JabRef Loads Very Slowly Windows 10 (4.3.1) and screen goes black.

[MazerRackhem]

JabRef version 4.3.1

Hi, I'm a relatively new JabRef user. I used to have a Mac machine at work and used Bibdesk before. I love all of the JabRef features. However, the program loads so slowly on my machine it's almost unusable. I only have about 50 entries total so far. However, it takes JabRef as long as 10 minutes to open up a database file. Just a few moments ago I loaded a database with just 12 entries. I went and made coffee, came back wrote an e-mail and then logged onto GitHub to post this request for help before JabRef came up.

I'm not sure what I need to change or what the issue is. I can't imagine everyone is experiencing this kind of performance. I would expect people would stop using the software if this was normal. So I don't know if this is a bug in what I have or a setting that's incorrect but any help on this would be greatly appreciated.

Additionally, I use a dual screen system. In whatever screen JabRef loads up in it works (once it loads). However, when I drag the window over to the other screen the JabRef window goes completely black and becomes inoperable. It works when I drag it back to the first screen.

[MazerRackhem]

A further note that may be relevant. Whenever I open a .bib file I get the message "A back for X.bib was found, do you want to restore X.bib from the backup?"

Every time I load a file this happens.

[Siedlerchr]

Please try the latest development version from http://builds.jabref.org/master/ there has been a lot of improvement regarding performance and other fixes.

[MazerRackhem]

I downloaded the development version. This did help the issue but not very much. What I am finding is that if I click on the Jabref Icon it loads in about 30 seconds to a minute. I can then click on File-> Open Library ->Appropriate File and that file will load up instantly. However, if I click a .bib file outside of Jabref it takes a very long time for Jabref to come up.

[MazerRackhem]

The backups issue is actually worse. Now whenever I open a file I get the "A back up was detected do you want to restore from the back up" message. However, after I click no the same message will sometime randomly reappear later and will also cause additional Jabref windows to keep popping up. As I am writing this I've actually had to close 3 Jabref windows that popped up just while I was writing this comment.

[Siedlerchr]

@MazerRackhem First of all you can manually delete the backup files. They are next to your bib files. The *.sav and *.bak file. JabRef usually asks if the instance was not shut down correctly.
You can also disable the auto save feature in the Settings which may sometimes cause this effect.
Starting JabRef may take some time depending on your last opened bib files. We are working on this. #4578 So you might wait a time or disable the option "Open last bib files at startup" in the settings.

Another known issue you might encounter is that JabRef is currently unable to detect an already running instance. So you may have accidentally started multiple instances of JabRef.

[MazerRackhem]

Thanks for your response Siedlerchr. I am trying to take the suggestions you have offered. However, I cannot find a settings tab in the current 5.0 version. Under "Options" I see "Preferences" however when I click on Preferences a status in the bottom of the JabrRef window says "Status: Opening preferences..." but does not actually open up preferences. I waited on it for around 5 minutes before giving up.

Am I missing the settings somewhere else?

As a point of reference I timed the start up of JabRef today, it took 5 minutes 11 seconds to open after being clicked on from the desktop. There was 1 Library file open at the time it was closed last night which opened with it.

[Siedlerchr]

No, you did all right. Are you using a Mac? Some Mac users reported problems with JabRef as well.
You might try this: http://help.jabref.org/en/FAQosx#q-jabref-slowhangs-on-macos-sierra

[MazerRackhem]

No, I'm on a Windows 10 machine.

[matthiasgeiger]

As @Siedlerchr has not made this clear IMHO: Loading times like the ones you report are faaaaaaar from being normal.
A database file with some hundreds of entries is usually loaded within 1-3 seconds. So there must be something terribly wrong here...

A wild guess from my side: Are you synching the folder of your bib file with Dropbox or a similar service? Or is it a network drive?

[denshion]

Hi, everyone.
Today I updated JabRef from 4.3.1 to the latest development release and the same problem popped out for me. 4.3.1 used to launch quickly, but the process would not shut down cleanly.

I have been trying to fiddle with the problem for the past hour. My OS is Windows 10, the JabRef version is JabRef 5.0-dev--snapshot--2019-03-12--master--930fa4efb. Here is what I've found out.

