mpiblast should work faster in general but there's no guarantee that the scaling would be better. Few factors are there:
- For parallel processing, you need to make sure that the nodes that are being used are not idle/not being used properly. That is one of the main reason for poor scaling!
- Also, it depends on the files you are using for BLAST. For instance, there are some parameters in mpiblast, you should go through them first.
But in general, mpiblast should scale well when the nodes are equally being used that means greatly load-balanced :)