batch_writer: Write a slurm batch script file

In OchoaLab/ochoalabtools: Handy plotting and other tools for scientific publications

Write a slurm batch script file

Description

A wrapper around writing the script given the desired command, a short name for the job, and many optional parameters. Defaults are for my current setup (latest R version on cluster).

Usage

batch_writer(
  commands,
  name,
  R = "4.0.0",
  mem = NA,
  time = NA,
  nodes = 1,
  threads = 1,
  array = NA,
  partition = "biostat",
  account = NA,
  email = NA
)

Arguments

commands	A character vector of commands to run, one per line.
name	Short name for for batch script file, job, and stdout/stderr output paths
R	Specify R version, to load module (NA prevents loading R).
mem	Memory limit. NA (default) is no memory limit. May be a string like ⁠1G⁠, whatever sbatch accepts.
time	Time limit. NA (default) is no time limit. May be a string like 1:00:00, whatever sbatch accepts.
nodes	Number of nodes to use (default 1).
threads	Number of tasks per node (default 1).
array	Value for array jobs (default NA is not an array job; typical values are numeric ranges passed as strings, such as "1-50", "0-90", or discontinuous ranges such as "1,4,10-20").
partition	The partition to submit to, by default biostat. If NA then no partition is declared (default partition will be used, common in DCC?).
account	Account to use. NA (default) is default account for user.
email	Address to receive emails about job completion.

See Also

batch_submit() to submit slurm batch scripts. batch_cleanup() to remove slurm batch scripts.

Examples

# set desired parameters
commands <- 'time echo "Hello world!"'
name <- 'hola'

# writes file `hola.q`
batch_writer(
    commands,
    name
)

# cleanup
batch_cleanup( name )

OchoaLab/ochoalabtools documentation built on July 28, 2024, 12:37 p.m.