segmentation fault 11 on Mavericks python Python 2.7.6rc1 #5396

venuktan · 2013-10-31T08:21:55Z

I get a segmentation fault 11 when I try to read from a csv.

Here is the full error report :

Process: Python [95313]
Path: /Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier: Python
Version: 2.7.6rc1 (2.7.6rc1)
Code Type: X86-64 (Native)
Parent Process: bash [94753]
Responsible: iTerm [160]
User ID: 501

Date/Time: 2013-10-31 01:16:01.018 -0700
OS Version: Mac OS X 10.9 (13A603)
Report Version: 11
Anonymous UUID: 592E522A-F4DC-667B-6F11-E35383BBC4BE

Sleep/Wake UUID: F91ECED6-C437-4874-B521-5F139FBA707A

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 0000000100000000-0000000100001000 [ 4K] r-x/rwx SM=COW /Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python

Thread 0 Crashed:: 0 umath.so 1 umath.so 2 umath.so 3 umath.so 4 org.python.python 5 org.python.python 6 multiarray.so 7 org.python.python 8 org.python.python 9 org.python.python 10 org.python.python 11 org.python.python 12 org.python.python 13 org.python.python 14 org.python.python 15 org.python.python 16 org.python.python 17 org.python.python 18 org.python.python 19 org.python.python 20 org.python.python 21 org.python.python 22 org.python.python 23 org.python.python 24 org.python.python 25 org.python.python Dispatch queue: com.apple.main-thread
0x0000000101293567 _extract_pyvals + 403
0x0000000101295ea4 _get_bufsize_errmask + 49
0x0000000101293ad4 PyUFunc_GenericFunction + 1181
0x00000001012977b7 ufunc_generic_call + 307
0x000000010000c702 PyObject_Call + 98
0x0000000100010e45 _PyObject_CallFunction_SizeT + 197
0x0000000101104500 array_richcompare + 761
0x000000010005ae9c try_rich_compare + 92
0x000000010005c86f PyObject_RichCompare + 95
0x00000001000bf443 PyEval_EvalFrameEx + 8355
0x00000001000c4746 PyEval_EvalCodeEx + 2118
0x00000001000c2b80 PyEval_EvalFrameEx + 22496
0x00000001000c338a PyEval_EvalFrameEx + 24554
0x00000001000c4746 PyEval_EvalCodeEx + 2118
0x00000001000c2b80 PyEval_EvalFrameEx + 22496
0x00000001000c4746 PyEval_EvalCodeEx + 2118
0x00000001000c2b80 PyEval_EvalFrameEx + 22496
0x00000001000c4746 PyEval_EvalCodeEx + 2118
0x00000001000c2b80 PyEval_EvalFrameEx + 22496
0x00000001000c4746 PyEval_EvalCodeEx + 2118
0x00000001000c4866 PyEval_EvalCode + 54
0x00000001000e8c1c PyRun_InteractiveOneFlags + 380
0x00000001000e8e7e PyRun_InteractiveLoopFlags + 78
0x00000001000e9691 PyRun_AnyFileExFlags + 161
0x000000010010040d Py_Main + 3101
0x0000000100000f14 0x100000000 + 3860

Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000103167d88 rbx: 0x0000000000000000 rcx: 0x00000001012b4326 rdx: 0x0000000000000000
rdi: 0x0000000000000000 rsi: 0x00007fff5fbfba70 rbp: 0x00007fff5fbfbbc0 rsp: 0x00007fff5fbfbb90
r8: 0x0000000000000000 r9: 0x0000000102f00000 r10: 0x0000000000000000 r11: 0x0000000001ec1f48
r12: 0x00007fff5fbfbdd8 r13: 0x00007fff5fbfbddc r14: 0x00007fff5fbfbdd8 r15: 0x0000000000000000
rip: 0x0000000101293567 rfl: 0x0000000000010202 cr2: 0x0000000000000000

