Jeremy, You are a genius! That did the trick. I've yet to test it on something really big, but all my small tests were successful. Now, of course, the question is why. (By the way, the directories on my Ubuntu installation are not encrypted.)
Let me know if I can help track down what the problem is with the file preferences, although I suspect that you have a few other things to do as well. Many thanks, Charles On Monday, March 22, 2021 at 4:11:20 PM UTC-4 jeremy...@northwestern.edu wrote: > Hey Charles, > > One thing I found in poking around at `FileSystemPreferences` is that > encrypted home directories can cause problems for them due to path length > limits. Do you know if your home directories on encrypted on the server > you're using? I believe it uses the `user.home` Java property as the place > to place the `.userPrefs/` folder (maybe under `.java/`), so if the home > folder location is the problem, setting that property to a non-encrypted > location might fix things. https://stackoverflow.com/a/13847337/1246011 > > In either case, to test out whether or not the file system prefs are the > issue I made a dummy one that doesn't do anything. It shouldn't matter for > what you're doing with BehaviorSpace headlessly. You can download the file > here: > https://github.com/LaCuneta/DummyPreferences/blob/main/dummypreferences_2.13-0.0.1.jar, > > or if you prefer you can clone that repo and build it yourself using `sbt > package` to avoid using a binary file from a stranger on the internet on > your server :-) (it'll be in `target/scala-2.13/` after packaging). > > To use it you'll need to add it to your classpath and then set the > `java.util.prefs.PreferencesFactory` Java option. Here is an example of > what I ran to use it: > > ``` > java -Xmx1024m -Dfile.encoding=UTF8 > -Djava.util.prefs.PreferencesFactory=org.nlogo.DummyPreferencesFactory -cp > "/path/to/NetLogo > 6.2.0/app/netlogo-6.2.0.jar:/path/to/dummypreferences_2.13-0.0.1.jar" > org.nlogo.headless.Main --model ~/WolfSheepPredation.nlogo --experiment > energy --spreadsheet ~/WSP-energy.csv > ``` > > To set the classpath I had to use colons to delimit the jars, surround the > string in double quotes, and then the full, absolute paths instead of the > home shortcut, `~`, as it doesn't work inside the quotes (dunno if you were > using that or not). > > If that helps, then we at least know the file prefs are the cause, even if > we don't exactly know why. It could be the encrypted home drive issue, or > possibly something else. In either case, let me know what you find. > Thanks. > > -Jeremy > > On Monday, March 22, 2021 at 10:33:40 AM UTC-5 Charles wrote: > >> Hi Jeremy. New information: I was able to work with my system >> administrator this morning to run NetLogo with root privilege. It worked! >> So, it may well be, then, that there is something peculiar to our grid's >> configuration that is preventing Java from cleaning up after NetLogo >> completes its job. We did notice that there was a .NFSxxxxx file that was >> locked while java was hanging and that it disappeared when he killed the >> job. (That hang seemed to arise from NetLogo itself being unable to delete >> a user file due to a permissions problem, which we fixed.) >> >> Do you have any suggestions as to where we should look for what NetLogo >> is trying to do that java can not clean up without root priviledge? Any >> other tests we might make? >> >> Thanks, >> Charles >> >> On Thursday, March 18, 2021 at 4:30:37 PM UTC-4 >> jeremy...@northwestern.edu wrote: >> >>> It could some kind of access issue, but my expectation would be that it >>> would just bomb out completely if it tried to open or write to something >>> that you don't have permissions for. But I can't say for sure. >>> >>> I think you're onto something with the FileSystemPreferences, those are >>> the default Preferences used by Java on Linux, and NetLogo does read and >>> write to them for a few things. It's possible to set a different >>> Preferences handler by Java switch, so I'll see if I can make up a dummy >>> one you can try out. If it doesn't hang, at least we'll know the culprit >>> even if we don't know why. >>> >>> -Jeremy >>> >>> On Thursday, March 18, 2021 at 2:54:59 PM UTC-5 Charles wrote: >>> >>>> I've run this under both JDK 11 and 1.8 (Java HotSpot(TM) 64-Bit Server >>>> VM (25.281-b09 mixed mode)), with the same results (attached). I know >>>> nothing abut reading these dumps, but the "DestroyJavaVM" is referencing >>>> java.util.prefs.FileSystemPreferences$4$1. I'm wondering if I run this >>>> (or >>>> have my system manager run it) with full root privs would be worth a try, >>>> just to make sure it's not a privilege problem. Another straw! >>>> >>>> Charles >>>> >>>> On Thursday, March 18, 2021 at 1:52:33 PM UTC-4 se...@tisue.net wrote: >>>> >>>>> There are no NetLogo threads in the thread dump, so this is rather >>>>> mystifying. >>>>> >>>>> The thread dump says "Full thread dump OpenJDK 64-Bit Server VM >>>>> (11.0.2+9 mixed mode)", is JDK 11 also what you're doing your other >>>>> testing >>>>> with...? (I'm grasping at straws.) >>>>> >>>>> Seth >>>>> >>>> -- You received this message because you are subscribed to the Google Groups "netlogo-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to netlogo-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/netlogo-devel/10ccaa3a-5e2b-4cac-94b3-f13b320d0d91n%40googlegroups.com.
