HPC multi-threading and parallelization?

Hi all,

I'm still trouble shooting some things for our laboratory. One thing that I was also tasked with was getting QIIME2 to run on the HPC at the medical center.

We run a Linux cluster of approximately 70 nodes. We've been trying to get it working in a pipeline so we can streamline our analysis and run DADA2 from these nodes.

I found a couple of threads in the past, but I was wondering what strategies that you all have used to run it on HPC/parallelization. Thank you. Again, greatly appreciate your input.

Sincerely, ben

Hey there @ben!

We have some long-term goals to support direct integration with various task schedulers, etc, but not quite sure when something like that would happen. Otherwise, I tend to submit q2cli-based QIIME 2 commands as torque jobs on our local cluster. Some actions in QIIME 2 expose parameters like n_threads or n_cores - I will allocate nodes accordingly, when applicable. Sorry I don’t have a more slick answer for you, but for now, we basically treat QIIME 2 like any other package on our HPC.

FWIW - we have generally found that analyses that utilize ASVs over OTUs have a significantly smaller computational burden (obviously there are plenty of examples where that isn’t the case, but, broadly speaking…).

Hope that helps. :t_rex: :qiime2:

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Thanks, that’s greatly appreciated. I was reading on the DADA command for pushing for more threads I think it was --p-n-threads. If helpful, I can put my commands on here. I have been submitting QIIME2 as batch commands through their SGE scheduler(?). The problem is that when issues arise I cannot see errors, but this isn’t an issue with QIIME2 it is an issue with the SGE scheduler.

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As an aside, most of the DADA2 and denoise takes less than 12 hours with the HPC (compared to almost running some over a whole day. I do however, run multiple threads option with DADA and that may have something to do with the speed at which it runs.

Yup, DADA2 scales pretty well with more threads!

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