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

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, ID.shift = 0L)

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

ID.shift

single integer value used to shift the array ID by a constant. Useful when there are array range limitation that must be specified in the shell files (e.g., array can only be 10000 but there are more rows in the design object). For example, if the array ID should be 10000 through 12000, but the cluster computer enviroment does not allow these indices, then including the arrange range as 1-2000 in the shell file with shift=9999 would add this constant to the detected arrayID, thereby indexing the remaining row elements in the design object

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