innobackupex --defaults-file

When you run innobackupex without the --defaults-file flag specified, what determines the location of my.cnf that will be used?

We originally had a master slave setup, the backup was being performed on the slave. The slave was then changed to master and the new setup is master master. On the original master we don’t have the ib_logfile size set in the my.cnf (on the slave it was set to 512M). When the backup script ran, we noticed that the log file size is now 5M instead of the usual 512M. The my.cnf has the ib_logfile size set to 5M as well. It was only after specifying the --defaults-file to /etc/mysql/my.cnf that we were able to get a backup with the correct file size. We think that the my.cnf was somehow pulled from the other master instead of from local on new master (originally slave).

No, my.cnf shouldn’t be pulled off from the master. May be you multiple my.cnf exists from where you started the backup i.e. slave ? Can you please show us slave my.cnf and command you used to took the backup please.