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linuxcluster-computingnetlogobehaviorspace

NetLogo netlogo-headless.sh file location

I am attempting to run Netlogo on headlessly using linux in order to send a job to a cluster. I have never used linux before, but I am attempting to follow the directions here (http://netlogo-users.18673.x6.nabble.com/Running-NetLogo-Headless-in-Behaviorspace-Sample-code-td4862232.html). 

#!/bin/bash
#SBATCH -N 1
#SBATCH -n 1  
#SBATCH -c 7
module load netlogo/5.3.1-64
~/netlogo-5.3.1-64/netlogo-headless.sh \
-- model /cluster/home/rfuda01/UM_model.nlogo \
--experiment UM
--table /cluster/home/rfuda01/UM_test.csv

When I submit the job, the output file contains an error message saying: 

line 7: /cluster/home/rfuda01/netlogo-5.3.1-64/netlogo-headless.sh: No such file or directory

I see that this file is not located in the folder I specified, but every example that I've looked at for using NetLogo on a cluster refers to this script. Where can I find the correct path to this file?

Solution

  • netlogo-headless.sh was inadvertently removed from the Linux install in 5.3.0: https://github.com/NetLogo/NetLogo/issues/979

    For now, you can use 5.2.1.

    Actually, you can probably just take the netlogo-headless.sh from a 5.2.1 download and put it in 5.3.1 without problems, but I haven't tested this.

    Edit: Taking the old netlogo-headless.sh should work if you put it in the app/ directory, under the main NetLogo directory. Thanks Nicolas!