profiling_wmma.R

## This script is for ncu-profiling MMA1Bit (wmma).
# We simulate a population with 1000k SNPs and 10k individuals.

library(miraculix)
# Global RFutils options
RFoptions(install="none", warn_parallel=FALSE)
RFoptions(centered=FALSE, normalized=FALSE, cores=12, helpinfo=FALSE, la_mode=LA_GPU, snpcoding=MMA1Bit)

# Number of individuals
n <- 10000
# Number of SNPs
snps <- 1e6
# magic number to avoid RAM overflow
divisor <- 100

#Simulate population
SNPs <- matrix(sample(0:2, n/divisor * snps, replace=T), ncol=n/divisor)
Z <- miraculix::genomicmatrix(snps, n)
for (j in 0:(divisor-1)) {
  fillGeno(Z, (1:(n/divisor)) + n/divisor * j, SNPs)
}

cat("snpcoding=MMA1Bit, wmma version\n")

print(system.time({
    G <- miraculix::relationshipMatrix(Z,
      warp = TRUE, shape = 6, n_streams = 6, tilesize = 1024, naive = TRUE
    )
  })[3]
)