getArrayID: Get job array ID (e.g., from SLURM or other HPC array...

In philchalmers/SimDesign: Structure for Organizing Monte Carlo Simulation Designs

Get job array ID (e.g., from SLURM or other HPC array distributions)

Description

Get the array ID from an HPC array distribution job (e.g., from SLURM or from optional command line arguments). The array ID is used to index the rows in the design object in runArraySimulation. For instance, a SLURM array with 10 independent jobs might have the following shell instructions.

Usage

getArrayID(type = "slurm", trailingOnly = TRUE)

Arguments

type	an integer indicating the element from the result of commandArgs to extract, or a character specifying the the type of. Default is 'slurm'
trailingOnly	logical value passed to commandArgs. Only used when type is an integer

Details

#!/bin/bash -l

#SBATCH --time=00:01:00

#SBATCH --array=1-10

which names the associated jobs with the numbers 1 through 10. getArrayID() then extracts this information per array, which is used as the runArraySimulation(design, ..., arrayID = getArrayID()) to pass specific rows for the design object.

See Also

runArraySimulation

Examples

## Not run: 

# get slurm array ID
arrayID <- getArrayID()

# get ID based on first optional argument in shell specification
arrayID <- getArrayID(type = 1)

# pass to
# runArraySimulation(design, ...., arrayID = arrayID)


## End(Not run)

philchalmers/SimDesign documentation built on April 29, 2024, 11:43 p.m.