Logical CPU: 0
Error Code: 0x00000006
Trap Number: 14

Binary Images:
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0x7fff8a6b2000 - 0x7fff8a6bcfff libcommonCrypto.dylib (60049) <8C4F0CA0-389C-3EDC-B155-E62DD2187E1D> /usr/lib/system/libcommonCrypto.dylib
0x7fff8a78f000 - 0x7fff8a79ffff libbsm.0.dylib (33) <2CAC00A2-1352-302A-88FA-C567D4D69179> /usr/lib/libbsm.0.dylib
0x7fff8a907000 - 0x7fff8a92effb libsystem_info.dylib (449.1.3) <7D41A156-D285-3849-A2C3-C04ADE797D98> /usr/lib/system/libsystem_info.dylib
0x7fff8b0c4000 - 0x7fff8b0c8fff libsystem_stats.dylib (93.1.26) /usr/lib/system/libsystem_stats.dylib
0x7fff8b821000 - 0x7fff8b863ff7 libauto.dylib (185.5) /usr/lib/libauto.dylib
0x7fff8bd2f000 - 0x7fff8bd49fff libdispatch.dylib (339.1.9) <46878A5B-4248-3057-962C-6D4A235EEF31> /usr/lib/system/libdispatch.dylib
0x7fff8bd4a000 - 0x7fff8bd51ff7 libsystem_pthread.dylib (53.1.4) /usr/lib/system/libsystem_pthread.dylib
0x7fff8c92a000 - 0x7fff8c92eff7 libcache.dylib (62) /usr/lib/system/libcache.dylib
0x7fff8cac1000 - 0x7fff8cca6ff7 com.apple.CoreFoundation (6.9 - 855.11) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
0x7fff8cca7000 - 0x7fff8cd86fff libcrypto.0.9.8.dylib (50) /usr/lib/libcrypto.0.9.8.dylib
0x7fff8ce15000 - 0x7fff8ce1cff7 liblaunch.dylib (842.1.4) /usr/lib/system/liblaunch.dylib
0x7fff8ce1d000 - 0x7fff8ce20ff7 libdyld.dylib (239.3) <62F4D752-4089-31A8-8B73-B95A68893B3C> /usr/lib/system/libdyld.dylib
0x7fff8d7e7000 - 0x7fff8d7e7fff com.apple.Accelerate.vecLib (3.9 - vecLib 3.9) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
0x7fff8dab8000 - 0x7fff8dab9fff libunc.dylib (28) <62682455-1862-36FE-8A04-7A6B91256438> /usr/lib/system/libunc.dylib
0x7fff8e8db000 - 0x7fff8e8e0ff7 libunwind.dylib (35.3) <78DCC358-2FC1-302E-B395-0155B47CB547> /usr/lib/system/libunwind.dylib

External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 2382784
thread_create: 0
thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=95.6M resident=25.9M(27%) swapped_out_or_unallocated=69.7M(73%)
Writable regions: Total=98.5M written=59.2M(60%) resident=66.6M(68%) swapped_out=0K(0%) unallocated=31.9M(32%)

REGION TYPE VIRTUAL
=========== =======
Kernel Alloc Once 4K
MALLOC 88.9M
MALLOC (admin) 16K
MALLOC_LARGE (reserved) 768K reserved VM address space (unallocated)
STACK GUARD 56.0M
Stack 8192K
VM_ALLOCATE 16K
__DATA 2648K
__LINKEDIT 68.5M
__TEXT 27.1M
__UNICODE 544K
shared memory 4K
=========== =======
TOTAL 252.5M
TOTAL, minus reserved VM space 251.7M

Model: MacBookPro10,1, BootROM MBP101.00EE.B03, 4 processors, Intel Core i7, 2.7 GHz, 16 GB, SMC 2.3f36
Graphics: Intel HD Graphics 4000, Intel HD Graphics 4000, Built-In, 1024 MB
Graphics: NVIDIA GeForce GT 650M, NVIDIA GeForce GT 650M, PCIe, 1024 MB
Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D5434314753364D465238432D50422020
Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D5434314753364D465238432D50422020
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0xEF), Broadcom BCM43xx 1.0 (5.106.98.100.22)
Bluetooth: Version 4.2.0f6 12982, 3 services, 15 devices, 1 incoming serial ports
Network Service: Wi-Fi, AirPort, en0
Serial ATA Device: APPLE SSD SM768E, 751.28 GB
USB Device: Hub
USB Device: FaceTime HD Camera (Built-in)
USB Device: Hub
USB Device: Hub
USB Device: Apple Internal Keyboard / Trackpad
USB Device: BRCM20702 Hub
USB Device: Bluetooth USB Host Controller
Thunderbolt Bus: MacBook Pro, Apple Inc., 23.4

jreback · 2013-10-31T10:17:33Z

you think that the contents of the csv, the code you are using to read, and your python/pandas version woulud be useful?

jtratner · 2013-10-31T11:26:20Z

Also, please consider whether AppNap is a factor (ie is Python specifically allowed? Are you letting the window slide out of focus?)

jtratner · 2013-10-31T11:29:22Z

finally, please tell us whether you see the same behavior in a stable Python version like 2.7.5 or 3.3. Bonus points if you edit down the size of your file to be just what's involved in this specific issue.

venuktan · 2013-10-31T17:45:43Z

yes , I am able to replicate the error with 2.7.5 too .

Here the full error info.
Process: Python [565]
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: pycharm [163]
Responsible: pycharm [163]
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: 2013-10-31 10:44:35.330 -0700
OS Version: Mac OS X 10.9 (13A603)
Report Version: 11
Anonymous UUID: 592E522A-F4DC-667B-6F11-E35383BBC4BE

