I’ve compiled mothur on 64 bit Ubuntu 10.04 and enabled mpi (I set CC=mpic++ in the makefile.) I am now trying to test whether all is well with running mothur under mpi. I’m running the commands on a single machine, dual core. Running mothur by just typing
on the command line, and then running a command, such as the align.seqs command, I can see a single process running, and it completes, for the sequence set I was using, in about 21 seconds.
If I run mothur using mpirun:
and then run the same align.seqs command, I still only see one process, and it completes in 21 seconds.
The above suggests that mpi is not relevant to the above command or that my build is not able to not really mpi enabled.
If I assume the former, can anyone tell me what commands might make use of mpi so that I can test my build of mothur will run as expected under mpirun?