Segmentation Fault in Pandas read_csv

Question

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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0x7fff867df000 -     0x7fff867e0ff7  libSystem.B.dylib (1197.1.1) <BFC0DC97-46C6-3BE0-9983-54A98734897A> /usr/lib/libSystem.B.dylib
0x7fff867fc000 -     0x7fff867feff7  libquarantine.dylib (71) <7A1A2BCB-C03D-3A25-BFA4-3E569B2D2C38> /usr/lib/system/libquarantine.dylib
0x7fff8689d000 -     0x7fff868a4ff7  liblaunch.dylib (842.1.4) <FCBF0A02-0B06-3F97-9248-5062A9DEB32C> /usr/lib/system/liblaunch.dylib
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

Answer 1

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.

Answer 2

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.