new_rscript {slurmR}

General purpose function to write R scripts

Description

This function will create an object of class slurmR_rscript that can be used to write the R component in a batch job.

Usage

new_rscript(
  njobs,
  tmp_path,
  job_name,
  pkgs = list_loaded_pkgs(),
  libPaths = .libPaths()
)

Arguments

njobs

Integer. Number of jobs to use in the job-array. This specifies the number of R sessions to initialize. This does not specify the number of cores to be used.

tmp_path

Character. Path to the directory where all the data (including scripts) will be stored. Notice that this path must be accessible by all the nodes in the network (See opts_slurmR).

job_name

Character. Name of the job to be passed to Slurm.

pkgs

A named list with packages to be included. Each element of the list must be a path to the R library, while the names of the list are the names of the R packages to be loaded.

libPaths

A character vector. See .libPaths.

Value

An environment of class slurmR_rscript. This has the following accessible components:

• add_rds Add rds files to be loaded in each job.", x is a named list with the objects that should be loaded in the jobs. If index = TRUE the function assumes that the user will be accessing a particular subset of x during the job, which is accessed according to INDICES[[ARRAY_ID]]. The option compress is passed to saveRDS.

  One important side effect is that when this function is called, the object will be saved in the current job directory, this is opts_slurmR$get_tmp_path().

• append Adds a line to the R script. Its only argument, x is a character vector that will be added to the R script.

• rscript A character vector. This is the actual R script that will be written at the end.

• finalize Adds the final line of the R script. This function receives a character scalar x which is used as the name of the object to be saved. If missing, the function will save a NULL object. The compress argument is passed to saveRDS.

• set_seed Adds a vector of seeds to be used across the jobs. This vector of seeds should be of length njobs. The other two parameters of the function are passed to set.seed. By default the seed is picked as follows:

  seeds <- sample.int(.Machine$integer.max, njobs, replace = FALSE)
  

• write Finalizes the process by writing the R script in the corresponding folder to be used with Slurm.