xx_comm_dist: Global Distance for Distributed Matrices

In pbdMPI: R Interface to MPI for HPC Clusters (Programming with Big Data Project)

Global Distance for Distributed Matrices

Description

These functions globally compute distance for all ranks.

Usage

comm.dist(X.gbd, method = "euclidean", diag = FALSE, upper = FALSE,
          p = 2, comm = .pbd_env$SPMD.CT$comm,
          return.type = c("common", "gbd"))

Arguments

X.gbd	a gbd matrix.
method	as in dist().
diag	as in dist().
upper	as in dist().
p	as in dist().
comm	a communicator number.
return.type	returning type for the distance.

Details

The distance function is implemented for a distributed matrix.

The return type common is only useful when the number of rows of the matrix is small since the returning matrix is N * N for every rank where N is the total number of rows of X.gbd of all ranks.

The return type gbd returns a gbd matrix (distributed across all ranks, and the gbd matrix has 3 columns, named "i", "j", and "value", where (i, j) is the global indices of the i-th and j-th rows of X.gbd, and value is the corresponding distance. The (i, j) is ordered as a distance matrix.

Value

A full distance matrix is returned from the common return type. Suppose N.gbd is total rows of X.gbd, then the distance will have N.gbd * (N.gbd - 1) / 2 elements and the distance matrix will have N.gbd^2 elements.

A gbd distance matrix with 3 columns is returned from the gbd return type.

Warning

The distance or distance matrix could be huge.

Author(s)

Wei-Chen Chen [e-mail], George Ostrouchov, Drew Schmidt, Pragneshkumar Patel, and Hao Yu.

References

Programming with Big Data in R Website: https://pbdr.org/

See Also

comm.allpairs() and comm.pairwise().

Examples

## Not run: 
### Save code in a file "demo.r" and run with 2 processors by
### SHELL> mpiexec -np 2 Rscript demo.r

spmd.code <- "
### Initialize
suppressMessages(library(pbdMPI, quietly = TRUE))

### Examples.
comm.set.seed(123456, diff = TRUE)

X.gbd <- matrix(runif(6), ncol = 3)
dist.X.common <- comm.dist(X.gbd)
dist.X.gbd <- comm.dist(X.gbd, return.type = \"gbd\")

### Verify.
dist.X <- dist(do.call(\"rbind\", allgather(X.gbd)))
comm.print(all(dist.X == dist.X.common))

### Verify 2.
dist.X.df <- do.call(\"rbind\", allgather(dist.X.gbd))
comm.print(all(dist.X == dist.X.df[, 3]))
comm.print(dist.X)
comm.print(dist.X.df)

### Finish.
finalize()
"
# execmpi(spmd.code, nranks = 2L)

## End(Not run)

pbdMPI documentation built on Sept. 18, 2024, 9:07 a.m.