Create a batch job template file — scaffold_batch

Generates a template file for batch job submission systems like SLURM. The template is used by batchtools to submit jobs to the cluster.

Usage

scaffold_batch_template(
  system = c("slurm"),
  out = file.path("batchtools", paste0("parade-", match.arg(system), ".tmpl")),
  modules = "R",
  exports = c(PARADE_SCRATCH =
    "${PARADE_SCRATCH:-${SCRATCH:-${SCRATCHDIR:-${PSCRATCH:-${WORK:-${SLURM_TMPDIR:-${TMPDIR:-/tmp}}}}}}}",
    OMP_NUM_THREADS = "1", MKL_NUM_THREADS = "1", OPENBLAS_NUM_THREADS = "1"),
  preamble = character(),
  overwrite = FALSE
)

Arguments

system: Character string specifying the batch system. Currently only "slurm" is supported.
out: Path where the template file should be written. Defaults to "batchtools/parade-slurm.tmpl".
modules: Character vector of modules to load. Default is "R".
exports: Named character vector of environment variables to export in the job script.
preamble: Character vector of additional shell commands to include in the template preamble.
overwrite: Logical indicating whether to overwrite an existing template file.

Value

Invisibly returns the normalized path to the created template file.

Examples

# \donttest{
# Create a basic SLURM template
template_path <- scaffold_batch_template(
  system = "slurm",
  out = tempfile(fileext = ".tmpl")
)

# Create a template with custom modules and exports
template_path <- scaffold_batch_template(
  system = "slurm",
  modules = c("R/4.3.0", "gcc/11.2"),
  exports = c(CUSTOM_VAR = "value"),
  out = tempfile(fileext = ".tmpl")
)
# }