Added file for choosing the slurm config

scripts/utils/choose_slurmConfig.R

+#######################################################################
+############### Select slurm partitiion ###############################
+#######################################################################
+
+get_line <- function(){
+  # gets characters (line) from the terminal or from a connection
+  # and returns it
+  if(interactive()){
+    s <- readline()
+  } else {
+    con <- file("stdin")
+    s <- readLines(con, 1, warn=FALSE)
+    on.exit(close(con))
+  }
+  return(s);
+}
+
+choose_slurmConfig <- function() {
+  
+  slurm <- suppressWarnings(ifelse(system2("srun",stdout=FALSE,stderr=FALSE) != 127, TRUE, FALSE))
+  if (slurm) {
+    modes <- c(" SLURM standby ",
+               " SLURM priority"
+               )
+
+    cat("\nCurrent cluster utilization:\n")
+    system("sclass")
+    cat("\n")
+
+    cat("\nPlease choose run submission type:\n")
+    cat(paste(1:length(modes), modes, sep=": " ),sep="\n")
+    cat("Number: ")
+    identifier <- get_line()
+    identifier <- as.numeric(strsplit(identifier,",")[[1]])
+    comp <- switch(identifier,
+                   "1" = "--qos=standby --nodes=1 --tasks-per-node=1"   ,
+                   "2" = "--qos=priority --nodes=1 --tasks-per-node=1"  )
+                  
+    if(is.null(comp)) stop("This type is invalid. Please choose a valid type")
+  } else {
+    comp <- "direct"
+  }
+
+  return(comp)
+}