I have Python 2.7.5 on Os X 10.9 with Pandas version 0.12.0-943-gaef5061. When I download this train.csv file and run read_csv, I get Segmentation Fault 11. I have experimented with the file encoding, putting values in the empty columns, and changing the options for quotes, but to no avail. From the error report, it looks as if the fault may be occurring in unmath.so
.
Does anyone have an explanation or workaround?
Python 2.7.5 (default, Aug 25 2013, 00:04:04)
[GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.0.68)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import pandas
>>> pandas.read_csv('train.csv')
Segmentation fault: 11
More information from the error report:
Process: Python [5400]
Path: /System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier: Python
Version: 2.7.5 (2.7.5)
Code Type: X86-64 (Native)
Parent Process: bash [4823]
Responsible: Terminal [321]
User ID: 501
PlugIn Path: /Library/Python/2.7/site-packages/numpy-1.9.0.dev_54d3559-py2.7-macosx-10.9-intel.egg/numpy/core/umath.so
PlugIn Identifier: umath.so
PlugIn Version: ??? (0)
Date/Time: 2013-10-26 09:02:45.350 -0700
OS Version: Mac OS X 10.9 (13A603)
Report Version: 11
Anonymous UUID: CAE885D2-2BCB-60AF-9133-E06FE6DD85A9
Sleep/Wake UUID: 2B9C017B-5FE4-4EA0-A2DF-EB279848BED9
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000000
VM Regions Near 0:
-->
__TEXT 0000000109030000-0000000109031000 [ 4K] r-x/rwx SM=COW /System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 umath.so 0x0000000109563567 _extract_pyvals + 403
1 umath.so 0x0000000109565ea4 _get_bufsize_errmask + 49
2 umath.so 0x0000000109563ad4 PyUFunc_GenericFunction + 1181
3 umath.so 0x00000001095677b7 ufunc_generic_call + 307
4 org.python.python 0x000000010903ef72 PyObject_Call + 101
5 org.python.python 0x00000001090b8df5 PyEval_EvalFrameEx + 15416
6 org.python.python 0x00000001090bb864 0x109035000 + 551012
7 org.python.python 0x00000001090b84d4 PyEval_EvalFrameEx + 13079
8 org.python.python 0x00000001090bb864 0x109035000 + 551012
9 org.python.python 0x00000001090b84d4 PyEval_EvalFrameEx + 13079
10 org.python.python 0x00000001090bb864 0x109035000 + 551012
11 org.python.python 0x00000001090b84d4 PyEval_EvalFrameEx + 13079
12 org.python.python 0x00000001090bb864 0x109035000 + 551012
13 org.python.python 0x00000001090b84d4 PyEval_EvalFrameEx + 13079
14 org.python.python 0x00000001090b5093 PyEval_EvalCodeEx + 1641
15 org.python.python 0x000000010905c796 0x109035000 + 161686
16 org.python.python 0x000000010903ef72 PyObject_Call + 101
17 org.python.python 0x00000001090499a7 0x109035000 + 84391
18 org.python.python 0x000000010903ef72 PyObject_Call + 101
19 org.python.python 0x00000001090b8df5 PyEval_EvalFrameEx + 15416
20 org.python.python 0x00000001090b5093 PyEval_EvalCodeEx + 1641
21 org.python.python 0x00000001090bb8c8 0x109035000 + 551112
22 org.python.python 0x00000001090b84d4 PyEval_EvalFrameEx + 13079
23 org.python.python 0x00000001090b5093 PyEval_EvalCodeEx + 1641
