R/main.R
In AthilaRocha/iracex:
Defines functions
readArgOrDefault
read.table.text
irace.main
irace.cmdline
# =========================================================================
# irace: An implementation in R of Iterated Race.
# -------------------------------------------------------------------------
#
# Copyright (C) 2010-2014
# Manuel López-Ibáñez <manuel.lopez-ibanez@ulb.ac.be>
# Jérémie Dubois-Lacoste <jeremie.dubois-lacoste@ulb.ac.be>
#
# -------------------------------------------------------------------------
# This program is free software (software libre); you can redistribute
# it and/or modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, you can obtain a copy of the GNU
# General Public License at:
# http://www.gnu.org/copyleft/gpl.html
# or by writing to the Free Software Foundation, Inc., 59 Temple Place,
# Suite 330, Boston, MA 02111-1307 USA
# -------------------------------------------------------------------------
# $Revision: 956 $
# =========================================================================
irace.license <-
'********************************************************************************
* irace: An implementation in R of Iterated Race *
* Copyright (C) 2010-2014 *
* Manuel Lopez-Ibanez <manuel.lopez-ibanez@ulb.ac.be> *
* Jeremie Dubois-Lacoste <jeremie.dubois-lacoste@ulb.ac.be> *
* *
* This is free software, and you are welcome to redistribute it under certain *
* conditions. See the GNU General Public License for details. There is NO *
* warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. *
* *
* irace builds upon previous code from the race package *
* Copyright (C) 2003 Mauro Birattari *
********************************************************************************
'
# Function to read command-line arguments.
readArgOrDefault <- function(args, short="", long="", default=NULL)
{
pos <- c()
if (length (short) > 0) {
pos <- grep (paste ("^", short, "$", sep=""), args)
if (length (pos) == 0) {
pos <- grep (paste ("^", short, "=", sep=""), args)
}
}
if (length (long) > 0 && length (pos) == 0) {
pos <- grep (paste ("^", long, "$", sep=""), args)
if (length (pos) == 0) {
pos <- grep (paste ("^", long, "=", sep=""), args)
}
}
if (length (pos) == 0) {
return (default)
} else if (length(pos) > 0) {
# Allow repeated parameters
pos <- max(pos)
}
value <- unlist(strsplit (args[pos], '=', fixed = TRUE))[2]
if (is.null (value) || is.na(value)) {
value <- args[pos + 1]
}
return(value)
}
read.table.text <- function(text, header = TRUE, stringsAsFactors = FALSE, ...)
{
con <- textConnection(text)
x <- read.table(con, header = header, stringsAsFactors = stringsAsFactors,
...)
close(con)
return(x)
}
# Non-variable options (such as --help and --version) have names starting with '.'
# Variables that do not have an option have description == ""
# FIXME: Add more columns with the type of the parameter: b(oolean),
# i(nteger), p(ath), r(eal), c(ategorical). For i, r, and c, add their
# range.
# FIXME: Align columns.
.irace.params.def <- read.table.text('
name short long default description
.help "-h" "--help" NA "Show this help."
.version "-v" "--version" NA "Show irace package version."
configurationFile "-c" "--config-file" "./tune-conf" "File that contains the configuration for irace."
parameterFile "-p" "--param-file" "./parameters.txt" "File that contains the description of the parameters to be tuned. See the template."
execDir "" "--exec-dir" "./" "Directory where the programs will be run."
"logFile" "-l" "--log-file" "./irace.Rdata" "File to save tuning results as an R dataset, either absolute path or relative to execDir."
"logFileagg" "-l" "--log-file" "./iraceagg.Rdata" "File to save aggregated tuning results as an R dataset, either absolute path or relative to execDir."
"recoveryFile" "" "--recovery-file" "" "Previously saved log file to recover the execution of irace, either absolute path or relative to the current directory. If empty or NULL, recovery is not performed."
"instances" "" "" "" ""
"instances.extra.params" "" "" "" ""
"instanceDir" "" "--instance-dir" "./Instances" "Folder where tuning instances are located either absolute or relative to working directory."
"instanceFile" "" "--instance-file" "" "File containing a list of instances and optionally additional parameters for them."
"candidatesFile" "" "--candidates-file" "" "File containing a list of initial candidates. If empty or NULL do not use a file."
"forbiddenExps" "" "" "" ""
"forbiddenFile" "" "--forbidden-file" "" "File containing a list of logical expressions that cannot be true for any evaluated candidate. If empty or NULL, do not use a file."
