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Problem with example distance

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Problem with example distance

Postby jhu_data_miner » Tue Sep 21, 2010 13:40

Hi

I'm on a Mac, (Intel-based), every time I connect a file to the example_distance widget orange crashes. Here is the crash report:


rocess: Python [13710]
Path: /Applications/Orange.app/Contents/Frameworks/Python.framework/Resources/Python.app/Contents/MacOS/Python
Identifier: si.ailab.Orange
Version: 2.5a0 (2.5alpha0)
Code Type: X86 (Native)
Parent Process: launchd [85]

Date/Time: 2010-09-21 08:39:33.152 -0400
OS Version: Mac OS X 10.6.4 (10F569)
Report Version: 6

Interval Since Last Report: 555 sec
Crashes Since Last Report: 3
Per-App Interval Since Last Report: 492 sec
Per-App Crashes Since Last Report: 3
Anonymous UUID: 25D05098-5341-4C0F-94E8-A0DAA6D76514

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

Application Specific Information:
abort() called

Thread 0 Crashed: Dispatch queue: com.apple.main-thread
0 libSystem.B.dylib 0x90da0ef6 __kill + 10
1 libSystem.B.dylib 0x90da0ee8 kill$UNIX2003 + 32
2 libSystem.B.dylib 0x90e3362d raise + 26
3 libSystem.B.dylib 0x90e496e4 abort + 93
4 libstdc++.6.dylib 0x98bcffda __gnu_cxx::__verbose_terminate_handler() + 433
5 libstdc++.6.dylib 0x98bce17a __cxxabiv1::__terminate(void (*)()) + 10
6 libstdc++.6.dylib 0x98bce1ba __cxxabiv1::__unexpected(void (*)()) + 0
7 libstdc++.6.dylib 0x98bce2b8 __gxx_exception_cleanup(_Unwind_Reason_Code, _Unwind_Exception*) + 0
8 libstdc++.6.dylib 0x98bce658 operator new(unsigned long) + 101
9 libstdc++.6.dylib 0x98bce703 operator new[](unsigned long) + 17
10 orange.so 0x032d05e8 SymMatrix_new(_typeobject*, _object*, _object*) + 168
11 org.python.python 0x00064e26 type_call + 54
12 org.python.python 0x0000e482 PyObject_Call + 50
13 org.python.python 0x000a180a PyEval_EvalFrameEx + 15130
14 org.python.python 0x000a40a0 PyEval_EvalFrameEx + 25520
15 org.python.python 0x000a40a0 PyEval_EvalFrameEx + 25520
16 org.python.python 0x000a40a0 PyEval_EvalFrameEx + 25520
17 org.python.python 0x000a40a0 PyEval_EvalFrameEx + 25520
18 org.python.python 0x000a494a PyEval_EvalCodeEx + 1962
19 org.python.python 0x000a28e5 PyEval_EvalFrameEx + 19445
20 org.python.python 0x000a494a PyEval_EvalCodeEx + 1962
21 org.python.python 0x000a28e5 PyEval_EvalFrameEx + 19445
22 org.python.python 0x000a494a PyEval_EvalCodeEx + 1962
23 org.python.python 0x00032d2a function_call + 330
24 org.python.python 0x0000e482 PyObject_Call + 50
25 org.python.python 0x000171d6 instancemethod_call + 422
26 org.python.python 0x0000e482 PyObject_Call + 50
27 org.python.python 0x0009cce6 PyEval_CallObjectWithKeywords + 118
28 sip.so 0x006e9472 sip_api_call_method + 76
