Submit jobs — bsub_chunk • bsub

Submit jobs

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,
  ask = TRUE
)

bsub_script(
  script,
  argv = "",
  name = NULL,
  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$local,
  sh_head = bsub_opt$sh_head,
  ask = TRUE,
  ...
)

bsub_cmd(
  cmd,
  sh = NULL,
  name = NULL,
  hours = 1,
  memory = 1,
  cores = 1,
  temp_dir = bsub_opt$temp_dir,
  output_dir = bsub_opt$output_dir,
  dependency = NULL,
  enforce = bsub_opt$enforce,
  local = bsub_opt$local,
  env_var = NULL,
  sh_head = bsub_opt$sh_head,
  ask = TRUE,
  ...
)

Arguments

code: The code chunk, it should be embraced by {}.
name: If name is not specified, an internal name calculated by digest::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: In bsub_chunk(), it is the path of a script where code chunks will be extracted and sent to the cluster. It is always used with start and end arguments. In bsub_script(), it is the path of the R script to submit.
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.
ask: Whether to promote.
argv: A string of command-line arguments.
...: Command-line arguments can also be specified as name-value pairs.
cmd: A single-line command.
sh: Path of the bash script.
env_var: Environment variables. It should be a named vector. Note environment variables can also be directly set in sh_head.

Value

A job ID.

Details

job_chunk() submits R code chunk.

job_script() submits R script with command-line arguments.

job_cmd() submits general bash commands.

Examples

# \dontrun{
bsub_chunk(name = "example", memory = 10, hours = 10, cores = 4,
{
    Sys.sleep(5)
})
#> Error in bsub_chunk(name = "example", memory = 10, hours = 10, cores = 4,     {        Sys.sleep(5)    }): Job can only be sumitted on the same file system as submission nodes.

# the R version is defined in bsub_opt$R_version
bsub_script("/path/of/foo.R", name = ..., memory = ..., cores = ..., ...)
#> Error in eval(expr, envir, enclos): '...' used in an incorrect context
# with command-line arguments
bsub_script("/path/of/foo.R", argv = "--a 1 --b 3", ...)
#> Error in eval(expr, envir, enclos): '...' used in an incorrect context

# put all arguments also in the command
bsub_cmd("some-tool -arg1 1 -arg2 2", name = ..., memory = ..., cores = ..., ...)
#> Error in eval(expr, envir, enclos): '...' used in an incorrect context
# }