24 org.python.python 0x000000010905c796 0x109035000 + 161686
25 org.python.python 0x000000010903ef72 PyObject_Call + 101
26 org.python.python 0x00000001090499a7 0x109035000 + 84391
27 org.python.python 0x000000010903ef72 PyObject_Call + 101
28 org.python.python 0x00000001090b8df5 PyEval_EvalFrameEx + 15416
29 org.python.python 0x00000001090b5093 PyEval_EvalCodeEx + 1641
30 org.python.python 0x00000001090bb8c8 0x109035000 + 551112
31 org.python.python 0x00000001090b84d4 PyEval_EvalFrameEx + 13079
32 org.python.python 0x00000001090b5093 PyEval_EvalCodeEx + 1641
33 org.python.python 0x00000001090bb8c8 0x109035000 + 551112
34 org.python.python 0x00000001090b84d4 PyEval_EvalFrameEx + 13079
35 org.python.python 0x00000001090bb864 0x109035000 + 551012
36 org.python.python 0x00000001090b84d4 PyEval_EvalFrameEx + 13079
37 org.python.python 0x00000001090bb864 0x109035000 + 551012
38 org.python.python 0x00000001090b84d4 PyEval_EvalFrameEx + 13079
39 org.python.python 0x00000001090b5093 PyEval_EvalCodeEx + 1641
40 org.python.python 0x000000010905c796 0x109035000 + 161686
41 org.python.python 0x000000010903ef72 PyObject_Call + 101
42 org.python.python 0x00000001090499a7 0x109035000 + 84391
43 org.python.python 0x000000010903ef72 PyObject_Call + 101
44 org.python.python 0x00000001090bb01f PyEval_CallObjectWithKeywords + 93
45 org.python.python 0x0000000109083d09 0x109035000 + 322825
46 org.python.python 0x000000010906dd34 _PyObject_Str + 127
47 org.python.python 0x000000010906ddca PyObject_Str + 15
48 org.python.python 0x00000001090769c2 0x109035000 + 268738
49 org.python.python 0x00000001090800f9 0x109035000 + 307449
50 org.python.python 0x000000010903ef72 PyObject_Call + 101
51 org.python.python 0x00000001090b8df5 PyEval_EvalFrameEx + 15416
52 org.python.python 0x00000001090b5093 PyEval_EvalCodeEx + 1641
53 org.python.python 0x000000010905c796 0x109035000 + 161686
54 org.python.python 0x000000010903ef72 PyObject_Call + 101
55 org.python.python 0x00000001090499a7 0x109035000 + 84391
56 org.python.python 0x000000010903ef72 PyObject_Call + 101
57 org.python.python 0x00000001090bb01f PyEval_CallObjectWithKeywords + 93
58 org.python.python 0x0000000109083a74 0x109035000 + 322164
59 org.python.python 0x000000010906dbde PyObject_Repr + 49
60 org.python.python 0x000000010906da93 0x109035000 + 232083
61 org.python.python 0x000000010905563f PyFile_WriteObject + 137
62 org.python.python 0x00000001090d9b5f 0x109035000 + 674655
63 org.python.python 0x000000010903ef72 PyObject_Call + 101
64 org.python.python 0x00000001090bb01f PyEval_CallObjectWithKeywords + 93
65 org.python.python 0x00000001090b7682 PyEval_EvalFrameEx + 9413
66 org.python.python 0x00000001090b5093 PyEval_EvalCodeEx + 1641
67 org.python.python 0x00000001090b4a24 PyEval_EvalCode + 54
68 org.python.python 0x00000001090d3c2c 0x109035000 + 650284
69 org.python.python 0x00000001090d3a4e PyRun_InteractiveOneFlags + 365
70 org.python.python 0x00000001090d353f PyRun_InteractiveLoopFlags + 188
