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turtles, patches, and links for kids, teachers, and scientists

Home Page: http://ccl.northwestern.edu/netlogo/

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netlogo's Introduction

NetLogo

This page is for open source developers interested in the source code for NetLogo.

Other users should visit the NetLogo home page at Northwestern and the NetLogo users group on Google.

The most recent version of NetLogo can be downloaded here.

I Need Help! Where Do I Look?

This depends on what you need help with. The NetLogo community have several different channels for communicating and the best way to get help quickly is to address your request to the proper channel.

I have encountered a bug
I am learning NetLogo and would like help
I am trying to model something or extend a model
I have a suggestion for a new feature
I am developing an extension or using the controlling API and would like support
I would like to build NetLogo from source
I'm interested in working on NetLogo with Google Summer of Code
I need help for some other reason

Reporting Bugs

If you have encountered a bug in the latest version of NetLogo, it might be worth checking the Known Issues page to see if other users have already reported the issue. If no one has reported the issue, please open a GitHub issue or email our bugs list. If possible, please include a model displaying the bug as well as information about what you were doing when the issue occurred. Including the model and information about the buggy interaction makes fixing the problem much easier and ensures we fix the exact problem you were experiencing. If the model isn't public, please send it to our bugs mailing list. This list is private and your model will not be shared publicly.

Learning NetLogo

We're excited that you're learning NetLogo! NetLogo comes with a tutorial which introduces the basic concepts and can help you get started. If you're looking for a textbook which explains the concepts underlying NetLogo you might look at Introduction to Agent-Based Modeling available as a paper book and/or ebook from MIT Press. The archives of an intro courses on NetLogo titled "Introduction to Agent-Based Modeling" are available on Complexity Explorer.

Help With Modeling

There are many good resources listed on the NetLogo resources page The Netlogo-Users Google group frequently tackles questions on modeling. Be aware that the the group is moderated, so most messages don't go through until at least the next business day. There is also a fairly active NetLogo community on StackOverflow. NetLogo Users tends to be a better place to ask more open-ended modeling questions, for instance "I'm interested in making a model of plate tectonics, can anyone offer advice?". StackOverflow tends to be best for asking specific questions with definite answers, for instance "How can I create a small-world network of turtles and links?".

Suggestions for New Features

While the resources we have to add new features are limited, we're happy to hear new ideas! You might quickly search our issue tracker to see if someone has suggested something similar in the past (if you find something, comment on the issue to let us know it's something people are interested in). Otherwise, please open an enhancement request on GitHub or email our feedback list.

Extension API and Controlling API support

A good place to start is in our wiki. For extension developers, see the page on the extensions API. If you're a developer of an existing extension and interested in porting it to NetLogo 6, please see the 6.0 transition guide. There is also a wiki page on the controlling API.

Often extension and embedding developers have fairly specific questions. We encourage those developers to post to the netlogo-devel Google Group or join us on Gitter.

Building from source

Our goal is that users are able to build NetLogo from source on their platform of choice (Mac, OS X, or Linux). More information can be found on our Building wiki page. If the information on this page doesn't work for you or you have trouble or are confused, please post to netlogo-devel Google Group or join us on Gitter and request help. We're trying to make building NetLogo easy, so we would love to hear any suggestions you have or problems you encounter!

Google Summer of Code

We're very excited to have been accepted to Google Summer of Code 2017 as a mentoring organization! We're even more excited that you're interested in contributing to NetLogo this summer. Please join us in our GSoC 2017 chat room if you have specific questions or are just interested in chatting. Student applications will open up on GSoC on March 20th, and that will be everyone's opportunity to formally declare their interest in working on NetLogo, and what projects they would like to contribute to. Guidelines for what we would like to see in proposals are covered on our organization page.

Please note that an accepted contribution to NetLogo or NetLogo Web is necessary for an application to be considered. Before working on a contribution, please discuss it with us in the GSoC 2017 Gitter channel. This helps us stay on top of things and might save you time working on something that someone else is already planning to do!

For Other Help

Please ask us!

You can email our feedback list or ask your question on Gitter.

Issues

We've all got them. NetLogo's are here: https://github.com/NetLogo/NetLogo/issues

Developer documentation

...is in the wiki.

Discussion group

To talk about NetLogo development, NetLogo internals, the NetLogo source code, usage of NetLogo APIs, etc., join netlogo-devel at Google Groups.

