Extraodrinary slow OSX clients

cvnZoterro

I am having severe usability issues with both Zotero standalone and Firefox apps on OSX but not on an up-to-date Linux client running a synced copy of the same database (without the PDFs, however).

It is my hope someone can provide some insight on how to resolve this issue.

I use both OSX client versions on a mid-2010 MacBook Pro running version 10.10.3 of Yosemite. Mostly, I use the standalone. The machine has 8Gb of memory and an upgraded hard drive but not a solid state drive. For comparison, the Linux version runs on a less powerful server system with an up-to-date installation of Ubuntu Trusty. I usually display the Zotero interface on the Macbook via ssh -X and XQuartz 2.7.7. Firefox is up-to-date on both systems. The libraries are stored in a folder just below the user home directory. On the OSX machine, I have symbolically linked the document store directory to a folder backed up by Dropbox. I imagine that as the PDF store is infrequently written to, this should not be a problem. The actual Zotero databases are not associated with Dropbox folders.

The issue is that both Zotero client versions on OSX stall excessively, rendering Zotero almost unusable. Switching between saved searches or category folders is very often painfully slow, whereas on the Linux version with the synchronized database it is almost instantaneous. Delays can range up to one minute or more. When composing notes, the embedded HTML editor frequently freezes after a word or two, permitting a further few words after a pause up to 30 seconds or more, followed by another lockup. Often, Firefox complains that the editor script is stalled. Every once and a while, Zotero inexplicably seems to speed back up only to fall back into the doldrums again.

The database is relatively large with 22784 total items. I switched back to Zotero from Papers2 about five months ago using bibtex as a go between. This resulted in a number of duplicate entries, but this should be irrelevant. Displaying the complete library (MyLibrary) in the Linux client takes about 10–15 seconds. I might as well make a pot of coffee when I try this with the OSX client(s).

adamsmith

we'll want a Debug ID for one action that takes unduly long (e.g. switching collections):
https://www.zotero.org/support/debug_output
post the ID here, let us know exactly what action it's covering.

cvnZoterro

Hi,

Thanks for your quick response. I've posted the debug output from a single action as requested, switching from the global library view to a saved search with 27 items. The debug ID is D1597652014.

Cheers,

Chris

dstillman

Switching to a saved search actually isn't a great example — that saved search in particular is doing a non-left-bound (i.e., 'contains') phrase search across all your items, which for a library the size of yours could easily be slow (though 50 seconds (which is the search part of that in your debug output) seems excessive).

Can you provide a Debug ID for another action?

dstillman

But just to clarify here, you're saying that the local OS X versions run much slower than a remote X11 version, with the same database, for the same actions?

cvnZoterro

Yes, the OSX version is running slower. I'll see if I can reproduce the error when the note pane slows to a crawl. Will that do?

jonschatz

I've also been having extremely poor performance, using a similar system: mid-2011 MacBook Pro, 8 gigs. Using as Firefox plugin only. I'm constantly staring at the spinning beachball when using Zotero, which locks up all of Firefox, even interrupts music streaming through Pandora, etc. I turned off syncing, which maybe helped a little, but this is approaching the point of being unusable.

dstillman

jonschatz: We can't tell you anything without Debug IDs for specific actions that are slow.

cvnZoterro

Update: In my quest to post a few good examples of slow behavior on the part of Zotero I have found the program to have become more responsive than in the past despite having added more entries to the database. Is it possible that the underlying database optimized indices? This still would not explain the occasional extremely slow performance of the note taking subsystem. During these episodes adding a few letters, let alone words, could take a minute. I'll continue to try to post a Debug ID that demonstrates such behavior.

cvnZoterro

One possible source of the trouble may be the number of active on-line documents (GoogleDocs) open in Firefox. Perhaps this is simply a resource issue. That said, no other application open slows down to the extent of Zotero under the load resulting in the marked slowing of Zotero's responsiveness.

The following Debug ID documents a long search time switching between collections: D1764438031.

dstillman

Temporarily disable all the extensions you've installed into Standalone, to start.

dstillman

And your use of Firefox shouldn't have any effect on the performance of Zotero Standalone.

cvnZoterro

OK and will do.

cjpoor

Thanks, Dan. I had this problem and needed to set Zotero Auto Export to "Batch mode - Export only manually".
Update - Sorry - it does nothing with that setting (but does not slow down zotero). I just have to do a normal manual export of my collection.

adamsmith

@cjpoor -- https://zotplus.github.io/better-bibtex/ offers smoother, automated export.

cjpoor

Thanks Adam. I tried zotplus Better Bib(La)Tex - for the last few hours. I tried removing it and reinstalling it, disabling all other plugins, all the different settings (that I could access and understand) - Also tried to see if any different zutilo and/or zotfile settings would make a difference. Eventually, with zotfile (I think) Better Bibtex format exported my collection with a good and updated .bib file but no pdf files (actually - the export deleted the previously exported files folder).
Reverting to plain BibTex export format restored an updated files folder and .bib file in my export folder.
I am on the latest Mac OS X, Firefox and plugins all updated.
I think I will probably save time by doing all exports manually in BibTex format. :-\

cvnZoterro

Dan,

I've submitted a debug report (# D387852889) with all of the extensions disabled as requested. Over the last week, Zotero has been running tolerably quickly, although not nearly as quickly as the Linux and Windows clients on the same synced database. After some cleanups of duplicate entries, the OSX client slowed to a snails crawl and has stayed there.

The debug report documents a search for an author across the entire database. The search term was "Otto." Although Zotero searched correctly for the term, the interface is blocked after the initial O and does not display the remaining "tto" until the search completes. Top reports zotero-bin stuck for the long duration of the search, while Activity Monitor reported that 90% of the CPU was unused and disk activity was at 50% for most of the search. Memory swapping did not occur during the test. I hope this helps isolate the problem with the OSX client.

Cheers,

Chris

adamsmith

Dan will have a look, but generally speaking, full text searches in quick search mode can do that. For large-ish databases, either switch to "Title, Creator, Year" mode for quicksearch, or begin your search with a straight quote (") which will disable real-time search and have Zotero wait until you've hit enter to search.

cvnZoterro

Hi Adam,

Thanks for the tip. I will try that. Other symptoms include stalling when entering text in notes, for instance.

Cheers,

Chris

adamsmith

The stalling in notes is, I think, the most interesting bit. If you can find a way to capture that in a debug, that might be helpful. I'm not aware of anything that should cause that, nor any other reports.

cvnZoterro

Will do …

emilianoeheyns

(the problem @cjpoor reported has been fixed in the interim -- PDF exports with BBT work again)