Fix use on SLURM by replacing parallel::detectCores()

Replaced parallel::detectCores() with length(parallelly::availableWorkers()). Since the former does not respect the allocations of queueing systems such as SLURM, it was not ready to be used on systems such as UBELIX that use e.g. SLURM (see https://stackoverflow.com/a/75923399)

R/map2tidy.R

@@ -24,7 +24,7 @@
 #' @param fileprefix A character string specifying the file name prefix.
 #' @param ncores Number of cores for parallel execution (distributing
 #' extraction of longitude slices). When set to \code{"all"}, the number of
-#' cores for parallelisation is determined by \code{parallel::detectCores()}.
+#' cores for parallelisation is determined by \code{length(parallelly::availableWorkers())}.
 #' Defaults to \code{1} (no parallelisation).
 #' @param fgetdate A function to derive the date used for the time dimension
 #' based on the file name.
@@ -114,7 +114,7 @@ map2tidy <- function(
 
 
   if (ncores=="all"){
-    ncores <- parallel::detectCores() - 1
+    ncores <- length(parallelly::availableWorkers()) - 1
   }
   ncores <- min(ncores, nrow(ilon_arg)) # No need to have more cores if we only produce 1 file
 

vignettes/parallel_computation.Rmd

@@ -127,7 +127,7 @@ print("getting data for longitude indices:")
 list_of_LON_str <- gsub(".*(LON_[0-9.+-]*).*.rds","\\1", res_tidy$data) # extract LONGITUDES from res_tidy
 
 # get all available cores
-ncores <- 3 # parallel::detectCores()
+ncores <- 3 # length(parallelly::availableWorkers())
 
 # set up the cluster, sending required objects to each core
 cl <- multidplyr::new_cluster(ncores) %>%