I tried launching the JabRef JAR from the command line without GUI and with debug messages enabled. The Java machine and the Application class started as it should: here is the output of the logger:

D:\Program Files\JabRef>java -jar JabRef-5.0-dev--snapshot--2019-03-12--master--930fa4efb.jar -v -n --debug
19:25:35.857 [JavaFX Application Thread] DEBUG org.jabref.logic.logging.JabRefLogger - Showing debug messages
JabRef 5.0-dev--snapshot--2019-03-12--master--930fa4efb

But after that the app hanged, while it should have terminated. In a few minutes while I was reading through the source code, the application crashed exited cleanly with the following stack trace:

19:30:35.257 [JavaFX Application Thread] DEBUG org.jabref.logic.remote.client.RemoteClient - Could not ping server at port 6050
java.net.SocketException: Malformed reply from SOCKS server
        at java.net.SocksSocketImpl.readSocksReply(Unknown Source) ~[?:1.8.0_201]
        at java.net.SocksSocketImpl.connect(Unknown Source) ~[?:1.8.0_201]
        at java.net.Socket.connect(Unknown Source) ~[?:1.8.0_201]
        at java.net.Socket.connect(Unknown Source) ~[?:1.8.0_201]
        at java.net.Socket.<init>(Unknown Source) ~[?:1.8.0_201]
        at java.net.Socket.<init>(Unknown Source) ~[?:1.8.0_201]
        at org.jabref.logic.remote.client.RemoteClient.openNewConnection(RemoteClient.java:64) ~[JabRef-5.0-dev--snapshot--2019-03-12--master--930fa4efb.jar:?]
        at org.jabref.logic.remote.client.RemoteClient.ping(RemoteClient.java:28) ~[JabRef-5.0-dev--snapshot--2019-03-12--master--930fa4efb.jar:?]
        at org.jabref.JabRefMain.handleMultipleAppInstances(JabRefMain.java:138) ~[JabRef-5.0-dev--snapshot--2019-03-12--master--930fa4efb.jar:?]
        at org.jabref.JabRefMain.start(JabRefMain.java:71) ~[JabRef-5.0-dev--snapshot--2019-03-12--master--930fa4efb.jar:?]
        at com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$161(LauncherImpl.java:863) ~[jfxrt.jar:?]
        at com.sun.javafx.application.PlatformImpl.lambda$runAndWait$174(PlatformImpl.java:326) ~[jfxrt.jar:?]
        at com.sun.javafx.application.PlatformImpl.lambda$null$172(PlatformImpl.java:295) ~[jfxrt.jar:?]
        at java.security.AccessController.doPrivileged(Native Method) ~[?:1.8.0_201]
        at com.sun.javafx.application.PlatformImpl.lambda$runLater$173(PlatformImpl.java:294) ~[jfxrt.jar:?]
        at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95) ~[jfxrt.jar:?]
        at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) ~[jfxrt.jar:?]
        at com.sun.glass.ui.win.WinApplication.lambda$null$147(WinApplication.java:177) ~[jfxrt.jar:?]
        at java.lang.Thread.run(Unknown Source) [?:1.8.0_201]
Mar 13, 2019 7:30:40 PM com.microsoft.applicationinsights.core.dependencies.http.impl.execchain.RetryExec execute
INFO: I/O exception (java.net.SocketException) caught when processing request to {tls}->http://*HTTP PROXY**:3128 ->https://dc.services.visualstudio.com:443: Socket Closed
Mar 13, 2019 7:30:40 PM com.microsoft.applicationinsights.core.dependencies.http.impl.execchain.RetryExec execute
INFO: Retrying request to {tls}->http://**HTTP PROXY**:3128->https://dc.services.visualstudio.com:443
19:30:40.282 [JavaFX Application Thread] DEBUG org.jabref.logic.remote.server.RemoteListenerServerThread - Interrupting JabRef - Remote Listener Server on port 6050

Apparently, the application was having some problems with the proxy server. I was indeed using a corporate HTTP proxy server (I left its IP address undisclosed), so I tried disabling it in Windows settings and launching JabRef again. This time it crashed exited in a few seconds after printing the first debug messages. The stack trace is now as follows:

