Warning
Iceberg reaches end-of-life on 30th November 2020. If you are running jobs on Iceberg then you need to take urgent action to ensure that your jobs/scripts will run on ShARC or Bessemer. If you have never used ShARC or Bessemer then now is the time to test your scripts. Not all software on Iceberg is available on ShARC/Bessemer.
NetLogo is a multi-agent programmable modeling environment. It is used by tens of thousands of students, teachers and researchers worldwide.
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
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.
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.
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/
The module file is on the system at /usr/local/modulefiles/apps/binapps/netlogo/5.3.1