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POpython segmentation fault when closing / quitting
 

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  1. POpython segmentation fault when closing / quitting
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    <p>I have a strange error that is now duplicated on 2 machines. It may be limited to python 2.7 64 bit, but that's not clear yet. On Mac OS X 10.7, I get: Segmentation fault: 11 and on 10.6 I get a simple "segmentation fault" whenever I close python.</p> <p>However, the error is hard to reproduce. Simple python scripts like: python -c "import sys; print sys.maxint" open and close without issue.</p> <p>I had suspected an issue with matplotlib, but similarly python -c "import pylab; pylab.plot(); pylab.show()" doesn't suffer any issues either.</p> <p>However, there are a number of different packages that DO cause segmentation faults when python closes, but not during an interactive session and not until the script is finished. So, the error doesn't affect any of my code - but it makes for a mess when running anything in 10.7 because focus-stealing error messages pop up.</p> <p>I'll make an effort to list and document the scripts / modules that lead to the crashes, but I thought I'd throw up the question now to see if anyone else has come across a similar issue.</p> <p>Here's a sample trackback (thanks for the suggestion Ned). </p> <pre><code>Process: python2.7 [42731] Path: /usr/local/bin/python Identifier: python2.7 Version: ??? (???) Code Type: X86-64 (Native) Parent Process: bash [1838] Date/Time: 2011-09-16 20:38:52.847 -0600 OS Version: Mac OS X 10.7.1 (11B2118) Report Version: 9 Interval Since Last Report: 11388 sec Crashes Since Last Report: 12 Per-App Crashes Since Last Report: 11 Anonymous UUID: CE462F4B-5DAF-482A-8901-28ADB7AB0AD6 Crashed Thread: 0 Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000008 VM Regions Near 0x8: --&gt; __TEXT 0000000100000000-0000000100001000 [ 4K] r-x/rwx SM=COW /Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7 Application Specific Information: objc[42731]: garbage collection is OFF Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 org.python.python 0x00000001000c3f71 new_threadstate + 305 1 org.python.python 0x00000001000c3fe8 PyGILState_Ensure + 40 2 h5e.so 0x0000000106558c21 __pyx_f_4h5py_3h5e_err_callback + 33 (h5e.c:2045) 3 libhdf5.7.dylib 0x0000000106323940 H5E_dump_api_stack + 144 4 libhdf5.7.dylib 0x0000000106320428 H5Eget_auto2 + 136 5 libhdf5.7.dylib 0x00000001062bf2f0 H5_term_library + 64 6 libsystem_c.dylib 0x00007fff8ff1b7d0 __cxa_finalize + 282 7 libsystem_c.dylib 0x00007fff8ff1b652 exit + 18 8 python 0x0000000100000e51 _start + 255 9 python 0x0000000100000d51 start + 33 Thread 1:: Dispatch queue: com.apple.libdispatch-manager 0 libsystem_kernel.dylib 0x00007fff8bcfd7e6 kevent + 10 1 libdispatch.dylib 0x00007fff8bdf760e _dispatch_mgr_invoke + 923 2 libdispatch.dylib 0x00007fff8bdf619e _dispatch_mgr_thread + 54 Thread 2: 0 libsystem_kernel.dylib 0x00007fff8bcfd192 __workq_kernreturn + 10 1 libsystem_c.dylib 0x00007fff8ff2a594 _pthread_wqthread + 758 2 libsystem_c.dylib 0x00007fff8ff2bb85 start_wqthread + 13 Thread 3: 0 libsystem_kernel.dylib 0x00007fff8bcfd192 __workq_kernreturn + 10 1 libsystem_c.dylib 0x00007fff8ff2a594 _pthread_wqthread + 758 2 libsystem_c.dylib 0x00007fff8ff2bb85 start_wqthread + 13 Thread 4: 0 libsystem_kernel.dylib 0x00007fff8bcfd192 __workq_kernreturn + 10 1 libsystem_c.dylib 0x00007fff8ff2a594 _pthread_wqthread + 758 2 libsystem_c.dylib 0x00007fff8ff2bb85 