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Segmentation Fault when calling md.compute_dssp #1574

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itaneja2 opened this issue Aug 5, 2020 · 6 comments
Closed

Segmentation Fault when calling md.compute_dssp #1574

itaneja2 opened this issue Aug 5, 2020 · 6 comments
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wontfix

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@itaneja2
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itaneja2 commented Aug 5, 2020 •
edited
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Running Mac OS 10.15.6 and python 3.7 and get a Seg Fault when calling compute_dssp on trajectory data for mdtraj 1.9.4. For reference, when I run this exact same setup and input on Ubuntu 18.04, I don't get the same issue.

Trace of the issue below:

Crashed Thread:        0  Dispatch queue: com.apple.main-thread

Exception Type:        EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:       KERN_INVALID_ADDRESS at 0x00007ffbe83ffff4
Exception Note:        EXC_CORPSE_NOTIFY

Termination Signal:    Segmentation fault: 11
Termination Reason:    Namespace SIGNAL, Code 0xb
Terminating Process:   exc handler [1818]

VM Regions Near 0x7ffbe83ffff4:
    MALLOC_LARGE           00007ffbe5900000-00007ffbe7660000 [ 29.4M] rw-/rwx SM=PRV  
--> 
    MALLOC_LARGE           00007ffbe8400000-00007ffbf0400000 [128.0M] rw-/rwx SM=PRV  

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   _geometry.cpython-37m-darwin.so	0x0000000126072a75 kabsch_sander + 629
1   _geometry.cpython-37m-darwin.so	0x000000012606491b dssp + 1339
2   _geometry.cpython-37m-darwin.so	0x0000000126055bf1 __pyx_pw_6mdtraj_8geometry_9_geometry_21_dssp(_object*, _object*, _object*) + 2225
3   org.python.python3            	0x000000010cadeb22 _PyMethodDef_RawFastCallKeywords + 722
4   org.python.python3            	0x000000010cadde99 _PyCFunction_FastCallKeywords + 41
5   org.python.python3            	0x000000010cbb3390 call_function + 656
6   org.python.python3            	0x000000010cbafb78 _PyEval_EvalFrameDefault + 28360
7   org.python.python3            	0x000000010cbb4108 _PyEval_EvalCodeWithName + 2888
8   org.python.python3            	0x000000010cadde54 _PyFunction_FastCallKeywords + 228
9   org.python.python3            	0x000000010cbb340c call_function + 780
10  org.python.python3            	0x000000010cbafb78 _PyEval_EvalFrameDefault + 28360
11  org.python.python3            	0x000000010cbb4108 _PyEval_EvalCodeWithName + 2888
12  org.python.python3            	0x000000010cadde54 _PyFunction_FastCallKeywords + 228
13  org.python.python3            	0x000000010cbb340c call_function + 780
14  org.python.python3            	0x000000010cbafc18 _PyEval_EvalFrameDefault + 28520
15  org.python.python3            	0x000000010cbb4108 _PyEval_EvalCodeWithName + 2888
16  org.python.python3            	0x000000010cadde54 _PyFunction_FastCallKeywords + 228
17  org.python.python3            	0x000000010cbb340c call_function + 780
18  org.python.python3            	0x000000010cbafc18 _PyEval_EvalFrameDefault + 28520
19  org.python.python3            	0x000000010cbb4108 _PyEval_EvalCodeWithName + 2888
20  org.python.python3            	0x000000010cba8c10 PyEval_EvalCode + 48
21  org.python.python3            	0x000000010cbebb9e PyRun_FileExFlags + 174
22  org.python.python3            	0x000000010cbeb13e PyRun_SimpleFileExFlags + 270
23  org.python.python3            	0x000000010cc0d8fe pymain_main + 6590
24  org.python.python3            	0x000000010cc0e2bf _Py_UnixMain + 111
25  libdyld.dylib                 	0x00007fff708e2cc9 start + 1

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x00007ffd39aa3e00  rbx: 0x00007ffbe56eafe0  rcx: 0x00000000ffffffff  rdx: 0xfffffffffffffffd
  rdi: 0x00007ffd39aa3e00  rsi: 0x00000000000001cb  rbp: 0x00007ffee3150160  rsp: 0x00007ffee3150020
   r8: 0x00007ffbe56eafe0   r9: 0x000000000000e71d  r10: 0x00000000e0000000  r11: 0x000000000000009a
  r12: 0x000000000000009a  r13: 0x00000000000003c4  r14: 0x00007ffd39665400  r15: 0x00007ffbe8400000
  rip: 0x0000000126072a75  rfl: 0x0000000000010246  cr2: 0x00007ffbe83ffff4
  
Logical CPU:     0
Error Code:      0x00000004 (no mapping for user data read)
Trap Number:     14
@rmcgibbo
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rmcgibbo commented Aug 6, 2020

Thanks for the bug report!