Package repository hosting is graciously provided by Cloudsmith.

netlogo's People

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netlogo's Issues

can't import world with an array containing strings with curly braces

there are now commented-out tests for this in TestImportExport and TokenizerTests.
a string like this: {{array: 0: "}}" "{{"}}

confuses the tokenizer because it doesn't know the }} are part of the string rather than terminating the array

I'm not sure how fixable this even is without redesigning the export format

add to TokenizerTests:

  test("array of strings containing doubled curly braces") {
    val tokens = tokenize("{{array: 0: \"}}\" \"{{\"}}")
    expect(1)(tokens.size)
    expect("Token({{array: 0: \"}}\" \"{{\"}},LITERAL,{{array: 0: \"}}\" \"{{\"}})")(
      tokens.mkString)

add to TestImportExport:

  test("testImportingArrayContainingStringsWithBraces") {
    roundTripHelper("set a array:from-list [\"}}\" \"{{\"]",
                    "extensions [array] globals [a]")
  }

Strings run with the `run` and `runresult` primitives are sometimes not able to read or set variables created with `let`

The chances are of this ever getting fixed are low. The specification and implementation difficulties are too great.

If a change were to be made, it would probably be in the direction of giving run on strings less access to local context, not more.

Disallowing access to the local lexical environment would be in line with how eval behaves in other Lisp dialects:

Common Lisp: "The form [passed to eval] is evaluated in the current dynamic environment and a null lexical environment" (CLtL2 20.1)
Scheme: eval requires an explicit environment argument and there is no standard provision for reifying the local lexical environment. (see R5RS 6.5 for details)

can't import world containing nested arrays or tables

(included in docs/issues.html)

add this to TestImportExport.scala:

  @Test def testImportingArrayInsideArray() {
    val filename = getUniqueFilename
    new java.io.File( filename ).delete()
    workspace.initForTesting(5, "globals [ar1] extensions [ array ]" )
    testCommand( "set ar1 array:from-list (list array:from-list [5])" )
    testCommand( "export-world \"" + filename + "\"" )
    testCommand( "ca" )
    testCommand( "import-world \"" + filename + "\"" )
    testReporter( "array:to-list array:item ar1 0", "[5]")
  }

result is:

got a nonfatal error Warning: Error importing arrays: Error Importing at Line 176: Expected breed
Action to be Taken: This array will be ignored
There was 1 failure:
1) testImportingArrayInsideArray(org.nlogo.headless.TestImportExport)
org.nlogo.nvm.EngineException: Extension exception: 0 is not a valid index into an array of length 0

the original exception is:

Expected breed at position 4 in 
    at org.nlogo.compiler.CompilerExceptionThrowers$.exception(CompilerExceptionThrowers.scala:12)
    at org.nlogo.compiler.CompilerExceptionThrowers$.cAssert(CompilerExceptionThrowers.scala:6)
    at org.nlogo.compiler.ConstantParser.parseConstantAgentOrAgentSet(ConstantParser.scala:206)
    at org.nlogo.compiler.ConstantParser.readConstantPrefix(ConstantParser.scala:99)
    at org.nlogo.compiler.ConstantParser.parseConstantList(ConstantParser.scala:127)
    at org.nlogo.compiler.ConstantParser.readConstantPrefix(ConstantParser.scala:97)
    at org.nlogo.compiler.ConstantParser.getConstantValue(ConstantParser.scala:64)
    at org.nlogo.compiler.Compiler$.readFromString(Compiler.scala:79)
    at org.nlogo.workspace.Evaluator.readFromString(Evaluator.java:290)
    at org.nlogo.workspace.AbstractWorkspace.readFromString(AbstractWorkspace.java:867)
    at org.nlogo.workspace.ExtensionManager.readFromString(ExtensionManager.java:527)
    at org.nlogo.extensions.array.ArrayExtension.readExtensionObject(ArrayExtension.java:184)
    at org.nlogo.workspace.ExtensionManager.readExtensionObject(ExtensionManager.java:560)
    at org.nlogo.compiler.ConstantParser.parseConstantLiteral(ConstantParser.scala:138)
    at org.nlogo.compiler.ConstantParser.readConstantPrefix(ConstantParser.scala:93)
    at org.nlogo.compiler.ConstantParser.getConstantValue(ConstantParser.scala:64)
    at org.nlogo.compiler.Compiler$.readFromString(Compiler.scala:79)
    at org.nlogo.workspace.Evaluator.readFromString(Evaluator.java:290)
    at org.nlogo.workspace.AbstractWorkspace.readFromString(AbstractWorkspace.java:867)
    at org.nlogo.workspace.ExtensionManager.readFromString(ExtensionManager.java:527)
    at org.nlogo.extensions.array.ArrayExtension.importWorld(ArrayExtension.java:151)
    at org.nlogo.workspace.ExtensionManager.importExtensionData(ExtensionManager.java:833)
    at org.nlogo.workspace.AbstractWorkspace.importExtensionData(AbstractWorkspace.java:111)
    at org.nlogo.agent.Importer.importExtensionData(Importer.java:471)
    at org.nlogo.agent.Importer.importWorld(Importer.java:177)
    at org.nlogo.agent.World.importWorld(World.java:193)
    at org.nlogo.workspace.AbstractWorkspace$4.doImport(AbstractWorkspace.java:650)
    at org.nlogo.workspace.AbstractWorkspace.doImport(AbstractWorkspace.java:713)
    at org.nlogo.workspace.AbstractWorkspace.importWorld(AbstractWorkspace.java:643)
    at org.nlogo.prim.etc._importworld$1.run(_importworld.java:28)
    at org.nlogo.headless.HeadlessWorkspace.waitFor(HeadlessWorkspace.java:162)
    at org.nlogo.prim.etc._importworld.perform(_importworld.java:23)
    at org.nlogo.nvm.Context.stepConcurrent(Context.java:95)
    at org.nlogo.nvm.ConcurrentJob.step(ConcurrentJob.java:95)
    at org.nlogo.job.JobThread.runPrimaryJobs(JobThread.java:194)
    at org.nlogo.job.JobThread.run(JobThread.java:117)

exported world has:

