Everything is slow in Zotero Standalone 3.0.14 on W7 64bit

I imported a 10,200+ entry file (currently about 10GB before final cleaning) from EndNote X6 as a user of EndNote for over 15 years, with a brief, failed interlude with Mendeley.

Overall, I am happy with Zotero and switched due to better service, group-sharing functions, and the capacity for web snapshots and storage of files other than pdf.

However, Zotero Standalone is very slow, whereas EndNote Desktop was always very fast, regardless of the number of entries and pdfs.

Here is the current situation:
(1) I have a Sony Vaio 500GB HD, 4GB RAM, Windows 7 Pro 64bit.
(2) In latest version of Zotero (3.0, with purchase of additional maximum storage): As the result of a couple of freezes during the import from Endnote, some items were imported as many as four times. I deleted the duplicates with no problems, but for individual items, some have four Zotero notes "The following values have no corresponding Zotero field" and four PDFs, Which I am about halfway through deleting. Many tags were also imported from EndNote keywords, and I think multiplied because I did not know to turn off the auto-tagging feature. I have deleted most of the tags that I did not create myself.
(3) Auto-sync, indexing, and tags are turned off, trash is deleted (and any time I delete items I also empty the trash)
(4) Searches are painfully slow and often freeze in the middle of typing a word. I have to wait for several minutes between letters in the search while Zotero says it is "not responding". Eventually it does kick back in and produce the results.
(5) Right clicking on an item produces the not responding response for a few minutes, then I am able to select and right click on several items and delete them.
(6) Deleting takes awhile and then I can interact with Zotero again, however, #5 repeats and I have to wait for a few minutes before I can do any cleaning again.
(7) Scrolling down is very slow
(8) Selecting a few citations and dragging to a collection or sub-collection folder is very slow, and selecting more than 10 results in only a few citations being transferred.
(9) Creating a new record is very, very slow. Zotero goes into "not responding" mode for a few minutes, then brings up the entry box. Tabbing or clicking on each new field results in hanging for 20-30 seconds in "not responding" mode. Here is an expert from error reports REPORT ID 2134945961 produced after this behavior:

[JavaScript Error: "[Exception... "'JavaScript component does not have a method named: "getCellValue"' when calling method: [nsITreeView::getCellValue]" nsresult: "0x80570030 (NS_ERROR_XPC_JSOBJECT_HAS_NO_FUNCTION_NAMED)" location: "native frame :: <unknown filename> :: <TOP_LEVEL> :: line 0" data: no]"]

(10) When I click between one field and another, onceI received this error message: "Warning: Unresponsive script"
"A script on this page may be busy, or it may have stopped responding. You can stop the script now, or you can continue to see if the script will complete. Script: jar:file:///C:/Program%20Files%20(x86)/Zotero%20Standalone/chrome/zotero.jar!/content/zotero/tinymce/tiny_mce.js:1494"

Stopping the script and continuing does not change the behavior.

(11) Normally, when I click between one child note and another, it simply takes a few minutes to become responsive again. Here is the debug ID for one of these behaviors:
The Debug ID is D1413170671.

(12) When I try to add a new entry I get the following Debug ID: D219431329.

(13) Periodically, Zotero truly freezes and I have to use Task Manager to close the program, which produces the following error message box: "XULRunner Has Stopped Working"
  • Dan will have to say more on the debug and error, but it would be useful to know how many items including attachments you have in Zotero

    For 2) Did you delete duplicate items or merge them? With merge the multiple notes/attachments are expected behavior, but not when deleting items.
    I don't have a good idea for quickly deleting the attached PDFs, but for the notes, you can search for "The following values have no corresponding Zotero field:" in the quick search bar, set to "all fields and tags" - you'll both the parten items and the notes in the search results, but the parent items will be greyed out. If you select all in the middle panel (ctrl+a) you'll be able to delete all those notes (of yours if you want to keep one per item that's going to be harder).
  • RE (2) see Tip under importing into Zotero
  • oh of course - I completely blanked there. Unless you've deleted that tag already, of course, in which case you'll have to use my clunkier version.
  • The total number of items is now 26098 (~10,000 records, with the rest as notes and pdfs. My original EndNote file had about 4,000 pdfs, and I believe I have deleted all duplicate pdfs within citations, so that should be about the same in Zotero).

    When I imported, I deleted duplicates in cases when they were identical and merged them when Zotero imported and recognized citations from pdfs that had not been recognized in Endnote.

    I did want to keep at least one of the note items per file, because in some cases they are from the "Research Notes" field in EndNote and some other custom fields. I have to look at each imported note individually to delete them.
  • After closing and opening Zotero again and after some syncing, the item list is now 11023.
  • That's 11,023 including child items, or just top-level?

    What column are you sorting by in the middle pane?

    Did you clear your full-text index in the Search pane of the preferences or just disable indexing?

