Repeated crashes on index

cantabrian · December 29, 2009, 5:59am

For weeks, I have been trying to either import or index folders containing mostly word documents and pdfs. Because the import crashed so often, I gave up and started just indexing, and that has worked about half of the time.

The only unusual thing about the files is that many of them are large word documents, for they contain embedded audio files created through the notebook view. It doesn’t seem that DTPO can read these very well, and so perhaps they are the problem. I assume that the files are creating a problem mostly because the index takes so long. Just 200 files or so can take as much as an hour.

But the index rarely completes, as DTPO continually crashes mid-index. It’s happened about 12 times today. At least two of the crashes messed up the database enough that I had to rebuild it. The most recent crash report is below.

I’d be grateful for any help.

Process: DEVONthink Pro [2184]
Path: /Applications/DEVONthink Pro.app/Contents/MacOS/DEVONthink Pro
Identifier: com.devon-technologies.thinkpro2
Version: 2.0 (2.0pb8)
Code Type: X86 (Native)
Parent Process: launchd [112]

Date/Time: 2009-12-29 00:47:33.642 -0500
OS Version: Mac OS X 10.6.2 (10C540)
Report Version: 6

Interval Since Last Report: 120028 sec
Crashes Since Last Report: 8
Per-App Interval Since Last Report: 419365 sec
Per-App Crashes Since Last Report: 8
Anonymous UUID: C5DFBEAA-35BA-4265-A9C9-E5A785CEB1D5

Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Application Specific Information:
Assertion failed: (pool->head!=NULL), function InitDendriformPoolWithCapacity, file /Users/criss/Documents/Projekte/Devon/…/DevonKernel/Dendriform-Internal.h, line 28.

Thread 0 Crashed: Dispatch queue: com.apple.main-thread
0 libSystem.B.dylib 0x993f8732 __kill + 10
1 libSystem.B.dylib 0x993f8724 kill$UNIX2003 + 32
2 libSystem.B.dylib 0x9948b98d raise + 26
3 libSystem.B.dylib 0x994a1a44 abort + 93
4 libSystem.B.dylib 0x9948e5ec __pthread_markcancel + 0
5 com.devon-technologies.kernel 0x0056a316 InitDendriformPoolWithCapacity + 198
6 com.devon-technologies.kernel 0x0056a355 -[NRN initNeuronInNeuralNet:atomic:setID:dendriformCapacities:::] + 53
7 com.devon-technologies.kernel 0x0058a3bf -[TNRN initNeuronInNeuralNet:atomic:setID:dendriformCapacities:::] + 95
8 com.devon-technologies.kernel 0x0056f79f -[NRN initContainerInNeuralNet:dendriformCapacities:::] + 79
9 com.devon-technologies.kernel 0x0053d9ed cCwNaC + 5981
10 com.devon-technologies.kernel 0x00545d99 -[NNT createContextWithNeuronsAndCount::count:mode:signalOperator:extraBytes:] + 121
11 com.devon-technologies.kernel 0x004e038f aC2N + 991
12 …evon-technologies.thinkpro2 0x001218ec 0x1000 + 1181932
13 …evon-technologies.thinkpro2 0x0011c9d9 0x1000 + 1161689
14 …evon-technologies.thinkpro2 0x000dd6eb 0x1000 + 902891
15 …evon-technologies.thinkpro2 0x000dbe1d 0x1000 + 896541
16 …evon-technologies.thinkpro2 0x000dbc3f 0x1000 + 896063
17 …evon-technologies.thinkpro2 0x000dbc3f 0x1000 + 896063
18 …evon-technologies.thinkpro2 0x000dafad 0x1000 + 892845
19 …evon-technologies.thinkpro2 0x000d746e 0x1000 + 877678
20 …evon-technologies.thinkpro2 0x0012f138 0x1000 + 1237304
21 com.apple.Foundation 0x9790aad9 __NSFireDelayedPerform + 537
22 com.apple.CoreFoundation 0x98d60edb __CFRunLoopRun + 8059
23 com.apple.CoreFoundation 0x98d5e864 CFRunLoopRunSpecific + 452
24 com.apple.CoreFoundation 0x98d5e691 CFRunLoopRunInMode + 97
25 com.apple.HIToolbox 0x95910f0c RunCurrentEventLoopInMode + 392
26 com.apple.HIToolbox 0x95910cc3 ReceiveNextEventCommon + 354
27 com.apple.HIToolbox 0x95910b48 BlockUntilNextEventMatchingListInMode + 81
28 com.apple.AppKit 0x90857ac5 _DPSNextEvent + 847
29 com.apple.AppKit 0x90857306 -[NSApplication nextEventMatchingMask:untilDate:inMode:dequeue:] + 156
30 com.apple.AppKit 0x9081949f -[NSApplication run] + 821
31 com.apple.AppKit 0x90811535 NSApplicationMain + 574
32 …evon-technologies.thinkpro2 0x000029d6 0x1000 + 6614