71 org.python.python 0x00000001090d33f0 PyRun_AnyFileExFlags + 60
72 org.python.python 0x00000001090e4363 Py_Main + 2995
73 libdyld.dylib 0x00007fff8821b5fd start + 1
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x000000010e1810e0 rbx: 0x0000000000000000 rcx: 0xc4002be6c4209f06 rdx: 0x0000000000000000
rdi: 0x0000000109584326 rsi: 0x00007fff56bca700 rbp: 0x00007fff56bca870 rsp: 0x00007fff56bca840
r8: 0x0000000000000000 r9: 0x0800000000000100 r10: 0x2000000000000200 r11: 0x0000000004c09dce
r12: 0x00007fff56bcaa88 r13: 0x00007fff56bcaa8c r14: 0x00007fff56bcaa88 r15: 0x0000000000000000
rip: 0x0000000109563567 rfl: 0x0000000000010206 cr2: 0x0000000000000000
Logical CPU: 4
Error Code: 0x00000006
Trap Number: 14
Binary Images:
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0x1097a3000 - 0x1097a4fff time.so (76) <60566D0D-485D-3EE6-BD9F-3C330C973922> /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/time.so
0x1097eb000 - 0x1097efff7 +_compiled_base.so (0) <907FD9FE-69CF-309F-BC37-7A7341740D39> /Library/Python/2.7/site-packages/numpy-1.9.0.dev_54d3559-py2.7-macosx-10.9-intel.egg/numpy/lib/_compiled_base.so
0x109833000 - 0x109836fff +lapack_lite.so (0) <12B329E7-CA0B-3D05-8580-AC8659BF1FBC> /Library/Python/2.7/site-packages/numpy-1.9.0.dev_54d3559-py2.7-macosx-10.9-intel.egg/numpy/linalg/lapack_lite.so
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0x7fff86925000 - 0x7fff86949fff libxpc.dylib (300.1.17) <4554927A-9467-365C-91F1-5A116989DD7F> /usr/lib/system/libxpc.dylib
0x7fff87b1b000 - 0x7fff87b2bfff libbsm.0.dylib (33) <2CAC00A2-1352-302A-88FA-C567D4D69179> /usr/lib/libbsm.0.dylib
0x7fff87b34000 - 0x7fff87b82fff libcorecrypto.dylib (161.1) <F3973C28-14B6-3006-BB2B-00DD7F09ABC7> /usr/lib/system/libcorecrypto.dylib
0x7fff87b83000 - 0x7fff87bd5fff libc++.1.dylib (120) <4F68DFC5-2077-39A8-A449-CAC5FDEE7BDE> /usr/lib/libc++.1.dylib
0x7fff87ea3000 - 0x7fff8805bff3 libicucore.A.dylib (511.25) <3ED7B656-416E-3071-AEC8-E85C90232F78> /usr/lib/libicucore.A.dylib
0x7fff88218000 - 0x7fff8821bff7 libdyld.dylib (239.3) <62F4D752-4089-31A8-8B73-B95A68893B3C> /usr/lib/system/libdyld.dylib
0x7fff8821c000 - 0x7fff88243ffb libsystem_info.dylib (449.1.3) <7D41A156-D285-3849-A2C3-C04ADE797D98> /usr/lib/system/libsystem_info.dylib
0x7fff88244000 - 0x7fff882f4ff7 libvMisc.dylib (423.32) <049C0735-1808-39B9-943F-76CB8021744F> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib
0x7fff884c1000 - 0x7fff884c1ff7 libkeymgr.dylib (28) <3AA8D85D-CF00-3BD3-A5A0-E28E1A32A6D8> /usr/lib/system/libkeymgr.dylib
0x7fff88952000 - 0x7fff88953ff7 libsystem_sandbox.dylib (278.10) <A47E7E11-3C76-318E-B67D-98972B86F094> /usr/lib/system/libsystem_sandbox.dylib
0x7fff88d28000 - 0x7fff88f0dff7 com.apple.CoreFoundation (6.9 - 855.11) <E22C6A1F-8996-349C-905E-96C3BBE07C2F> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
0x7fff8a102000 - 0x7fff8a11eff7 libsystem_kernel.dylib (2422.1.72) <D14913DB-47F1-3591-8DAF-D4B4EF5F8818> /usr/lib/system/libsystem_kernel.dylib