D:\Program Files\JabRef>java -jar JabRef-5.0-dev--snapshot--2019-03-12--master--930fa4efb.jar -v -n --debug
19:49:57.625 [JavaFX Application Thread] DEBUG org.jabref.logic.logging.JabRefLogger - Showing debug messages
JabRef 5.0-dev--snapshot--2019-03-12--master--930fa4efb
19:49:58.634 [JavaFX Application Thread] DEBUG org.jabref.logic.remote.client.RemoteClient - Could not ping server at port 6050
java.net.ConnectException: Connection refused: connect
        at java.net.DualStackPlainSocketImpl.connect0(Native Method) ~[?:1.8.0_201]
        at java.net.DualStackPlainSocketImpl.socketConnect(Unknown Source) ~[?:1.8.0_201]
        at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source) ~[?:1.8.0_201]
        at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source) ~[?:1.8.0_201]
        at java.net.AbstractPlainSocketImpl.connect(Unknown Source) ~[?:1.8.0_201]
        at java.net.PlainSocketImpl.connect(Unknown Source) ~[?:1.8.0_201]
        at java.net.SocksSocketImpl.connect(Unknown Source) ~[?:1.8.0_201]
        at java.net.Socket.connect(Unknown Source) ~[?:1.8.0_201]
        at java.net.Socket.connect(Unknown Source) ~[?:1.8.0_201]
        at java.net.Socket.<init>(Unknown Source) ~[?:1.8.0_201]
        at java.net.Socket.<init>(Unknown Source) ~[?:1.8.0_201]
        at org.jabref.logic.remote.client.RemoteClient.openNewConnection(RemoteClient.java:64) ~[JabRef-5.0-dev--snapshot--2019-03-12--master--930fa4efb.jar:?]
        at org.jabref.logic.remote.client.RemoteClient.ping(RemoteClient.java:28) ~[JabRef-5.0-dev--snapshot--2019-03-12--master--930fa4efb.jar:?]
        at org.jabref.JabRefMain.handleMultipleAppInstances(JabRefMain.java:138) ~[JabRef-5.0-dev--snapshot--2019-03-12--master--930fa4efb.jar:?]
        at org.jabref.JabRefMain.start(JabRefMain.java:71) ~[JabRef-5.0-dev--snapshot--2019-03-12--master--930fa4efb.jar:?]
        at com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$161(LauncherImpl.java:863) ~[jfxrt.jar:?]
        at com.sun.javafx.application.PlatformImpl.lambda$runAndWait$174(PlatformImpl.java:326) ~[jfxrt.jar:?]
        at com.sun.javafx.application.PlatformImpl.lambda$null$172(PlatformImpl.java:295) ~[jfxrt.jar:?]
        at java.security.AccessController.doPrivileged(Native Method) ~[?:1.8.0_201]
        at com.sun.javafx.application.PlatformImpl.lambda$runLater$173(PlatformImpl.java:294) ~[jfxrt.jar:?]
        at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95) ~[jfxrt.jar:?]
        at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) ~[jfxrt.jar:?]
        at com.sun.glass.ui.win.WinApplication.lambda$null$147(WinApplication.java:177) ~[jfxrt.jar:?]
        at java.lang.Thread.run(Unknown Source) [?:1.8.0_201]
19:50:02.607 [JavaFX Application Thread] DEBUG org.jabref.logic.remote.server.RemoteListenerServerThread - Interrupting JabRef - Remote Listener Server on port 6050

Apparently something is wrong the remote server connection, but I am not familiar with JavaFX, so I am afraid I cannot locate the problem further by myself.
I hope this helps.

[denshion]

Just now I have also tried running

java -jar JabRef-5.0-dev--snapshot--2019-03-12--master--930fa4efb.jar  --debug

with and without proxy. The JVM printed the same stack traces, but the GUI launched normally. So in the previous post I made a mistake when said that the application crashed - actually, it exited cleanly because of the -n flag.

So, basically: with the proxy turned off JabRef launched within reasonble time, while with HTTP proxy turned on, it only launched after a few minutes.