"EXTENSIONS"

"array"
"{{array: 0: 5}}"
"{{array: 1: {{array: 0}}}}"

Java Web Start: pegdown jar doesn't work when signed

for now we worked around this for ABMPLUS by using a special build that doesn't have rich info tabs, but obviously that's no good

bundle Java 6 Update 30 for Windows users

when an (unhandled) runtime error occurs, all open files should be closed

As file-close doesn't throw errors if you try to close file that isn't open, an easy workaround is to use file-close before code like this:

; Delete a file if exists
if [file-exists filename][
   file-delete filename
]

Although the workaround exists, it would still really be better if the system closed all open files when a runtime error (unhandled by carefully) occurs.

reported by Onno Steenbergen

export/import-world should save/restore default shapes

export-world is supposed to save all state, but this is a piece of state that isn't being saved.

(included in docs/issues.html)

on Linux, the exp primitive may not always return consistent answers

We have discovered a problem on at least some versions of Linux where the exp primitive sometimes returns a slightly different answer (differing only in the last decimal place) for the same input. According to an engineer at Sun, this should only happen on Linux kernel versions 2.4.19 and earlier, but we have observed the problem on more recent kernel versions. We imagine the problem is Linux-specific and does not happen on other Unix-based systems. We are not sure if the problem ever occurs in practice during actual NetLogo model runs, or only occurs in the context of our automated test regimen. The bug is in Sun's Java VM, and not in NetLogo itself. We hope that only the exp is affected, but we can't be entirely sure.

Users are encouraged to visit http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5023712 (free registration required) and vote for Sun to fix this bug.

some unit tests fail when the system language isn't English

with my system language set to Russian on Mac OS X, I get:

> test-fast
[info] == org.nlogo.plot.PlotPenTests ==
[info] PlotPenTests:
[info] - PlotModeConstants *** FAILED *** (28 milliseconds)
[info]   Expected "[Line]", but got "[Линия]" (PlotPenTests.scala:8)
[info] 
[info] == org.nlogo.window.UpdateManagerTests ==
[info] UpdateManagerTests:
[info] - tick-based: default speed *** FAILED *** (36 milliseconds)
[info]   "...0, frameRateGap = 30[,00 fps, nanoGap = Infinity fps, slowdown = 0,0 ms, every 1,]000 ticks" did not equal "...0, frameRateGap = 30[.00 fps, nanoGap = Infinity fps, slowdown = 0.0 ms, every 1.]000 ticks" (UpdateManagerTests.scala:28)
[info] - tick-based: max speed *** FAILED *** (1 millisecond)
[info]   "...rameRateGap = 498256[,10 fps, nanoGap = 0,33 fps, slowdown = 0,0 ms, every 1000026,]000 ticks" did not equal "...rameRateGap = 498256[.10 fps, nanoGap = 0.33 fps, slowdown = 0.0 ms, every 1000026.]000 ticks" (UpdateManagerTests.scala:32)
[info] - tick-based: min speed *** FAILED *** (1 millisecond)
[info]   "...50, frameRateGap = 0[,15 fps, nanoGap = Infinity fps, slowdown = 9000,0 ms, every 0,]010 ticks" did not equal "...50, frameRateGap = 0[.15 fps, nanoGap = Infinity fps, slowdown = 9000.0 ms, every 0.]010 ticks" (UpdateManagerTests.scala:36)
[info] - tick-based: all speeds *** FAILED *** (25 milliseconds)
[info]   "...50, frameRateGap = 0[,15 fps, nanoGap = Infinity fps, slowdown = 9000,0 ms, every 0,010 ticks
[info] speed = -49, frameRateGap = 0,17 fps, nanoGap = Infinity fps, slowdown = 7501,0 ms, every 0,011 ticks
[info] speed = -48, frameRateGap = 0,19 fps, nanoGap = Infinity fps, slowdown = 6252,0 ms, every 0,012 ticks
...

perhaps there are more failing tests that aren't part of test-fast. all of nightly.sh should be checked.

in-cone is broken in 3D when turtle's pitch isn't 0

Christoph Möslinger reports:

I was trying to implement my own flocking simulation with the latest
NetLogo 3D version and came upon a bug with the "in-cone" primitive:

