Nothing
# File name: dist_pony.r
# Run: mpiexec -np 4 Rscript dist_pony.r
rm(list = ls()) # Clean environment
library(pbdMPI, quietly = TRUE) # Load library
library(phyclust, quietly = TRUE) # Load library
if(comm.size() != 4)
comm.stop("4 processors are required.")
### Load data
data.path <- paste(.libPaths()[1], "/phyclust/data/pony524.phy", sep = "")
pony.524 <- read.phylip(data.path)
X <- pony.524$org
### Distribute data
jid <- get.jid(nrow(X))
X.gbd <- X[jid,] # GBD row-major format
### Compute distance
X.dist.common <- phyclust.edist(X)
### User-defined distance
my.dist <- function(x, y){
as.vector(phyclust.edist(rbind(x, y)))
}
X.gbd.dist <- comm.pairwise(X.gbd, FUN = my.dist)
### Verify
X.dist <- unlist(allgather(X.gbd.dist[, 3]))
n.diff <- sum(X.dist.common != X.dist)
### Neighbor Joining
X.nj <- nj(X.dist.common)
if(comm.rank() == 0){
set.seed(1234)
pony.phyclust <- phyclust(X, 3)
pdf("dist_pony.pdf", width = 6, height = 5)
par(mar = c(0, 0, 2, 0))
plotnj(X.nj, X.class = pony.phyclust$class.id)
title("Pony 524 & K = 3")
dev.off()
cat("Difference of common and gbd: ", n.diff, "\n", sep = "")
}
### Finish
finalize()
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