    Also, there's a tremendous amount of debug output in each of those Debug IDs that you provided—which, if it really is for just the actions you said, would certainly be related to the problem, but it looks like there might be other things going on. For starters, can you temporarily disable auto-sync in the Sync pane of the Zotero preferences and provide two new Debug IDs for those two actions, restarting Zotero immediately before you reproduce each one?
  • Another report ID: 2058882211

    Same "not responding" behavior after reduced item list and restart, saving a search and trying to delete notes by right-clicking.
  • Also, are you doing these things within a saved search or within the library root? As a baseline, I'd want to know within the library root.
  • 1. 11,023 including child items - sorting by author
    2. I cleared the index (and have done so periodically) and set Maximum pages to index per file to 0, and all index numbers are "0" and Unindexed: 5698
    3. The debug reports I sent were in the library root AND all but the last were done with syncing off. I have since reproduced the behavior on a saved search "Zotero field" in Notes.

    NEW DEBUGS IDS after turning off sync again, with indexing cleared and disabled, clearing output between each action:

    ACTION 1: Creating a new record (book). "Not responding" for 20-30 secs. Debug ID: D977364714.

    ACTION 2: Adding something to a record. Added the word "test" to an abstract. "Not responding for 20-30 secs" Debug ID: D467023703.

    ACTION 3: Went to saved search "Zotero field", right click on a note I want to delete, select "delete selected item", Zotero hangs with "not responding for almost a minute. Debug ID: D432321307.

    ACTION 4: Selected 4 notes, right click and select delete for all of them. Debug ID: D1498535643 (produces a lot of lines of code!)

    ACTION 5: Right click on a "full text (pdf)" file and select "rename from parent metadata" GET Dialogue box:

    A script on this page may be busy, or it may have stopped responding. You can stop the script now, or you can continue to see if the script will complete.

    Script: jar:file:///C:/Program%20Files%20(x86)/Zotero%20Standalone/chrome/zotero.jar!/content/zotero/tinymce/tiny_mce.js:3716

    DEBUG ID: D682784913

    I hope this helps us get to the bottom of the problem!
  • Yeah, there appears to be something extremely wrong in those logs.

    You might have done this already, but can you check your database integrity in the Advanced pane of the Zotero preferences? Even if that passes, it might be worth running your database (if it's under 100MB) through the DB Repair Tool to see if that improves matters.

    If you've only tried this in Zotero Standalone, it might also worth be trying in Zotero for Firefox, which by default should share your existing data directory. (You just need to close Zotero Standalone before running it.) That should work identically, but if there's some sort of issue related to your settings in Zotero Standalone, trying in Firefox, which won't start with the same settings, may be instructive.

    If none of that helps, we can try some other things.
  • The database integrity check within Standalone produces no errors. I uploaded, repaired, and replaced file using the repair tool (Upload ID 513dafca7371e).

    I opened Zotero, and the problems outlined above still occur (just moving from selecting one note to another, not responding on right-click of a note and after deletion, hanging when selecting notes, etc.). Strangely, the error report option is grayed out after this behavior, which is unusual.

    A Debug ID for the hanging behavior is here: The Debug ID is D1128852055.

    I am not sure what you mean by checking database integrity within Firefox. When I open my library, I don't see any settings optioins where that can be done.
  • Do you have the Zotero for Firefox plugin installed? If so, you can open Zotero by clicking on the "Zotero" icon on the bottom right of the screen (you'll need to have closed Zotero Standalone).
  • Here's another Standalone Debug ID: D1233673220.

    I usually use Chrome for a number of reasons so I just installed the Firefox add-in, and the database integrity check says there are no errors there either.

    When I clicked on a saved search, the Firefox version also froze up.
  • I am getting the same behavior in Firefox. When I clicked on one of the notes I wanted to delete, the following error message came up:

    "A script on this page may be busy, or it may have stopped responding. You can stop the script now, or you can continue to see if the script will complete.

    Script: chrome://zotero/content/xpcom/itemTreeView.js:1729"

    Strange that it is saying Chrome when I'm using the Firefox version.
  • Here is the report ID after deleting a couple of notes: 1993037425
  • (chrome is a protocoll used by Firefox. The name similarity to the browser is a coincidence).
  • That last ID was for Zotero Firefox, and here is a Debug ID after doing the same thing (selecting, right clicking, and deleting a couple of notes):

    The Debug ID is D1256917695.
  • OK, I've looked into this a bit more. A bunch of things:

    1) The library you uploaded to the DB Repair Tool still had 26.8K total items, not 11K.

    2) Currently, at least, many things you do within a saved search that matches thousands of child items will be very slow. I'm looking into this.

    3) The same goes for things you do within the library root if you have a search in the quick search bar that matches many child items. You appear to have been doing that with at least one of the new-item actions above.

    4) There seems to be an issue in which, if you perform a search in the library root that matches many child items and then clear the search, that view remains slow. Regardless of the slowdown with the search, it certainly shouldn't have an effect after it's cleared, so I'm going to look into why that's happening.

    5) If you start Zotero with the library root selected and just create a new item, I would expect that to be close to instantaneous. (That's why it's important for debug outputs to be immediately preceded by Zotero restarts, but it sounds like you were just clearing the debug output between each run, which would allow previously triggered problems to affect the results.)

    6) If Zotero is running slowly within the library root due to a previous search, I believe that switching to a collection and switching back would cause it to return to its initial speed.

    I'm going to look into the performance problems you're seeing in the searches and am going to try to speed things up for 3.1, which will be out later this month. For now, though, you should know that those are what are causing your issues. When you don't need to search child items, you can also change the quick search mode to "Title, Creator, Year" to avoid matching child items.

    Does this all square with what you're seeing?
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