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nspope / radish

Fast gradient-based optimization of resistance surfaces
BSD 3-Clause "New" or "Revised" License
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Cholmod error 'problem too large' when creating conductance surface #6

Open sbreitbart opened 1 year ago

sbreitbart commented 1 year ago

Hi Nate,

I'm running a script on the HPC and have encountered this error:

Error in Matrix::Cholesky(Qn, LDL = TRUE) :
  Cholmod error 'problem too large' at file ../Core/cholmod_change_factor.c, line 536
Calls: conductance_surface -> <Anonymous> -> <Anonymous>

I believe it occurs after running the equivalent of this line (from the tutorial):

surface <- conductance_surface(covariates = scale_covs,
                               coords = sites_select,
                               directions = 8)

From what I'm reading online, I'm getting this error because this is a memory issue related to the output matrix. My input raster is pretty big, so I will decrease the resolution of my input raster and then try again, but I'm not sure of other potential next steps. I realize this issue isn't directly related to radish, but thought you might have some advice.

Thanks so much! Sophie