Search for unlinked local files fails after large result & SaveException due to "Too many open files"

[hongmiao-wu]

JabRef version

Latest development branch build (please note build date below)

Operating system

macOS

Details on version and operating system

Mac OS X 13.4 aarch64 JabRef 6.0-alpha.65--2025-01-29--5ace0ef

Checked with the latest development build (copy version output from About dialog)

• I made a backup of my libraries before testing the latest development version.
• I have tested the latest development version and the problem persists

Steps to reproduce the behaviour

1. Open a non-empty library
2. Click Search for unlinked local files under Lookup
3. Search using the root directory and any file types (in my case, 50k+ files)
4. Close the search window
5. Re-open the Search for unlinked local files window, now search with any directory, or limit the file type
6. Search result always shows 0 file(s)
7. Make any changes to your library, and try to save it, JabRef could not save files.

Appendix

First search result using the root directory and any file types:

The following search result using the same directory as the first one, shows 0 file(s)

Save library error details

org.jabref.logic.exporter.SaveException: Problems saving: java.io.FileNotFoundException: /Users/xxx/test.bib.tmp (Too many open files)
	at org.jabref@6.0.15065/org.jabref.gui.exporter.SaveDatabaseAction.saveDatabase(SaveDatabaseAction.java:282)
	at org.jabref@6.0.15065/org.jabref.gui.exporter.SaveDatabaseAction.save(SaveDatabaseAction.java:235)
	at org.jabref@6.0.15065/org.jabref.gui.exporter.SaveDatabaseAction.save(SaveDatabaseAction.java:210)
	at org.jabref@6.0.15065/org.jabref.gui.exporter.SaveDatabaseAction.save(SaveDatabaseAction.java:80)
	at org.jabref@6.0.15065/org.jabref.gui.exporter.SaveAction.execute(SaveAction.java:54)
	at org.jabref@6.0.15065/org.jabref.gui.actions.JabRefAction.lambda$new$1(JabRefAction.java:25)
	at org.jabref.merged.module@6.0.15065/org.controlsfx.control.action.Action.handle(Action.java:423)
	at org.jabref.merged.module@6.0.15065/org.controlsfx.control.action.Action.handle(Action.java:64)
	at javafx.base@23.0.1/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
	at javafx.base@23.0.1/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:232)
	at javafx.base@23.0.1/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:189)
	at javafx.base@23.0.1/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
	at javafx.base@23.0.1/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at javafx.base@23.0.1/com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
	at javafx.base@23.0.1/com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
	at javafx.base@23.0.1/javafx.event.Event.fireEvent(Event.java:199)
	at javafx.controls@23.0.1/javafx.scene.control.MenuItem.fire(MenuItem.java:459)
	at javafx.controls@23.0.1/com.sun.javafx.scene.control.GlobalMenuAdapter.lambda$bindMenuItemProperties$2(GlobalMenuAdapter.java:150)
	at javafx.base@23.0.1/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
	at javafx.base@23.0.1/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:232)
	at javafx.base@23.0.1/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:189)
	at javafx.base@23.0.1/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
	at javafx.base@23.0.1/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at javafx.base@23.0.1/com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
	at javafx.base@23.0.1/com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
	at javafx.base@23.0.1/javafx.event.Event.fireEvent(Event.java:199)
	at javafx.controls@23.0.1/javafx.scene.control.MenuItem.fire(MenuItem.java:459)
	at javafx.graphics@23.0.1/com.sun.javafx.tk.quantum.GlassSystemMenu$1.action(GlassSystemMenu.java:266)
Caused by: java.io.FileNotFoundException: /Users/xxx/test.bib.tmp (Too many open files)
	at java.base/java.io.FileOutputStream.open0(Native Method)
	at java.base/java.io.FileOutputStream.open(FileOutputStream.java:295)
	at java.base/java.io.FileOutputStream.<init>(FileOutputStream.java:237)
	at java.base/java.io.FileOutputStream.<init>(FileOutputStream.java:185)
	at org.jabref@6.0.15065/org.jabref.logic.exporter.AtomicFileOutputStream.<init>(AtomicFileOutputStream.java:83)
	at org.jabref@6.0.15065/org.jabref.logic.exporter.AtomicFileWriter.<init>(AtomicFileWriter.java:29)
	at org.jabref@6.0.15065/org.jabref.gui.exporter.SaveDatabaseAction.saveDatabase(SaveDatabaseAction.java:259)
	... 27 more