start_wqthread + 13 Thread 5: 0 libsystem_kernel.dylib 0x00007fff8bcfcdf2 __select + 10 1 Tcl 0x00000001022eb80b NotifierThreadProc + 558 2 libsystem_c.dylib 0x00007fff8ff288bf _pthread_start + 335 3 libsystem_c.dylib 0x00007fff8ff2bb75 thread_start + 13 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000001 rbx: 0x0000000000000001 rcx: 0x0000000000000b00 rdx: 0x00007fff5fbff034 rdi: 0x00000a0000000b03 rsi: 0x00000b0000000b00 rbp: 0x00007fff5fbff0c0 rsp: 0x00007fff5fbff0a0 r8: 0x00007fff5fbff03c r9: 0x00007fff5fbff038 r10: 0x0000000000000081 r11: 0x00000000e33a913f r12: 0x00000001062bf2b0 r13: 0x0000000000000000 r14: 0x0000000000000000 r15: 0x0000000101bd05a0 rip: 0x00000001000c3f71 rfl: 0x0000000000010202 cr2: 0x0000000000000008 Logical CPU: 0 Binary Images: 0x100000000 - 0x100000fff +python (??? - ???) &lt;BA9D2124-1753-3A21-91BE-15C8CD5FE7F3&gt; /usr/local/bin/python 0x100003000 - 0x100142fe7 +org.python.python (, [c] 2004-2011 Python Software Foundation. - ???) &lt;C6142A6D-0D50-32D9-A058-2A2BA484D94E&gt; /Library/Frameworks/Python.framework/Versions/2.7/Python --SNIP - TOO LONG-- 0x7fff98338000 - 0x7fff9841cdef libobjc.A.dylib (228.0.0 - compatibility 1.0.0) &lt;C5F2392D-B481-3A9D-91BE-3D039FFF4DEC&gt; /usr/lib/libobjc.A.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 6 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: 1288178 thread_create: 1 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=170.9M resident=77.2M(45%) swapped_out_or_unallocated=93.7M(55%) Writable regions: Total=169.1M written=87.2M(52%) resident=111.0M(66%) swapped_out=1536K(1%) unallocated=58.2M(34%) REGION TYPE VIRTUAL =========== ======= CG image 4K CG raster data 64K CG shared images 3416K CoreGraphics 16K CoreServices 1800K MALLOC 140.4M MALLOC guard page 48K Memory tag=242 12K Memory tag=251 8K STACK GUARD 56.0M Stack 10.1M VM_ALLOCATE 16.1M __CI_BITMAP 80K __DATA 15.6M __IMAGE 1256K __LINKEDIT 53.4M __TEXT 117.5M __UNICODE 544K mapped file 30.4M shared memory 308K =========== ======= TOTAL 446.8M </code></pre> <p>C code that produces the same (approximately) error: helloworld.cpp - </p> <pre><code>#include&lt;iostream&gt; using namespace std; int main() { char *blah; cout &lt;&lt; "Hello World" &lt;&lt; endl &lt;&lt; "I am the C sea" &lt;&lt; endl; cin &gt;&gt; blah; cout &lt;&lt; blah &lt;&lt; endl; return 0; } </code></pre> <p>compiled by:</p> <pre><code>g++ helloworld.cpp -o helloworld.out ./helloworld.out </code></pre> <p>Error Report #2: </p> <pre><code>Process: helloworld.out [10982] Path: /Users/USER/*/helloworld.out Identifier: helloworld.out Version: ??? (???) Code Type: X86-64 (Native) Parent Process: bash [10803] Date/Time: 2011-09-24 09:36:43.979 -0600 OS Version: Mac OS X 10.7.1 (11B2118) Report Version: 9 Interval Since Last Report: 271170 sec Crashes Since Last Report: 119 Per-App Crashes Since Last Report: 4 Anonymous UUID: CE462F4B-5DAF-482A-8901-28ADB7AB0AD6 Crashed Thread: 0 Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: 0x000000000000000d, 0x0000000000000000 VM Regions Near 0: --&gt; __TEXT 0000000104ca3000-0000000104ca4000 [ 4K] r-x/rwx SM=COW /Users/USER/*/*.out Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 helloworld.out 0x0000000104ca3d79 main + 169 1 ??? 