29 QtGui.so 0x02006331 sipVH_QtGui_27(PyGILState_STATE, _object*, QMouseEvent*) + 91
30 QtGui.so 0x0227cac3 sipQGraphicsView::mouseReleaseEvent(QMouseEvent*) + 119
31 QtGui 0x02878af8 QWidget::event(QEvent*) + 3208
32 QtGui 0x02bd0435 QFrame::event(QEvent*) + 37
33 QtGui 0x02c56e7f QAbstractScrollArea::viewportEvent(QEvent*) + 447
34 QtGui 0x02ddc592 QGraphicsView::viewportEvent(QEvent*) + 114
35 QtGui.so 0x0227c37b sipQGraphicsView::viewportEvent(QEvent*) + 97
36 QtGui 0x02c59e65 QAbstractScrollAreaFilter::eventFilter(QObject*, QEvent*) + 53
37 QtCore 0x012e6c37 QCoreApplicationPrivate::sendThroughObjectEventFilters(QObject*, QEvent*) + 151
38 QtGui 0x02835b46 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 150
39 QtGui 0x02837c6d QApplication::notify(QObject*, QEvent*) + 1261
40 QtGui.so 0x023a8bb6 sipQApplication::notify(QObject*, QEvent*) + 104
41 QtCore 0x012e69e1 QCoreApplication::notifyInternal(QObject*, QEvent*) + 145
42 QtGui 0x0288944b QApplicationPrivate::globalEventProcessor(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*) + 5771
43 com.apple.HIToolbox 0x99264f2f DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 1567
44 com.apple.HIToolbox 0x992641f6 SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*) + 411
45 com.apple.HIToolbox 0x992869bb SendEventToEventTarget + 52
46 com.apple.HIToolbox 0x992984db ToolboxEventDispatcherHandler(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*) + 1257
47 com.apple.HIToolbox 0x99265380 DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 2672
48 com.apple.HIToolbox 0x992641f6 SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*) + 411
49 com.apple.HIToolbox 0x992869bb SendEventToEventTarget + 52
50 QtGui 0x02884351 qt_mac_send_event(QFlags<QEventLoop::ProcessEventsFlag>, OpaqueEventRef*, OpaqueWindowPtr*) + 97
51 QtGui 0x02892842 QEventDispatcherMac::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 658
52 QtCore 0x012e60a1 QEventLoop::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 65
53 QtCore 0x012e616d QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 157
54 QtCore 0x012e9eb1 QCoreApplication::exec() + 161
55 QtGui.so 0x023abfba meth_QApplication_exec_ + 104
56 org.python.python 0x000a2ec0 PyEval_EvalFrameEx + 20944
57 org.python.python 0x000a494a PyEval_EvalCodeEx + 1962
58 org.python.python 0x000a28e5 PyEval_EvalFrameEx + 19445
59 org.python.python 0x000a494a PyEval_EvalCodeEx + 1962
60 org.python.python 0x000a4a57 PyEval_EvalCode + 87
61 org.python.python 0x000c8a97 PyRun_FileExFlags + 263
62 org.python.python 0x000c8e43 PyRun_SimpleFileExFlags + 659
63 org.python.python 0x000d7507 Py_Main + 3031
64 org.python.python 0x00001f82 0x1000 + 3970
65 org.python.python 0x00001ea9 0x1000 + 3753

