Support for multiple cores in cluster and clearcut commands

Commands in mothur
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System(s): Ubuntu Server 22.04 and CentOS 7
mothur version: 1.48.0

Good afternoon mothur dev team.

I have noticed that a couple of steps in the mothur SOP, e.g. the cluster step (using the default OptiClust, not agc or dgc) and clearcut steps, seem to be limited to 1 core. As such, these steps can seemingly take forever with large datasets and can drain users of “service units” when dealing with computing clusters within our institutions.

Out of curiosity and the desire to optimize my mothur workflow, I was wondering if there is a way, or will be a way, to run these steps with multiple cores. I am far from being a software developer and I admire the hard work that you all do to maintain and improve mothur, so I mean no ill will by asking.

Thank you for your time and efforts,
Elek

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Hi Elek,

You are correct. The way these algorithms are designed, they cannot be parallelized. Alternatively, you could use cluster.split to make use of parallelization.

Pat

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