dofuture: Interface for parallel computations

In spaMM: Mixed-Effect Models, with or without Spatial Random Effects

Interface for parallel computations

Description

interface to apply some function fn in parallel on columns of a matrix. It is not logically restricted to mixed-effect applications, hence it can be used more widely. Depending on the nb_cores argument, parallel or serial computation is performed, calling the future.apply::future_apply function. A socket cluster is used by default for parallel computations, but a fork cluster can be requested on linux and alike operating systems by using argument cluster_args=list(type="FORK").

Usage

dofuture(newresp, fn, nb_cores=NULL, fit_env, control=list(), 
      cluster_args=NULL, debug.=FALSE, iseed=NULL, 
      showpbar="ignored", pretest_cores="ignored",
      ... )

Arguments

newresp	A matrix on whose columns fn will be applied (e.g., as used internally in spaMM, the return value of a simulate.HLfit() call); or an integer, then converted to a trivial matrix matrix(seq(newresp),ncol=newresp,nrow=1).
fn	Function whose first argument is named y. The function will be applied for y taken to be each column of newresp.
nb_cores	Integer. Number of cores to use for parallel computations. If >1, a cluster of nb_cores nodes is used. Otherwise, no parallel computation is performed.
fit_env	(for socket clusters only:) An environment, or a list, containing variables to be exported on the nodes of the cluster (by parallel::clusterExport).
control	A list. The only effective control is .combine="rbind" (mimicking the foreach syntax used in the alternative interface dopar).
cluster_args	A list of arguments passed to parallel::makeCluster or parallel::makeForkCluster. E.g., outfile="log.txt" may be useful to collect output from the nodes, and type="FORK" to force a fork cluster on linux(-alikes).
debug.	(for socket clusters only:) For debugging purposes. Effect, if any, is to be defined by the fn as provided by the user.
iseed	Integer, or NULL. If an integer, it is used to initialize "L'Ecuyer-CMRG" random-number generator (iseed argument of clusterSetRNGStream), with identical effect across different models of parallelisation. If iseed is NULL, the seed is not controlled.
showpbar,pretest_cores	Currently ignored; for consistency with dopar formal arguments.
...	Further arguments to be passed (unevaluated) to future.apply (and then possibly to fn).

Value

The result of calling future.apply. If the progressr package is loaded, a side-effect of dofuture is to show a progress bar with character 'S' or 'P' or 'F' depending on parallelisation status (serial/socket/fork).

See Also

dopar for an alternative implementation of (essentially) the same functionalities, and wrap_parallel for its differences from dofuture.

Examples

## Not run: 
if (requireNamespace("future.apply", quietly = TRUE)) {

 # Useless function, but requiring some argument beyond the first
 foo <- function(y, somearg, ...) {
   if ( is.null(somearg) || TRUE ) length(y)
 }

 # Whether FORK can be used depends on OS and whether Rstudio is used:
   dofuture(matrix(1,ncol=4,nrow=3), foo, fit_env=list(), somearg=NULL, 
     nb_cores=2, cluster_args=list(type="FORK"))
}

## End(Not run)

spaMM documentation built on Aug. 30, 2023, 1:07 a.m.