0x0073657261757173 0 + 32481164257489267 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x0000000000000000 rcx: 0x0000000000000008 rdx: 0x0000000000000000 rdi: 0x00007fff7c8e24e8 rsi: 0x00007fab53000000 rbp: 0x00007fff648a28e0 rsp: 0x00007fff648a28d8 r8: 0x00000000fb343fb8 r9: 0x0000000000000000 r10: 0x0000000053000000 r11: 0x0000000000000246 r12: 0x0000000000000000 r13: 0x0000000000000000 r14: 0x0000000000000000 r15: 0x0000000000000000 rip: 0x0000000104ca3d79 rfl: 0x0000000000010202 cr2: 0x00007fab53001000 Logical CPU: 1 Binary Images: 0x104ca3000 - 0x104ca3ff7 +helloworld.out (??? - ???) &lt;68FD4206-E8D6-340F-B25B-E2DE6FB1D3BC&gt; /Users/USER/*/helloworld.out 0x7fff648a3000 - 0x7fff648d7ac7 dyld (195.5 - ???) &lt;4A6E2B28-C7A2-3528-ADB7-4076B9836041&gt; /usr/lib/dyld 0x7fff8bce6000 - 0x7fff8bd06fff libsystem_kernel.dylib (1699.23.2 - compatibility 1.0.0) &lt;55377210-60A0-3F33-9D45-B2D19AA91859&gt; /usr/lib/system/libsystem_kernel.dylib 0x7fff8bdf4000 - 0x7fff8be02fff libdispatch.dylib (187.5.0 - compatibility 1.0.0) &lt;698F8EFB-7075-3111-94E3-891156C88172&gt; /usr/lib/system/libdispatch.dylib 0x7fff8c415000 - 0x7fff8c41cfff libcopyfile.dylib (85.1.0 - compatibility 1.0.0) &lt;65602684-33B1-32DE-802B-050CE07659AC&gt; /usr/lib/system/libcopyfile.dylib 0x7fff8cf65000 - 0x7fff8cfa7ff7 libcommonCrypto.dylib (55010.0.0 - compatibility 1.0.0) &lt;A5B9778E-11C3-3F61-B740-1F2114E967FB&gt; /usr/lib/system/libcommonCrypto.dylib 0x7fff8cfcc000 - 0x7fff8cfccfff libkeymgr.dylib (23.0.0 - compatibility 1.0.0) &lt;61EFED6A-A407-301E-B454-CD18314F0075&gt; /usr/lib/system/libkeymgr.dylib 0x7fff8cfcd000 - 0x7fff8cfd1fff libmathCommon.A.dylib (2026.0.0 - compatibility 1.0.0) &lt;FF83AFF7-42B2-306E-90AF-D539C51A4542&gt; /usr/lib/system/libmathCommon.A.dylib 0x7fff8d001000 - 0x7fff8d006fff libcompiler_rt.dylib (6.0.0 - compatibility 1.0.0) &lt;98ECD5F6-E85C-32A5-98CD-8911230CB66A&gt; /usr/lib/system/libcompiler_rt.dylib 0x7fff8e5bb000 - 0x7fff8e5c3fff libsystem_dnssd.dylib (??? - ???) &lt;1FA8F861-9D0D-33D2-939F-5BD382718B97&gt; /usr/lib/system/libsystem_dnssd.dylib 0x7fff8e5d2000 - 0x7fff8e5d6fff libdyld.dylib (195.5.0 - compatibility 1.0.0) &lt;F1903B7A-D3FF-3390-909A-B24E09BAD1A5&gt; /usr/lib/system/libdyld.dylib 0x7fff8e67d000 - 0x7fff8e69aff7 libxpc.dylib (77.16.0 - compatibility 1.0.0) &lt;1FEBB79D-8537-38A4-882D-1E2AE212CD31&gt; /usr/lib/system/libxpc.dylib 0x7fff8e999000 - 0x7fff8e99fff7 libunwind.dylib (30.0.0 - compatibility 1.0.0) &lt;1E9C6C8C-CBE8-3F4B-A5B5-E03E3AB53231&gt; /usr/lib/system/libunwind.dylib 0x7fff8ebdd000 - 0x7fff8ebe8ff7 libc++abi.dylib (14.0.0 - compatibility 1.0.0) &lt;8FF3D766-D678-36F6-84AC-423C878E6D14&gt; /usr/lib/libc++abi.dylib 0x7fff8f110000 - 0x7fff8f111fff libsystem_sandbox.dylib (??? - ???) &lt;8D14139B-B671-35F4-9E5A-023B4C523C38&gt; /usr/lib/system/libsystem_sandbox.dylib 0x7fff8f21e000 - 0x7fff8f21ffff libunc.dylib (24.0.0 - compatibility 1.0.0) &lt;0482C762-746D-37EB-A8C9-E1048CF70462&gt; /usr/lib/system/libunc.dylib 0x7fff8f5d0000 - 0x7fff8f5d1ff7 libsystem_blocks.dylib (53.0.0 - compatibility 1.0.0) &lt;8BCA214A-8992-34B2-A8B9-B74DEACA1869&gt; /usr/lib/system/libsystem_blocks.dylib 0x7fff8feda000 - 0x7fff8ffb7fef libsystem_c.dylib (763.11.0 - compatibility 1.0.0) &lt;D48352AB-D1F1-3D8F-875C-2C807425CB8C&gt; /usr/lib/system/libsystem_c.dylib 0x7fff907e1000 - 0x7fff907e6fff libcache.dylib (47.0.0 - compatibility 1.0.0) &lt;3D114C8A-AD1F-3C78-9E8C-B8F3810740E5&gt; /usr/lib/system/libcache.dylib 0x7fff908ec000 - 0x7fff9095ffff libstdc++.6.dylib (52.0.0 - compatibility 7.0.0) &lt;6BDD43E4-A4B1-379E-9ED5-8C713653DFF2&gt; /usr/lib/libstdc++.6.dylib 0x7fff90e9b000 - 0x7fff90ec8fe7 libSystem.B.dylib (159.0.0 - compatibility 1.0.0) &lt;B4654B67-7521-3CD2-A67D-E1393C459D23&gt; /usr/lib/libSystem.B.dylib 0x7fff9165c000 - 0x7fff9165dfff libdnsinfo.dylib (395.7.0 - compatibility 