I am glad you said all your data is InnoDB so I can answer as follows: If max_allowed_packet is maxed out at 1G and you are still having issues, there is really only two places to look:

1. innodb_log_buffer_size : The size in bytes of the buffer that InnoDB uses to write to the log files on disk. The default value is 8MB. A large log buffer enables large transactions to run without a need to write the log to disk before the transactions commit. Thus, if you have big transactions, making the log buffer larger saves disk I/O.
2. innodb_log_file_size : The size in bytes of each log file in a log group. The combined size of log files must be less than 4GB. The default value is 5MB. Sensible values range from 1MB to 1/N-th of the size of the buffer pool, where N is the number of log files in the group. The larger the value, the less checkpoint flush activity is needed in the buffer pool, saving disk I/O. But larger log files also mean that recovery is slower in case of a crash.

I addressed something like about 2 years ago

• Aug 01, 2011 : How does max_allowed_packet affect the backup and restore of a database?
• Apr 20, 2011 : MySQL gives "Out of Memory" error when inserting a large file. From where is this filesize limitation arising?

SUGGESTIONS

You need to increase the InnoDB transaction logs. Here are the steps to safely increase innodb_log_buffer_size and innodb_log_file_size:

Step 01 : Add these to /etc/my.cnf

[mysqld]
innodb_log_buffer_size = 32M
innodb_log_file_size = 2047M

Step 02 : Run this in mysql

mysql> SET GLOBAL innodb_fast_shutdown = 0;

Step 03 : Shutdown mysql

service mysql stop

Step 04 : Move the old logs aside

mv ib_logfile0 ib_logfile0.bak
mv ib_logfile1 ib_logfile1.bak

Step 05 : Start mysql

service mysql start

That's it.

The InnoDB Infrastructure should now have enough logging space for different size BLOBs.

Give it a Try !!!

For my situation, the master met with the error timeout, but the slave run the same sql successfully. The sql is about load data, so the master actually finished reading the whole packet?