Thread 1: Dispatch queue: com.apple.libdispatch-manager
0 libSystem.B.dylib 0x90d66942 kevent + 10
1 libSystem.B.dylib 0x90d6705c _dispatch_mgr_invoke + 215
2 libSystem.B.dylib 0x90d66519 _dispatch_queue_invoke + 163
3 libSystem.B.dylib 0x90d662be _dispatch_worker_thread2 + 240
4 libSystem.B.dylib 0x90d65d41 _pthread_wqthread + 390
5 libSystem.B.dylib 0x90d65b86 start_wqthread + 30

Thread 0 crashed with X86 Thread State (32-bit):
eax: 0x00000000 ebx: 0x90e49693 ecx: 0xbfffc75c edx: 0x90da0ef6
edi: 0xa00c6b30 esi: 0x98bd2e2f ebp: 0xbfffc778 esp: 0xbfffc75c
ss: 0x0000001f efl: 0x00000286 eip: 0x90da0ef6 cs: 0x00000007
ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037
cr2: 0xa0afbfc0

Binary Images:
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0x98b84000 - 0x98beefe7 libstdc++.6.dylib 7.9.0 (compatibility 7.0.0) <411D87F4-B7E1-44EB-F201-F8B4F9227213> /usr/lib/libstdc++.6.dylib
0x98bef000 - 0x98bf6ff3 com.apple.print.framework.Print 6.1 (237.1) <97AB70B6-C653-212F-CFD3-E3816D0F5C22> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Print.framework/Versions/A/Print
0x98bf7000 - 0x98c08ff7 com.apple.LangAnalysis 1.6.6 (1.6.6) <97511CC7-FE23-5AC3-2EE2-B5479FAEB316> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/LangAnalysis.framework/Versions/A/LangAnalysis
0x98c09000 - 0x98c17ff7 com.apple.opengl 1.6.8 (1.6.8) <EBB7B411-60DD-DB9D-20C0-3E6258762EF0> /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
0x98c18000 - 0x98c5bff7 libGLU.dylib ??? (???) <B50572FF-3EAC-FD98-1A01-6B718D98F67F> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
0x98c9d000 - 0x98cfefe7 com.apple.CoreText 3.1.0 (???) <1372DABE-F183-DD03-03C2-64B2464A4FD5> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreText.framework/Versions/A/CoreText
0x98cff000 - 0x98d50ff7 com.apple.HIServices 1.8.0 (???) <10C85B88-C6AF-91DB-2546-34661BA35AC5> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices
0x99191000 - 0x991a6fff com.apple.ImageCapture 6.0 (6.0) <0E86F45E-E656-9015-7AD4-A2C5F8D8A2FA> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ImageCapture.framework/Versions/A/ImageCapture
0x991a7000 - 0x99254fe7 libobjc.A.dylib 227.0.0 (compatibility 1.0.0) <DF8E4CFA-3719-3415-0BF1-E8C5E561C3B1> /usr/lib/libobjc.A.dylib
0x99255000 - 0x99255ff7 com.apple.ApplicationServices 38 (38) <8012B504-3D83-BFBB-DA65-065E061CFE03> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
0x9925d000 - 0x99581fef com.apple.HIToolbox 1.6.3 (???) <0A5F56E2-9AF3-728D-70AE-429522AEAD8A> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/HIToolbox
0x99582000 - 0x995a3fe7 com.apple.opencl 12.1 (12.1) <DA2AC3FA-ED11-2D10-21E9-7BDF4778B228> /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
0x99606000 - 0x99609ff7 libCoreVMClient.dylib ??? (???) <420D9D10-B00E-202D-AA98-026996AB97DD> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
0x99704000 - 0x9970dff7 com.apple.DiskArbitration 2.3 (2.3) <E9C40767-DA6A-6CCB-8B00-2D5706753000> /System/Library/Frameworks/DiskArbitration.framework/Versions/A/DiskArbitration
0x99765000 - 0x9979dff7 libcups.2.dylib 2.8.0 (compatibility 2.0.0) <76C02F5C-98FD-BD64-B5FB-C698FB76EA25> /usr/lib/libcups.2.dylib
0x9979e000 - 0x99854ffb libFontParser.dylib ??? (???) <067DC1A2-764B-41EA-B07E-4205472749B7> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.dylib
0x99855000 - 0x99947ff7 libcrypto.0.9.8.dylib 0.9.8 (compatibility 0.9.8) <D2C86308-F998-C83D-F49B-CD484D4EFE6A> /usr/lib/libcrypto.0.9.8.dylib
0x99948000 - 0x9998bff7 com.apple.NavigationServices 3.5.4 (182) <753B8906-06C0-3AE0-3D6A-8FF5AC18ED12> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/NavigationServices.framework/Versions/A/NavigationServices
0x9998c000 - 0x9999cff7 libsasl2.2.dylib 3.15.0 (compatibility 3.0.0) <C8744EA3-0AB7-CD03-E639-C4F2B910BE5D> /usr/lib/libsasl2.2.dylib
0xba900000 - 0xba916ff7 libJapaneseConverter.dylib 49.0.0 (compatibility 1.0.0) <12C58901-CCF3-4E8E-30CA-92A10CD55DF1> /System/Library/CoreServices/Encodings/libJapaneseConverter.dylib
0xbab00000 - 0xbab21fe7 libKoreanConverter.dylib 49.0.0 (compatibility 1.0.0) <7FFF4AFA-6522-C7D5-760F-A8F13D6EF032> /System/Library/CoreServices/Encodings/libKoreanConverter.dylib
0xffff0000 - 0xffff1fff libSystem.B.dylib ??? (???) <3441F338-2218-6D36-3F95-3A16FBF6713D> /usr/lib/libSystem.B.dylib

