Batching up on BC3

aggregate_results.R

library(dplyr)

arguments <- commandArgs(T)
splits <- as.numeric(arguments[1])
outdir <- arguments[2]
savefile <- arguments[3]

l <- list()
for(i in 1:splits)
{
	cat(i, "\n")
	filename <- outdir, paste("/results", i, ".RData", sep="")
	if(file.exists(filename))
	{
		load(filename)
		l[[i]] <- parameters
	} else {
		message("Missing ", filename)
	}
}

parameters <- rbind_all(l)
save(parameters, file = savefile)

run_analysis.R

main <- function()
{
	# Create parameters to test
	parameters <- expand.grid(
		start1 = 1:3700,
		start2 = 1:3700,
		treatment = c(14, 60),
		measure1 = NA,
		measure2 = NA
	)
	# Only keep days when start1 is less than or equal to start2
	# When start1 == start2 this is the 1 day scenario
	parameters <- subset(parameters, start1 < start2)


	# Parallel
	arguments <- commandArgs(T)
	jid <- "all"
	outdir <- "./"
	if(length(arguments) > 0)
	{
		jid <- as.numeric(arguments[1])
		splits <- as.numeric(arguments[2])
		outdir <- arguments[3]
		stopifnot(all(!is.na(jid), !is.na(splits), !is.na(outfile)))

		first <- (jid - 1) * splits + 1
		last <- min(nrow(parameters), jid * splits)
		parameters <- parameters[first:last, ]
	}

	# Set output file
	outfile <- paste(outdir, "/results", jid, ".RData", sep="")
	message("Running ", jid, ": ", nrow(parameters), " rows")
	message("Saving in ", outfile)

	for(i in 1:nrow(parameters))
	{
		message(i)
		res <- with(parameters[i, ],
			get_measures(start1, start2, treatment, countdata)
		)
		parameters$measure1[i] <- res$measure1
		parameters$measure2[i] <- res$measure2
	}

	save(parameters, file=outfile)
}


# Get data needed to calculate measures
load(countdata)

# Write function to get measures
get_measures <- function(start1, start2, treatment, countdata)
{

	return(list(measure1=measure1, measure2=measure2))
}




# Run everything
main()

submit.sh

#!/bin/bash

#PBS -N jobname
#PBS -o job_reports/jobname-output
#PBS -e job_reports/jobname-error
#PBS -l walltime=12:00:00
#PBS -t 1-1000
#PBS -l nodes=1:ppn=4
#PBS -S /bin/bash

set -e

echo "Running on ${HOSTNAME}"

if [ -n "${1}" ]; then
  echo "${1}"
  PBS_ARRAYID=${1}
fi

i=${PBS_ARRAYID}
splits=13687
outdir="~/path/to/dir"

R --no-save --args ${i} ${splits} ${outdir} < ~/path/to/run_analysis.R