When the pitch of the turtle is 0 degrees then it works as it should,
but as soon as the pitch of the turtle increases, the cone is more and
more "cut" and is (much) less than half of its usual size if the turtle
pitch is 90 degrees.

the bug is demonstrated visually in models/benchmarks/other/3D Cone Tester.nlogo

a test should also be added to tests/commands/InCone.txt

performance: "one-of turtles" is O(n), should be O(1)-ish

both TreeAgentSet and ArrayAgentSet are affected

I made a benchmark to measure it, models/test/other/One-Of Turtles Benchmark.nlogo

TreeAgentSet and ArrayAgentSet are different problems.

in the TreeAgentSet case, we know the sets contain no dead agents. we could go straight to a random agent in O(log n) time if we were using a tree that knew the size of it's subtrees. e.g. starting at root if we have 10 agents on the left and 7 on the right, we have a 1 in 18 chance to stop, a 10 in 18 to go left, and a 7 in 18 to go right. but java's TreeMap.Entry doesn't store this information.

in the ArrayAgentSet case, the array may contain dead agents. we could pick randomly and if we hit a dead agent pick again, but then the worst-case runtime is unbounded. can we be cleverer? we can't pick a random location and scan forward for the next live turtle, because that would favor live turtles that follow clusters of dead ones.

models changes for 5.0RC5

promote Sandpile (as CC0)
promote Bug Hunt Predators and Invasive Species

5.0 speed regression: primitives that use tasks are slower (especially ? variables)

example code that's substantially slower in 5.0 than 4.1: sort-by [[p] of ?1 < [p] of ?2] my-patch-set

incorrect `carefully` example in NetLogo Dictionary

The carefully example doesn't work in 5.0RC4:

carefully [ show 1 / 0 ] [ print error-message ]

Gives:
ERROR: Runtime error: Division by zero.

recompiling Code tab doesn't recompile tasks stored in variables

this is a missing feature.

but there is also a bug in that the old tasks might not even work anymore, if the declarations in the Code tab changed, because the tasks might have references to the old indices of agent variables

5.0RC3 regression: double-clicking models on Windows doesn't work

multiple users are reporting:

Startup error
An error has occurred during startup:
java.lang.IllegalStateException: Error parsing command line arguments: you can only specify one model to open at startup.
    at org.nlogo.app.App$.processCommandLineArguments(App.scala:172)
    at org.nlogo.app.App$.main(App.scala:82)

perhaps an accidental side effect of c278463

5.0 regression: NetLogo 3D: turtle trails rendered incorrectly

run Trails Example 3D to see the problem. the line segments in the trail are oriented incorrectly

the regression happened between 5.0beta4 and 5.0RC1

GoGo extension: Mac OS X native library lacks 64-bit support (UnsatisfiedLinkError)

it's NetLogo/GoGo-RXTX-Extension#1

GIS extension: 5.0 regression: applet not working: out-of-date jar name in GISExtension.additionalJars

see NetLogo/GIS-Extension#3

Mac OS X: in fullscreen mode, zooming messes up the window size

...making it no longer fullscreen

steps to reproduce:

open a model with a small enough interface (e.g. Fire) on a big enough monitor
switch to fullscreen mode (click the two-arrows icon in the upper right corner, in the title bar)
zoom in or out (with the Zoom menu)

although NetLogo remains in fullscreen mode, the window doesn't actually fill the screen anymore

reported by Nathan Holbert

model with empty tick counter label can't be loaded

that line in the file ends up blank, so the model loader thinks it marks the end of the GRAPHICS-WINDOW section

reported by Jim Lyons

the sizing of interface elements varies from platform to platform

this means that button names, slider names, and so on that look fine on the model author's computer might be cut off when somebody else looks at the model.

for now, it is advisable to leave some extra space in the sizes of buttons, sliders, etc. in any model that isn't intended merely for personal use.

include Eric's fix for GIS extension issue #1 (bug reported by Jim Westervelt)

NetLogo/GIS-Extension#1

making ticket in this repo so it gets included in the main change list

5.0 regression: stop inside foreach not working properly

these tests (if added to test/commands/Stop.txt) fail.

StopFromForeach2
  to test foreach [1 2 3] [ if ? = 2 [ stop ] set glob1 glob1 + ? ] end
  O> test
  glob1 => 1

StopFromForeach3
  to test1 test2 test2 end
  to test2 foreach [1 2 3 4 5] [ set glob1 glob1 + ? stop ] end
  O> test1
  glob1 => 2

reported by Onno Steenbergen

app always comes up in English even if another language is available

Francisco J. Miguel Quesada reports that this was working before in 5.0beta2 on Windows, but had stopped working by 5.0RC2.