Model: MacPro4,1, BootROM MP41.0081.B08, 4 processors, Quad-Core Intel Xeon, 2.93 GHz, 16 GB, SMC 1.39f5
Graphics: NVIDIA GeForce GT 120, NVIDIA GeForce GT 120, PCIe, 512 MB
Memory Module: global_name
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x8E), Broadcom BCM43xx 1.0 (5.10.91.27)
Bluetooth: Version 2.3.3f8, 2 service, 19 devices, 1 incoming serial ports
Network Service: Ethernet 1, Ethernet, en0
PCI Card: NVIDIA GeForce GT 120, Display, Slot-1
Serial ATA Device: HL-DT-ST DVD-RW GH41N
Serial ATA Device: Hitachi HDE721010SLA330, 931.51 GB
Serial ATA Device: Hitachi HDE721010SLA330, 931.51 GB
USB Device: Hub, 0x05ac (Apple Inc.), 0x9136, 0xfd100000
USB Device: Keyboard Hub, 0x05ac (Apple Inc.), 0x1006, 0xfd130000
USB Device: Apple Keyboard, 0x05ac (Apple Inc.), 0x0220, 0xfd132000
USB Device: USB-PS/2 Optical Mouse, 0x046d (Logitech Inc.), 0xc00e, 0xfd110000
USB Device: Hub, 0x05ac (Apple Inc.), 0x9137, 0xfd140000
USB Device: Display iSight, 0x05ac (Apple Inc.), 0x8508, 0xfd142000
USB Device: Apple LED Cinema Display, 0x05ac (Apple Inc.), 0x9236, 0xfd143000
USB Device: Display Audio, 0x05ac (Apple Inc.), 0x2912, 0xfd141000
USB Device: BRCM2046 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0x5a100000
USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.), 0x8215, 0x5a110000
FireWire Device: built-in_hub, Up to 800 Mb/sec


Any ideas?

Postby Ales » Wed Sep 22, 2010 10:10

How large is your dataset?

Postby jhu_data_miner » Thu Sep 23, 2010 14:09

I tried different size datasets, the smallest having 5,000 objects and only 1-3 features, and the largest having 30,000 objects with only 1-3 features.

I'm not sure how memory allocation works in Python, but is there some kind of virtual machine limit, like Java or does the heap just continually grow until no memory is left? I ask, cause I may just write my own program to compute distances and load them into orange, I'm just worried if orange can handle the large matrices...

Postby Janez » Fri Sep 24, 2010 11:06

The error is triggered by 'new' that tries to allocate memory for (dim+1)(dim+2)/2 floats. For 5000 objects this is around 50 megabytes (assuming 4-byte float). This code is in C, so the limit on memory allocation would be imposed by OS X, not Python.

The number of features does not matter, what matters is only the number of objects, that is, the matrix dimension.

Ale, can you replicate this problem?

Postby Ales » Mon Sep 27, 2010 9:51

Yes I can replicate this, but only for dimensions exceeding 30000 (roughly 2.2 GB). Also the error output when running orange from the command line is
Code: Select all
python2.6(327) malloc: *** mmap(size=2450210816) 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():  std::bad_alloc
Abort trap

This seems to be a common problem on Mac OSX (at least for 32bit processes). numpy also cannot create an array of similar size, but instead of crashing raises an "array to big" exception.


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