Memory problem in Jabref

[bernhard-kleine]

• I have tested the latest master version from http://builds.jabref.org/master/ and the problem persists

JabRef 5.0-dev--snapshot--2018-09-06--docbookfive--ee248ae75
Windows 7 6.1 amd64
Java 1.8.0_181

Steps to reproduce:

1. Open two libraries and the select one entry and open it with crtl-e in the entry editor
2. Put something (like a doi in my case) into the clipboard
3. Switch to the other library
4. Try to open the entry editor by double clicking one entry.

Jabref chokes and the program can only be shut down from the task manager. It only increases available RAM up to 4.4 Gb (and even further, but I did not wait for it) without doing anything. A log file or error report is not possible.

[xiaodongcentury]

The same phenomenon appears in JabRef 5.0-dev--snapshot--2018-09-08 (Debian GNU/Linux).
terminal reads,

i search the error "java.lang.OutOfMemoryError: GC overhead limit exceeded", over the stackoverflow.com (https://stackoverflow.com/questions/1393486/error-java-lang-outofmemoryerror-gc-overhead-limit-exceeded), Mnementh gives a solution: A simple solution could be simply to give some more Heap-memory to the Java-Engine (-Xmx) but this only helps, if the application needs exactly as much memory, as the heap-limit before was set. while Adelin (https://stackoverflow.com/questions/11091516/exception-in-thread-main-java-lang-outofmemoryerror-gc-overhead-limit-exceede) just increase the memory that the virtual machine needs to compile the project.
I dont understand the app development, so i dont know what to do, may the information above be useful to resolve the problem.

[Siedlerchr]

Hi, Thanks for your reports, could you please try to tell when exactly the problem occurs?

If you want to debug this a bit further, you could try to use the YourKit java Profiler.
Launch JabRef, start Yourkit and attach it to the application. When the error occurs, take a Memory Snapshot and upload it somewhere for us, so we can analyze it in detail.
You can send the link to developers@jabref.org

https://www.yourkit.com/docs/java/help/memory_snapshots.jsp
https://www.yourkit.com/java/profiler/download/ (15 day free evaluation key)

[xiaodongcentury]

Thanks your advice, i try the latest version (JabRef 5.0-dev--snapshot--2018-09-09--master--4c7194a39), and the error is gone. Now everything looks fine, though the RSS is higher, or maybe just my opinon (BTW, i have 2000+ entries in my JabRef.).
Here is the task manage screen shot:

Oh, NO!!!
After i open a library, which contains 1000+ entries, then double click one entry, sadly, the JabRef was freeded.
the task manager screen shot:

and the terminal reads:

I can do nothing but kill JabRef.
Maybe the memory JabRef allocated is fixed, or limited, what about dynamic?

[Siedlerchr]

Hi, I found an error when opening a new library, which could be the problem here as well. I fixed it as part of another PR. https://builds.jabref.org/storeColumnSortOrder/
It seems like that on the Threading Error JabRef consumes all memory until it runs out of it. could be unix related, because on Windows the memory stays constant even when JabRef freezes

[xiaodongcentury]

Thanks! Now i'll try the stable version, JabRef 4.3.1, it seems like fine.

though the RSS is more higher, maybe.

[xiaodongcentury]

I'm sorry, man, the https://builds.jabref.org/storeColumnSortOrder/ version doesn't work. I cann't make the JabRef version screenshot( through "Option" > "About") in that the JabRef is freezed. Here's the terminal reads:



I can do nothing but kill JabRef.

[Siedlerchr]

@xiaodongcentury Could you please test again with the latest master version?
https://builds.jabref.org/master/
And then please try to call with the following options:
java -XX:+UseG1GC -XX:+UseStringDeduplication -XX:StringTableSize=1000003 -jar JabRef.jar

[xiaodongcentury]

no problem. I'll try it.
After i download the latest master version (2018-09-13), then java -jar xxxx.jar. At first, it seems like normal. Later, my debian OS freeze, ALL apps freeze, chromium, evince document viewer, task manager, terminal, emacs freeze. So, there is NO screenshot, and i manually shutdown debian OS.

[xiaodongcentury]

Once i reboot my OS, java -jar xxxx.jar (2018-09-13). Task manager reads: CPU, 100%,

So i kill Jabref.
Then try your given options, and the JabRef (2018-09-13) freezes, the same phenomenon as above, though the CPU is about 25%.

And a new "dbind-warning" appears, whether use your given option.
.
May the information above be useful to resolve the problem.
Then i google "dbind-warning", on a french Ubuntu website ( i use chromium 'translate to english'), maybe, https://forum.ubuntu-fi.org/index.php?topic=53591.0. According to nm's explanation: "accessibility bus are related to GNOME's accessibility support and communication between applications and the desktop system". The exact case I REALLY don't know, because i am new to Linux. And i "sudo apt install at-spi2-core", the terminal reads:

So i've no idea what can i do.

[Siedlerchr]

Hi, I recently had the same problem with it and found that this switch helps:
java -Djavafx.embed.singleThread=true -jar JabRef.jar

[xiaodongcentury]

OK, Thanks, I'll try your suggestion.

[bernhard-kleine]

I have tested the master snapshot of yesterday. (2018-09-13) And I encounter memory problems by a very small excerpt of my database which is included. I suspected an error with unescaped % signs in the abstract, but when I escaped the offending % signs manually using Notepad++, the strange behavior remained. I click on all entry in the file and nothing strange happened. Then I clicked on the entry NS86
and suddenly the RAM for Jabref goes from about 350.000 K to 1.500.000 K and I had to shut down Jabref via the taskmanager. I tested for longer since I have 16 Gb and seems to stop at 4.470.692 K of the RAM. But JabRef does not become aktiv again.

I ran the snapshot with the switch proposed, but it does not help.
testjabref.bib.txt

[bernhard-kleine]

after I let run java for a prolonged time I can no longer restart jabref 5dev since an java error occurs:

java.lang.ClassNotFoundException: org.jabref.JabRefMain
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:81)
at com.exe4j.runtime.WinLauncher.main(WinLauncher.java:94)
at com.install4j.runtime.launcher.WinLauncher.main(WinLauncher.java:25).

Please advise what to do.

[tobiasdiez]

Thanks @bernhard-kleine. This narrows down the problem. In fact,

author          = {Nambu, J R and Scheller, R H},

leads to the freeze while

author          = {Nambu, J. R. and Scheller, R. H.},

works fine (I just added dots after the first name initials). Moreover, removing the last dot in the working example also results in the freeze. Hence, I guess our integrity checks are the reason for the problem.

@bernhard-kleine: system restart?