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@jakob-r /runMBO.R
Last active Mar 22, 2017

What would you like to do?
optimizing a executable shell script with mlrMBO
library(mlrMBO)
library(stringi)
library(jsonlite)
# read command line args (in a not very safe way)
# Script can be called like that:
# Rscript runMBO.R iters=20 time=10 seed=1
args = commandArgs(TRUE)
# defaults:
iters = 50
time = 30
seed = 123
# parse args (and possibly overwrite defaults)
for (arg in args) {
eval(parse(text = arg))
}
set.seed(seed)
# write bash script
lines = '#!/bin/bash
fun ()
{
x1=$1
x2=$2
command="(s($x1-1) + ($x1^2 + $x2^2))"
result=$(bc -l <<< $command)
}
echo "Start calculation."
fun $1 $2
echo "The result is $result!" > "result.txt"
echo "Finish calculation."
'
writeLines(lines, "fun.sh")
system("chmod +x fun.sh")
# runScript function to execute bash script
runScript = function(x) {
# console output file output_1490030005_1.1_2.4.txt
output_file = sprintf("output_%i_%.1f_%.1f.txt", as.integer(Sys.time()), x[['x1']], x[['x2']])
# redirect output with ./fun.sh 1.1 2.4 > output.txt
# alternative: ./fun.sh 1.1 2.4 > /dev/null to drop it
command = sprintf("./fun.sh %f %f > %s", x[['x1']], x[['x2']], output_file)
error.code = system(command)
if (error.code != 0) {
stop("Simulation had error.code != 0!")
}
result = readLines("result.txt")
# the pattern matches 12 as well as 12.34 and .34
# the ?: makes the decimals a non-capturing group.
result = stri_match_first_regex(result, pattern = "\\d*(?:\\.\\d+)?(?=\\!)")
as.numeric(result)
}
# define mlrMBO optimization
par.set = makeParamSet(
makeNumericParam("x1", lower = -3, upper = 3),
makeNumericParam("x2", lower = -2.5, upper = 2.5)
)
fn = makeSingleObjectiveFunction(
id = "fun.sh",
fn = runScript,
par.set = par.set,
has.simple.signature = FALSE
)
ctrl = makeMBOControl()
ctrl = setMBOControlInfill(ctrl, crit = crit.ei)
ctrl = setMBOControlTermination(ctrl, iters = iters, time.budget = time)
configureMlr(show.info = FALSE, show.learner.output = FALSE)
run = mbo(fun = fn, control = ctrl)
# save result to json
write_json(run[c("x","y")], "mbo_res.json")
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