Tuning your algorithm with irace on the IRIDIA cluster
From IridiaWiki
Jump to navigationJump to searchYou should really read the README file, and take a look on the examples and templates in the irace directory. Or you can just follow this walk-through for a quick start but you will miss many options and configuration possibilities. You can start from this example and then adapt it to the algorithm you want to configure.
Installation
First of all, you have to install the irace R package on majorana:
$ ssh majorana
$ R
> install.packages("multicore")
> install.packages("irace")
select the belgian mirror and test the installation with
> library(irace) > CTRL+d
Once installed, exit R, and add at the end of your .bash_profile or .bashrc or .profile the local R package folder where irace was installed (e.g. '~/R/x86_64-redhat-linux-gnu-library/2.15/irace/'):
export IRACE_HOME=~/R/x86_64-redhat-linux-gnu-library/2.15/irace/ # export PATH=$IRACE_HOME/bin/:$PATH
and run:
source ~/.bash_profile
to load the changes without the need to logout an login again.
The algorithm to be tuned
You have to create a directory where you do the tuning
$ mkdir ~/tuning $ cd ~/tuning
you copy here the program you are tuning, in this case it's just a simple C program
$ cat > algo.c
#include <stdio.h>
int main(int argc, char **argv) {
// call me with ./algo -i instance --whatever <integer_parameter>
printf("Best %d\n", atoi(argv[4]));
}
CTRL+d
$ make algo
cc algo.c -o algo
Prepare for the tuning
Copy some of the template and example files in the current (tuning) directory
$ cd ~/tuning $ cp $IRACE_HOME/templates/tune-conf.tmpl tune-conf $ cp $IRACE_HOME/examples/mpi/tune-main-cluster-mpi tune-main-cluster-mpi $ cp $IRACE_HOME/examples/acotsp/hook-run . $ mkdir temp
in hook-run change the two environment variables like below
EXE=~/tuning/algo FIXED_PARAMS=""
create some dummy instances
$ mkdir Instances
$ for i in {1..100}; do touch Instances/$i; done
create a parameters file
$ cat > parameters.txt dummy_par "--whatever " i (1, 100) CTRL+d
you should look in the examples/acotsp directory for a more complete example...
Tuning time!
Now you are ready to run irace:
$ ./tune-main-cluster-mpi $IRACE_HOME/bin temp --parallel 10
take a look at tune-main-cluster-mpi and change cluster queues and qsub parameters to better suit your needs. If you have issues with your code or irace try to run it by specifying a debug level (e.g. 1, or 2, or more):
$ ./tune-main-cluster-mpi $IRACE_HOME/bin temp --parallel 10 --debug-level 1
You can check if the job is waiting, running, or complete with the qstat command. In the directory ~/tuning/temp you will find an irace-$PID.stdout and an irace-$PID.stderr file. In the stdout file you should have an output like the one below:
-catch_rsh /opt/gridengine/default/spool/compute-3-14/active_jobs/7718068.1/pe_hostfile
compute-3-14
compute-3-14
compute-3-14
compute-3-14
compute-3-14
compute-3-14
compute-3-14
compute-3-14
compute-3-14
compute-3-14
compute-3-14
irace version 1.0.560
irace: An implementation in R of Iterated Race
Copyright (C) 2010, 2011
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.
Warning: A default configuration file ' ./tune-conf ' has been found and will be read
Note: Reading configuration file ' ./tune-conf '....... done!
### CONFIGURATION STATE TO BE USED
configurationFile <- "./tune-conf"
parameterFile <- "/home/mascia/tuning/./parameters.txt"
execDir <- "temp"
logFile <- "./irace.Rdata"
instances <- "/home/mascia/tuning/./Instances//1"
instanceDir <- "/home/mascia/tuning/./Instances"
instanceFile <- ""
candidatesFile <- ""
hookRun <- "/home/mascia/tuning/./hook-run"
expName <- "Experiment Name"
expDescription <- "Experiment Description"
maxExperiments <- 1000
timeBudget <- 0
timeEstimate <- 0
digits <- 4
debugLevel <- 0
nbIterations <- 0
nbExperimentsPerIteration <- 0
sampleInstances <- TRUE
testType <- "friedman"
firstTest <- 5
eachTest <- 1
minNbSurvival <- 0
nbCandidates <- 0
mu <- 5
seed <- "NA"
parallel <- 10
sgeCluster <- FALSE
mpi <- TRUE
softRestart <- TRUE
### end of configuration
# 2012-03-02 14:41:13 CET: INITIALIZATION
# nbIterations: 2
# minSurvival: 2
# nbParameters: 1
# Seed: 1110701261
# 2012-03-02 14:41:13 CET: ITERATION 1 of 2
# experimentsUsedSoFar: 0
# timeUsedSoFar: 0
# timeEstimate: 0
# remainingBudget: 1000
# currentBudget: 500
# nbCandidates: 83
Racing methods for the selection of the best
Copyright (C) 2003 Mauro Birattari
This software comes with ABSOLUTELY NO WARRANTY
Race name: Experiment Name
Number of candidates: 83
Number of available tasks: 1000
Max number of experiments: 500
Statistical test: Friedman test
Tasks seen before discarding: 5
Initialization function: ok
Experiment Description
Markers:
x No test is performed.
- The test is performed and
some candidates are discarded.
= The test is performed but
no candidate is discarded.
