I've been trying to get a parallelized foreach loop running in R, it works fine for approximately ten iterations but then crashes, showing the error:
Error in { : task 7 failed - "missing value where TRUE/FALSE needed"
Calls: %dopar% -> <Anonymous>
Execution halted
I append the results of each loop to a file, which does show the output to be as expected. My script is as followed,using the combn_sub function from this post:
LBRA <- fread(
input = "LBRA.012",
data.table = FALSE)
str_bra <- nrow(LBRA)
br1sums <- colSums(LBRA)
b1non <- which(br1sums == 0)
LBRA_trim <- LBRA[,-b1non]
library(foreach)
library(doMC)
registerDoMC(28)
foreach(X = seq(2, (nrow(LBRA)-1))) %dopar% {
com <- combn_sub(
x = nrow(LBRA),
m = X,
nset = 1000)
out_in <- matrix(
ncol = 2,
nrow = 1)
colnames(out) <- c("SNPs", "k")
for (A in seq(1, ncol(com))){
rowselect <- com[, A]
sub <- LBRA_trim[rowselect, ]
subsum <- colSums(sub)
length <- length(which(subsum != 0)) - 1
out_in <- rbind(out_in, c(length, X))
}
write.table(
file = "plateau.csv",
sep = "\t",
x = out_in,
append = TRUE)
}
I had a similar problem with my foreach call...
tmpcol <- foreach(j = idxs:idxe, .combine=cbind) %dopar% { imp(j) }
Error in { : task 18 failed - "missing value where TRUE/FALSE needed"
Changing the .errorhandling parameter only ignores the error
tmpcol <- foreach(j = idxs:idxe, .combine=cbind, .errorhandling="pass") %dopar% { imp(j) }
Warning message:
In fun(accum, result.18) :
number of rows of result is not a multiple of vector length (arg 2)
I suggest running the function in your foreach call for X=7. The problem in my case was my function, imp(j), was throwing an error (for j=18, it was hitching on an NA calculation) which resulted in the vague output from foreach.
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