Saving abstract change takes 60 seconds...

jonscomo

Hello,

I just changed the abstract on an article and saved, and it took roughly 60 seconds before the browser unfroze. Moving items to a collection in the left pane takes between 20 and 30 seconds, as well. Adding items to collection sometimes also never comes back - browser freezes, and I have to Force Quit. In looking at system stats, firefox is taking up 100% of one of my two CPU cores when this happens.

I am working within search results for a simple search ("news network"). I have the tag search box in the lower left closed. It looks like performance is better once I clear the search box...

Debug output is posted: D324181676

My system is a Mac running OS 10.6.5, Firefox 3.6.13, Zotero 2.0.9.

I have the PDF indexing files in place in my installation.

Any help will be greatly appreciated.

Thanks,

Jonathan

dstillman

How many items do you have in your library?

jonscomo

550 items, many with one or more associated PDFs.

In case it matters, here are my index statistics:
Indexed: 461
Partial: 5
Unindexed: 235
Words: 113429

In Firefox, I have the following extensions installed:
Firebug (all panels disabled)
Drupal for Firebug
Firefox PDF Plugin for Mac OS X
Firefox Sync
Fox to Phone
Gmail Watcher
Google Gears
JSView
MeasureIt
Personas
Tab Mix Plus
Web Developer
...And the Zotero and Zotero python plugins.

Hope this helps.

Jon

dstillman

Have you emptied your trash?

jonscomo

Yes, trash is empty.

dstillman

Is that your total items (i.e., with children expanded, as the page explains)?

dstillman

If you don't mind, upload your DB to the DB Repair Tool and send the Upload ID to support@zot....org. (Don't post the Upload ID here.) There's a particular (repeated) query that's taking way too long on your database.

jonscomo

OK. I did not have that expanded to include all items. I have 2720 total, so that might be more the size where you have problems.

I'll upload my database now.

Thanks,

Jon

dstillman

Something is very strange in your output. Is this a stock version of 2.0.9?

Disable all your other extensions and try again.

jonscomo

I made modifications to RIS.js so EndNote would import better. Other than that I haven't changed anything.

I'll post the debug ID in a second here.

Jon

jonscomo

Another one with extensions enabled: D730759293

After disabling all extensions other than the 3 zotero plugins and python:
- debug for saving abstract with all extensions disabled: D169008311
- I also got error messages: 1223103840

dstillman

Is that not much faster? It looks it. The 120 or so half-second queries are all gone.

jonscomo

Another one with all extensions disabled, in case I screwed something up (I couldn't remember if I actually changed the abstract or not): D1410059254

jonscomo

Yes, it is much faster.

dstillman

OK, so something is interfering with Zotero. Find out what it is.

jonscomo

So do you think it is an add-on? Should I try enabling them one-by-one?

dstillman

Well it's clearly one of your extensions, since it went away when you disabled them. So yes, enable them one by one.

jonscomo

Well, I went through one-by-one, using a window that was not full screen zotero, and it was fine even after all were enabled.

Then I moved the browser window to my 2nd monitor, made the browser window full-screen, then clicked the little full-screen button in the upper right of zotero, and now it is slow again - adding to a collection and changing an abstract just both froze the browser (I'm doing this in chrome, so I can type while Firefox is busted).

So, I will remove all extensions again and try in full-screen.

Jon

jonscomo

And now it is doing it with no add-ons enabled except for:
PythonExt 2.6.2.20100203
Zotero 2.0.9
Zotero MacWord Integration 3.0b7
Zotero OpenOffice Integration 3.0b2

dstillman

You'll have to figure out what's changing. I can't reproduce it.

jonscomo

Happening with all plugins disabled, too, and the MacWord and OpenOffice add-ons disabled as well. Not sure what to do now. Thanks for trying to help.

Jon

jonscomo

OK. At this point, It is happening regardless of add-on or plugin, and starting right when browser starts up. Might it help to try re-installing the plugins, or installing them in a new profile?

Thanks again for your help.

DWL-SDCA

I began having a similar problem a couple of days ago. I turned off Google Toolbar and everything went back to speedy activity. I also had a problem after a recent Skype update. I can't have Skype as a start-up program and have Zotero respond properly. The Skype issue also affected connections with publisher and other literature databases. Apple Care helped me identify and fix the Skype issue. The most recent versions of Google Toolbar are known to have problems on some Mac OS 10.6 systems leading to serious slowdowns for form filling and similar activities.

dstillman

Try deleting localstore.rdf in your Firefox profile directory and restarting Firefox—it stores window settings and will be recreated automatically.