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 000000010b025000-000000010b026000 [ 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 0x000000010b4ff567 _extract_pyvals + 403
1 umath.so 0x000000010b501ea4 _get_bufsize_errmask + 49
2 umath.so 0x000000010b4ffad4 PyUFunc_GenericFunction + 1181
3 umath.so 0x000000010b5037b7 ufunc_generic_call + 307
4 org.python.python 0x000000010b034f72 PyObject_Call + 101
5 org.python.python 0x000000010b0aedf5 PyEval_EvalFrameEx + 15416
6 org.python.python 0x000000010b0ab093 PyEval_EvalCodeEx + 1641
7 org.python.python 0x000000010b0aaa24 PyEval_EvalCode + 54
8 org.python.python 0x000000010b0bf0bc PyImport_ExecCodeModuleEx + 247
9 org.python.python 0x000000010b0c1c00 0x10b02b000 + 617472
10 org.python.python 0x000000010b0c2649 0x10b02b000 + 620105
11 org.python.python 0x000000010b0c2225 0x10b02b000 + 619045
12 org.python.python 0x000000010b0c0522 PyImport_ImportModuleLevel + 1153
13 org.python.python 0x000000010b0a6776 0x10b02b000 + 505718
14 org.python.python 0x000000010b034f72 PyObject_Call + 101
15 org.python.python 0x000000010b0b101f PyEval_CallObjectWithKeywords + 93
16 org.python.python 0x000000010b0ae110 PyEval_EvalFrameEx + 12115
17 org.python.python 0x000000010b0ab093 PyEval_EvalCodeEx + 1641
18 org.python.python 0x000000010b0aaa24 PyEval_EvalCode + 54
19 org.python.python 0x000000010b0bf0bc PyImport_ExecCodeModuleEx + 247
20 org.python.python 0x000000010b0c1c00 0x10b02b000 + 617472
21 org.python.python 0x000000010b0c2649 0x10b02b000 + 620105
22 org.python.python 0x000000010b0c2225 0x10b02b000 + 619045
23 org.python.python 0x000000010b0c0522 PyImport_ImportModuleLevel + 1153
24 org.python.python 0x000000010b0a6776 0x10b02b000 + 505718
25 org.python.python 0x000000010b034f72 PyObject_Call + 101
26 org.python.python 0x000000010b0b101f PyEval_CallObjectWithKeywords + 93
27 org.python.python 0x000000010b0ae110 PyEval_EvalFrameEx + 12115
28 org.python.python 0x000000010b0ab093 PyEval_EvalCodeEx + 1641
29 org.python.python 0x000000010b0aaa24 PyEval_EvalCode + 54
30 org.python.python 0x000000010b0bf0bc PyImport_ExecCodeModuleEx + 247
31 org.python.python 0x000000010b0c1c00 0x10b02b000 + 617472
32 org.python.python 0x000000010b0c1e7c 0x10b02b000 + 618108
33 org.python.python 0x000000010b0c2649 0x10b02b000 + 620105
34 org.python.python 0x000000010b0c2225 0x10b02b000 + 619045
35 org.python.python 0x000000010b0c0522 PyImport_ImportModuleLevel + 1153
36 org.python.python 0x000000010b0a6776 0x10b02b000 + 505718
37 org.python.python 0x000000010b034f72 PyObject_Call + 101
38 org.python.python 0x000000010b0b101f PyEval_CallObjectWithKeywords + 93
39 org.python.python 0x000000010b0ae110 PyEval_EvalFrameEx + 12115
40 org.python.python 0x000000010b0ab093 PyEval_EvalCodeEx + 1641
41 org.python.python 0x000000010b0aaa24 PyEval_EvalCode + 54
42 org.python.python 0x000000010b0bf0bc PyImport_ExecCodeModuleEx + 247
43 org.python.python 0x000000010b0c1c00 0x10b02b000 + 617472
44 org.python.python 0x000000010b0c2649 0x10b02b000 + 620105
45 org.python.python 0x000000010b0c2225 0x10b02b000 + 619045
46 org.python.python 0x000000010b0c0522 PyImport_ImportModuleLevel + 1153
47 org.python.python 0x000000010b0a6776 0x10b02b000 + 505718
48 org.python.python 0x000000010b034f72 PyObject_Call + 101
49 org.python.python 0x000000010b0b101f PyEval_CallObjectWithKeywords + 93
50 org.python.python 0x000000010b0ae110 PyEval_EvalFrameEx + 12115
51 org.python.python 0x000000010b0ab093 PyEval_EvalCodeEx + 1641
52 org.python.python 0x000000010b0aaa24 PyEval_EvalCode + 54
53 org.python.python 0x000000010b0bf0bc PyImport_ExecCodeModuleEx + 247
54 org.python.python 0x000000010b0c1c00 0x10b02b000 + 617472
55 org.python.python 0x000000010b0c1e7c 0x10b02b000 + 618108
56 org.python.python 0x000000010b0c2649 0x10b02b000 + 620105
57 org.python.python 0x000000010b0c2225 0x10b02b000 + 619045
58 org.python.python 0x000000010b0c0522 PyImport_ImportModuleLevel + 1153
59 org.python.python 0x000000010b0a6776 0x10b02b000 + 505718
60 org.python.python 0x000000010b034f72 PyObject_Call + 101
61 org.python.python 0x000000010b0b101f PyEval_CallObjectWithKeywords + 93
62 org.python.python 0x000000010b0ae110 PyEval_EvalFrameEx + 12115
63 org.python.python 0x000000010b0ab093 PyEval_EvalCodeEx + 1641
64 org.python.python 0x000000010b0aaa24 PyEval_EvalCode + 54
65 org.python.python 0x000000010b0bf0bc PyImport_ExecCodeModuleEx + 247
66 org.python.python 0x000000010b0c1c00 0x10b02b000 + 617472
67 org.python.python 0x000000010b0c2649 0x10b02b000 + 620105
68 org.python.python 0x000000010b0c2225 0x10b02b000 + 619045
69 org.python.python 0x000000010b0c0522 PyImport_ImportModuleLevel + 1153
70 org.python.python 0x000000010b0a6776 0x10b02b000 + 505718
71 org.python.python 0x000000010b034f72 PyObject_Call + 101
72 org.python.python 0x000000010b0b101f PyEval_CallObjectWithKeywords + 93
73 org.python.python 0x000000010b0ae110 PyEval_EvalFrameEx + 12115
74 org.python.python 0x000000010b0ab093 PyEval_EvalCodeEx + 1641
75 org.python.python 0x000000010b0aaa24 PyEval_EvalCode + 54
76 org.python.python 0x000000010b0bf0bc PyImport_ExecCodeModuleEx + 247
77 org.python.python 0x000000010b0c1c00 0x10b02b000 + 617472
78 org.python.python 0x000000010b0c1e7c 0x10b02b000 + 618108
79 org.python.python 0x000000010b0c2649 0x10b02b000 + 620105
80 org.python.python 0x000000010b0c2225 0x10b02b000 + 619045
81 org.python.python 0x000000010b0c0557 PyImport_ImportModuleLevel + 1206
82 org.python.python 0x000000010b0a6776 0x10b02b000 + 505718
83 org.python.python 0x000000010b034f72 PyObject_Call + 101
84 org.python.python 0x000000010b0b101f PyEval_CallObjectWithKeywords + 93
85 org.python.python 0x000000010b0ae110 PyEval_EvalFrameEx + 12115
86 org.python.python 0x000000010b0ab093 PyEval_EvalCodeEx + 1641
87 org.python.python 0x000000010b0aaa24 PyEval_EvalCode + 54
88 org.python.python 0x000000010b0c9c2c 0x10b02b000 + 650284
89 org.python.python 0x000000010b0c9cd3 PyRun_FileExFlags + 137
90 org.python.python 0x000000010b0c9821 PyRun_SimpleFileExFlags + 718
91 org.python.python 0x000000010b0da363 Py_Main + 2995
92 libdyld.dylib 0x00007fff96a985fd start + 1

Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x000000010ce0fa28 rbx: 0x0000000000000000 rcx: 0x460010815b3857f5 rdx: 0x0000000000000000
rdi: 0x000000010b520326 rsi: 0x00007fff54bd5c70 rbp: 0x00007fff54bd5de0 rsp: 0x00007fff54bd5db0
r8: 0x0000000000000000 r9: 0x0800000000000100 r10: 0x2000000000000200 r11: 0x0000000001901a59
r12: 0x00007fff54bd5ff8 r13: 0x00007fff54bd5ffc r14: 0x00007fff54bd5ff8 r15: 0x0000000000000000
rip: 0x000000010b4ff567 rfl: 0x0000000000010202 cr2: 0x0000000000000000

Logical CPU: 2
Error Code: 0x00000006
Trap Number: 14

Binary Images:
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External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 308
thread_create: 0
thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=97.4M resident=36.3M(37%) swapped_out_or_unallocated=61.1M(63%)
Writable regions: Total=100.8M written=24.1M(24%) resident=29.6M(29%) swapped_out=0K(0%) unallocated=71.2M(71%)

REGION TYPE VIRTUAL
=========== =======
Kernel Alloc Once 4K
MALLOC 91.9M
MALLOC (admin) 16K
STACK GUARD 56.0M
Stack 8192K
VM_ALLOCATE 16K
__DATA 2768K
__LINKEDIT 68.6M
__TEXT 28.8M
__UNICODE 544K
shared memory 4K
=========== =======
TOTAL 256.6M

Model: MacBookPro10,1, BootROM MBP101.00EE.B03, 4 processors, Intel Core i7, 2.7 GHz, 16 GB, SMC 2.3f36
Graphics: Intel HD Graphics 4000, Intel HD Graphics 4000, Built-In, 1024 MB
Graphics: NVIDIA GeForce GT 650M, NVIDIA GeForce GT 650M, PCIe, 1024 MB
Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D5434314753364D465238432D50422020
Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D5434314753364D465238432D50422020
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0xEF), Broadcom BCM43xx 1.0 (5.106.98.100.22)
Bluetooth: Version 4.2.0f6 12982, 3 services, 15 devices, 1 incoming serial ports
Network Service: Wi-Fi, AirPort, en0
Serial ATA Device: APPLE SSD SM768E, 751.28 GB
USB Device: Hub
USB Device: FaceTime HD Camera (Built-in)
USB Device: Hub
USB Device: Hub
USB Device: BRCM20702 Hub
USB Device: Bluetooth USB Host Controller
USB Device: Apple Internal Keyboard / Trackpad
Thunderbolt Bus: MacBook Pro, Apple Inc., 23.4

jtratner · 2013-10-31T21:17:35Z

you still haven't posted the code you used to generate this. There's no
effective way to determine what's going on if you don't have a minimal
reproducible example.