A few quick questions (some of which may be easier than others):
(1) What version of the clang compiler do you have?
(2) Do you think there's any way you could get a backtrace with line numbers? That would help a lot.
(3) What input triggers this? Could you make a test case to go in https://github.com/mdtraj/mdtraj/blob/master/tests/test_dssp.py that would trigger this? Do those tests run successfully for you? (i.e. either the test suite is missing something important or there's an important difference between your machine and the OS X CI environment)

@itaneja2
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itaneja2 commented Aug 6, 2020 •
edited by rmcgibbo
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  1. 11.0.3 (clang-1103.0.32.62)
  2. Not sure if this is of help, but pasting more of the error report I didn't include in the original thread:
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    0x7fff44391000 -     0x7fff4440bff7  com.apple.SystemConfiguration (1.19 - 1.19) <84F9B3BB-F7AF-3B7C-8CD0-D3C22D19619F> /System/Library/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration
    0x7fff4837b000 -     0x7fff48440fe7  com.apple.APFS (1412.141.1 - 1412.141.1) <C86A3423-E61C-335A-9D17-0B3CE5BB6467> /System/Library/PrivateFrameworks/APFS.framework/Versions/A/APFS
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    0x7fff6ea34000 -     0x7fff6eadbff7  libmecab.dylib (883.11) <2DF2B2E9-438D-326E-89C8-DD5247ABFE08> /usr/lib/libmecab.dylib
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    0x7fff6f20a000 -     0x7fff6f686ff5  libnetwork.dylib (1880.120.4) <F2B8AAA5-E093-37F1-885B-EDCD9783F1C0> /usr/lib/libnetwork.dylib
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    0x7fff6f774000 -     0x7fff6f7aaff7  libpcap.A.dylib (89.120.1) <A748C246-1484-3CBC-94DD-B4C47877AA78> /usr/lib/libpcap.A.dylib
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    0x7fff6fcdd000 -     0x7fff6fce0ffb  libutil.dylib (57) <F01467F6-23A7-37EE-A170-33CE1577B41D> /usr/lib/libutil.dylib
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    0x7fff6fe03000 -     0x7fff6fe15ff3  libz.1.dylib (76) <793D9643-CD83-3AAC-8B96-88D548FAB620> /usr/lib/libz.1.dylib
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    0x7fff706ca000 -     0x7fff706d5fff  libcommonCrypto.dylib (60165.120.1) <C095BD55-1D27-337F-9B02-885E1C7FF87A> /usr/lib/system/libcommonCrypto.dylib
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    0x7fff706e8000 -     0x7fff7077afdb  libcorecrypto.dylib (866.140.1) <0B6C52DB-5A50-3FCD-8B5E-C0C2F35857E3> /usr/lib/system/libcorecrypto.dylib
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    0x7fff70919000 -     0x7fff70930ff3  libsystem_asl.dylib (377.60.2) <7A07FF86-658E-35D7-8136-829737E98B7B> /usr/lib/system/libsystem_asl.dylib
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    0x7fff70b1a000 -     0x7fff70b4fffe  libxpc.dylib (1738.140.1) <58E276A9-EE11-3F02-9D3E-5371E604E677> /usr/lib/system/libxpc.dylib
  1. I'm pretty sure the input isn't the issue. I got this error from multiple .xtc files that didn't occur when running them on an Ubuntu machine. Btw, not sure if this is any useful information, but there are some .xtc files where I don't get the seg fault when running on Mac OS 10.15.6. I will try and get back to you on the tests though...

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rmcgibbo commented Aug 6, 2020

Thanks. I think in order to get a backtrace, you'd need to run it inside the debugger. In gdb, you can do gdb python --args /path/to/script.py, hit r and then hit bt when it crashes. On OS X I think you need to use lldb, the LLVM/clang debugger, and I don't have any experience with that, unfortunately.

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rmcgibbo commented Aug 6, 2020 •
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It looks like our OS X CI is running with Clang 10 (which already has problems -- #1572), whereas you have Clang 11. So it's possible that this is the reason we're not seeing these crashes on the CI environment.

I don't mean to pour too much work on you (I don't have a recent-ish Mac), but can you confirm whether or not you get the crash when you run the current test suite?

@itaneja2
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itaneja2 commented Aug 7, 2020

When I run the current test suite, tests 4-7 passed:

tests/test_dssp.py::test_1 SKIPPED                                                                                                                                                                   [ 13%]
tests/test_dssp.py::test_2 SKIPPED                                                                                                                                                                   [ 13%]
tests/test_dssp.py::test_3 SKIPPED                                                                                                                                                                   [ 13%]
tests/test_dssp.py::test_4 PASSED                                                                                                                                                                    [ 13%]
tests/test_dssp.py::test_5 PASSED                                                                                                                                                                    [ 13%]
tests/test_dssp.py::test_7 PASSED

@mattwthompson mattwthompson mentioned this issue Nov 4, 2020
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stale bot commented Feb 4, 2021

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

@stale stale bot added the wontfix label Feb 4, 2021
@stale stale bot closed this as completed Mar 7, 2021
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