[Siedlerchr]

The error log above is related to the instance detection of a potential second JabRef instance. This is a known bug which has not yet been fixed.
Regarding the proxy: Have you tried specifying the proxy as parameter to the jvm?
e.g.:

java -Dhttp.proxyHost=webcache.example.com
-Dhttp.proxyPort=8080 -jar JabRef.jar 

See here for detailas:;
https://docs.oracle.com/javase/8/docs/technotes/guides/net/proxies.html

[denshion]

Thank you for the reply.
I tried passing the proxy server a parameters, but it made no effect.

I have skimmed through the link you provided. It seems to me that only a SOCKS proxy would work that way, and one should make use of the Proxy class in order to specify HTTP proxy for TCP socket.

[denshion]

I confirm the issue to be fixed in the version JabRef-5.0-dev--snapshot--2019-03-16--master--d7dd41b00.

For your information, now the stack trace is

03:41:20.697 [JavaFX Application Thread] DEBUG org.jabref.logic.logging.JabRefLogger - Showing debug messages
03:41:20.909 [JavaFX Application Thread] DEBUG org.jabref.logic.remote.client.RemoteClient - Could not ping server at port 6050
java.net.SocketTimeoutException: connect timed out
        at java.net.DualStackPlainSocketImpl.waitForConnect(Native Method) ~[?:1.8.0_201]
        at java.net.DualStackPlainSocketImpl.socketConnect(Unknown Source) ~[?:1.8.0_201]
        at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source) ~[?:1.8.0_201]
        at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source) ~[?:1.8.0_201]
        at java.net.AbstractPlainSocketImpl.connect(Unknown Source) ~[?:1.8.0_201]
        at java.net.PlainSocketImpl.connect(Unknown Source) ~[?:1.8.0_201]
        at java.net.SocksSocketImpl.connect(Unknown Source) ~[?:1.8.0_201]
        at java.net.Socket.connect(Unknown Source) ~[?:1.8.0_201]
        at org.jabref.logic.remote.client.RemoteClient.openNewConnection(RemoteClient.java:67) ~[JabRef-5.0-dev--snapshot--2019-03-16--master--d7dd41b00.jar:?]
        at org.jabref.logic.remote.client.RemoteClient.ping(RemoteClient.java:29) ~[JabRef-5.0-dev--snapshot--2019-03-16--master--d7dd41b00.jar:?]
        at org.jabref.JabRefMain.handleMultipleAppInstances(JabRefMain.java:138) ~[JabRef-5.0-dev--snapshot--2019-03-16--master--d7dd41b00.jar:?]
        at org.jabref.JabRefMain.start(JabRefMain.java:71) ~[JabRef-5.0-dev--snapshot--2019-03-16--master--d7dd41b00.jar:?]
        at com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$161(LauncherImpl.java:863) ~[jfxrt.jar:?]
        at com.sun.javafx.application.PlatformImpl.lambda$runAndWait$174(PlatformImpl.java:326) ~[jfxrt.jar:?]
        at com.sun.javafx.application.PlatformImpl.lambda$null$172(PlatformImpl.java:295) ~[jfxrt.jar:?]
        at java.security.AccessController.doPrivileged(Native Method) ~[?:1.8.0_201]
        at com.sun.javafx.application.PlatformImpl.lambda$runLater$173(PlatformImpl.java:294) ~[jfxrt.jar:?]
        at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95) ~[jfxrt.jar:?]
        at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) ~[jfxrt.jar:?]
        at com.sun.glass.ui.win.WinApplication.lambda$null$147(WinApplication.java:177) ~[jfxrt.jar:?]
        at java.lang.Thread.run(Unknown Source) [?:1.8.0_201]
03:41:21.048 [JavaFX Application Thread] DEBUG org.jabref.JabRefGUI - Initializing frame
03:41:23.327 [JavaFX Application Thread] DEBUG org.jabref.JabRefGUI - Finished adding panels

for the proxy being either enabled or disabled. The stack trace is printed after the first debug message without any delay. The first debug message itself is printed in half a minute after the launch, though.

Thank you for the fix!