I have a few questions as far as which compiled version of mothur is appropriate to run. As far as I can tell, the commands that can use multiple processors (multiple cores) are align.seqs, chimera.slayer, chimera.uchime, classify.seqs, dist.seqs, filter.seqs, screen.seqs, and trim.seqs. From a note in the forum, trim.seqs will run with multiple cores, but not with mpi enabled, is this true for all the commands?
When I input any commands using an mpi-enabled build of mothur on my linux machine I never see it using more than one processor or thread. When run on my mac it seems to use multiple processors. Would a build of mothur with mpi not enabled, allow it to run on multiple cores on a linux box?
Which commands would be able to use mpi, launched from a mpirun command line or a shell script using sge?