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Simon-Coetzee / motifBreakR

A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.
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multiple cores do not seem to be used #33

Closed paul-shannon closed 3 years ago

paul-shannon commented 3 years ago

@scoetzee @Simon-Coetzee First, thanks for this package. It has been very helpful.

In scaling up our use to explore eQTLs from Alzheimer's loci, I cannot seem to make good use of the BPPARAM argument.

With MulticoreParam(workers=40) on a linux box with 84 cores, watching top I see multiple R processes appear very briefly, and then disappear, leaving only one R process, running for an additional 10 minutes. The total execution time seems to be linear.
I am using 40 rsids at a time, against 80 motifs from MotifDb.

Any suggestions?

Simon-Coetzee commented 3 years ago

I had a problem with how I was implementing the parallel code, It should be fixed here (on github) now, and should be propagating to Bioconductor devel soon.

paul-shannon commented 3 years ago

Thanks, Simon!

I’m trying it out now.

On Sep 10, 2021, at 12:42 PM, Simon Coetzee @.***> wrote:

I had a problem with how I was implementing the parallel code, It should be fixed here (on github) now, and should be propagating to Bioconductor devel soon.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

paul-shannon commented 3 years ago

Works great! Fast!

Thanks, Simon.

On Sep 10, 2021, at 12:56 PM, Paul Shannon @.***> wrote:

Thanks, Simon!

I’m trying it out now.

  • Paul

On Sep 10, 2021, at 12:42 PM, Simon Coetzee @.***> wrote:

I had a problem with how I was implementing the parallel code, It should be fixed here (on github) now, and should be propagating to Bioconductor devel soon.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.