Enable parallelization on batch systems

Description

This class is used to parameterize scheduler options on managed high-performance computing clusters.

Usage

BatchJobsParam(workers, catch.errors = TRUE, cleanup = TRUE, 
    work.dir = getwd(), stop.on.error = FALSE, seed = NULL,
    resources = NULL, conffile = NULL, cluster.functions = NULL, 
    progressbar = TRUE, ...) 

Arguments

Number of workers on with Multicore and SSH backend which defaults here to all workers available. On managed HPC workers defaults to NA but can be set to control chunking of jobs. See argument n.chunks in chunk and submitJobs for more information.

Flag to determine in apply-like functions (see e.g. bplapply) whether to quit with an error as soon as one application fails or encapsulation of function calls in try blocks which triggers a resume mechanism (see bpresume). Defaults to TRUE.

BatchJobs creates temporary directories in the work.dir. If cleanup is set to TRUE (default), the directories are removed from the file systems automatically. Set this to FALSE whenever it might become necessary to utilize any special functionality provided by BatchJobs. To retrieve the registry, call loadRegistry on the temporary directory.

Directory to store temporary files. Note that this must be shared across computational nodes if you use a distributed computing backend. Default ist the current working directory of R, see getwd.

Stop all jobs as soon as one jobs fails (stop.on.error == TRUE) or wait for all jobs to terminate. Default is FALSE.

Set an initial seed for the RNG. See makeRegistry for more information. Default is NULL where a random seed is chosen upon initialization.

List of job specific resources passed to submitJobs. Default is NULL where the resources defined in the configuration are used.

URI to a custom BatchJobs configuration file used for execution. Default is NULL which relies on BatchJobs to handle configuration files.

Specify a specific cluster backend using on of the constructors provided by BatchJobs, see ClusterFunctions. Default is NULL where the default cluster functions defined in the configuration are used.

Suppress the progress bar used in BatchJobs and be less verbose. Default is FALSE.

BatchJobsParam constructor

Return an object with specified values. The object may be saved to disk or reused within a session.

Methods

The following generics are implemented and perform as documented on the corresponding help page: bpworkers, bpstart, bpstop, bpisup, bpbackend, bpbackend<-

Author(s)

Martin Morgan mailto:mtmorgan@fhcrc.org

See Also

getClass("BiocParallelParam") for additional parameter classes.

register for registering parameter classes for use in parallel evaluation.

Examples

p <- BatchJobsParam(progressbar=FALSE)
bplapply(1:10, sqrt, BPPARAM=p)

## Not run: 
register(BatchJobsParam(catch.errors = FALSE), default=TRUE)

## End(Not run)