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Parallel Processing Parameters

Source: R/parallel.R
parallel_params.Rd

tileApply() is parallelized through either future.apply::future_lapply() (default) or BiocParallel::bplapply().

Additional parameters to control parallelization can be passed as a list through the parallel_params argument in tileApply() methods.

Usage

getTileworkParMethod()

setTileworkParMethod(method)

Arguments

method

character. Either "future" (default) or "biocparallel". Which parallelization framework to use.

Value

getTileworkParMethod returns character. The parallelization method being used.

setTileworkParMethod returns NULL invisibly

Parameters

Available parameters for the parallel_params list:

  • method - character. Either "future" (default) or "biocparallel". Which parallelization framework to use. Overrides setTileworkParMethod()

  • future_seed - logical (default = TRUE). Passed to the future.seed parameter in future.apply::future_lapply(). Only used when method = "future".

  • BPPARAM - a {BiocParallel} parallelization parameter object. Only used when method = "biocparallel".

Additional parameters relevant to the underlying functions may also be passed in the list and will be forwarded via ....

Package Options

  • "tilework.warn_sequential" - logical (default = TRUE). Whether to warn when using parallelization defaults that run sequentially (i.e., future::sequential() or BiocParallel::SerialParam()).

  • "tilework.par_method" - character (default = "future"). Either "future" or "biocparallel". Which parallelization framework to use.

  • "tilework.bpparam" - a {BiocParallel} parameter object. Set this to automatically use a specific BPPARAM, analogous to setting a future::plan() for the {future} backend.

See also

tileApply()

Other parallel settings: tilework_management

Examples

getTileworkParMethod()
#> [1] "future"

# Set to BiocParallel
setTileworkParMethod("biocparallel")
getTileworkParMethod()
#> [1] "biocparallel"

if (FALSE) { # \dontrun{
# Using future backend with multisession
future::plan(future::multisession, workers = 4)
tileApply(x, tiles, fun)

# Using BiocParallel backend
setTileworkParMethod("biocparallel")
options(tilework.bpparam = BiocParallel::SnowParam(workers = 4))
tileApply(x, tiles, fun)

# Or override per-call
setTileworkParMethod("future")  # global default is future
tileApply(x, tiles, fun, 
    parallel_params = list(method = "biocparallel")
) # but use BiocParallel here

# Suppress sequential warnings
options(tilework.warn_sequential = FALSE)
} # }