If that doesn't help, yes, try a new profile. For testing, you can point Zotero in the new profile to your existing data directory from the Advanced pane of the Zotero prefs.

dstillman

You might also try disabling auto-sync in the old profile.

Exact steps to reproduce might also help, including exactly what's selected and what you're clicking on from startup.

jonscomo

Interesting. DWL-SDCA's comment got me thinking. Google.com is my home page, and it was set to always keep me logged in. I just signed out of google, and that did, at least for the moment, bring everything up to speed. This actually could be what was going on last night. While I was disabling and re-enabling add-ons, I had set it to not load any page on start up, and so google wasn't even loading in my browser, so it wouldn't be able to start any background javascript activity. In disabling all add-ons, I think I also stopped loading the google.com page as home page.

Is there a way similar to unix ps to look inside firefox to see what scripts are running, what is loaded into memory inside the browser?

I just logged back into google, and the problem started up again, but logging out didn't fix it this time. I also started top, and I briefly saw a "stuck" process that bubbled up and then disappeared when firefox froze. I'm going to sort the top output so status "stuck" stays on top, see if that tells me anything.

It looks like it doesn't matter which items I use. Once the problem starts, it happens regardless of item. I will start recording exact steps, too, to see if it is reproduce-able.

If stuck doesn't tell me anything, then I'll:
- try closing browser and re-opening, not logging in to google at all, and then work, to see if the problem comes back (it seems to start within a minute or two of loading browser, regardless of configuration).
- If it starts again, then I'll delete localstore.rdf, then try making a new profile. With new profile, if I place my old zotero folder in there, will it just accept that library, or do I need to do something more involved?

More in a bit.

ajlyon

The JavaScript debugger (https://addons.mozilla.org/en-US/firefox/addon/216/) gives you some idea of what's going on in the JavaScript engine.

dstillman

I wouldn't recommend trying to use the debugger for this. It's very clear from the debug output what's happening—just not why. We need exact steps to reproduce, as with any bug.

With new profile, if I place my old zotero folder in there, will it just accept that library

Yes, but I said you can just point it at your existing one from the Advanced pane of the preferences.

ajlyon

My pointing out the debugger was really just in answer to Jonathan's question as to whether such a tool exists. I have never used it in understanding Zotero problems, but it might be useful to him more generally.

jonscomo

Right.

Specific steps to reproduce problem:
- Start Firefox (home page is google.com, with my user auto-signed in - logging out and not auto-signing in didn't seem to matter on subsequent reload, nor did a different home page).
- Open Zotero pane.
- Click on the search box at the top right of the middle pane.
- Enter a search (I use the search "news network". In my library, this returns 209 total items including notes, PDF files, etc. Specific search text doesn't seem to matter - "Social network" brings back 190 items and behaves the same, for instance).

At this point, there are a number of ways to cause freeze. A few specific examples:

1) update abstract.
- Click on the main line in the search results for a given reference. This brings up its info in the right pane.
- In the right pane, click the Abstract field. If zotero not maximized within browser window, this bounces the pane to the bottom, then you have to scroll back up to the field.
- Enter text at the end of the abstract field. I enter "trest" so it is not a word, so I can search on it later in case I forget to change on back.
- Click on the Publication field (or click on another reference in the center pane - either one seems to start the ajax update of the abstract in the database).
- wait.

2) Try to move a reference into a collection.
- Click and hold on reference, drag it to collection, let up on mouse.
- wait.

A few more notes:
- deleting localstore.rdf had no effect.
- turning off auto-update had no effect.
- sometimes when I start browser, I get three messages saying that python components didn't load, but not all the time (For example. I haven't since I've wanted to capture them to post them here).
- Clearing Mac system caches didn't change anything.
- New profile, fresh install of zotero, python, word plugin, pointing at same database doesn't change behavior.
- Within that profile, pointing at a different copy of the zotero directory (made last night as a backup) did change the behavior, but only for about 4 changes (changed the abstract on four different stories). Then the problem started again, though not as bad.
- In my original profile, then, pointing at that separate copy of the zotero directory also fixed the problem initially, but then ongoing changes got progressively slower (though not near as slow as with the old database), and the slowdown accrued across subsequent restarts of the browser. Here, too, it isn't as slow as it was with old profile, but it is slowing down.

Thanks again for the help. I sure hope there isn't a "slow down" button I have clicked or something.

ajlyon

Actually, frequent temporary lock-ups when working from within saved search results are something I've seen pretty often as well. I try not to do anything significant while looking at search results.

As for the slow down button, my understanding is that it's a feature scheduled for Zotero 3.0.