+-+-----------+-----------+-----------+-----------+-----------+
| | Task| Alive| Best| Mean best| Exp so far|
+-+-----------+-----------+-----------+-----------+-----------+
10 slaves are spawned successfully. 0 failed.
master (rank 0 , comm 1) of size 11 is running on: compute-3-14
slave1 (rank 1 , comm 1) of size 11 is running on: compute-3-14
slave2 (rank 2 , comm 1) of size 11 is running on: compute-3-14
slave3 (rank 3 , comm 1) of size 11 is running on: compute-3-14
slave4 (rank 4 , comm 1) of size 11 is running on: compute-3-14
slave5 (rank 5 , comm 1) of size 11 is running on: compute-3-14
slave6 (rank 6 , comm 1) of size 11 is running on: compute-3-14
slave7 (rank 7 , comm 1) of size 11 is running on: compute-3-14
slave8 (rank 8 , comm 1) of size 11 is running on: compute-3-14
slave9 (rank 9 , comm 1) of size 11 is running on: compute-3-14
slave10 (rank 10, comm 1) of size 11 is running on: compute-3-14
|x| 1| 83| 7| 1| 83|
|x| 2| 83| 7| 1| 166|
|x| 3| 83| 7| 1| 249|
|x| 4| 83| 7| 1| 332|
|-| 5| 1| 7| 1| 415|
+-+-----------+-----------+-----------+-----------+-----------+
Selected candidate: 7 mean value: 1
Description of the selected candidate:
[1] 1
# Elite candidates:
dummy_par
7 1
# 2012-03-02 14:41:17 CET: ITERATION 2 of 2
# experimentsUsedSoFar: 415
# timeUsedSoFar: 0
# timeEstimate: 0
# remainingBudget: 585
# currentBudget: 585
# nbCandidates: 83
# Computing similarity of candidates .................................................................................. DONE
# 2012-03-02 14:41:21 CET: Soft restart: 7 85 86 87 88 89 90 91 92 93 94 95 96 98 100 102 103 104 105 108 109 110 111 112 113 115 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 135 136 138 139 140 142 145 146 147 148 149 150 152 153 154 155 156 158 159 160 161 163 164 84 97 99 101 106 107 114 116 134 137 141 143 144 151 157 162 165 !
Racing methods for the selection of the best
Copyright (C) 2003 Mauro Birattari
This software comes with ABSOLUTELY NO WARRANTY
Race name: Experiment Name
Number of candidates: 83
Number of available tasks: 1000
Max number of experiments: 585
Statistical test: Friedman test
Tasks seen before discarding: 5
Initialization function: ok
Experiment Description
Markers:
x No test is performed.
- The test is performed and
some candidates are discarded.
= The test is performed but
no candidate is discarded.
+-+-----------+-----------+-----------+-----------+-----------+
| | Task| Alive| Best| Mean best| Exp so far|
+-+-----------+-----------+-----------+-----------+-----------+
|x| 1| 83| 1| 1| 83|
|x| 2| 83| 1| 1| 166|
|x| 3| 83| 1| 1| 249|
|x| 4| 83| 1| 1| 332|
|-| 5| 59| 1| 1| 415|
|=| 6| 59| 1| 1| 474|
|=| 7| 59| 1| 1| 533|
+-+-----------+-----------+-----------+-----------+-----------+
Selected candidate: 1 mean value: 1
Description of the selected candidate:
[1] 1
# Elite candidates:
dummy_par
7 1
84 1
# 2012-03-02 14:41:25 CET: Limit of iterations reached
# 2012-03-02 14:41:25 CET: ITERATION 3 of 3
# experimentsUsedSoFar: 948
# timeUsedSoFar: 0
# timeEstimate: 0
# remainingBudget: 52
# currentBudget: 52
# nbCandidates: 6
# Computing similarity of candidates ..... DONE
# 2012-03-02 14:41:25 CET: Soft restart: 7 84 166 167 168 169 !
Racing methods for the selection of the best
Copyright (C) 2003 Mauro Birattari
This software comes with ABSOLUTELY NO WARRANTY
Race name: Experiment Name
Number of candidates: 6
Number of available tasks: 1000
Max number of experiments: 52
Statistical test: Friedman test
Tasks seen before discarding: 5
Initialization function: ok
Experiment Description
Markers:
x No test is performed.
- The test is performed and
some candidates are discarded.
= The test is performed but
no candidate is discarded.
+-+-----------+-----------+-----------+-----------+-----------+
| | Task| Alive| Best| Mean best| Exp so far|
+-+-----------+-----------+-----------+-----------+-----------+
|x| 1| 6| 1| 1| 6|
|x| 2| 6| 1| 1| 12|
|x| 3| 6| 1| 1| 18|
|x| 4| 6| 1| 1| 24|
|-| 5| 2| 1| 1| 30|
+-+-----------+-----------+-----------+-----------+-----------+
Selected candidate: 1 mean value: 1
Description of the selected candidate:
[1] 1
# Elite candidates:
dummy_par
7 1
84 1
# 2012-03-02 14:41:25 CET: Limit of iterations reached
# 2012-03-02 14:41:25 CET: Stopped because there is no enough budget to sample new candidates
# number of elites: 2
# indexIteration: 4
# mu: 5
# nbIterations: 4
# experimentsUsedSoFar: 978
# timeUsedSoFar: 0
# timeEstimate: 0
# remainingBudget: 22
# currentBudget: 22
# nbCandidates: 2
# Best candidates
dummy_par
7 1
84 1
# Best candidates (as commandlines)
command
7 --whatever 1
84 --whatever 1
# Finalize MPI...
[1] "Exiting Rmpi. Rmpi cannot be used unless relaunching R."
