Nice, I'm glad we at least have a better workaround! Debugging this would be tough as the code that's hanging is inside the `FileSystemPreferences`, not anything in the NetLogo code. I'll make a note to look for any existing issues with it that sound similar, and I'll reach out if I need any tests done. Thanks for the offer and for following up.
-Jeremy On Wednesday, March 24, 2021 at 11:39:08 AM UTC-5 Charles wrote: > 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/769d7eaf-4990-4d9f-9882-4b7dce68f30bn%40googlegroups.com.
