You could execute them all at the same time if you had a computer (or cluster) with at least 6001 CPUs (or 3001 CPUs that had hyperthreading turned on.)
There are some programs that work faster with parallel computing, but it is not uncommon for programs to work slower in parallel, because there is a lot of communications overhead in talking to the extra processes.
Do they need to all be run simultaneously, or do you just have 6000 independent files to get through and would like to keep your system running at maximum capacity?
