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#191 2GB (after decompression) .lsm stack crashes bxd

Pre-beta
open
nobody
Input / Output (63)
5
2012-09-10
2008-01-24
Dan White
No

svn 1357
OSX 10.5 macbook pro core duo 32 bit 2GB RAM
self build of VTK and ITK

large 1 timepoint z stack (2GB after decompression, 500 MB compressed) .lsm file 8 bit
crashes BXD on opening it.

looks like memory error..

Dan

mainWindow.fileTree.unselectAll()
mainWindow.fileTree.selectChannelsByName(ur'/Users/dan/Desktop/20x05NAZebFishEmb.lsm', ['TV'])
MainWindow.py:488: Setting dataset for visualizer= lib.DataUnit.DataUnit.DataUnit
VISUALIZER SETDATAUNIT
Visualizer.py:1104: Hiding time slider, because only one timepoint
Visualizer.py:1131: Setting zslider value
Visualizer.py:1157: Will set up mode later
Visualizer.py:1042: Setting enabled status of current window to True
PreviewFrame.py:165: Calculating buffer from client size 442,580
PreviewFrame.py:196: Making buffer the size of 442,580
InteractivePanel.py:1045: Requested size = 442, 580, client size = 442, 580
InteractivePanel.py:1063: Setting size of preview to 442 580 virtual size to 442 580
Visualizer.py:1170: Setting dataunit to current mode
PreviewFrame.py:365: Setting dataunit of PreviewFrame to <lib.dataunit.dataunit.dataunit instance="" at="" 0x1d54c4e0="">
PreviewFrame.py:165: Calculating buffer from client size 442,580
PreviewFrame.py:196: Making buffer the size of 442,580
InteractivePanel.py:1045: Requested size = 442, 580, client size = 442, 580
InteractivePanel.py:1063: Setting size of preview to 442 580 virtual size to 442 580
PreviewFrame.py:247: Selected item 0
PreviewFrame.py:443: Using timepoint 0 as preview
PreviewFrame.py:503: Mapping trough ctf
Update extent= (0, 1387, 0, 1039, 0, 0)
optimize.py:83: Using update extent (0, 1387, 0, 1039, 0, 0)
optimize.py:131: Setting update extent to (0, 1387, 0, 1039, 0, 0)
Python(894,0xa05d4f60) malloc: *** mmap(size=1993502720) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
terminate called after throwing an instance of 'std::bad_alloc'
what(): St9bad_alloc
Abort trap</lib.dataunit.dataunit.dataunit>

Discussion

  • Dan White

    Dan White - 2008-01-28

    Logged In: YES
    user_id=1557534
    Originator: YES

    OSX crash reporter says:

    Process: Python [5486]
    Path: /System/Library/Frameworks/Python.framework/Versions/2.5/Resources/Python.app/Contents/MacOS/Python
    Identifier: org.python.pythonapp
    Version: 2.5.0 (2.5.0a0)
    Build Info: python-300000~42
    Code Type: X86 (Native)
    Parent Process: bash [5454]

    Date/Time: 2008-01-28 15:10:19.835 +0100
    OS Version: Mac OS X 10.5.1 (9B18)
    Report Version: 6

    Exception Type: EXC_CRASH (SIGABRT)
    Exception Codes: 0x0000000000000000, 0x0000000000000000
    Crashed Thread: 0

    Thread 0 Crashed:
    0 libSystem.B.dylib 0x939e947a __kill + 10
    1 libSystem.B.dylib 0x93a60782 raise + 26
    2 libSystem.B.dylib 0x93a6fd3f abort + 73
    3 libstdc++.6.dylib 0x90d6e005 0x90d26000 + 294917
    4 libstdc++.6.dylib 0x90d6c10c __gxx_personality_v0 + 1108
    5 libstdc++.6.dylib 0x90d6c14b std::terminate() + 29
    6 libstdc++.6.dylib 0x90d6c261 __cxa_throw + 101
    7 libstdc++.6.dylib 0x90d6c5d8 operator new(unsigned long) + 100
    8 libstdc++.6.dylib 0x90d6c689 operator new + 17

