#696 Crash on MacOS: Import multi-molecule PDB file

v_1.1.0
open
nobody
None
1
2013-11-19
2013-11-16
Anonymous
No

I was having frequent crashes on Mac (change view type, especially) with 1.1.0 running on MacOS 10.9/Mavericks, most of which were resolved upon switching to nightly builds.

However on the current/last nightly - 11/15 git rev c1fcc5b - I am getting repeatable crashes when I try to open a multi-molecule PDB file. Avogadro starts opening the file, displays "opening multi-molecule file, this may take a while," and then crashes with:

...
Crashed Thread: 11
Exception Type: EXC_BAD_ACCESS (SIGBUS)
Exception Codes: KERN_PROTECTION_FAILURE at 0x000000010e5f5ff0

VM Regions Near 0x10e5f5ff0:
IOKit 000000010e575000-000000010e5f5000 [ 512K] rw-/rw- SM=SHM
--> STACK GUARD 000000010e5f5000-000000010e5f6000 [ 4K] ---/rwx SM=NUL stack guard for thread 11
Stack 000000010e5f6000-000000010e678000 [ 520K] rw-/rwx SM=COW thread 11
...

I am attaching the full (I think) crash dump to this ticket.

Thanks for the amazing work on this program!

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Discussion

  • I'd really need an example file. Also, the current nightly builds don't give much debugging information (to help out a friend, these have full optimizations turned on). I'd be happy to send a fully-debug build if you're willing to test.

    Thanks!

     
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      Anonymous
      2014-09-01

      I've experienced this kind of crash with the Mac OSX version of Avagadro but when I switched to the Windows version of Avagadro there was no problem.

      There are several examples demonstrating this crash on the following website:
      http://www.ime.unicamp.br/~martinez/packmol/
      For example, look for the following half-way down the page
      Output file: bilayer.pdb
      I've also attempted to attach that bilayer.pdb file to this message. Here's the first part of the crash report:
      Process: Avogadro [59405]
      Path: /Applications/Avogadro.app/Contents/MacOS/Avogadro
      Identifier: net.sourceforge
      Version: ??? (1.1.1)
      Code Type: X86-64 (Native)
      Parent Process: launchd [225]
      Responsible: Avogadro [59405]
      User ID: 1053

      Date/Time: 2014-09-01 12:25:01.523 -0700
      OS Version: Mac OS X 10.9.4 (13E28)
      Report Version: 11
      Anonymous UUID: 2A9AC301-04DD-DADC-68C2-E53C054BE4C3

      Sleep/Wake UUID: 2F111874-DB4F-4E78-84D3-A4A46DDC8887

      Crashed Thread: 14 Avogadro::ReadFileThread

      Exception Type: EXC_BAD_ACCESS (SIGBUS)
      Exception Codes: KERN_PROTECTION_FAILURE at 0x000000010e268fd8

       
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  • Anonymous
    2013-11-19

    Sounds great! I'm happy to test with a verbosely logging nightly build, though at this point I may want to test on a newer nightly once I'm home to make sure the problem persists. Likewise the example/input file I was working with isn't accessible to me right now but will be later this evening; I will update then.

    Jon

     


Anonymous


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