"hookRun" "" "--hook-run" "./hook-run" "The script called for each candidate that launches the program to be tuned. See templates/."
hookRunData "" "" "" ""
hookRunParallel "" "" "" ""
hookEvaluate "" "--hook-evaluate" "" "Optional script that provides a numeric value for each candidate. See templates/hook-evaluate.tmpl"
"maxExperiments" "" "--max-experiments" 1000 "The maximum number of runs (invocations of hookRun) that will be performed. It determines the maximum budget of experiments for the tuning unless timeBudget is positive."
"timeBudget" "" "--time-budget" 0 "The maximum computation time that should be used for tuning. This only works when tuning for time. 0 means no time limit (then it uses maxExperiments)."
"timeEstimate" "" "--time-estimate" 0 "An estimation of the average time required for one experiment. Only required if timeBudget is positive."
"digits" "" "--digits" 4 "Indicates the number of decimal places to be considered for the real parameters."
"debugLevel" "" "--debug-level" 0 "A value of 0 silences all debug messages. Higher values provide more verbose debug messages."
"nbIterations" "" "--iterations" 0 "Number of iterations."
"nbExperimentsPerIteration" "" "--experiments-per-iteration" 0 "Number of experiments per iteration."
"sampleInstances" "" "--sample-instances" 1 "Sample the instances or take them always in the same order."
"testType" "" "--test-type" "F-test" "Specifies the statistical test type: F-test or t-test."
"firstTest" "" "--first-test" 12 "Specifies how many instances are seen before the first elimination test. It must be a multiple of eachTest."
"eachTest" "" "--each-test" 3 "Specifies how many instances are seen between elimination tests."
"minNbSurvival" "" "--min-survival" 0 "The minimum number of candidates that should survive to continue one iteration."
"nbCandidates" "" "--num-candidates" 0 "The number of candidates that should be sampled and evaluated at each iteration."
"nbCandidatesagg" "" "--num-candidatesagg" 0 "The number of candidates of the agregated test that should be sampled and evaluated at each iteration."
"mu" "" "--mu" 5 "This value is used to determine the number of candidates to be sampled and evaluated at each iteration."
"confidence" "" "--confidence" 0.95 "Confidence level for the elimination test."
"seed" "" "--seed" NA "Seed of the random number generator (must be a positive integer, NA means use a random seed)."
"parallel" "" "--parallel" 0 "Number of calls to hookRun to execute in parallel. 0 or 1 mean disabled."
"mpi" "" "--mpi" 0 "Enable/disable MPI. Use Rmpi to execute hookRun in parallel (parameter parallel is the number of slaves)."
"sgeCluster" "" "--sge-cluster" 0 "Enable/disable SGE cluster mode. Use qstat to wait for cluster jobs to finish (hookRun must invoke qsub)."
"softRestart" "" "--soft-restart" 1 "Enable/disable the soft restart strategy that avoids premature convergence of the probabilistic model."
')
rownames (.irace.params.def) <- .irace.params.def[,"name"]
.irace.params.names <- rownames(.irace.params.def)[substring(rownames(.irace.params.def), 1, 1) != "."]
## read commandline parameters
readCmdLineParameter <- function (args, params.def, paramName, default)
{
return (readArgOrDefault (args = args,
short = params.def[paramName, "short"],
long = params.def[paramName,"long"],
default = if (is.null(default))
params.def[paramName, "default"] else default))
}
irace.usage <- function ()
{
# FIXME: It would be nice to put the version number in the license
# message to avoid having this extra line.
cat ("irace\tversion: ", irace.version, "\n", sep="")
cat (irace.license)
# FIXME: The output would be nicer if we used cat(sprintf()) to
# print short and long within a fixed width field. The description
# can be wrapped with strwrap to the remainder space up to 80
# columns. We can calculate the field width from the largest string
# for each of short and long.
for (i in seq_len(nrow(.irace.params.def))) {
if (.irace.params.def[i,"description"] != "")
cat(.irace.params.def[i,"short"], ", ", .irace.params.def[i,"long"],
"\t", .irace.params.def[i,"description"], "\n")
}
}
irace.main <- function(tunerConfig = defaultConfiguration(), output.width = 9999)
{
##overall mean for the performance of algorithms to the family problems (instances)
mi <- 5
print("Mean of the algorithms on the instances: ")
cat("\n")
cat(mi)
cat("\n")
op <- options(width = output.width) # Do not wrap the output.
