Mothur is a “project [which] seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.”

Some of the Mothur functions support OpenMPI to provide parallelism. There are two steps to take advantage of this feature:

  1. Allocate enough nodes in the Torque/Slurm job file, i.e:

    PBS -l nodes=16

or

#SBATCH -N 16
  1. In your Mothur batchfile, call the functions with the processors parameter, i.e:

    summary.seqs(fasta=amazon.fasta,processors=16)

Note that not all Mothur functions support multi-processor parallelism. Attempting to call unsupported functions with the processors parameter will produce an error message.