5.0 regression: error recompiling models using temporary plot pens

steps to reproduce:

open Models Library, HubNet, Disease
make any change to the code tab (add a space somewhere )
go to the interface tab (you will get an error)

bug is reproducible in 5.0RC1 and 5.0RC6, but not 5.0beta1

the bug still happens if you resave the model in 5.0RC6 first

the bug doesn't happen until after reset-ticks has run. (you can test this by renaming startup so it doesn't run automatically, then running the commands in the body manually, testing for the bug after each one)

I was unable to reproduce the bug with two other HubNet models (Gridlock, Tragedy of the Commons.)

reported by Corey Brady

the following error details seem to indicate that temporary plot pens are the culprit ("run 1" is the name of a temporary pen)


java.util.NoSuchElementException: key not found: PlotPen(run 1, Plot(Number Sick))
 at scala.collection.MapLike$class.default(MapLike.scala:224)
 at scala.collection.JavaConversions$JMapWrapper.default(JavaConversions.scala:792)
 at scala.collection.MapLike$class.apply(MapLike.scala:135)
 at scala.collection.JavaConversions$JMapWrapper.apply(JavaConversions.scala:792)
 at org.nlogo.plot.PlotManager.getPenSetupError(PlotManager.scala:179)
 at org.nlogo.plot.PlotManager.hasErrors(PlotManager.scala:177)
 at org.nlogo.plot.PlotManager$$anonfun$hasErrors$1.apply(PlotManager.scala:172)
 at org.nlogo.plot.PlotManager$$anonfun$hasErrors$1.apply(PlotManager.scala:172)
 at scala.collection.LinearSeqOptimized$class.exists(LinearSeqOptimized.scala:79)
 at scala.collection.immutable.List.exists(List.scala:45)
 at org.nlogo.plot.PlotManager.hasErrors(PlotManager.scala:172)
 at org.nlogo.window.AbstractPlotWidget.anyErrors(AbstractPlotWidget.scala:287)
 at org.nlogo.window.AbstractPlotWidget.recolor(AbstractPlotWidget.scala:269)
 at org.nlogo.window.AbstractPlotWidget.handle(AbstractPlotWidget.scala:282)
 at org.nlogo.window.Events$CompiledEvent.beHandledBy(Events.java:213)
 at org.nlogo.window.Event.doRaise(Event.java:198)
 at org.nlogo.window.Event.raise(Event.java:122)
 at org.nlogo.window.CompilerManager.compileProcedures(CompilerManager.java:124)
 at org.nlogo.window.CompilerManager.compileAll(CompilerManager.java:88)
 at org.nlogo.window.CompilerManager.handle(CompilerManager.java:310)
 at org.nlogo.window.Events$CompileAllEvent.beHandledBy(Events.java:175)
 at org.nlogo.window.Event.doRaise(Event.java:198)
 at org.nlogo.window.Event.raise(Event.java:122)
 at org.nlogo.app.ProceduresTab.recompile(ProceduresTab.scala:125)
 at org.nlogo.app.ProceduresTab.handle(ProceduresTab.scala:103)
 at org.nlogo.app.Events$SwitchedTabsEvent.beHandledBy(Events.java:42)

import-world should be able to import tasks

and anyway export-world doesn't export enough information for a re-import to be possible anyway

this is a missing feature, not merely a bug

some SDM models behave incorrectly when running headless

Kevin Zollman supplied the example System Dynamics Modeler diagram below.

in the GUI, this is read in by JHotDraw, which handles it correctly. but we can't use JHotDraw from org.nlogo.headless, so we rolled our own code in sdm.AggregateManagerLite to read SDM diagrams, and that code fails on this case.

NetLogo 4.1 has the same issue.

0.01
    org.nlogo.sdm.gui.AggregateDrawing 9
        org.nlogo.sdm.gui.ConverterFigure "attributes" "attributes" 1 "FillColor" "Color" 130 188 183 242 296 50 50
            org.nlogo.sdm.gui.WrappedConverter "type-1 + ( type-2 * 3)" "type-1-fitness"
        org.nlogo.sdm.gui.ConverterFigure "attributes" "attributes" 1 "FillColor" "Color" 130 188 183 369 293 50 50
            org.nlogo.sdm.gui.WrappedConverter "type-2 * 2" "type-2-fitness"
        org.nlogo.sdm.gui.StockFigure "attributes" "attributes" 1 "FillColor" "Color" 225 225 182 177 107 60 40
            org.nlogo.sdm.gui.WrappedStock "type-1" "0.01" 0
        org.nlogo.sdm.gui.StockFigure "attributes" "attributes" 1 "FillColor" "Color" 225 225 182 479 108 60 40
            org.nlogo.sdm.gui.WrappedStock "type-2" "0.99" 0
        org.nlogo.sdm.gui.ConverterFigure "attributes" "attributes" 1 "FillColor" "Color" 130 188 183 501 286 50 50
            org.nlogo.sdm.gui.WrappedConverter "(type-1 * type-1-fitness) + (type-2 * type-2-fitness)" "ave-fitness"
        org.nlogo.sdm.gui.ReservoirFigure "attributes" "attributes" 1 "FillColor" "Color" 192 192 192 103 101 30 30
        org.nlogo.sdm.gui.RateConnection 3 133 117 149 119 165 121 NULL NULL 0 0 0
            org.jhotdraw.figures.ChopEllipseConnector REF 11
            org.jhotdraw.standard.ChopBoxConnector REF 5
            org.nlogo.sdm.gui.WrappedRate "type-1 * (type-1-fitness - ave-fitness)" "t1-replicator"
                org.nlogo.sdm.gui.WrappedReservoir  REF 6 0
        org.nlogo.sdm.gui.ReservoirFigure "attributes" "attributes" 1 "FillColor" "Color" 192 192 192 396 110 30 30
        org.nlogo.sdm.gui.RateConnection 3 426 125 446 125 467 126 NULL NULL 0 0 0
            org.jhotdraw.figures.ChopEllipseConnector REF 17
            org.jhotdraw.standard.ChopBoxConnector REF 7
            org.nlogo.sdm.gui.WrappedRate "type-2 * (type-2-fitness - ave-fitness)" "t2-replicator"
                org.nlogo.sdm.gui.WrappedReservoir  REF 8 0