on.exit(options(op), add = TRUE)
tunerConfig <- checkConfiguration (tunerConfig)
debug.level <- tunerConfig$debugLevel
if (debug.level >= 1) printConfiguration (tunerConfig)
##obtaining the number of Instances
nbInstances <- length(tunerConfig$instances)
effects <- matrix(data=NA,nrow=1000,ncol=nbInstances)
effectsagg<-matrix(data=NA,nrow=1000,ncol=nbInstances)
# Read parameters definition
parameters <- readParameters (file = tunerConfig$parameterFile,
digits = tunerConfig$digits,
debugLevel = debug.level)
if (tunerConfig$debugLevel >= 2) { cat("Parameters have been read\n") }
eliteCandidates <- irace (tunerConfig = tunerConfig,
parameters = parameters,
media = mi,
effects = effects,
effectsagg=effectsagg)
cat("# Best candidates - Non Aggregated Tests\n")
candidates.print(eliteCandidates)
cat("# Best candidates (as commandlines)\n")
candidates.print.command (eliteCandidates, parameters)
invisible(eliteCandidates)
}
irace.cmdline <- function(args = commandArgs (trailingOnly = TRUE))
{
if (!is.null(readArgOrDefault (args, short = "-h", long = "--help"))) {
irace.usage()
return(invisible(NULL))
}
if (!is.null(readArgOrDefault (args, short = "-v", long = "--version"))) {
# FIXME: It would be nice to put the version number in the license
# message to avoid having this extra line.
cat ("irace\tversion: ", irace.version, "\n", sep="")
cat (irace.license)
return(invisible(NULL))
}
# FIXME: It would be nice to put the version number in the license
# message to avoid having this extra line.
cat ("irace\tversion: ", irace.version, "\n", sep="")
cat (irace.license)
# Read the configuration file and the command line
configurationFile <-
readArgOrDefault(args = args,
short = .irace.params.def["configurationFile","short"],
long = .irace.params.def["configurationFile","long"],
default = "")
tunerConfig <- readConfiguration(configurationFile)
for (param in .irace.params.names) {
tunerConfig[[param]] <-
readCmdLineParameter (args = args,
params.def = .irace.params.def,
paramName = param,
default = tunerConfig[[param]])
}
irace.main(tunerConfig)
}
AthilaRocha/iracex documentation built on May 5, 2019, 8:12 a.m.
R Package Documentation
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Defines functions readArgOrDefault read.table.text irace.main irace.cmdline
# =========================================================================
# irace: An implementation in R of Iterated Race.
# -------------------------------------------------------------------------
#
# Copyright (C) 2010-2014
# Manuel López-Ibáñez <manuel.lopez-ibanez@ulb.ac.be>
# Jérémie Dubois-Lacoste <jeremie.dubois-lacoste@ulb.ac.be>
#
# -------------------------------------------------------------------------
# This program is free software (software libre); you can redistribute
# it and/or modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, you can obtain a copy of the GNU
# General Public License at:
# http://www.gnu.org/copyleft/gpl.html
# or by writing to the Free Software Foundation, Inc., 59 Temple Place,
# Suite 330, Boston, MA 02111-1307 USA
# -------------------------------------------------------------------------
# $Revision: 956 $
# =========================================================================
irace.license <-
'********************************************************************************
* irace: An implementation in R of Iterated Race *
* Copyright (C) 2010-2014 *
* Manuel Lopez-Ibanez <manuel.lopez-ibanez@ulb.ac.be> *
* Jeremie Dubois-Lacoste <jeremie.dubois-lacoste@ulb.ac.be> *
* *
* This is free software, and you are welcome to redistribute it under certain *
* conditions. See the GNU General Public License for details. There is NO *
* warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. *
* *
* irace builds upon previous code from the race package *
* Copyright (C) 2003 Mauro Birattari *
********************************************************************************
'
# Function to read command-line arguments.
readArgOrDefault <- function(args, short="", long="", default=NULL)
{
pos <- c()
if (length (short) > 0) {
pos <- grep (paste ("^", short, "$", sep=""), args)
if (length (pos) == 0) {
pos <- grep (paste ("^", short, "=", sep=""), args)
}
}
if (length (long) > 0 && length (pos) == 0) {
pos <- grep (paste ("^", long, "$", sep=""), args)
if (length (pos) == 0) {
pos <- grep (paste ("^", long, "=", sep=""), args)
}
}
if (length (pos) == 0) {
return (default)
} else if (length(pos) > 0) {
# Allow repeated parameters
pos <- max(pos)
}
value <- unlist(strsplit (args[pos], '=', fixed = TRUE))[2]
if (is.null (value) || is.na(value)) {
value <- args[pos + 1]
}
return(value)
}
read.table.text <- function(text, header = TRUE, stringsAsFactors = FALSE, ...)
