What sort of scaling can be expected with mpiblast?

On our HPC cluster, one of the users runs mpiblast jobs on upward of 30 cores. These will typically end up on about 10 different nodes, the nodes normally being shared between users. Although these jobs occasionally scale fairly well and can effectively use about 90% of the cores available, often scaling is very bad with jobs only accumulating CPU-time corresponding to around 10% of the cores available.

Should mpiblast scale better in general? Does anyone know what factors might lead to poor scaling?

Solution

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 :)