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const-ae / glmGamPoi

Fit Gamma-Poisson Generalized Linear Models Reliably
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Core Usage #36

Open NKalavros opened 2 years ago

NKalavros commented 2 years ago

Hello!

Insanely useful package. Thank you so much for this!

I wanted to ask, when fitting a model with glm_gp on slightly larger datasets, during the final fitting step, all cores on the machine are hogged. Sometimes this can cause problems with other processes. Is there any way to limit core usage by gamPoi? I tried through future, and biocParallel but was unable to limit core usage.

Thanks again, Nikolas

const-ae commented 2 years ago

Hi Nikolas,

sorry for the delay. I just got back from holidays.

Thank you for highlighting this issue. Could you say a bit more with what kind of data are you calling glmGamPoi? Is it by any chance data stored on disk using the DelayedArray package?

If yes, please try the following setting, before calling glmGamPoi:

DelayedArray::setAutoBPPARAM(BiocParallel::SerialParam())

If no, could you maybe provide a small reproducible example so that I can investigate the issue?

Best, Constantin