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Customize at runtime the number of cores nlmeans is using #608

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fmorency opened this Issue Mar 19, 2015 · 8 comments

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@fmorency

fmorency commented Mar 19, 2015

This is a feature request to be able to customize at runtime the number of cores nlmeans is using.

Use case: We are running a dMRI pipeline on a massively parallel cluster and we need more control over the number of core each task is using in order to be performance efficient.

@samuelstjean

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samuelstjean commented Mar 19, 2015

That would be in https://github.com/nipy/dipy/blob/master/dipy/denoise/denspeed.pyx line 84 for the records, we need to add a num_cores variable to the parallel function http://docs.cython.org/src/userguide/parallelism.html

Of course we'll also need to put a new variable to carry around the value, add a valid default and everything in between.

@fmorency

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fmorency commented Oct 16, 2015

Hey guys, I don't think this feature request has been fixed...

@arokem

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arokem commented Oct 16, 2015

Oh yeah - you're right. Mind making a quick PR with the fix?

@samuelstjean

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samuelstjean commented Oct 16, 2015

We actually looked at it two weeks ago or so, and it involves playing with setup.py options to bind it with openmp. We also realized it does not work out of the box on a mac because the llvm version they use by default has no openmp support (and it also means that nothing is parallelized for these guys by default sadly). And well, it is fixable in the cython version, but the building and binding part to actualy use the option just made us give up in the end as the suggestion on the cython website itself was not working.

@jchoude

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jchoude commented Oct 16, 2015

Ok so just to correct what Sam is saying, it IS doable. We didn't do it for our internal codebase because it was not a priority, but it is true that it is more that juste 1 or 2 lines.

@Garyfallidis

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Garyfallidis commented Oct 18, 2015

I am looking at it. Will try to get it in before the release.

@skoudoro

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skoudoro commented Jun 12, 2017

Should we close this one @Garyfallidis @fmorency ?

@samuelstjean

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samuelstjean commented Jun 12, 2017

It was indeed fixed ages ago, new nlmeans is not parallel so it's probably also fine to close the issue anyway.

@skoudoro skoudoro closed this Jun 12, 2017

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