venuktan · 2013-11-01T03:11:49Z

Here the code that is generating the error:

Python 2.7.6rc1 (v2.7.6rc1:4913d0e9be30+, Oct 27 2013, 20:52:11)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

import pandas as pd
pd.read_csv('/Users/venuktangirala/ratings.csv')
Segmentation fault: 11

venuktan · 2013-11-01T03:13:20Z

here is the head of the ratings file

1,809,4.0
1,601,5.0
1,238,5.0
1,664,4.5
1,3049,3.0
1,121,4.5
1,85,4.5
1,4327,2.5
1,329,5.0
1,13,4.0
1,63,3.5

jtratner · 2013-11-01T03:20:07Z

So if you read just those lines in, you get the segmentation fault? Just need to see whether it's some issue with length/width/whatever. Maybe you could put the data on Dropbox/gist or something? [if it's not private] Just need to be able to reproduce it.

venuktan · 2013-11-01T03:29:12Z

Here is the google drive link:
https://drive.google.com/file/d/0B73X9MAO_G8yRVpza0RtRTJoMlU/edit?usp=sharing

venuktan · 2013-11-01T03:33:44Z

I get the same error even with just 10 lines in the file.

jreback · 2013-11-01T10:14:24Z

this is a bug in mavericks; try the test and solution here

http://stackoverflow.com/questions/19531969/segmentation-fault-11-in-os-x

jtratner · 2013-11-01T11:54:50Z

To be clear, if you run this as a script it doesn't fail?

As an aside, I think you also might be able to get around this by
installing Python with homebrew (because I believe it comes with its own
libedit).

TomAugspurger · 2013-11-01T13:19:52Z

Homebrew python works fine on Mavericks.

ned-deily · 2013-11-01T17:26:22Z

Unless I am missing something, there is no indication in the crash traces that this is related to the readline segfault. In any case, the first crash is with 2.7.6rc1 in which the readline problem is fixed and the second is with the Apple-supplied system python which does not have the problem anyway.

ned-deily · 2013-11-01T17:32:38Z

Googling for umath.so finds this: numpy/numpy#3962

venuktan · 2013-11-01T17:38:14Z

It fails even when running as a script, I will try the homebrew version of python

ned-deily · 2013-11-01T17:47:54Z

venuktan, you should only need to install a newer version of Numpy. The problem is there.

rjurney · 2013-11-01T22:06:49Z

I built numpy from latest source, and the problem still exists.

jtratner · 2013-11-01T22:09:23Z

are we saying this is a numpy issue?

ned-deily · 2013-11-01T22:10:12Z

Are you sure that that particular fix is actually in the source you used? You need to show the stack trace from the python crash to be able to tell where the segfault really happened.

rjurney · 2013-11-01T22:11:41Z

It was committed to master, and I checked out master. Not sure otherwise. How do I show the stack trace?

ned-deily · 2013-11-01T22:14:13Z

jratner, the traces that venuktan provided above indicate a crash in Numpy that is consistent with the Numpy issue I linked above. rjurney, there may be log files in ~/Library/Logs/DiagnosticReports. Without a stack trace, it's not certain that rjurney is seeing the same problem, of course.

jtratner · 2013-11-01T22:20:17Z

okay, then probably beneficial to move this issue to numpy instead? Going to close this for now unless it's demonstrated that it's a pandas issue.

rjurney · 2013-11-01T22:20:36Z

I checked, my version of numpy is '1.9.0.dev-54d3559'

rjurney · 2013-11-01T22:27:37Z

Process: Python [10688]
Path: /Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier: Python
Version: 2.7.6rc1 (2.7.6rc1)
Code Type: X86-64 (Native)
Parent Process: bash [10210]
Responsible: Terminal [424]
User ID: 501

Date/Time: 2013-11-01 00:09:12.322 -0700
OS Version: Mac OS X 10.9 (13A603)
Report Version: 11
Anonymous UUID: 0EDCD4EC-A236-45AB-8B7F-E007D20296B5

