How many cores does deblur or dada2 use?

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How many cores does deblur or dada2 use? I know some plugins can use more than one core, so I wanted to see how much these used so I can optimize my processing. Furthermore, the more cores I ask my supercomputer center for, the longer it takes for them to actually start the processing, so I want to ask for the most it can use but no more. Thanks!

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Hello Mike,

Both deblur and dada2 are pretty efficient, so they will use as many cores as you can give them!
(Well, as many cores on a single node!)

You could ask your supercomputer center how many cores/threads are on one node, then pass that to dada2 and deblur.

Some supercomputer centers have a ‘short queue’ especially for programs like deblur and dada2 that only run on a single node. This short queue is often very fast to start processing, so it’s a perfect fit for your programs.

Colin

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Thanks,

What about the plugin demux?

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Take a look at the Methods section for the plugin.
https://docs.qiime2.org/2019.7/plugins/available/demux/

If you see a --p-cores or --p-threads option, then it can use multiple cores. If not, just one core is used.

Let me know what you conclude!
Colin

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They don’t seem to be there, so I’ll assume 1 then. Thanks!
Link: https://docs.qiime2.org/2019.7/plugins/available/deblur/denoise-16S/

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deblur denoise-16S supports multiple jobs via the --p-jobs-to-start flag.

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What do you mean jobs? Multiple denoising if I had multiple files to denoise?

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Not sure (I am just quoting the plugin doc), you’ll have to check the deblur docs to check their definition of “jobs” out:

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Deblur can operate in parallel. The number of threads can be specified by the -O NNN flag (default it 1). Running more threads than available cores is not advised.

Looks like "jobs" means "threads" here.

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