{
con <- textConnection(text)
x <- read.table(con, header = header, stringsAsFactors = stringsAsFactors,
...)
close(con)
return(x)
}
# Non-variable options (such as --help and --version) have names starting with '.'
# Variables that do not have an option have description == ""
# FIXME: Add more columns with the type of the parameter: b(oolean),
# i(nteger), p(ath), r(eal), c(ategorical). For i, r, and c, add their
# range.
# FIXME: Align columns.
.irace.params.def <- read.table.text('
name short long default description
.help "-h" "--help" NA "Show this help."
.version "-v" "--version" NA "Show irace package version."
configurationFile "-c" "--config-file" "./tune-conf" "File that contains the configuration for irace."
parameterFile "-p" "--param-file" "./parameters.txt" "File that contains the description of the parameters to be tuned. See the template."
execDir "" "--exec-dir" "./" "Directory where the programs will be run."
"logFile" "-l" "--log-file" "./irace.Rdata" "File to save tuning results as an R dataset, either absolute path or relative to execDir."
"logFileagg" "-l" "--log-file" "./iraceagg.Rdata" "File to save aggregated tuning results as an R dataset, either absolute path or relative to execDir."
"recoveryFile" "" "--recovery-file" "" "Previously saved log file to recover the execution of irace, either absolute path or relative to the current directory. If empty or NULL, recovery is not performed."
"instances" "" "" "" ""
"instances.extra.params" "" "" "" ""
"instanceDir" "" "--instance-dir" "./Instances" "Folder where tuning instances are located either absolute or relative to working directory."
"instanceFile" "" "--instance-file" "" "File containing a list of instances and optionally additional parameters for them."
"candidatesFile" "" "--candidates-file" "" "File containing a list of initial candidates. If empty or NULL do not use a file."
"forbiddenExps" "" "" "" ""
"forbiddenFile" "" "--forbidden-file" "" "File containing a list of logical expressions that cannot be true for any evaluated candidate. If empty or NULL, do not use a file."
"hookRun" "" "--hook-run" "./hook-run" "The script called for each candidate that launches the program to be tuned. See templates/."
hookRunData "" "" "" ""
hookRunParallel "" "" "" ""
hookEvaluate "" "--hook-evaluate" "" "Optional script that provides a numeric value for each candidate. See templates/hook-evaluate.tmpl"
"maxExperiments" "" "--max-experiments" 1000 "The maximum number of runs (invocations of hookRun) that will be performed. It determines the maximum budget of experiments for the tuning unless timeBudget is positive."
"timeBudget" "" "--time-budget" 0 "The maximum computation time that should be used for tuning. This only works when tuning for time. 0 means no time limit (then it uses maxExperiments)."
"timeEstimate" "" "--time-estimate" 0 "An estimation of the average time required for one experiment. Only required if timeBudget is positive."
"digits" "" "--digits" 4 "Indicates the number of decimal places to be considered for the real parameters."
"debugLevel" "" "--debug-level" 0 "A value of 0 silences all debug messages. Higher values provide more verbose debug messages."
"nbIterations" "" "--iterations" 0 "Number of iterations."
"nbExperimentsPerIteration" "" "--experiments-per-iteration" 0 "Number of experiments per iteration."
"sampleInstances" "" "--sample-instances" 1 "Sample the instances or take them always in the same order."
"testType" "" "--test-type" "F-test" "Specifies the statistical test type: F-test or t-test."
"firstTest" "" "--first-test" 12 "Specifies how many instances are seen before the first elimination test. It must be a multiple of eachTest."
"eachTest" "" "--each-test" 3 "Specifies how many instances are seen between elimination tests."
"minNbSurvival" "" "--min-survival" 0 "The minimum number of candidates that should survive to continue one iteration."
"nbCandidates" "" "--num-candidates" 0 "The number of candidates that should be sampled and evaluated at each iteration."
"nbCandidatesagg" "" "--num-candidatesagg" 0 "The number of candidates of the agregated test that should be sampled and evaluated at each iteration."
"mu" "" "--mu" 5 "This value is used to determine the number of candidates to be sampled and evaluated at each iteration."
"confidence" "" "--confidence" 0.95 "Confidence level for the elimination test."
