batchtools (version 0.9.0)

btlapply: Synchronous Apply Functions

Description

This is a set of functions acting as counterparts to the sequential popular apply functions in base R: btlapply for lapply and btmapply for link[base]{mapply}.

Internally, jobs are created using batchMap on the provided registry. If no registry is provided, a temporary registry (see argument file.dir of makeRegistry) and batchMap will be used. After all jobs are terminated (see waitForJobs), the results are collected and returned as a list.

Note that these functions are one suitable for short and fail-safe operations on batch system. If some jobs fail, you have to retrieve partial results from the registry directory yourself.

Usage

btlapply(X, fun, ..., resources = list(), n.chunks = NULL,
  chunk.size = NULL, reg = makeRegistry(file.dir = NA))
btmapply(fun, ..., more.args = list(), simplify = FALSE, use.names = TRUE,
  resources = list(), n.chunks = NULL, chunk.size = NULL,
  reg = makeRegistry(file.dir = NA))

Arguments

X

[vector] Vector to apply over.

fun

[function] Function to apply.

...

[ANY] Additional arguments passed to fun (btlapply) or vectors to map over (btmapply).

resources

[named list] Computational resources for the batch jobs. The elements of this list (e.g. something like “walltime” or “nodes”) depend on your template file. See notes for reserved special resource names. Defaults can be stored in the configuration file by providing the named list default.resources. Settings in resources overwrite those in default.resources.

n.chunks

[integer(1)] Requested number of chunks. If more chunks than elements in ids are requested, empty chunks are ignored. Mutually exclusive with chunks.size.

chunk.size

[integer(1)] Requested number of elements in each chunk. If ids cannot be chunked evenly, some chunks will have less elements than others. Mutually exclusive with with n.chunks.

reg

[Registry] Registry. If not explicitly passed, uses the default registry (see setDefaultRegistry).

more.args

[list] Additional arguments passed to fun.

simplify

[logical(1)] Simplify the results using simplify2array?

use.names

[logical(1)] Use names of the input to name the output?

Value

[list] List with the results of the function call.

Examples

btlapply(1:3, function(x) x^2)
btmapply(function(x, y, z) x + y + z, x = 1:3, y = 1:3, more.args = list(z = 1), simplify = TRUE)