#' Batch job script creation
#'
#' Generate headers for running batch PBS jobs
#'
#' @param jobName name of job
#' @param jobDescription description of job
#' @param Nnodes number of nodes requested
#' @param Nproc number of cores requested
#' @param Memory size of memory requested
#' @param Walltime limit to run time
#' @param email address to notify of job progress
#' @param logDir directory output logs
#'
#' @export
genSlurmHead <- function(jobName="myrun", jobDescription="My analysis",
Nnodes=1, Nproc=16, Memory="32gb", Walltime="24:00:00",
email="pieta.schofield@cruk.manchester.ac.uk",emailMode="END",
logDir="/home/camp/schofip/logs",Partition="compute")
{
header <- c(
"#!/bin/sh ",
paste0('# ', jobDescription),
paste0('#SBATCH --job-name=', jobName),
paste0('#SBATCH --nodes=', 1),
paste0('#SBATCH --ntasks=', Nnodes),
paste0('#SBATCH --cpus-per-task=',Nproc),
paste0('#SBATCH --time=',Walltime),
paste0('#SBATCH --mem=',Memory),
paste0('#SBATCH --mail-user=', email),
paste0('#SBATCH --partition=', Partition),
paste0('#SBATCH --mail-type=', emailMode),
paste0('#SBATCH --output=', file.path(logDir,paste0(jobName,"_%j.log"))),
paste0('#')
)
header
}
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