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/b3a63b02-5011-4c1b-81be-1b35db37cf9dn%40googlegroups.com.
