Issues with mysqldump after upgrade 5.5 -> 5.6

Question

A few months ago I updated a MySQL setup from 5.5 to 5.6. Since then I've been having problems with a script that I use to dump the various databases so that I can back them up.

The script is a short piece of perl that gets a list of all databases and then calls mysqldump for each as follows:

mysqldump -udb_account -pdb_pw -hserver.com --single-transaction --flush-logs 
   --routines --triggers --quick $fn 2> $fn.err | gzip > $fn.mysql.gz

Issue: many of these databases have hundreds of tables (ever increasing). For these larger dbs the mysqldump command often exits after only a single table. If I run the command from a terminal session it executes correctly. (typically it runs as a cron job 1x/wk)

The .err file contains no messages. Neither does the server.err file in the MySQL root dir.

Note: this script had been running fine on MySQL 5.5 for several years. This problem started happening when I upgraded to 5.6.

Also: the --flush-logs portion isn't working. The mysql_bin folder has never been emptied since this system was brought online.

One variable that I haven't controlled for yet: when run as a CRON job the script forks 3 processes at a time. When I test the command in a term session I'm only doing one at a time.

System in question:

• CentOS 6.4
• x64
• 64Gb RAM