0x7fff8a558000 - 0x7fff8a561ff3 libsystem_notify.dylib (121) <52571EC3-6894-37E4-946E-064B021ED44E> /usr/lib/system/libsystem_notify.dylib
0x7fff8a5ca000 - 0x7fff8a60cff7 libauto.dylib (185.5) <F45C36E8-B606-3886-B5B1-B6745E757CA8> /usr/lib/libauto.dylib
0x7fff8a92d000 - 0x7fff8a947fff libdispatch.dylib (339.1.9) <46878A5B-4248-3057-962C-6D4A235EEF31> /usr/lib/system/libdispatch.dylib
0x7fff8ab42000 - 0x7fff8ab46ff7 libcache.dylib (62) <BDC1E65B-72A1-3DA3-A57C-B23159CAAD0B> /usr/lib/system/libcache.dylib
0x7fff8ab47000 - 0x7fff8ab48fff libffi.dylib (18.1) <FEB76C94-97BA-39BC-B713-D086B9757BA5> /usr/lib/libffi.dylib
0x7fff8ab49000 - 0x7fff8ab4afff com.apple.TrustEvaluationAgent (2.0 - 25) <334A82F4-4AE4-3719-A511-86D0B0723E2B> /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
0x7fff8ab73000 - 0x7fff8abd6ff7 com.apple.SystemConfiguration (1.13 - 1.13) <F05F4149-981B-380B-8F50-51CE804BBB89> /System/Library/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration
0x7fff8aeb9000 - 0x7fff8aec3fff libcommonCrypto.dylib (60049) <8C4F0CA0-389C-3EDC-B155-E62DD2187E1D> /usr/lib/system/libcommonCrypto.dylib
0x7fff8bd81000 - 0x7fff8bd82ff7 libDiagnosticMessagesClient.dylib (100) <4CDB0F7B-C0AF-3424-BC39-495696F0DB1E> /usr/lib/libDiagnosticMessagesClient.dylib
0x7fff8be54000 - 0x7fff8be59fff libmacho.dylib (845) <1D2910DF-C036-3A82-A3FD-44FF73B5FF9B> /usr/lib/system/libmacho.dylib
0x7fff8bfaa000 - 0x7fff8bfd9fd2 libsystem_m.dylib (3047.16) <B7F0E2E4-2777-33FC-A787-D6430B630D54> /usr/lib/system/libsystem_m.dylib
0x7fff8c6ba000 - 0x7fff8c6bcff3 libsystem_configuration.dylib (596.12) <C4F633D9-94C8-35D9-BB2D-84C5122533C7> /usr/lib/system/libsystem_configuration.dylib
0x7fff8d7e0000 - 0x7fff8d810fff libncurses.5.4.dylib (42) <BF763D62-9149-37CB-B1D2-F66A2510E6DD> /usr/lib/libncurses.5.4.dylib
0x7fff8d811000 - 0x7fff8d9bef27 libobjc.A.dylib (551.1) <AD7FD984-271E-30F4-A361-6B20319EC73B> /usr/lib/libobjc.A.dylib
0x7fff8dcc0000 - 0x7fff8dcdbff7 libsystem_malloc.dylib (23.1.10) <FFE5C472-B23A-318A-85BF-77CDE61900D1> /usr/lib/system/libsystem_malloc.dylib
0x7fff8dd15000 - 0x7fff8dd1cfff libcompiler_rt.dylib (35) <4CD916B2-1B17-362A-B403-EF24A1DAC141> /usr/lib/system/libcompiler_rt.dylib
0x7fff8dd1d000 - 0x7fff8dd25fff libsystem_dnssd.dylib (522.1.11) <270DCF6C-502D-389A-AA9F-DE4624A36FF7> /usr/lib/system/libsystem_dnssd.dylib
0x7fff8dd26000 - 0x7fff8dd2dff3 libcopyfile.dylib (103) <5A881779-D0D6-3029-B371-E3021C2DDA5E> /usr/lib/system/libcopyfile.dylib
0x7fff8e589000 - 0x7fff8e59aff7 libz.1.dylib (53) <42E0C8C6-CA38-3CA4-8619-D24ED5DD492E> /usr/lib/libz.1.dylib
0x7fff8e5ae000 - 0x7fff8e68dfff libcrypto.0.9.8.dylib (50) <B95B9DBA-39D3-3EEF-AF43-44608B28894E> /usr/lib/libcrypto.0.9.8.dylib
0x7fff8e80b000 - 0x7fff8e834ff7 libc++abi.dylib (48) <8C16158F-CBF8-3BD7-BEF4-022704B2A326> /usr/lib/libc++abi.dylib
0x7fff8f319000 - 0x7fff8f487ff7 libBLAS.dylib (1094.5) <DE93A590-5FA5-32A2-A16C-5D7D7361769F> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
