BatchJobsParam-class

Enable parallelization on batch systems

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 = TRUE, seed = NULL, resources = NULL, conffile = NULL, cluster.functions = NULL, progressbar = TRUE, jobname = "BPJOB", reg.pars=list(seed=seed, work.dir=work.dir), conf.pars=list(conffile=conffile, cluster.functions=cluster.functions), submit.pars=list(resources=resources), ...)
Arguments
workers
integer(1)
catch.errors
DEPRECATED. logical(1)
cleanup
logical(1)
work.dir
character(1)
stop.on.error
logical(1)
seed
integer(1L)
resources
list()
conffile
character(1)
cluster.functions
ClusterFunctions
progressbar
logical(1)
jobname
character(1)
reg.pars
list()
conf.pars
list()
submit.pars
list()
...
Addition arguments, currently not handled.

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, bpnworkers, bpstart, bpstop, bpisup, bpbackend, bpbackend<-

See Also

getClass("BiocParallelParam") for additional parameter classes.

register for registering parameter classes for use in parallel evaluation.

Aliases
  • BatchJobsParam-class
  • BatchJobsParam
  • bpbackend,BatchJobsParam-method
  • bpbackend<-,BatchJobsParam
  • bpisup,BatchJobsParam-method
  • bpstart,BatchJobsParam-method
  • bpstop,BatchJobsParam-method
  • bpworkers,BatchJobsParam-method
  • bpschedule,BatchJobsParam-method
  • show,BatchJobsParam-method
Examples
p <- BatchJobsParam(progressbar=FALSE)
bplapply(1:10, sqrt, BPPARAM=p)

## Not run: 
# ## see vignette for additional explanation
# funs <- makeClusterFunctionsSLURM("~/slurm.tmpl")
# param <- BatchJobsParam(4, cluster.functions=funs)
# register(param)
# bplapply(1:10, function(i) sqrt)
# ## End(Not run)
Documentation reproduced from package BiocParallel, version 1.6.2, License: GPL-2 | GPL-3

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