register: Maintain a global registry of available back-end Params

In BiocParallel: Bioconductor facilities for parallel evaluation

Description

Use functions on this page to add to or query a registry of back-ends, including the default for use when no BPPARAM object is provided to functions.

Usage

register(BPPARAM, default=TRUE)
registered(bpparamClass)
bpparam(bpparamClass)

Arguments

BPPARAM	An instance of a BiocParallelParam class, e.g., MulticoreParam, SnowParam, DoparParam.
default	Make this the default BiocParallelParam for subsequent evaluations? If FALSE, the argument is placed at the lowest priority position.
bpparamClass	When present, the text name of the BiocParallelParam class (e.g., “MulticoreParam”) to be retrieved from the registry. When absent, a list of all registered instances is returned.

Details

The registry is a list of back-ends with configuration parameters for parallel evaluation. The first list entry is the default and is used by BiocParallel functions when no BPPARAM argument is supplied.

At load time the registry is populated with default backends. On Windows these are SnowParam and SerialParam and on non-Windows MulticoreParam, SnowParam and SerialParam. When snowWorkers() or multicoreWorkers returns a single core, only SerialParm is registered.

The BiocParallelParam objects are constructed from global options of the corresponding name, or from the default constructor (e.g., SnowParam()) if no option is specified. The user can set customizations during start-up (e.g., in an .Rprofile file) with, for instance, options(MulticoreParam=quote(MulticoreParam(workers=8))).

The act of “registering” a back-end modifies the existing BiocParallelParam in the list; only one param of each type can be present in the registry. When default=TRUE, the newly registered param is moved to the top of the list thereby making it the default. When default=FALSE, the param is modified 'in place' vs being moved to the top.

bpparam(), invoked with no arguments, returns the default BiocParallelParam instance from the registry. When called with the text name of a bpparamClass, the global options are consulted first, e.g., options(MulticoreParam=MulticoreParam()) and then the value of registered(bpparamClass).

Value

register returns, invisibly, a list of registered back-ends.

registered returns the back-end of type bpparamClass or, if bpparamClass is missing, a list of all registered back-ends.

bpparam returns the back-end of type bpparamClass or,

Author(s)

Martin Morgan mailto:[e-mail].

See Also

BiocParallelParam for possible values of BPPARAM.

Examples

## ----------------------------------------------------------------------
## The registry 
## ----------------------------------------------------------------------

## The default registry.
default <- registered()
default

## When default = TRUE the last param registered becomes the new default.
snowparam <- SnowParam(workers = 3, type = "SOCK")
register(snowparam, default = TRUE)
registered()

## Retrieve the default back-end,
bpparam()

## or a specific BiocParallelParam.
bpparam("SnowParam")

## restore original registry -- push the defaults in reverse order
for (param in rev(default))
    register(param)

## ----------------------------------------------------------------------
## Specifying a back-end for evaluation
## ----------------------------------------------------------------------

## The back-end of choice is given as the BPPARAM argument to
## the BiocParallel functions. None, one, or multiple back-ends can be
## used.

bplapply(1:6, sqrt, BPPARAM = MulticoreParam(3))

## When not specified, the default from the registry is used.
bplapply(1:6, sqrt)

BiocParallel documentation built on Nov. 8, 2020, 5:46 p.m.