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Initialize parade for HPC use

parade_init_hpc.Rd

A one-command setup helper for running parade on HPC clusters. This function:

  • Initializes path aliases in "hpc" mode (prefer shared scratch over node-local tmp).

  • Optionally creates required directories and runs a quick doctor check.

  • Optionally scaffolds a batchtools SLURM template and persists it to parade.json.

  • Optionally sets SLURM defaults and persists them to parade.json.

Usage

parade_init_hpc(
  scratch = NULL,
  artifacts = NULL,
  registry = NULL,
  create = TRUE,
  persist = TRUE,
  template = TRUE,
  template_path = "project://batchtools/parade-slurm.tmpl",
  overwrite_template = FALSE,
  slurm_defaults = NULL,
  quiet = FALSE
)

Arguments

scratch

Optional shared scratch root. If NULL, parade auto-detects using PARADE_SCRATCH / SCRATCH / scheduler variables.

artifacts

Optional artifacts root. Default is file.path(scratch, "parade-artifacts").

registry

Optional registry root. Default is file.path(scratch, "parade-registry").

create

Whether to create missing directories for configured roots.

persist

Whether to persist paths/template/defaults to parade.json.

template

Whether to scaffold a SLURM batchtools template file.

template_path

Where to write the template (default: "project://batchtools/parade-slurm.tmpl").

overwrite_template

Whether to overwrite an existing template file.

slurm_defaults

Optional named list of defaults for SLURM resources (e.g., list(mem = NA, time = "2h")).

quiet

Whether to suppress messages.

Value

A list containing the configured paths, config path (if persisted), template path (if created), and doctor results.

Examples

# \donttest{
# Minimal HPC init (best-effort autodetect)
parade_init_hpc(quiet = TRUE, persist = FALSE, template = FALSE, create = FALSE)

# With explicit scratch + a temp template path (safe outside a cluster)
parade_init_hpc(
  scratch = tempdir(),
  persist = FALSE,
  create = FALSE,
  template = TRUE,
  template_path = tempfile(fileext = ".tmpl"),
  overwrite_template = TRUE
)
#> parade_init_hpc
#> --------------
#> - Paths initialized (profile='hpc')
#> - Project:   /home/runner/work/parade/parade/docs/reference
#> - Scratch:   /tmp/RtmpfrGA9U
#> - Artifacts: /tmp/RtmpfrGA9U/parade-artifacts
#> - Registry:  /tmp/RtmpfrGA9U/parade-registry
#> - Template:  /tmp/RtmpfrGA9U/file1b7a6ba42a55.tmpl
#> 
#> Warnings
#> --------
#> - Missing directory for: data, config, cache 
# }