Sleep/Wake UUID: 89AC84A0-9F0B-40E8-890F-4FC2B6FB598F

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 0000000100000000-0000000100001000 [ 4K] r-x/rwx SM=COW /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 0x000000010374b567 _extract_pyvals + 403
1 umath.so 0x000000010374dea4 _get_bufsize_errmask + 49
2 umath.so 0x000000010374bad4 PyUFunc_GenericFunction + 1181
3 umath.so 0x000000010374f7b7 ufunc_generic_call + 307
4 org.python.python 0x000000010000c702 PyObject_Call + 98
5 org.python.python 0x00000001000c03f0 PyEval_EvalFrameEx + 12368
6 org.python.python 0x00000001000c338a PyEval_EvalFrameEx + 24554
7 org.python.python 0x00000001000c338a PyEval_EvalFrameEx + 24554
8 org.python.python 0x00000001000c338a PyEval_EvalFrameEx + 24554
9 org.python.python 0x00000001000c338a PyEval_EvalFrameEx + 24554
10 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
11 org.python.python 0x000000010003e280 function_call + 176
12 org.python.python 0x000000010000c702 PyObject_Call + 98
13 org.python.python 0x000000010001eded instancemethod_call + 365
14 org.python.python 0x000000010000c702 PyObject_Call + 98
15 org.python.python 0x00000001000c03f0 PyEval_EvalFrameEx + 12368
16 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
17 org.python.python 0x00000001000c2b80 PyEval_EvalFrameEx + 22496
18 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
19 org.python.python 0x000000010003e280 function_call + 176
20 org.python.python 0x000000010000c702 PyObject_Call + 98
21 org.python.python 0x000000010001eded instancemethod_call + 365
22 org.python.python 0x000000010000c702 PyObject_Call + 98
23 org.python.python 0x00000001000c03f0 PyEval_EvalFrameEx + 12368
24 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
25 org.python.python 0x00000001000c2b80 PyEval_EvalFrameEx + 22496
26 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
27 org.python.python 0x00000001000c2b80 PyEval_EvalFrameEx + 22496
28 org.python.python 0x00000001000c338a PyEval_EvalFrameEx + 24554
29 org.python.python 0x00000001000c338a PyEval_EvalFrameEx + 24554
30 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
31 org.python.python 0x000000010003e280 function_call + 176
32 org.python.python 0x000000010000c702 PyObject_Call + 98
33 org.python.python 0x000000010001eded instancemethod_call + 365
34 org.python.python 0x000000010000c702 PyObject_Call + 98
35 org.python.python 0x00000001000bc0e7 PyEval_CallObjectWithKeywords + 87
36 org.python.python 0x000000010007a75a slot_tp_str + 58
37 org.python.python 0x000000010005beba _PyObject_Str + 106
38 org.python.python 0x000000010005bf85 PyObject_Str + 21
39 org.python.python 0x000000010006bca2 string_new + 98
40 org.python.python 0x0000000100075e53 type_call + 51
41 org.python.python 0x000000010000c702 PyObject_Call + 98
42 org.python.python 0x00000001000c03f0 PyEval_EvalFrameEx + 12368
43 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
44 org.python.python 0x000000010003e280 function_call + 176
45 org.python.python 0x000000010000c702 PyObject_Call + 98
46 org.python.python 0x000000010001eded instancemethod_call + 365
47 org.python.python 0x000000010000c702 PyObject_Call + 98
48 org.python.python 0x00000001000bc0e7 PyEval_CallObjectWithKeywords + 87
49 org.python.python 0x000000010007a6ba slot_tp_repr + 58
50 org.python.python 0x000000010005bb75 PyObject_Repr + 117
51 org.python.python 0x00000001000c31a9 PyEval_EvalFrameEx + 24073
52 org.python.python 0x00000001000c338a PyEval_EvalFrameEx + 24554
53 org.python.python 0x00000001000c338a PyEval_EvalFrameEx + 24554
54 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
55 org.python.python 0x000000010003e280 function_call + 176
56 org.python.python 0x000000010000c702 PyObject_Call + 98
57 org.python.python 0x000000010001eded instancemethod_call + 365
58 org.python.python 0x000000010000c702 PyObject_Call + 98
59 org.python.python 0x000000010007a4ba slot_tp_call + 74
60 org.python.python 0x000000010000c702 PyObject_Call + 98
61 org.python.python 0x00000001000c03f0 PyEval_EvalFrameEx + 12368
62 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
63 org.python.python 0x00000001000c2b80 PyEval_EvalFrameEx + 22496
64 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
65 org.python.python 0x00000001000c2b80 PyEval_EvalFrameEx + 22496
66 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
67 org.python.python 0x000000010003e280 function_call + 176
68 org.python.python 0x000000010000c702 PyObject_Call + 98
69 org.python.python 0x000000010001eded instancemethod_call + 365
70 org.python.python 0x000000010000c702 PyObject_Call + 98
71 org.python.python 0x000000010007a4ba slot_tp_call + 74
72 org.python.python 0x000000010000c702 PyObject_Call + 98
73 org.python.python 0x00000001000bc0e7 PyEval_CallObjectWithKeywords + 87
74 org.python.python 0x00000001000c1cc8 PyEval_EvalFrameEx + 18728
75 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
76 org.python.python 0x00000001000c3aba PyEval_EvalFrameEx + 26394
77 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
78 org.python.python 0x00000001000c2b80 PyEval_EvalFrameEx + 22496
79 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
80 org.python.python 0x00000001000c2b80 PyEval_EvalFrameEx + 22496
81 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
82 org.python.python 0x00000001000c2b80 PyEval_EvalFrameEx + 22496
83 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
84 org.python.python 0x00000001000c2b80 PyEval_EvalFrameEx + 22496
85 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
86 org.python.python 0x00000001000c2b80 PyEval_EvalFrameEx + 22496
87 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
88 org.python.python 0x00000001000c2b80 PyEval_EvalFrameEx + 22496
89 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
90 org.python.python 0x000000010003e280 function_call + 176
91 org.python.python 0x000000010000c702 PyObject_Call + 98
92 org.python.python 0x00000001000beeef PyEval_EvalFrameEx + 6991
93 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
94 org.python.python 0x00000001000c2b80 PyEval_EvalFrameEx + 22496
95 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
96 org.python.python 0x00000001000c4866 PyEval_EvalCode + 54
97 org.python.python 0x00000001000e90ee PyRun_FileExFlags + 174
98 org.python.python 0x00000001000e938a PyRun_SimpleFileExFlags + 458
99 org.python.python 0x000000010010040d Py_Main + 3101
100 org.python.python 0x0000000100000f14 0x100000000 + 3860