0x7fff8f4b0000 - 0x7fff8f4b7ff7 libsystem_pthread.dylib (53.1.4) <AB498556-B555-310E-9041-F67EC9E00E2C> /usr/lib/system/libsystem_pthread.dylib
0x7fff8f64a000 - 0x7fff8f64fff7 libunwind.dylib (35.3) <78DCC358-2FC1-302E-B395-0155B47CB547> /usr/lib/system/libunwind.dylib
0x7fff8f9df000 - 0x7fff8fdc0ffe libLAPACK.dylib (1094.5) <7E7A9B8D-1638-3914-BAE0-663B69865986> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
0x7fff8fdcd000 - 0x7fff8fe56ff7 libsystem_c.dylib (997.1.1) <61833FAA-7281-3FF9-937F-686B6F20427C> /usr/lib/system/libsystem_c.dylib
0x7fff8feb7000 - 0x7fff8feb8ffb libremovefile.dylib (33) <3543F917-928E-3DB2-A2F4-7AB73B4970EF> /usr/lib/system/libremovefile.dylib
0x7fff8feb9000 - 0x7fff9018dfc7 com.apple.vImage (7.0 - 7.0) <D241DBFA-AC49-31E2-893D-EAAC31890C90> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
0x7fff90baa000 - 0x7fff90baefff libsystem_stats.dylib (93.1.26) <B9E26A9E-FBBC-3938-B8B7-6CF7CA8C99AD> /usr/lib/system/libsystem_stats.dylib
0x7fff91031000 - 0x7fff91058ff7 libsystem_network.dylib (241.3) <8B1E1F1D-A5CC-3BAE-8B1E-ABC84337A364> /usr/lib/system/libsystem_network.dylib
0x7fff9236d000 - 0x7fff9237aff0 libbz2.1.0.dylib (29) <0B98AC35-B138-349C-8063-2B987A75D24C> /usr/lib/libbz2.1.0.dylib
0x7fff9237b000 - 0x7fff9237cff7 libsystem_blocks.dylib (63) <FB856CD1-2AEA-3907-8E9B-1E54B6827F82> /usr/lib/system/libsystem_blocks.dylib
0x7fff9237d000 - 0x7fff9238eff7 libsystem_asl.dylib (217.1.4) <655FB343-52CF-3E2F-B14D-BEBF5AAEF94D> /usr/lib/system/libsystem_asl.dylib
0x7fff92436000 - 0x7fff92436fff com.apple.Accelerate.vecLib (3.9 - vecLib 3.9) <F8D0CC77-98AC-3B58-9FE6-0C25421827B6> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
0x7fff92437000 - 0x7fff9246bfff libssl.0.9.8.dylib (50) <B15F967C-B002-36C2-9621-3456D8509F50> /usr/lib/libssl.0.9.8.dylib
0x7fff92843000 - 0x7fff92844fff libunc.dylib (28) <62682455-1862-36FE-8A04-7A6B91256438> /usr/lib/system/libunc.dylib
0x7fff931b6000 - 0x7fff93281fff libvDSP.dylib (423.32) <3BF732BE-DDE0-38EB-8C54-E4E3C64F77A7> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
Have you tried switching to the 'python' parser?
pandas.read_csv('train.csv', engine='python')
Explanation: The default C parsing engine is faster while the python engine is currently more feature-complete. And since the Seg Fault error is a C error message, trying with the Python engine may solve the problem.
I have noticed the same issue with pandas and other modules. At: http://www.python.org/download/releases/2.7.6/ they state:
Python 2.7.6 release candidate 1 was released on October 26, 2013. This is a 2.7 series bugfix release. Most importantly, it resolves an issue that caused the interactive prompt to crash.
So, I just downloaded the binary package for mac. The segfault never occurred again since then. I tried with pandas and other modules since.
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