worker initialization failed: there is no package in parallel processing

Question

I'm trying to parallelise a function in R using the R function focal_hpc from the 'spatial.tools' R package. I'm using this script in a SLURM server. This is an example of what I have run.

f_mean = function(x){mean(x)}

sfQuickInit(cpus=6)
res_mean<-focal_hpc(x=raster,fun=f_mean,window_dims=c(7,7))[[1]]
sfQuickStop()

However, I do get the following error and I do not understand why:

Error in e$fun(obj, substitute(ex), parent.frame(), e$data) : 
  worker initialization failed: there is no package called ‘spatial.tools’
Calls: system.time ... focal_hpc_focal_processing -> %dopar% -> <Anonymous>

I have installed the 'spatial.tools' package in a local library within the server, so my guess is that the function is not able to load the package from the local library.

What do you think?

Answer 1

Are you able to load the spatial.tools package from a compute node? You should try by allocating compute resources with the command salloc and then start R and try to see if you can load the package spatial.tools . Whatever you install you need to make sure that all the compute nodes have access (read access at least) to it.