I am trying to write values at a certain GDS node in parallel. I was not able to figure out what I am doing wrong. I have tried the following:

​# Load data
data(hapmap_geno)

# Create a gds file
snpgdsCreateGeno("test.gds", genmat = hapmap_geno$genotype,
    sample.id = hapmap_geno$sample.id, snp.id = hapmap_geno$snp.id,
    snp.chromosome = hapmap_geno$snp.chromosome,
    snp.position = hapmap_geno$snp.position,
    snp.allele = hapmap_geno$snp.allele, snpfirstdim=TRUE)

# Open the GDS file
(genofile <- snpgdsOpen("test.gds", allow.fork=TRUE, readonly=FALSE))

snps.included <- read.gdsn(index.gdsn(genofile, "snp.id"))
all.samples <- read.gdsn(index.gdsn(genofile, "sample.id"))

LRR.matrix <- matrix(0, nrow = length(snps.included),
                      ncol = length(all.samples))

nLRR <- gdsfmt::add.gdsn(genofile, "LRR", LRR.matrix, replace=TRUE)
gdsfmt::read.gdsn(nLRR)

lrr.import <- function(lo, genofile, snps.included, nLRR){
message(lo)
LRR.x <- rnorm(length(snps.included))
gdsfmt::write.gdsn(nLRR, LRR.x, start=c(1,lo), count=c(length(snps.included),1))

}

### Working
multicoreParam <-  BiocParallel::MulticoreParam(workers = 1)
message("Start the parallel import of LRR/BAF values")
BiocParallel::bplapply(1:length(all.samples), lrr.import, BPPARAM = multicoreParam, genofile=genofile,
                           snps.included=snps.included, nLRR=nLRR)

### NOT Working
multicoreParam <-  BiocParallel::MulticoreParam(workers = 3)
message("Start the parallel import of LRR/BAF values")
BiocParallel::bplapply(1:length(all.samples), lrr.import, BPPARAM = multicoreParam, genofile=genofile,
                           snps.included=snps.included, nLRR=nLRR)

Error: BiocParallel errors
  element index: 1, 2, 3, 4, 5, 6, ...
  first error: Creating/Opening and writing the GDS file should be in the same process.

I would be grateful for some help.

The answer is simple: I have not implemented GDS writing with multiple processes at the same time so far.

We usually create multiple independent GDS files, and each process writes data to each separate GDS file. After all child processes are done, multiple GDS files are merged in the main process.