1.0.0) &lt;37FEFE78-BCB5-37EC-8E99-747469BCA4C7&gt; /usr/lib/system/libdnsinfo.dylib 0x7fff91704000 - 0x7fff91740fff libsystem_info.dylib (??? - ???) &lt;BC49C624-1DAB-3A37-890F-6EFD46538424&gt; /usr/lib/system/libsystem_info.dylib 0x7fff920e2000 - 0x7fff920e3ff7 libremovefile.dylib (21.0.0 - compatibility 1.0.0) &lt;AACAD200-A346-3653-89E2-D9D10FE4DC06&gt; /usr/lib/system/libremovefile.dylib 0x7fff92227000 - 0x7fff92230fff libnotify.dylib (80.0.0 - compatibility 1.0.0) &lt;BD08553D-8088-38A8-8007-CF5C0B8F0404&gt; /usr/lib/system/libnotify.dylib 0x7fff92e3e000 - 0x7fff92e40fff libquarantine.dylib (36.0.0 - compatibility 1.0.0) &lt;A6B3CF07-A0D0-3C56-9BEC-33CBDD63CB89&gt; /usr/lib/system/libquarantine.dylib 0x7fff9385e000 - 0x7fff93864fff libmacho.dylib (800.0.0 - compatibility 1.0.0) &lt;548BAEB6-8C4C-3B0F-AB0C-7E1C960BCAB5&gt; /usr/lib/system/libmacho.dylib 0x7fff95371000 - 0x7fff9537bff7 liblaunch.dylib (392.18.0 - compatibility 1.0.0) &lt;EB5C4B29-D3B7-38AC-A646-3D445C767F03&gt; /usr/lib/system/liblaunch.dylib 0x7fff9777d000 - 0x7fff97782ff7 libsystem_network.dylib (??? - ???) &lt;4ABCEEF3-A3F9-3E06-9682-CE00F17138B7&gt; /usr/lib/system/libsystem_network.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: 8407398 thread_create: 1 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=50.0M resident=14.0M(28%) swapped_out_or_unallocated=36.1M(72%) Writable regions: Total=17.4M written=60K(0%) resident=104K(1%) swapped_out=0K(0%) unallocated=17.3M(99%) REGION TYPE VIRTUAL =========== ======= MALLOC 9396K MALLOC guard page 16K STACK GUARD 56.0M Stack 8192K __DATA 516K __LINKEDIT 47.1M __TEXT 3000K shared memory 12K =========== ======= TOTAL 123.8M Model: MacBookAir4,2, BootROM MBA41.0077.B00, 2 processors, Intel Core i7, 1.8 GHz, 4 GB, SMC 1.73f63 Graphics: Intel HD Graphics 3000, Intel HD Graphics 3000, Built-In, 384 MB Memory Module: BANK 0/DIMM0, 2 GB, DDR3, 1333 MHz, 0x80AD, 0x484D54333235533642465238432D48392020 Memory Module: BANK 1/DIMM0, 2 GB, DDR3, 1333 MHz, 0x80AD, 0x484D54333235533642465238432D48392020 AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0xE9), Broadcom BCM43xx 1.0 (5.100.98.75.10) Bluetooth: Version 4.0.0f4, 2 service, 11 devices, 1 incoming serial ports Serial ATA Device: APPLE SSD SM256C, 251 GB USB Device: FaceTime Camera (Built-in), apple_vendor_id, 0x850a, 0xfa200000 / 3 USB Device: hub_device, 0x0424 (SMSC), 0x2513, 0xfa100000 / 2 USB Device: BRCM20702 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0xfa110000 / 5 USB Device: Bluetooth USB Host Controller, apple_vendor_id, 0x821f, 0xfa113000 / 6 USB Device: Apple Internal Keyboard / Trackpad, apple_vendor_id, 0x024c, 0xfa120000 / 4 USB Device: hub_device, 0x0424 (SMSC), 0x2513, 0xfd100000 / 2 USB Device: Internal Memory Card Reader, apple_vendor_id, 0x8404, 0xfd110000 / 3 </code></pre>
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    1. COYou could try compiling or downloading the debug version of the python interpreter and run the scripts using GDB. You could at least traceback what's causing the problem then.
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    2. COIf the Python in use on OS X is a framework build, the "focus-stealing" error message should include a complete stack trace. Save and post the trace. It is not normal to get a segfault on quitting python.
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    3. COIt looks like it could have something to do with hdf5, the scientific data format. Maybe it's when you access the a certain file or data object with matplotlib?
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