in the generated code, in system-dynamics-go in the GUI we see:

  let new-type-1 ( type-1 + local-t1-replicator )
  let new-type-2 ( type-2 + local-t2-replicator )

but from headless (adding println(source) to AggregateManagerLite.load and running headless.Main with run --model /Users/tisue/Desktop/PD-replicator.nlogo --experiment experiment) we see:

  let new-type-1 ( type-1 + local-t1-replicator )
  let new-type-2 ( type-2 )

Linux: GUI issues under some window managers (e.g. DWM)

Under window managers which do not reparent root windows, such as DWM, there will be various menu and window drawing issues. Windows may appear blank, and menus may pop-up and disappear.

Users wanting to work around these issues should refer to the solutions suggested at http://awesome.naquadah.org/wiki/Problems_with_Java

add Chinese localization contributed by Yu Yanfei

Linux: shell script to run app can't be run from a symlink

the problem line is:

cd "`dirname "$0"`"

it's there to ensure that when NetLogo starts, the NetLogo installation directory is the current working directory, since the app expects that. but if there's a symlink to the script, $0 points to the symlink, rather than to the target, so we end up in the wrong directory

reported by Fred Drueck

file-read and read-from-string don't support extension types (e.g. tables and arrays)

so for example read-from-string (word table:make) results in:

java.lang.NumberFormatException: For input string: "[]"
 at java.lang.NumberFormatException.forInputString(NumberFormatException.java:48)
 at java.lang.Long.parseLong(Long.java:410)
 at java.lang.Long.parseLong(Long.java:468)
 at org.nlogo.extensions.table.TableExtension.readExtensionObject(TableExtension.java:406)
 at org.nlogo.workspace.ExtensionManager.readExtensionObject(ExtensionManager.java:504)
 at org.nlogo.compiler.ConstantParser.parseConstantLiteral(ConstantParser.scala:140)

this isn't just a bug, it's a missing feature.

we may need to rethink our whole approach on serializing extension types; see also #12, #13

NetLogo 3D on Mac OS X 10.6/7: menu items grayed out, unusable with mouse

WORKAROUND: Corey Brady discovered that you can re-enable the menus by opening a modal dialog and then closing it again. For example, a quick way is to press Command-M to open the Models Library dialog with Command-M, then press Esc key to dismiss it.

the keyboard shortcuts for the grayed out menu items still work, so it's clearly Apple's bug. though it would be good if we could find some kind of workaround to put in the code so users don't have to use the workaround above

a user reports that Mac OS X 10.5 works fine. it's broken on 10.6 and 10.7

both NetLogo 3D 4 and 5 are affected

the Command Center should allow reporters to be entered

and insert the show command automatically

advantages:

you get the answer you wanted
we don't have to resort to the traditional "You don't say what to do with" Logo thing which I think mainly comes across as pedantic
we still educate users about the existence of the show command, which they'll need in the Code tab

5.0 regression: file reading doesn't work in applets

it worked in 5.0beta3:

http://ccl.northwestern.edu/netlogo/5.0beta3/applet/File%20Input%20Example.html works

it's broken in 5.0beta5 and all of the release candidates:

the error is an AccessControlException in org.nlogo.api.RemoteFile.getAbsolutePath(RemoteFile.scala:72): http://cl.ly/3D1F100G3z160m3Q1H1u

thanks to Jim Westervelt for discovering and reporting this

plot with initial space in update code can't be loaded

e.g. this line:

"" " set-plot-x-range min [fitness] of individuals  - 20 max [fitness] of individuals + 20"

won't load because of the space before set-plot-x-range:

Caused by: java.lang.RuntimeException: Plot 'fitness histogram' contains invalid setup and/or update code: "" " set-plot-x-range min [fitness] of individuals  - 20 max [fitness] of individuals + 20"
 at scala.sys.package$.error(package.scala:27)
 at org.nlogo.plot.PlotLoader$.parsePlot(PlotLoader.scala:32)
 at org.nlogo.window.AbstractPlotWidget.load(AbstractPlotWidget.scala:255)

the mode of failure is different is you begin pen update code (instead of plot update code) with a space; there is no exception, but the code doesn't load and is lost.

models changes for 5.0RC6

promoted:

Connected Chemistry Atmosphere

Mac OS X: opening model from Finder intermittently fails

If NetLogo is not already running, then the model may or may not open; the bug is intermittent. (If NetLogo is already running, the model always opens.)

