setup_cluster {adaptr}R Documentation

Setup default cluster for use in parallelised adaptr functions

Description

This function setups (or removes) a default cluster for use in all parallelised functions in adaptr using the parallel package. The function also exports objects that should be available on the cluster and sets the random number generator appropriately. See Details for further info on how adaptr handles sequential/parallel computation.

Usage

setup_cluster(cores, export = NULL, export_envir = parent.frame())

Arguments

cores

can be either unspecified, NULL, or a single integer ⁠> 0⁠. If NULL or 1, an existing default cluster is removed (if any), and the default will subsequently be to run functions sequentially in the main process if cores = 1, and according to getOption("mc.cores") if NULL (unless otherwise specified in individual functions calls). The parallel::detectCores() function may be used to see the number of available cores, although this comes with some caveats (as described in the function documentation), including that the number of cores may not always be returned and may not match the number of cores that are available for use. In general, using less cores than available may be preferable if other processes are run on the machine at the same time.

export

character vector of names of objects to export to each parallel core when running in parallel; passed as the varlist argument to parallel::clusterExport(). Defaults to NULL (no objects exported), ignored if cores == 1. See Details below.

export_envir

environment where to look for the objects defined in export when running in parallel and export is not NULL. Defaults to the environment from where the function is called.

Details

Using sequential or parallel computing in adaptr

All parallelised adaptr functions have a cores argument that defaults to NULL. If a non-NULL integer ⁠> 0⁠ is provided to the cores argument in any of those (except setup_cluster()), the package will run calculations sequentially in the main process if cores = 1, and otherwise initiate a new cluster of size cores that will be removed once the function completes, regardless of whether or not a default cluster or the global "mc.cores" option have been specified.

If cores is NULL in any adaptr function (except setup_cluster()), the package will use a default cluster if one exists or run computations sequentially if setup_cluster() has last been called with cores = 1. If setup_cluster() has not been called or last called with cores = NULL, then the package will check if the global "mc.cores" option has been specified (using ⁠options(mc.cores = <number of cores>)⁠). If this option has been set with a value ⁠> 1⁠, then a new, temporary cluster of that size is setup, used, and removed once the function completes. If this option has not been set or has been set to 1, then computations will be run sequentially in the main process.

Generally, we recommend using the setup_cluster() function as this avoids the overhead of re-initiating new clusters with every call to one of the parallelised adaptr functions. This is especially important when exporting many or large objects to a parallel cluster, as this can then be done only once (with the option to export further objects to the same cluster when calling run_trials()).

Type of clusters used and random number generation

The adaptr package solely uses parallel socket clusters (using parallel::makePSOCKcluster()) and thus does not use forking (as this is not available on all operating systems and may cause crashes in some situations). As such, user-defined objects that should be used by the adaptr functions when run in parallel need to be exported using either setup_cluster() or run_trials(), if not included in the generated trial_spec object.

The adaptr package uses the "L'Ecuyer-CMRG" kind (see RNGkind()) for safe random number generation for all parallelised functions. This is also the case when running adaptr functions sequentially with a seed provided, to ensure that the same results are obtained regardless of whether sequential or parallel computation is used. All functions restore both the random number generator kind and the global random seed after use if called with a seed.

Value

Invisibly returns the default parallel cluster or NULL, as appropriate. This may be used with other functions from the parallel package by advanced users, for example to load certain libraries on the cluster prior to calling run_trials().

Examples


# Setup a cluster using 2 cores
setup_cluster(cores = 2)

# Get existing default cluster (printed here as invisibly returned)
print(setup_cluster())

# Remove existing default cluster
setup_cluster(cores = NULL)

# Specify preference for running computations sequentially
setup_cluster(cores = 1)

# Remove default cluster preference
setup_cluster(cores = NULL)

# Set global option to default to using 2 new clusters each time
# (only used if no default cluster preference is specified)
options(mc.cores = 2)


[Package adaptr version 1.3.2 Index]