Known Issues - NetLogo/NetLogo GitHub Wiki

When bugs come up, we try to address them as quickly as possible. However, our resources are limited and we are often unable to address them as quickly as users would like. This page is intended to serve as a sort of repository for information about known issues, workarounds, and potential fixes. We hope this will help users know whether or not their bug has been reported by another user as well as consolidate information about causes and workarounds in one easy-to-access, easy-to-search location.

NetLogo Won't Start on Mac OS Catalina, Mojave, High Sierra, and Sierra

  • Reported in: Issue 1302, and 1788
  • Affects: NetLogo 5.3.1, NetLogo 6.0 (all), NetLogo 6.1 (all), NetLogo 6.2 (all), NetLogo 6.3 (all)
  • Fix Version: ???
  • Symptoms: NetLogo refuses to open on Mac OS Catalina, Mojave, High Sierra, and Sierra (10.12 - 10.15).
  • Additional information:

Update: We made changes to our build process for 6.0.2, hoping these would fix this issue. However, they seem to have been ineffective for at least some users. We're continuing to think about the problem, but don't have any promising avenues to fixing it at the moment.

There is a workaround for fixing this. Running the following command in the the Terminal app will enable you to run NetLogo without turning Gatekeeper completely off. For the latest NetLogo 6.3.0, the command is:

sudo xattr -dr com.apple.quarantine /Applications/NetLogo\ 6.3.0/NetLogo\ 6.3.0.app

Note that if you plan to run NetLogo 3D, HubNet Client, or NetLogo Logging, you may also need to re-run that command once for each of those applications. Additionally, if the workaround is not effective for you, please comment on Issue 1302 with the versions of NetLogo and Mac OS you are running and let us know!

Also note that the above fix only affects NetLogo 6.3.0. If you are trying to fix NetLogo 6.0 (or 5.3.1, or 6.2.2), change "6.3.0" in the above commands to "6.0" (or "5.3.1", or "6.2.2" respectively).

NetLogo slow start up behind proxy

  • Reported in: Issue 2298
  • Affects: NetLogo 6.34 (Linux) May affect other versions.
  • Fix Version:
  • Symptoms: NetLogo startup takes several minutes when behind a proxy.
  • Additional information: This happens when NetLogo makes a request over the network to update information about extensions and their latest versions and there is a problem getting the response.

There is a workaround for fixing this. Turn off the request to update the extensions information by setting the java preference netlogo.libraries.disabled=true by editing the NetLogo configuration file. There is one configuration file for each sub-application (NetLogo, NetLogo 3D, HubNet Client, etc.) Add the following line to the section with java-options (order doesn’t matter)

    java-options=-Dnetlogo.libraries.disabled=true

If you want to allow the updates again, you can set the value to false, or remove that preference.

Platform specific information for locating the NetLogo configuration files:

  • Windows: The file will typically be in C:\Program Files\NetLogo 6.4.0\app, unless you are running 32 bit NetLogo on a 64 bit Windows, then it will be in C:\Program Files (x86)\NetLogo 6.4.0\app.
  • Mac OS X: The file for NetLogo will be located at: /Applications/NetLogo 6.4.0/NetLogo 6.4.0.app/Contents/app/NetLogo 6.4.0.cfg For NetLogo 3D and the other applications, you will find the file in the corresponding location for each application package. You can reach the configuration file by control-clicking the application in the Finder and choosing "Show Package Contents" from the popup menu.
  • Linux: The configuration files will be located in the lib/app directory of your NetLogo installation.

NetLogo won't start on Ubuntu 16 (and various other Linux systems)

  • Reported in: Issue 1427
  • Affects: NetLogo 6.0.1 (Confirmed), NetLogo 5.3-6.0 (Likely)
  • Fix Version: N/A
  • Symptoms: NetLogo crashes immediately upon startup. The crash may report SIGSEGV (segmentation fault) and/or trigger a core dump. This crash starts happening after an update and after June 20, 2017
  • Additional Information:

This seems to have been caused by a security-related kernel update which has some incompatibilities with the bundled version of Java that we include with NetLogo. We are waiting for more information from Debian, Ubuntu, and/or Oracle before attempting to fix this problem, as it doesn't originate in NetLogo's code. In the meantime, affected users may work around the issue by installing Java 8 (Oracle Java recommended, but OpenJDK will most likely work as well) and taking the following steps to make a launcher script:

  • Copy the netlogo-headless.sh file to netlogo-gui.sh
  • Edit the copied file replacing org.nlogo.headless.Main with org.nlogo.app.App. Note that using this launcher requires having the java executable on your path.

HubNet Interface Import makes HubNet Client Editor Non-Functional

  • Reported in: Issue 1145
  • Affects: NetLogo 5.3.1-6.0.2
  • Fix Version:
  • Symptoms: After using "Import > Import HubNet Client Interface...", the HubNet client editor can perform some operations on the widget (repositioning for instance) but cannot perform others (like editing).
  • Additional information: It is possible to workaround this by saving the model, opening a different model (or a new model), then reopening the saved model.

Fixed - Number-too-large causes NullPointerException

  • Reported in: Issue 1277
  • Affects: NetLogo 6.0
  • Fix Version: NetLogo 6.0.1
  • Symptoms: NetLogo errors displaying a stack trace with the following lines first:
java.lang.NullPointerException
at org.nlogo.nvm.StackTraceBuilt.computeRuntimeErrorMessage(EngineException.scala:37)
at org.nlogo.nvm.StackTraceBuilt.computeRuntimeErrorMessage$(EngineException.scala:36)
at org.nlogo.nvm.RuntimePrimitiveException.computeRuntimeErrorMessage(EngineException.scala:51)
  • Additional information: This happens when the numeric values in a model are out of the numeric range NetLogo is capable of representing. This seems to happen frequently with the acos primitive, but could potentially happen with any of the mathematical primitives. This can often be worked around by ensuring that numeric values stay "small enough".

Fixed - NetLogo freezes on 41st Command Center entry

  • Affects: NetLogo 5.3.1-6.0.2
  • Fix Version: NetLogo 6.0.3
  • Symptoms: On entering the 41st unique command in the command center, NetLogo will become unresponsive and have to be terminated. Halt doesn't work to stop the problem.
  • Additional information: Users are advised to save / restart frequently when working extensively with the command center. Note that clicking the "Down Arrow" to the right of the command center and choosing "Clear History" will reset the history. By clearing history before the 41st entry, this problem can be effectively worked around.

Fixed - NetLogo Won't Start on Windows 10

  • Report in: Issue 1603
  • Affects: NetLogo 6.0.3
  • Fix Version: NetLogo 6.0.4
  • Symptoms: NetLogo does not start on Windows 10, instead gives an error message about a missing jvm.dll
  • Additional information:

On certain versions of Windows 10, NetLogo 6.0.3 fails to open, giving an error that it failed to find the library C:\Program Files\NetLogo 6.0.3\runtime\bin\server\jvm.dll. This is very likely this issue with Java 8. It looks like it affects more versions of Windows 10 than just those listed in that issue. I confirmed it on Windows 10 Pro 64 bit running in VirtualBox. Our possible solutions are limited, but the best is to wait for 8u172 which should resolve this completely.

Until 8u172 is in general release, our best workaround is to use the prior version of NetLogo, 6.0.2, on Windows 10 computers that encounter the problem. Some users reported, and the CCL confirmed in one case, that after installing 6.0.2, 6.0.3 will begin working when it didn't before. So it's worth a try to re-open 6.0.3 once 6.0.2 is installed.