I don't think PHPMyAdmin is really designed for running huge scripts -- it's limited to the file upload limits set in PHP. How big is your load script? You should also make sure it isn't trying to do things that aren't allowed in a script, like creating the database or defining users (you do these things from panel.dreamhost.com).
I'd suggest that you upload the script to the server using SFTP, then SSH in and execute the script on the command line.
More info here:
You might check the knowledge base as well (https://panel.dreamhost.com, link on upper-right) -- this is a pretty common requirement.