Netlogo¶

Interactive Usage¶

After connecting to Iceberg (see Establishing a SSH connection), start an interactive session with the qrshx command.

The latest version of NetLogo, currently 5.3.1, is made available with the command

module load apps/binapps/netlogo/

Alternatively, you can load a specific version with

module load apps/binapps/netlogo/5.3.1

This command makes the NetLogo executables available to your session by adding the install directory to your PATH variable. Start the NetLogo Graphical User Interface with the command

NetLogo

Batch usage¶

Here is an example batch submission file for a Netlogo model that contains a BehaviourSpace experiment called ParallelExperiment1. Using BehaviourSpace is the easiest way to exploit parallel processors in Netlogo.

#!/bin/bash
# Request 3 Gigabytes of RAM per core
#$ -l rmem=3G
#Combine stderr and stdout into one file
#$ -j y
#Make sure that the value below matches the number of threads
#$ -pe openmp 4
#Make sure this matches the number of openmp slots requested
threads=4

module load apps/binapps/netlogo/5.3.1

#Set the filename of the output csv file
#Will be called out_4.csv in this case
output_table=out_$threads.csv
#Experiment and model names
experiment=ParallelExperiment1
model=ParallelPredation.nlogo

echo "$threads threads requested"

#You have to run netlogo from its install directory in order for extensions to work
cd $NETLOGO_DIR
java -Xmx1024m -Dfile.encoding=UTF-8 -cp $NETLOGO_DIR/NetLogo.jar org.nlogo.headless.Main --model $SGE_O_WORKDIR/$model --experiment $experiment --table $SGE_O_WORKDIR/$output_table --threads $threads

Call the above file submit_netlogo.sh and submit it with qsub submit_netlogo.sh. All files required to run this example can be found in the HPC Examples repository.

Netlogo uses shared memory parallelism. As such, the maximum number of OpenMP slots can request on our current system is 16.

Troubleshooting¶

Problems with X Windows

When you run the NetLogo command, you get the following error

NetLogo Error invoking method.
NetLogo Failed to launch JVM

This could be because you have not requested an X session properly. Ensure that you have logged into the system using the -X flag e.g.

ssh -X abcd1@iceberg.sheffield.ac.uk

Also ensure that you have requested a qrshx session rather than a qrsh session.

Installation notes¶

Download and untar the installer to /usr/local/packages6/apps/binapps/netlogo/netlogo-5.3.1-64

post installation actions

One netlogo user required the Dynamic scheduler extension. Installed by doing

wget https://github.com/colinsheppard/Dynamic-Scheduler-Extension/archive/v0.2.1.tar.gz
tar -xvzf ./v0.2.1.tar.gz
mv Dynamic-Scheduler-Extension ./dynamic-scheduler
mv ./dynamic-scheduler/ /usr/local/packages6/apps/binapps/netlogo/netlogo-5.3.1-64/app/extensions/

Modulefile¶

• The module file is on the system at /usr/local/modulefiles/apps/binapps/netlogo/5.3.1