Zotero 7.0.11 (64-bit) tarball quitting on Linux (Fedora 41)

edited January 29, 2025
Hi,

Zotero 7.0.11 (64-bit) tarball is quitting unexpectedly approximately 10 seconds after opening. It stays open long enough for me to put it into Troubleshooting Mode, but after a similar time period, it quits.

It quits without doing anything - merely opening the program and leaving it open causes it to quit unexpectedly.

I have tried to have debug logging on, but when I go to open the debug log in Zotero, it causes it to freeze.

System: Fedora 41, Wayland, GNOME 47, kernel 6.12.10-200.fc41.x86_64

Any ideas?

Thanks

  • @dstillman - thanks

    From terminal:

    Missing chrome or resource URL: chrome://zotero/skin/16/white/loading.svg
    /home/research/Zotero_linux-x86_64/zotero: line 20: 59120 Segmentation fault (core dumped) "$CALLDIR/zotero-bin" -app "$CALLDIR/app/application.ini" "$@"

    zotero-debug.txt is 36,249 lines.
  • Probably not much to go on, but you can send the log file to support@zotero.org with a link to this thread.
  • @qallunaat: Was it working on this computer previously? What version? What happened between then and now?

    Does the same thing happen with the Zotero beta?
  • @dstillman: Yes, it was working fine on this computer. For years.

    Interestingly, the 7.1 beta tar ball works without issue.

    I have no idea what changed ... I will continue using the beta and hopefully 7.1 stable will land soon so I can switch over to something with greater stability as soon as possible.

    Thank you.

    (I also emailed support with the debug file.)
  • edited 5 days ago
    I've been experiencing this for a long time, too, starting sometime around 7.0.10, however that was too long ago to be sure (many months at least). I did not have time to properly debug this, so even had to switch to using a Windows version in the meanwhile, hoping it will resolve itself over time. It didn't, so I spent some time debugging and below are the points, hopefully helpful. I can do further troubleshooting if needed.

    Here's how it looks like:

    1) The crash is very consistent and 100% repeatable, happens at the same address in libxul.so. It's enough to just start Zotero and wait for a bit (order of 10 to 30 seconds), clicking collection names or entries in collections seems to speed it up a bit. Zotero seems to do some initialization at the beginning, with some CPU activity, and then crashes with SIGSEGV: "Thread 1 "zotero-bin" received signal SIGSEGV, Segmentation fault.".

    2) It seems like my particular Zotero data directory contents triggers this, and only on Linux (Fedora 41 and 42, XFCE, to be specific). Windows works fine and never exhibited this problem.

    3) The data dir is synchronized using simple file copy. Database integrity checks always pass.

    4) Creating new profile and attaching the same data dir doesn't help. Using Safe Mode doesn't help. Creating new profile, with empty storage dir, and populating it with randomly collected items does not reproduce the problem.

    5) Using the current 7.1 beta does help in my case too - no issue observed. Moreover, opening the same data dir with 7.0.22 afterwards seems to not exhibit the problem any more. EDIT: the second sentence is not really true, that was a sporadic "no crash" that I also observed once under the GDB but considered a fluke. So while 7.1 beta reproducibly does not crash, the 7.0.22 reproducibly crashes even on that same data/profile afterwards.

    6) I managed to get some relatively meaningful stack trace (I can send the full one as needed, let me know, small snippet below, though it seems to be mangled by the website's input sanitizationTIL it's DokuWiki!), and the crash seems to be related to a known signature [1], and there is some non-trivial underlying issue covered in the following BZ entries: [2], [3], [4], with the latter two still open.

    What else can I do to help debugging and fixing this?


    Thread 1 (Thread 0x7ffff7e89780 (LWP 14619) "zotero-bin"):
    #0 mozilla::CycleCollectedJSContext::CleanupIDBTransactions (this=0x7fffe9d3e000, aRecursionDepth=<optimized out>) at /builds/worker/checkouts/gecko/xpcom/base/CycleCollectedJSContext.cpp:452
    localQueue = {<nsTArray_Impl<mozilla::CycleCollectedJSContext::PendingIDBTransactionData, nsTArrayInfallibleAllocator>> = {<nsTArray_base<nsTArrayInfallibleAllocator, nsTArray_RelocateUsingMemutils>> = {mHdr = 0x7ffff6fe2900 <_pt_root>}, <nsTArray_TypedBase<mozilla::CycleCollectedJSContext::PendingIDBTransactionData, nsTArray_Impl<mozilla::CycleCollectedJSContext::PendingIDBTransactionData, nsTArrayInfallibleAllocator> >> = {<nsTArray_SafeElementAtHelper<mozilla::CycleCollectedJSContext::PendingIDBTransactionData, nsTArray_Impl<mozilla::CycleCollectedJSContext::PendingIDBTransactionData, nsTArrayInfallibleAllocator> >> = {<detail::nsTArray_CopyDisabler> = {<No data fields>}, <No data fields>}, <No data fields>}, static NoIndex = 18446744073709551615}, <No data fields>}