Thread 1:
0 libsystem_kernel.dylib 0x00007fff8b992716 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff8ce39c3b _pthread_cond_wait + 727
2 org.python.python 0x00000001000fd824 PyThread_acquire_lock + 116
3 org.python.python 0x0000000100102215 lock_PyThread_acquire_lock + 69
4 org.python.python 0x00000001000c273d PyEval_EvalFrameEx + 21405
5 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
6 org.python.python 0x00000001000c2b80 PyEval_EvalFrameEx + 22496
7 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
8 org.python.python 0x00000001000c2b80 PyEval_EvalFrameEx + 22496
9 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
10 org.python.python 0x000000010003e280 function_call + 176
11 org.python.python 0x000000010000c702 PyObject_Call + 98
12 org.python.python 0x00000001000beeef PyEval_EvalFrameEx + 6991
13 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
14 org.python.python 0x00000001000c2b80 PyEval_EvalFrameEx + 22496
15 org.python.python 0x00000001000c338a PyEval_EvalFrameEx + 24554
16 org.python.python 0x00000001000c338a PyEval_EvalFrameEx + 24554
17 org.python.python 0x00000001000c4746 PyEval_EvalCodeEx + 2118
18 org.python.python 0x000000010003e280 function_call + 176
19 org.python.python 0x000000010000c702 PyObject_Call + 98
20 org.python.python 0x000000010001eded instancemethod_call + 365
21 org.python.python 0x000000010000c702 PyObject_Call + 98
22 org.python.python 0x00000001000bc0e7 PyEval_CallObjectWithKeywords + 87
23 org.python.python 0x0000000100102727 t_bootstrap + 71
24 libsystem_pthread.dylib 0x00007fff8ce37899 _pthread_body + 138
25 libsystem_pthread.dylib 0x00007fff8ce3772a _pthread_start + 137
26 libsystem_pthread.dylib 0x00007fff8ce3bfc9 thread_start + 13

Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000105ac2680 rbx: 0x0000000000000000 rcx: 0x000000010376c326 rdx: 0x0000000000000000
rdi: 0x0000000000000000 rsi: 0x00007fff5fbf5cf0 rbp: 0x00007fff5fbf5e40 rsp: 0x00007fff5fbf5e10
r8: 0x0000000000000000 r9: 0x00007fff5fbf5f48 r10: 0x00000000996c66fd r11: 0x000000000235cd9e
r12: 0x00007fff5fbf6058 r13: 0x00007fff5fbf605c r14: 0x00007fff5fbf6058 r15: 0x0000000000000000
rip: 0x000000010374b567 rfl: 0x0000000000010206 cr2: 0x0000000000000000

Logical CPU: 2
Error Code: 0x00000006
Trap Number: 14

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jtratner · 2013-11-01T22:28:23Z

General note - if you're using a dev version of numpy, please build pandas with a supported version (which should include 1.8 soon) before posting a bug report, so we can:

Tell whether it's a numpy or pandas issue.
Figure out how to debug it.

Also, please post your stack traces as gists so they don't pollute inboxes and such. I strongly recommend you move this to numpy - nothing pandas devs can do to resolve this for you.

rjurney · 2013-11-01T22:30:12Z

Sorry about the pastie. I just switched from the latest stable/pip install of numpy to the latest dev in an attempt to resolve the issue. If this was a numpy issue, that should have fixed it. It seems not to be?

jtratner · 2013-11-01T22:32:26Z

not necessarily, maybe a mavericks issue? I and others use OSX (though I'm using an earlier version) and I don't see this problem.

rjurney · 2013-11-01T22:32:53Z

Looks like it is a numpy issue. It is a Mavericks issue, though.

venuktan · 2013-11-01T22:33:56Z

rjurney,

are you getting the same problem with numpy?
what is the numpy function that is giving you this problem.

ned-deily · 2013-11-01T22:36:51Z

rjurney, your stack trace shows the same crash as venuktan's. I'm no expert on Numpy or pandas but it sure looks to me like the Numpy problem in that linked issue. I only got involved here to establish that it was not the Mavericks readline problem in Python. I'm going to bow out now. Good luck!

venuktan · 2013-11-01T22:44:02Z

I dont think its a numpy issue as this works flawlessly

data = np.genfromtxt('/Users/venuktangirala/rat1.csv', dtype=float, delimiter=',', names=True)

the same does not work with pandas and crashes with segmentation fault 11.
Have no idea how you can say its a numpy issue.

jtratner · 2013-11-01T22:46:20Z

thought it was numpy because @ned-deily and other links to numpy issues. So everything else works but read_csv?

