spaMM: dofuture – R documentation

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dofuture

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).
`fn`	Function, whose first argument is named `y`, to be applied to 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).

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

Mixed-Effect Models, with or without Spatial Random Effects

v3.10.0

CeCILL-2

Authors

François Rousset [aut, cre, cph] (<https://orcid.org/0000-0003-4670-0371>), Jean-Baptiste Ferdy [aut, cph], Alexandre Courtiol [aut] (<https://orcid.org/0000-0003-0637-2959>), GSL authors [ctb] (src/gsl_bessel.*)

Initial release

2022-02-06