MarvinSpace experiences Segmentation Fault

I just began using the Marvin suite of programs a few days back. I'm quite pleased with both MarvinSketch and MarvinView, but I can't get MarvinSpace to work for the life of me.





I'm on Ubuntu Feisty and running the Sun Java 6 JRE, which doesn't cause a problem with either of the other Marvin programs. Nevertheless, when opening MarvinSpace (from command line or from MarvinSketch), the window pops up, the buttons load, and then the program shuts itself off. The command line echos "Segmentation Fault (core aborted)" at this point, which isn't all that helpful in diagnosing the problem. The same behavior happens when trying to open the program from the website (the online trial).





I've installed and tried Sun Java 1.5 JRE, but exactly the same behavior persists in all instances. If anybody knows how I might solve this problem, or at least start debugging it, help would be much appreciated.

Hi Natume,





we can not reproduce this behavior with Ubuntu Feisty, but the same problem appears on several Ubuntu Feisty forums.





Are you sure Sun Java is used when you try to start the application?


(For example Help->About in MarvinSketch displays information about Java in use.)





Some hints from the Ubuntu forums: Do you start the application as root? Does it work with JDK 7? Does NetBeans start correctly?


Please tell us how this goes on.





Kind regards,


Judit

I don't typically run applications as root, but just to check, I did run MarvinSpace as root a couple times (using sudo) and didn't find any different behavior from running it with normal permissions. Likewise, I checked to make sure that MarvinSketch was using Sun Java 6, which it indeed does. As for JDK 7, where might I get that? I have 6 installed, but I can't find 7 on the Sun website or in the Ubuntu repositories.





As for Netbeans, I don't believe that I had it installed earlier, so I recently installed Netbeans 6.0.1 using Sun's shell installer. The Netbeans IDE works fine, but it doens't make cause anything to run differently in MarvinSketch, or in MarvinSpace. Not to mention, the list of running processes doesn't include Netbeans, even though Java is clearly visible.





Aside from the Netbeans IDE, is there any other software that I need to properly run the Marvin program suite?





In any case, thanks for the inquiry. It prompted me to do a little more exploration as to why I can't get MarvinSpace working.

Hi Natume,





thank you for the checks, I'm sorry that it doesn't seem to give more idea about the nature of the problem.


NetBeans is not necessary form the Marvin applications, it was just a tip from an Ubuntu forum to get closer to the problem.





Can you please try this Java Web Start demo from JOGL?


http://download.java.net/media/jogl/builds/archive/jsr-231-webstart-current/Gears.jnlp





I wonder if JDK7 makes any sense to install, though if you wish to, JDK 7 can be reached from the "early access snapshots" of Sun at https://jdk7.dev.java.net/





Kind regards,


Judit

It seems like the sample doesn't work either. It crashes in roughly the same way as MarvinSpace. To see if I could find out exactly what the issue was, I saved the .jnlp file and opened it using java web start (javaws) from the command line, with verbose output. When it crashed, it gave me the following :





# An unexpected error has been detected by Java Runtime Environment:


#


# SIGSEGV (0xb) at pc=0xb7e93e77, pid=6621, tid=3027135376


#


# Java VM: Java HotSpot(TM) Client VM (1.6.0-b105 mixed mode, sharing)


# Problematic frame:


# C [libc.so.6+0x6ee77] memset+0x37


#


# An error report file with more information is saved as hs_err_pid6621.log


#


# If you would like to submit a bug report, please visit:


# http://java.sun.com/webapps/bugreport/crash.jsp


#





I have no idea what to make of this, but if the nitty gritty helps, the error log's attached, too. When I asked for verbose output on MarvinSpace, similar output was given. (And the log file was changed to a txt file, seeing as it wouldn't allow a log file to be attached)

Hi,





thank you for spending time with some investigations. The error message you got clearly indicates that the problem you experienced exists even when you are not using MarvinSpace. At this point we refer to the Ubuntu forums again that may give some clue how to fix the problem that's probably specific to your system.





We are sorry that we cannot further assist you in this particular matter. If you manage to find a solution, please get back to the forum and share the information with other MarvinSpace users. Thank you!








Regards,


Miklos