TABLES:
180824 14:52:53 Executing FLUSH NO_WRITE_TO_BINLOG TABLES...
180824 14:52:53 Executing FLUSH TABLES WITH READ LOCK...
180824 14:58:55 Executing UNLOCK TABLES
180824 14:58:55 All tables unlocked
And with --rsync, it became less than a second.
180824 13:07:28 Executing FLUSH NO_WRITE_TO_BINLOG TABLES...
180824 13:07:28 Executing FLUSH TABLES WITH READ LOCK...
180824 13:07:28 Starting to backup non-InnoDB tables and files
180824 13:07:28 Starting rsync as: rsync -t . --files-
180824 13:07:28 Executing UNLOCK TABLES
180824 13:07:28 All tables unlocked
I've had the exact same issue you had, and found your question & answer, which together with the lack of a consistent documentation, made me believe it wasn't available and I ended up wasting a day looking for alternative solutions, since innobackupex is outdated and doesn't have some functions I need, like the aforementioned --databases-exclude.
Posting this answer so that if someone else find themselves with this same exact issue, they'll know they can use the parameter even though it's not on the docs.