aa_allgather-method: All Ranks Gather Objects from Every Rank

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

All Ranks Gather Objects from Every Rank

Description

This method lets all ranks gather objects from every rank in the same communicator. The default return is a list of length equal to comm.size(comm).

Usage

allgather(x, x.buffer = NULL, x.count = NULL, displs = NULL,
          comm = .pbd_env$SPMD.CT$comm,
          unlist = .pbd_env$SPMD.CT$unlist)

Arguments

x	an object to be gathered from all ranks.
x.buffer	a buffer to hold the return object which probably has 'size of x' times 'comm.size(comm)' with the same type as x.
x.count	a vector of length 'comm.size(comm)' containing all object lengths.
displs	c(0L, cumsum(x.count)) by default.
comm	a communicator number.
unlist	apply unlist function to the gathered list before return.

Details

The arguments x.buffer, x.count, and displs can be left unspecified or NULL and are computed for you.

If x.buffer is specified, its type should be one of integer, double, or raw according to the type of x. Serialization and unserialization is avoided for atomic vectors if they are all the same size and x.buffer is specified, or if different sizes and both x.buffer and x.count are specified. A single vector instead of a list is returned in these cases.

Class array objects are gathered without serialization.

Complex objects can be gathered as serialization and unserialization is used on objects that are not of class "array" or atomic vectors.

The allgather is efficient due to the underlying MPI parallel communication and recursive doubling gathering algorithm that results in a sublinear (log2(comm.size(comm))) number of communication steps. Also, serialization is applied only locally and in parallel.

See methods{"allgather"} for S4 dispatch cases and the source code for further details.

Value

A list of length comm.size(comm), containing the gathered objects from each rank, is returned to all ranks by default. An exception is for atomic vectors, when x.buffer is specified, where a list is never formed and a single vector is returned. In other cases, the unlist = TRUE parameter simply applies the unlist() function to this list before returning.

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

gather(), allreduce(), reduce().

Examples

### 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))
.comm.size <- comm.size()
.comm.rank <- comm.rank()

### Examples
N <- 5
x <- (1:N) + N * .comm.rank
y <- allgather(matrix(x, nrow = 1))
comm.print(y)

y <- allgather(x, double(N * .comm.size))
comm.print(y)

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

RBigData/pbdMPI documentation built on Jan. 31, 2024, 10:34 p.m.