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Preset of Configuration for the RSPH Cluster

Source: R/slurmworkflow_helpers.R
swf_configs_rsph.Rd

Preset of Configuration for the RSPH Cluster

Usage

swf_configs_rsph(
  partition = "preemptable",
  r_version = "4.5.1",
  mail_user = NULL,
  cleanup_workers = TRUE
)

Arguments

partition

Which partition to use on RSPH (either "compute" or "epimodel")

r_version

Which version of R to load

mail_user

The mail address to send the messages to, default is NULL (see 'sbatch –mail-type' argument)

cleanup_workers

If TRUE (the default), append swf_cleanup_r_workers to r_loader so each step reaps its own R workers on cancel or timeout. RSPH has no cgroup containment, so without this, workers survive scancel and squat on cores SLURM has re-allocated, starving later tasks. See swf_cleanup_r_workers.

Value

a list containing default_sbatch_opts, renv_sbatch_opts and r_loader (see the "hpc_configs" section)

Node setup

r_loader sources the shared spack environment, unloads everything, and loads R. It deliberately does not load git: git is on the default path on RSPH, and the project template has not loaded it for some time. The git_version argument was removed accordingly.

hpc_configs

  1. default_sbatch_opts is a list of sbatch options to be passed to slurmworkflow::create_workflow.

  2. renv_sbatch_opts is a list of sbatch options to be passed to slurmworkflow::step_tmpl_renv_restore. It provides sane defaults for building the dependencies of an R project using renv

  3. r_loader is a set of bash lines to make the R software available. This is passed to the setup_lines arguments of the slurmworkflow::step_tmpl_ functions that requires it.