Parallel in core-metrics-phylogenetic

Hi All,

I’m trying to run Core diversity metrics (phylogenetic and non-phylogenetic) with passing parallel feature --p-n-jobs -1 to use all available CPUs, but I got this error.

Usage: qiime diversity core-metrics-phylogenetic [OPTIONS]

Error: Invalid value for "--p-n-jobs": -1 is smaller than the minimum valid value 0.

But from the document:

–p-n-jobs INTEGER RANGE [beta/beta-phylogenetic methods only,
excluding weighted_unifrac] - The number of
jobs to use for the computation. This works
by breaking down the pairwise matrix into
n_jobs even slices and computing them in
parallel. If -1 all CPUs are used. If 1 is
given, no parallel computing code is used at
all, which is useful for debugging. For
n_jobs below -1, (n_cpus + 1 + n_jobs) are
used. Thus for n_jobs = -2, all CPUs but one
are used. (Description from
sklearn.metrics.pairwise_distances)
[default: 1]

I’m using QIIME2-2018.2. I don’t know is this a bug or I did some thing wrong ?

Thanks,

Hey @Faisal!

That’s definitely on us. Thanks for letting us know our help text is all wrong! I’ve created an issue to track this. It looks like auto-detection may entirely not work.

In the meanwhile you’ll need to supply the total you want manually.

Sorry for the inconvenience!

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