This bug has been a problem for many years now.

reduce default stack size for 5.0 (and don't set it VM-wide)

we have two reports now (from Steve Railsback and Rainer Joswig) of errors on Windows that went away when the -Xss parameter was reduced.

and on Linux, I had OutOfMemoryErrors on Ubuntu (running under VirtualBox) until I reduced the setting

currently we have -Xss16m; try 8m, or even 4m?

also, at http://groups.yahoo.com/group/netlogo-users/message/13628 Ivan Sopov suggests setting the stack size for NetLogo job threads only using an alternate Thread constructor, rather than setting it VM-wide. he's right.

new reporters-in-command-center stuff thinks profiler:start is a reporter

add extensions [profiler] to the Code tab then type profiler:start in the command center.

or add this to headless/TestCompiler.Scala:

  test("isReporter on extension prims") {
    workspace.initForTesting(-5, 5, -5, 5, "extensions [profiler]")
    expect(false) { workspace.isReporter("profiler:start") }
    expect(true) { workspace.isReporter("profiler:report") }
  }

it fails.

our Pegdown version (1.0.2) is out of date

https://github.com/sirthias/pegdown/blob/master/CHANGELOG shows 1.1.0 has been out for a few weeks now

let + nested scopes + run/runresult of task = error

to bomb
  ca crt 1
  ask turtles [
    let c 0
    ask self [ set label task [c] ]
    __ignore runresult label
  ]
end

It bombs running the task, trying to access c

the outer ask can equally well be a foreach

error (NullPointerException)
 while observer running ASK
  called by procedure BOMB
  called by Button 'bomb'

java.lang.NullPointerException
 at org.nlogo.nvm.Context.getLet(Context.java:278)
 at org.nlogo.nvm.Context.getLet(Context.java:278)
 at org.nlogo.prim._asm_procedurebomb_letvariable_6.report(:1)
 at org.nlogo.nvm.ReporterTask.report(Task.scala:51)
 at org.nlogo.prim.etc._runresult.report(_runresult.scala:51)
 at org.nlogo.prim.etc._ignore.perform(_ignore.java:24)
 at org.nlogo.nvm.Context.runExclusive(Context.java:118)
 at org.nlogo.nvm.ExclusiveJob.run(ExclusiveJob.java:54)
 at org.nlogo.nvm.Context.runExclusiveJob(Context.java:160)
 at org.nlogo.prim._asm_procedurebomb_ask_1.perform(:1)
 at org.nlogo.nvm.Context.stepConcurrent(Context.java:90)
 at org.nlogo.nvm.ConcurrentJob.step(ConcurrentJob.java:80)
 at org.nlogo.job.JobThread.org$nlogo$job$JobThread$$runPrimaryJobs(JobThread.scala:125)

parallel BehaviorSpace doesn't work with extensions that use native libraries

amackenzieus writes:

I'm in the midst of some changes to my linear programming
solver extension, and it was brought to my attention that
there were some issues when using the extension in a model
with behaviorspace, specifically when spread across
multiple processors.

Since the extension makes a call to a native library (.dll), the
initial thread's classloader already has the .dll loaded.
As I understand it, only a single classloader can have a
native library open and be calling to it.

Is there a potential to identify the specific classloader
that's calling the native library and then utilize that
classloader to make multiple calls to the library, or
does the architecture behind behaviorspace make
that impossible?

I'm not sure yet if it will be fixable by changing the code in the extension, or if we'll need to make some change to NetLogo in a 5.0.x release

MissingResourceException when system language is Russian

you can start up NetLogo OK, but then when you try to open almost any model it blows up with e.g.

java.util.MissingResourceException: Can't find bundle for base name Errors, locale ru_RU
 at java.util.ResourceBundle.throwMissingResourceException(ResourceBundle.java:1427)
 at java.util.ResourceBundle.getBundleImpl(ResourceBundle.java:1250)
 at java.util.ResourceBundle.getBundle(ResourceBundle.java:777)
 at org.nlogo.api.I18N$BundleKind.getBundle(I18N.scala:60)
 at org.nlogo.api.I18N$BundleKind.<init>(I18N.scala:58)
 at org.nlogo.api.I18N$.errors(I18N.scala:94)
 at org.nlogo.compiler.SetVisitor.<init>(SetVisitor.scala:18)

the problem is also reproducible simply by running test-fast in sbt with the system language set to Russian