"seed" "" "--seed" NA "Seed of the random number generator (must be a positive integer, NA means use a random seed)."
"parallel" "" "--parallel" 0 "Number of calls to hookRun to execute in parallel. 0 or 1 mean disabled."
"mpi" "" "--mpi" 0 "Enable/disable MPI. Use Rmpi to execute hookRun in parallel (parameter parallel is the number of slaves)."
"sgeCluster" "" "--sge-cluster" 0 "Enable/disable SGE cluster mode. Use qstat to wait for cluster jobs to finish (hookRun must invoke qsub)."
"softRestart" "" "--soft-restart" 1 "Enable/disable the soft restart strategy that avoids premature convergence of the probabilistic model."
')
rownames (.irace.params.def) <- .irace.params.def[,"name"]
.irace.params.names <- rownames(.irace.params.def)[substring(rownames(.irace.params.def), 1, 1) != "."]
## read commandline parameters
readCmdLineParameter <- function (args, params.def, paramName, default)
{
return (readArgOrDefault (args = args,
short = params.def[paramName, "short"],
long = params.def[paramName,"long"],
default = if (is.null(default))
params.def[paramName, "default"] else default))
}
irace.usage <- function ()
{
# FIXME: It would be nice to put the version number in the license
# message to avoid having this extra line.
cat ("irace\tversion: ", irace.version, "\n", sep="")
cat (irace.license)
# FIXME: The output would be nicer if we used cat(sprintf()) to
# print short and long within a fixed width field. The description
# can be wrapped with strwrap to the remainder space up to 80
# columns. We can calculate the field width from the largest string
# for each of short and long.
for (i in seq_len(nrow(.irace.params.def))) {
if (.irace.params.def[i,"description"] != "")
cat(.irace.params.def[i,"short"], ", ", .irace.params.def[i,"long"],
"\t", .irace.params.def[i,"description"], "\n")
}
}
irace.main <- function(tunerConfig = defaultConfiguration(), output.width = 9999)
{
##overall mean for the performance of algorithms to the family problems (instances)
mi <- 5
print("Mean of the algorithms on the instances: ")
cat("\n")
cat(mi)
cat("\n")
op <- options(width = output.width) # Do not wrap the output.
on.exit(options(op), add = TRUE)
tunerConfig <- checkConfiguration (tunerConfig)
debug.level <- tunerConfig$debugLevel
if (debug.level >= 1) printConfiguration (tunerConfig)
##obtaining the number of Instances
nbInstances <- length(tunerConfig$instances)
effects <- matrix(data=NA,nrow=1000,ncol=nbInstances)
effectsagg<-matrix(data=NA,nrow=1000,ncol=nbInstances)
# Read parameters definition
parameters <- readParameters (file = tunerConfig$parameterFile,
digits = tunerConfig$digits,
debugLevel = debug.level)
if (tunerConfig$debugLevel >= 2) { cat("Parameters have been read\n") }
eliteCandidates <- irace (tunerConfig = tunerConfig,
parameters = parameters,
media = mi,
effects = effects,
effectsagg=effectsagg)
cat("# Best candidates - Non Aggregated Tests\n")
candidates.print(eliteCandidates)
cat("# Best candidates (as commandlines)\n")
candidates.print.command (eliteCandidates, parameters)
invisible(eliteCandidates)
}
irace.cmdline <- function(args = commandArgs (trailingOnly = TRUE))
{
if (!is.null(readArgOrDefault (args, short = "-h", long = "--help"))) {
irace.usage()
return(invisible(NULL))
}
if (!is.null(readArgOrDefault (args, short = "-v", long = "--version"))) {
# FIXME: It would be nice to put the version number in the license
# message to avoid having this extra line.
cat ("irace\tversion: ", irace.version, "\n", sep="")
cat (irace.license)
return(invisible(NULL))
}
# FIXME: It would be nice to put the version number in the license
# message to avoid having this extra line.
cat ("irace\tversion: ", irace.version, "\n", sep="")
cat (irace.license)
# Read the configuration file and the command line
configurationFile <-
readArgOrDefault(args = args,
short = .irace.params.def["configurationFile","short"],
long = .irace.params.def["configurationFile","long"],
default = "")
tunerConfig <- readConfiguration(configurationFile)
for (param in .irace.params.names) {
tunerConfig[[param]] <-
readCmdLineParameter (args = args,
params.def = .irace.params.def,
paramName = param,
default = tunerConfig[[param]])
}
irace.main(tunerConfig)
}
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