pbdMPI (version 0.3-0)

global distance function: 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.

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.

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.

References

Programming with Big Data in R Website: http://r-pbd.org/

See Also

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

Examples

### Save code in a file "demo.r" and run with 2 processors by
### SHELL> mpiexec -np 2 Rscript demo.r

### Initial.
suppressMessages(library(pbdMPI, quietly = TRUE))
init()

### 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()