    Thread 1:
    0 libSystem.B.dylib 0x93982ace __semwait_signal + 10
    1 libSystem.B.dylib 0x939acced pthread_cond_wait$UNIX2003 + 73
    2 com.apple.ColorSync 0x94396460 pthreadSemaphoreWait(t_pthreadSemaphore) + 42
    3 com.apple.ColorSync 0x943a8d92 CMMConvTask(void    ) + 54
    4 libSystem.B.dylib 0x939ac075 _pthread_start + 321
    5 libSystem.B.dylib 0x939abf32 thread_start + 34

    Thread 0 crashed with X86 Thread State (32-bit):
    eax: 0x00000000 ebx: 0x93a6fcff ecx: 0xbfffbd8c edx: 0x939e947a
    edi: 0xa05a0578 esi: 0x90d83128 ebp: 0xbfffbda8 esp: 0xbfffbd8c
    ss: 0x0000001f efl: 0x00000286 eip: 0x939e947a cs: 0x00000007
    ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037
    cr2: 0xffe2accc

    Binary Images:
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    0xffff0000 - 0xffff1780 libSystem.B.dylib ??? (???) /usr/lib/libSystem.B.dylib</fb5f572243dbc370a0ea5efc8e81ae11></c508c60fafca17824c0017b2e4369802></e064f94d969ce25cb7de3cfb980c3249></aa08b52d2a84b44dc6ee5d544a53fe8a></f8d0f6d0bb5ac092f48f42ca684bdb54></bdc6d70bf4ed3dace321b4ff76a353b3></acee7fc534674498dcac211318aa23e8></d25c63378a5029648ffd4b4669be31bf></cbeb17ab39f28351fe2ab5b82bf465bc></f53c808e87d1184c0f9df63aef53ce0b></fe87a9dede38db00e6c8949942c6bd4f></c35172175abbe554ddadd9b6401351fa></cc6bd78eabf1e2e7166914e9f12f5850></e2f71720ae1dad06a8883ac80775b21a></ad0aa0252e3323d182e17f50defe56fc></df82fc093e498a9eb5490761cb292218></a26683d121ee0f96df9a9d0bfca36049></afcea652ff2ec36885b2c81c57d06d4c></d468bc4a8a69343f1748c293db1b57fb></d4234e6f5e5f530bdafb969157f1f17b></e8bc0af671427cf2b6279a035805a086></bf3fa8927b4b8baae92381a976fd2079></ea0665f57cd267609466ed8b2b20e893></b8e553df643f2aec68fa968b3b459b2b></d3180f9edbd9a5e6f283d6156aa3c602></a4e63784275e25e62f57e75e0af0b94d></b6abcac36ec7654ff3e1cfa786b0117b></deb61cbeb3f734a1b2f4669f6268b9de></d74aa73e4cfd30a08fb169198a8d2539></b507b08e484cb89033e9cf23062d77de></a3b573eb950ca583290f7b2b4c486d09></fdb5c0e5fc8d4699b80a62f8116d3da5></fdd51d8c44078244791b73f51e525048></ebbc01c4f74991892c0eea9fd04ee229></bbe640520443fe246d6688c01990dc15></b3f33c9500be9506bc47fe0548e69ed9></e6346b7641557786a1745c3ff00c737d></fcb1e4bbf6d3f87e2e52e045b2acea3a></ca738aca3936a9c6e1d729662354d2a6></b42064a20bcfa11c62d074349b45668f></dae0eb454235c0cbf2913b258c7e8a3e></eff8a63a23a7d07af62b36fdb329e393></cfd5a59e5c9ce50c5a7a8888acfbd15d></fc8ec4ce8b7a647ff52cf997ad695c15></a2ccf04a940c23b34c33d7fe108d773e>

     

  • Dan White

    Dan White - 2011-04-26

    if this crash is hard to prevent, need to check available memory vs what the dataset will take to load, and not even try but give error message if its not gonna work.

     

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