bsub_chunk: Submit R code

In bsub: Submitter and Monitor of the 'LSF Cluster'

Description

Submit R code

Usage

bsub_chunk(code,
    name = NULL,
    packages = bsub_opt$packages,
    image = bsub_opt$image,
    variables = character(),
    share = character(),
    working_dir = bsub_opt$working_dir,
    hours = 1,
    memory = 1,
    cores = 1,
    R_version = bsub_opt$R_version,
    temp_dir = bsub_opt$temp_dir,
    output_dir = bsub_opt$output_dir,
    dependency = NULL,
    enforce = bsub_opt$enforce,
    local = bsub_opt$local,
    script = NULL,
    start = NULL,
    end = NULL,
    save_var = FALSE,
    sh_head = bsub_opt$sh_head)

Arguments

code	The code chunk, it should be embraced by { }.
name	If name is not specified, an internal name calculated by digest on the chunk is automatically assigned.
packages	A character vector with package names that will be loaded before running the script. There is a special name _in_session_ that loads all the packages loaded in current R session.
image	A character vector of RData/rda files that will be loaded before running the script. When image is set to TRUE, all variables in .GlobalEnv will be saved into a temporary file and all attached packages will be recorded. The temporary files will be removed after the job is finished.
variables	A character vector of variable names that will be loaded before running the script. There is a special name _all_functions_ that saves all functions defined in the global environment.
share	A character vector of variables names for which the variables are shared between jobs. Note the temporary .RData files are not deleted automatically.
working_dir	The working directory.
hours	Running time of the job.
memory	Memory usage of the job. It is measured in GB.
cores	Number of cores.
R_version	R version.
temp_dir	Path of temporary folder where the temporary R/bash scripts will be put.
output_dir	Path of output folder where the output/flag files will be put.
dependency	A vector of job IDs that current job depends on.
enforce	If a flag file for the job is found, whether to enforce to rerun the job.
local	Run job locally (not submitting to the LSF cluster)?
script	Path of a script where code chunks will be extracted and sent to the cluster.It is always used with start and end arguments.
start	A numeric vector that contains line indices of the starting code chunk or a character vector that contain regular expression to match the start of code chunks.
end	Same setting as start.
save_var	Whether save the last variable in the code chunk? Later the variable can be retrieved by retrieve_var.
sh_head	Commands that are written as head of the sh script.

Value

Job ID.

See Also

• bsub_script submits R scripts.

• bsub_cmdsubmits shell commands.

Examples

## Not run: 
bsub_chunk(name = "example", memory = 10, hours = 10, cores = 4,
{
    Sys.sleep(5)
})

## End(Not run)

bsub documentation built on July 1, 2021, 5:07 p.m.