    #1 mozilla::CycleCollectedJSContext::AfterProcessMicrotasks (this=0x7fffe9d3e000) at /builds/worker/checkouts/gecko/xpcom/base/CycleCollectedJSContext.cpp:523
    runnable = {mRawPtr = <optimized out>}

    #2 mozilla::CycleCollectedJSContext::PerformMicroTaskCheckPoint (this=0x7fffe9d3e000, aForce=<optimized out>) at /builds/worker/checkouts/gecko/xpcom/base/CycleCollectedJSContext.cpp:649
    raiiObject677 = {mCategoryString = 0x5555555a69c3 <malloc+355> "M\205\344\017\204\263\032", mMarkerName = 0x60 <error: Cannot access memory at address 0x60>, mCategoryPair = {mCategoryPair = 3287885568}, mInnerWindowID = {<mozilla::detail::MaybeStorage<unsigned long, true>> = {<mozilla::detail::MaybeStorageBase<unsigned long, true>> = {mStorage = {val = 15087974807078774528, dummy = 0 '\000'}}, mIsSome = 56 '8'}, <mozilla::detail::Maybe_CopyMove_Enabler<unsigned long, true, true, true>> = {<No data fields>}, <No data fields>}}
    aso = {mIsMainThread = 101, mScriptActivity = {<mozilla::detail::MaybeStorage<xpc::AutoScriptActivity, false>> = {<mozilla::detail::MaybeStorageBase<xpc::AutoScriptActivity, false>> = {mStorage = {val = {mActive = 149, mOldValue = 90}}}, mIsSome = 85 'U'}, <mozilla::detail::Maybe_CopyMove_Enabler<xpc::AutoScriptActivity, false, true, true>> = {<No data fields>}, <No data fields>}}
    restore = {mLocation = <optimized out>, mValue = <optimized out>}
    didProcess = <optimized out>
    currentDepth = <optimized out>

    #3 0x00007fffefa395d7 in mozilla::CycleCollectedJSContext::BeforeProcessTask (this=0x7fffe9d3e000, aMightBlock=<optimized out>) at /builds/worker/checkouts/gecko/xpcom/base/CycleCollectedJSContext.cpp:486

    #4 XPCJSContext::BeforeProcessTask (this=0x7fffe9d3e000, aMightBlock=<optimized out>) at /builds/worker/checkouts/gecko/js/xpconnect/src/XPCJSContext.cpp:1444

    #5 nsThread::ProcessNextEvent (this=0x7ffff7893200, aMayWait=true, aResult=0x7fffffffb79f) at /builds/worker/checkouts/gecko/xpcom/threads/nsThread.cpp:1145

    <...>


    [1] https://crash-stats.mozilla.org/signature/?signature=mozilla::CycleCollectedJSContext::CleanupIDBTransactions&amp;date=>=2025-01-26T22:14:00.000Z&amp;date=<2025-07-26T22:14:00.000Z&amp;_columns=date&amp;_columns=product&amp;_columns=version&amp;_columns=build_id&amp;_columns=platform&amp;_columns=reason&amp;_columns=address&amp;_columns=install_time&amp;_columns=startup_crash&amp;_sort=-date&amp;page=1

    [2] https://bugzilla.mozilla.org/show_bug.cgi?id=1443429

    [3] https://bugzilla.mozilla.org/show_bug.cgi?id=1509341

    [4] https://bugzilla.mozilla.org/show_bug.cgi?id=1513582
  • @alex-ter: Thanks for the debugging, but if it's fixed in the beta, that's the fix.
  • edited 3 days ago
    Thanks for following up. Fair enough, I wonder if it *is* fixed, though. Given no root cause and the plausible upstream bug not yet fixed, it may simply be that it's not triggering, just yet. However I also understand that with limited resources and in these circumstances it's more reasonable to wait and see if it resurfaces in 7.1.

    What's the plan for getting it out of beta? I unfortunately can't switch to beta as a daily driver just yet.
  • edited today at 3:04pm
    Ok, I have my answer in this thread: https://forums.zotero.org/discussion/125837/zotero-7-1-beta-vs-zotero-8-beta.

    All right then, will be testing 8.0 and get back if this reproduces there. Thanks for all the work on this wonderful app in any case! :)
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