You tried phpmyadmin, you tried cat some_large_file | mysql -uuser -p -Ddatabase but it complains too? Then simply do SOURCE <large file name> while in the mysql console and it will work.
The only problem could be if you still get the error on some lines is to increase the max_allowed_packet if there are large blob’s in your dump.
There are some alternatives like BigDump, but that’s installing additional tools for the job which is not always necessary.
