Function Not Found in R Doparallel 'Foreach' - Error in {:Task 1 Failed - "Could Not Find Function "Raster""

Function not found in R doParallel 'foreach' - Error in { : task 1 failed - could not find function raster

In the vignette of foreach and the help page of foreach, the argument .packages is pointed out as necessary to provide when using parallel computation with functions that are not loaded by default. So your code in the first example should be:

ptime<-system.time({
  r <- foreach(z = 1:length(files),
               .combine=cbind, 
               .packages='raster') %dopar% {
      # some code
      # and more code
  }
})

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Some more explanation

The foreach package does a lot of setting up behind the scenes. What happens is the following (in principle, technical details are a tad more complicated):

• foreach sets up a system of "workers" that you can see as separate R sessions that are each committed to a different core in a cluster.

• The function that needs to be carried out is loaded into each "worker" session, together with the objects needed to carry out the function

• each worker calculates the result for a subset of the data

• The results of the calculation on the different workers is put together and reported in the "master" R session.

As the workers can be seen as separate R sessions, packages from the "master" session are not automatically loaded. You have to specify which packages should be loaded in those worker sessions, and that's what the .package argument of foreach is used for.

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Note that when you use other packages (e.g. parallel or snowfall), you'll have to set up these workers explicitly, and also take care of passing objects and loading packages on the worker sessions.

permutation error with parallel and foreach package task 1 failed - could not find error

The code below should work. The reason you are getting this error is that the foreach function creates new workers in new sessions, and in those sessions functions and packages in the main session aren't exported. So note the .export argument, and the .packages argument.

# Permutations function ---------------------------------------------------
doNullPermutations <- function(nit, snps, estuaries) {
    x <- foreach(iteration = 1:3, # do 100 iterations
               .combine = rbind,
               .export = ls(globalenv()),
               .packages = 'tidyverse') %dopar% one_iteration(snps, estuaries)
    return(x)
}

perms_res_3est_10kperm <- doNullPermutations(1, snps = 20083, estuaries = 3)

R Parallel Programming: Error in { : task 1 failed - could not find function % %

you have to use .packages = c("magrittr", ...) and include all the packages, which are necessary to run the code within the foreach loop. However, .packages = "foreach" is not helping.

See, you can imagine that all the packages you define in .packages are forwareded / loaded in each parallel worker.

Error in { : task 1 failed - could not find function init_status.icm

I changed the numbers of cores (ncores) to 1 in both functions (simulate and baseline) and succeed it.

control.icm actually set the core to 1 as you can see it in the image below:

https://i.stack.imgur.com/xnx69.png

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