Submit an R script to SLURM or run locally

Submits an R script as a SLURM job using batchtools or runs it locally, with configurable resources and environment. Returns a handle for monitoring and retrieving results.

Usage

submit_slurm(
  script,
  args = character(),
  name = NULL,
  engine = c("slurm", "local"),
  template = NULL,
  resources = NULL,
  registry_dir = NULL,
  env = character(),
  lib_paths = .libPaths(),
  rscript = file.path(R.home("bin"), "Rscript"),
  wd = NULL,
  .as_jobset = FALSE,
  .error_policy = NULL
)

Arguments

script: Path to R script file to execute
args: Character vector of command line arguments to pass to script
name: Optional job name (defaults to script basename)
engine: Execution engine: "slurm" or "local" (default: "slurm")
template: Path to SLURM template file (uses default if NULL)
resources: Named list of SLURM resource specifications (ignored for local)
registry_dir: Directory for batchtools registry (auto-generated if NULL)
env: Named character vector of environment variables to set
lib_paths: Character vector of library paths to use
rscript: Path to Rscript executable
wd: Working directory for script execution
.as_jobset: Logical indicating whether to return a single-element jobset instead of a bare job object. Defaults to FALSE for backward compatibility.
.error_policy: Error policy object for retry logic (from on_error())

Value

A parade_script_job or parade_local_job object for monitoring the job, or a parade_jobset containing the job if .as_jobset = TRUE.

Examples

# Create a simple R script
script_path <- tempfile(fileext = ".R")
writeLines("cat('Hello from parade!')", script_path)

# Run locally (no SLURM required)
job <- submit_slurm(script_path, engine = "local")

# \donttest{
# Submit to SLURM (only if available)
if (Sys.which("squeue") != "") {
  job <- submit_slurm(script_path, resources = list(time = "5min"))
}
# }