batchtools: batchMap – R documentation

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batchMap

Map Operation for Batch Systems

Description

A parallel and asynchronous Map/mapply for batch systems. Note that this function only defines the computational jobs. The actual computation is started with submitJobs. Results and partial results can be collected with reduceResultsList, reduceResults or loadResult.

For a synchronous Map-like execution, see btmapply.

Usage

batchMap(
  fun,
  ...,
  args = list(),
  more.args = list(),
  reg = getDefaultRegistry()
)

Arguments

`fun`	[`function`] Function to map over arguments provided via `...`. Parameters given via `args` or `...` are passed as-is, in the respective order and possibly named. If the function has the named formal argument “.job”, the `Job` is passed to the function on the slave.
`...`	[ANY] Arguments to vectorize over (list or vector). Shorter vectors will be recycled (possibly with a warning any length is not a multiple of the longest length). Mutually exclusive with `args`. Note that although it is possible to iterate over large objects (e.g., lists of data frames or matrices), this usually hurts the overall performance and thus is discouraged.
`args`	[`list` \| `data.frame`] Arguments to vectorize over as (named) list or data frame. Shorter vectors will be recycled (possibly with a warning any length is not a multiple of the longest length). Mutually exclusive with `...`.
`more.args`	[`list`] A list of further arguments passed to `fun`. Default is an empty list.
`reg`	[`Registry`] Registry. If not explicitly passed, uses the default registry (see `setDefaultRegistry`).

Value

[data.table] with ids of added jobs stored in column “job.id”.

Examples

# example using "..." and more.args
tmp = makeRegistry(file.dir = NA, make.default = FALSE)
f = function(x, y) x^2 + y
ids = batchMap(f, x = 1:10, more.args = list(y = 100), reg = tmp)
getJobPars(reg = tmp)
testJob(6, reg = tmp) # 100 + 6^2 = 136

# vector recycling
tmp = makeRegistry(file.dir = NA, make.default = FALSE)
f = function(...) list(...)
ids = batchMap(f, x = 1:3, y = 1:6, reg = tmp)
getJobPars(reg = tmp)

# example for an expand.grid()-like operation on parameters
tmp = makeRegistry(file.dir = NA, make.default = FALSE)
ids = batchMap(paste, args = data.table::CJ(x = letters[1:3], y = 1:3), reg = tmp)
getJobPars(reg = tmp)
testJob(6, reg = tmp)

batchtools

Tools for Computation on Batch Systems

v0.9.15

LGPL-3

Authors

Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>), Bernd Bischl [aut], Dirk Surmann [ctb] (<https://orcid.org/0000-0003-0873-137X>)

Initial release