5.0 regression: temporary plot pens don't appear in legend

compare e.g. Crystallization Basic in 4.1 versus 5.0

reported by Christopher Watts

attempting to use `?0` crashes compiler

this should give a nice error message instead:

% make goshell
NetLogo 5.0RC4 (November 4, 2011)
print task [?0]
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -1
    at scala.collection.mutable.ResizableArray$class.apply(ResizableArray.scala:45)
    at scala.collection.mutable.ArrayBuffer.apply(ArrayBuffer.scala:44)
    at org.nlogo.prim._reportertask.getFormal(_reportertask.scala:25)
    at org.nlogo.compiler.TaskVisitor.visitReporterApp(TaskVisitor.scala:33)
    at org.nlogo.compiler.ReporterApp.accept(AstNode.scala:168)
    at org.nlogo.compiler.DefaultAstVisitor$$anonfun$visitReporterApp$1.apply(AstVisitor.scala:27)
    at org.nlogo.compiler.DefaultAstVisitor$$anonfun$visitReporterApp$1.apply(AstVisitor.scala:27)
    at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:60)
    at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:44)
    at scala.collection.TraversableProxyLike$class.foreach(TraversableProxyLike.scala:28)
    at org.nlogo.compiler.ReporterApp.foreach(AstNode.scala:158)
    at org.nlogo.compiler.DefaultAstVisitor.visitReporterApp(AstVisitor.scala:27)
    at org.nlogo.compiler.TaskVisitor.visitReporterApp(TaskVisitor.scala:22)
    at org.nlogo.compiler.ReporterApp.accept(AstNode.scala:168)
    at org.nlogo.compiler.DefaultAstVisitor$$anonfun$visitReporterApp$1.apply(AstVisitor.scala:27)
    at org.nlogo.compiler.DefaultAstVisitor$$anonfun$visitReporterApp$1.apply(AstVisitor.scala:27)
    at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:60)
    at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:44)
    at scala.collection.TraversableProxyLike$class.foreach(TraversableProxyLike.scala:28)
    at org.nlogo.compiler.ReporterApp.foreach(AstNode.scala:158)
    at org.nlogo.compiler.DefaultAstVisitor.visitReporterApp(AstVisitor.scala:27)
    at org.nlogo.compiler.TaskVisitor.visitReporterApp(TaskVisitor.scala:38)
    at org.nlogo.compiler.ReporterApp.accept(AstNode.scala:168)
    at org.nlogo.compiler.DefaultAstVisitor$$anonfun$visitStatement$1.apply(AstVisitor.scala:29)
    at org.nlogo.compiler.DefaultAstVisitor$$anonfun$visitStatement$1.apply(AstVisitor.scala:29)
    at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:60)
    at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:44)
    at scala.collection.TraversableProxyLike$class.foreach(TraversableProxyLike.scala:28)
    at org.nlogo.compiler.Statement.foreach(AstNode.scala:99)
    at org.nlogo.compiler.DefaultAstVisitor.visitStatement(AstVisitor.scala:29)
    at org.nlogo.compiler.Statement.accept(AstNode.scala:106)
    at org.nlogo.compiler.DefaultAstVisitor$$anonfun$visitStatements$1.apply(AstVisitor.scala:30)
    at org.nlogo.compiler.DefaultAstVisitor$$anonfun$visitStatements$1.apply(AstVisitor.scala:30)
    at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:60)
    at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:44)
    at scala.collection.TraversableProxyLike$class.foreach(TraversableProxyLike.scala:28)
    at org.nlogo.compiler.Statements.foreach(AstNode.scala:75)
    at org.nlogo.compiler.DefaultAstVisitor.visitStatements(AstVisitor.scala:30)
    at org.nlogo.compiler.Statements.accept(AstNode.scala:92)
    at org.nlogo.compiler.DefaultAstVisitor.visitProcedureDefinition(AstVisitor.scala:25)
    at org.nlogo.compiler.TaskVisitor.visitProcedureDefinition(TaskVisitor.scala:15)
    at org.nlogo.compiler.ProcedureDefinition.accept(AstNode.scala:66)
    at org.nlogo.compiler.CompilerMain$$anonfun$compile$2.apply(CompilerMain.scala:43)
    at org.nlogo.compiler.CompilerMain$$anonfun$compile$2.apply(CompilerMain.scala:39)
    at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:60)
    at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:44)
    at org.nlogo.compiler.CompilerMain$.compile(CompilerMain.scala:39)
    at org.nlogo.compiler.Compiler$.compileMoreCode(Compiler.scala:35)

Linux: shell script to run app handles relative paths incorrectly

because this happens:

cd "`dirname "$0"`

before the line that starts NetLogo runs, any relative pathnames passed on the command line will no longer point to the right place

it's not clear to me if this is even fixable as long as the app expects that the NetLogo directory must be the current working directory when NetLogo starts