What version of pandas are you using?

venuktan · 2013-11-01T22:55:45Z

pandas (0.12.0-943-gaef5061)
numpy (1.9.0.dev-54d3559)

jtratner · 2013-11-01T23:08:05Z

Can you import pandas or do anything else?
What happens if you pass read_csv a buffer?
What happens if you do read_csv and specify the Python engine?
Can you check out v0.12.0, build it and see if you still see the same thing? If that doesn't work, please try v0.11.0.
Can you make sure that you're building with the right compiler (i.e. clang vs. gcc)?

After that, going to need to use git bisect to locate the commit that introduced the issue (if possible) - I'm not sure how you write a script to test for segfaults -- but if I can figure it out, I'd ask you to run that with git bisect in the background.

rjurney · 2013-11-01T23:32:40Z

Check this out - you need to try the latest version of numpy:
numpy/numpy#3962

On Fri, Nov 1, 2013 at 3:55 PM, Venu K Tangirala
notifications@github.comwrote:

pandas (0.12.0-943-gaef5061)
numpy (1.9.0.dev-54d3559)

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/5396#issuecomment-27607393
.

Russell Jurney twitter.com/rjurney russell.jurney@gmail.com datasyndrome.com

venuktan · 2013-11-03T17:47:30Z

I can now for sure say this is a pandas issue and not a numpy issue from the tests below.
numpy works perfect. pandas test fails instantly.

>>> import numpy as np
>>> np.test('full')
Running unit tests for numpy
NumPy version 1.9.0.dev-54d3559
NumPy is installed in /Library/Python/2.7/site-packages/numpy-1.9.0.dev_54d3559-py2.7-macosx-10.9-intel.egg/numpy
Python version 2.7.5 (default, Nov  2 2013, 14:54:49) [GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.2.79)]
nose version 1.3.0
.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................S................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K................................................................................................................K...SK.S.......S.................................................................................SSSSSSSSSSSSSSSSSSSSS........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................S.........................................................................................................S............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K....................................................
----------------------------------------------------------------------
Ran 4682 tests in 81.786s

OK (KNOWNFAIL=5, SKIP=27)
<nose.result.TextTestResult run=4682 errors=0 failures=0>


========================================================================================================================================================================

pandas test follows:

$ nosetests pandas
Segmentation fault: 11

venuktan · 2013-11-03T17:50:09Z

@rjurney
why do you say its numpy issue ?

jtratner · 2013-11-03T18:00:30Z

I think you both have different errors. @venuktan please run through these steps and tell us what you get:

Can you import pandas or do anything else?
What happens if you pass read_csv a buffer?
What happens if you do read_csv and specify the Python engine?
Can you check out v0.12.0, build it and see if you still see the same thing? If that doesn't work, please try v0.11.0.
Can you make sure that you're building with the right compiler (i.e. clang vs. gcc)?

jtratner · 2013-11-04T12:14:56Z

Also, please make sure that your version of xcode is up to date and also try installing the scientific python stack (or just whatever you need for pandas) in a fresh virtualenv.

I've asked around and there are a number of Mavericks users who have no problems running pandas, so it seems more likely that it's something about your setup in particular.

rjurney · 2013-11-04T18:35:44Z

We may have different errors, but it seems noteworthy to me that Venuktan
and I both had the same version of numpy, which also causes Segmentation
fault 11. I think it is worth trying for him to upgrade to the very latest
numpy from github. Just my 2 cents. That resolved my problem.

On Mon, Nov 4, 2013 at 4:15 AM, Jeff Tratner notifications@github.comwrote:

Also, please make sure that your version of xcode is up to date and also
try installing the scientific python stack (or just whatever you need for
pandas) in a fresh virtualenv.

I've asked around and there are a number of Mavericks users who have no
problems running pandas, so it seems more likely that it's something about
your setup in particular.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/5396#issuecomment-27680966
.

Russell Jurney twitter.com/rjurney russell.jurney@gmail.com datasyndrome.com

jtratner · 2013-11-04T22:09:47Z

yeah, that could definitely be it. I'm also thinking it could be an environment issue (i.e. mismatched versions or something) b/c @venuktan is working with 2.7.6rc, suggesting more advanced packaging use. (maybe - I'm definitely not sure)

jtratner closed this as completed Nov 1, 2013

jtratner mentioned this issue Nov 4, 2013

segmentation fault 11 on Mavericks when reading csv with pandas fonnesbeck/ScipySuperpack#42

Closed

venuktan mentioned this issue Nov 5, 2013

numpy fails test on Mac Mavericks and default python; causes segmentaion fault 11 for pandas.read_csv numpy/numpy#4011

Closed

jreback mentioned this issue Jan 27, 2014

Installing 0.13.0 failed while building 'pandas.msgpack' extension. #6102

Closed

segmentation fault 11 on Mavericks python Python 2.7.6rc1 #5396

segmentation fault 11 on Mavericks python Python 2.7.6rc1 #5396

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