Thread 1: Dispatch queue: com.apple.libdispatch-manager
0 libSystem.B.dylib 0x993be0ea kevent + 10
1 libSystem.B.dylib 0x993be804 _dispatch_mgr_invoke + 215
2 libSystem.B.dylib 0x993bdcc3 _dispatch_queue_invoke + 163
3 libSystem.B.dylib 0x993bda68 _dispatch_worker_thread2 + 234
4 libSystem.B.dylib 0x993bd4f1 _pthread_wqthread + 390
5 libSystem.B.dylib 0x993bd336 start_wqthread + 30

Thread 2:
0 libSystem.B.dylib 0x993bd182 __workq_kernreturn + 10
1 libSystem.B.dylib 0x993bd718 _pthread_wqthread + 941
2 libSystem.B.dylib 0x993bd336 start_wqthread + 30

Thread 0 crashed with X86 Thread State (32-bit):
eax: 0x00000000 ebx: 0x994a19f3 ecx: 0xbfffd7fc edx: 0x993f8732
edi: 0x0000001c esi: 0x005d9fd0 ebp: 0xbfffd818 esp: 0xbfffd7fc
ss: 0x0000001f efl: 0x00000286 eip: 0x993f8732 cs: 0x00000007
ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037
cr2: 0x305c3000

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0x992e9000 - 0x99396fe7 libobjc.A.dylib ??? (???) /usr/lib/libobjc.A.dylib
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0x99587000 - 0x995b8ff3 libTrueTypeScaler.dylib ??? (???) <6C8916A2-8F85-98E0-AAD5-0020C39C0FC9> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libTrueTypeScaler.dylib
0xba900000 - 0xba916ff7 libJapaneseConverter.dylib ??? (???) <4FB5CEEB-8D3E-8C57-1718-81D7CAFBFE69> /System/Library/CoreServices/Encodings/libJapaneseConverter.dylib
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Model: MacBookPro3,1, BootROM MBP31.0070.B07, 2 processors, Intel Core 2 Duo, 2.2 GHz, 4 GB, SMC 1.16f11
Graphics: NVIDIA GeForce 8600M GT, GeForce 8600M GT, PCIe, 128 MB
Memory Module: global_name
AirPort: spairport_wireless_card_type_airport_extreme (0x168C, 0x87), Atheros 5416: 2.0.19.8
Bluetooth: Version 2.2.4f3, 2 service, 0 devices, 1 incoming serial ports
Network Service: AirPort, AirPort, en1
PCI Card: pci168c,24, sppci_othernetwork, PCI Slot 5
Serial ATA Device: FUJITSU MHW2120BH, 111.79 GB
Parallel ATA Device: HL-DT-ST DVDRW GSA-S10N, 7.76 GB
USB Device: Built-in iSight, 0x05ac (Apple Inc.), 0x8502, 0xfd400000
USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.), 0x8205, 0x1a100000
USB Device: IR Receiver, 0x05ac (Apple Inc.), 0x8242, 0x5d100000
USB Device: Apple Internal Keyboard / Trackpad, 0x05ac (Apple Inc.), 0x021a, 0x5d200000

korm · December 29, 2009, 11:41am

I have had similar problems, though not as severe, with Word documents that contain embedded media files. In my case the media files were embedded GIFS. As far as I know, DT is calling an in-built OS X engine to process these files and that engine chokes on Word documents of this sort. In response to the problem I had with very long synchronize times for indexed folders, I heard from DTech that:

If you can identify and exclude the problematic files from your import and/or index, you should find relief. If the OS X engine that DT is using is actually “choking”, as DTech implies, I assume not much will happen to fix it other than users such as us submitting bug or feature requests to Apple or (worse) Microsoft. (GLWT )

Sandy_Santra · December 29, 2009, 11:42pm

I clean installed Snow Leopard on my machine a week ago and have been adding my apps back in. I’m very disappointed with Yep 2 and downloaded DEVONThink Pro Office today to try it out. There have been so many great reviews of it! And especially now that Tagging has been added, and I can import PDFs from Yep2 and have the OpenMeta tags carry across.

But I’m having the same problems as the OP: crashing on an Index import. This is happening with a folder that contains only 2 PDFs, sizes 102K, 328K respectively. We are not talking huge documents at all here.

Each time I have to completely delete my database. Now the corruption is so bad, DT wants me to delete the inbox database. I have no idea where that is.

It’s very disconcerting to be trying this famous, amazing program to have it crash 3x within the first 20 minutes of use. I can’t even open it anymore; I get the error message “Database ‘Inbox.dtBase2’ seems to be already in use!” No idea how to fix that. How do you force quit something that’s not even running?

Sandy_Santra · December 29, 2009, 11:58pm

I now see that there are dozens of threads on the issue of Inbox.dtBase2 causing problems.

How does anyone even use DT when it’s crashing every 10 minutes?

DT Pro Office is coming up on version 2 (final) and costs US$150, so why would I even consider buying it if I can’t even use it?

Granted, it’s beautiful and feature-rich, but it’s so unstable that it won’t even stay up and running for 10 minutes? My God, I have Microsoft apps running on my Mac (natively, without Parallels or anything) that are more stable than that.

I am really starting to wonder about this company. (Especially since I’me forced to log in TWICE to post in these forums. Are the devs doing the web coding, too?)

Sandy_Santra · December 30, 2009, 12:12am

OK, this time I tried Import instead of Index. Worked beautifully. The addition of tagging is great.

But I thought Import MOVED the files and folders off your hard drive and into the DT database. This did not happen. ???

korm · December 30, 2009, 2:41am

Import copies documents. Index creates aliases to documents. In both cases DT respects your original data and does not move it. Many people import then go back and delete the source.

Depends on your data archival needs, workflow, etc.

Sandy_Santra · December 30, 2009, 6:04pm

Is all the data stored in [filename].dtBase2? That’s going to be one huge file if I import my 8000 PDFs.

Bill_DeVille · December 30, 2009, 6:34pm

Yes, that’s correct. Import means that your 8000 PDFs will be copied into the database and stored as PDF files inside the database package file.

A package file looks like a file, but is actually a special kind of folder. It can be opened by selecting it, Control-clicking and choosing ‘Show Package Contents’. NOTE: Please don’t monkey around inside the package file, as the database doesn’t have any way of knowing what you have done and problems will result. If you wish to delete a file, for example, always do that within the application, not directly by trashing it from the package file.

DEVONthink allows one to capture external files either by Import or Index. Personally, I prefer the Import capture mode, as my database is then completely self-contained and I can move it freely among my computers, without the need to copy other files as well, as would be required for a database containing Indexed material.

As korm noted, once I’ve captured files from the Finder into a database, I no longer care about the original external files and will delete them or archive them somewhere else. Another advantage of a self-contained database is that I’m free to organize it in any way I wish, without the constraints imposed by the organization of the external folders and files in an Indexed database.

Whether your PDFs are Indexed and left externally in the Finder, or Imported (and the external files then deleted after capture), the PDF files themselves use the same amount of storage space.

At any time you wish, you can select all the contents of your database and choose File > Export > Files & Folders. The result will be that the Finder now holds a copy of all the documents in the database, with the folder/file structure corresponding to your organization of groups and documents in the database.

Of course, I always recommend backups of databases. I use Time Machine, and also use File > Export > Database Archive. The Database Archive file is the smallest possible compressed and dated complete copy of the database. I’ll store it on an external medium, including a copy made to a portable FireWire drive that I store offsite. Backups are good insurance against a hard drive crash, theft of one’s computer equipment or a fire or flood.