#163 output from clang 3.6's -fsanitize=undefined

[Jack Howarth]

Building pymol svn with the clang 3.6 using -fsanitize=undefined (which also requires the additional linkage on -lc++abi for _cmd.so), produces the following output at runtime.

1) On starting pymol...

ov/src/OVLexicon.cpp:108:12: runtime error: left shift of 647690595356847671 by 5 places cannot be represented in type 'ov_word' (aka 'long')
PyMOL(TM) Molecular Graphics System, Version 1.7.5.0.
Copyright (c) Schrodinger, LLC.
All Rights Reserved.

Created by Warren L. DeLano, Ph.D.

PyMOL is user-supported open-source software.  Although some versions
are freely available, PyMOL is not in the public domain.

If PyMOL is helpful in your work or study, then please volunteer 
support for our ongoing efforts to create open and affordable scientific
software by purchasing a PyMOL Maintenance and/or Support subscription.

More information can be found at "http://www.pymol.org".

Enter "help" for a list of commands.
Enter "help <command-name>" for information on a specific command.

Hit ESC anytime to toggle between text and graphics.

Detected OpenGL version 2.0 or greater. Shaders available.
Detected GLSL version 1.20.
OpenGL graphics engine:
GL_VENDOR: ATI Technologies Inc.
GL_RENDERER: ATI Radeon HD 2600 OpenGL Engine
GL_VERSION: 2.1 ATI-10.0.28
Adjusting settings to improve performance for ATI cards.
Detected 8 CPU cores. Enabled multithreaded rendering.

2) On executing the Sculpting demos menu item...

layer2/SculptCache.cpp:82:19: runtime error: left shift of negative value -1
layer2/SculptCache.cpp:108:19: runtime error: left shift of negative value -1
layer2/SculptCache.cpp:122:21: runtime error: left shift of negative value -1
PyMOL>edit_mode
mouse: three_button_editing
layer2/Sculpt.cpp:2125:22: runtime error: left shift of negative value -17
layer2/Sculpt.cpp:2150:41: runtime error: left shift of negative value -21

3) On executing the Scripted Animation menu item...

/sw/opt/llvm-3.6.0/bin/../include/c++/v1/tree:834:16: runtime error: downcast of address 0x00010c660948 with insufficient space for an object of type 'std::1::__tree_node<long, void="" *="">'
0x00010c660948: note: pointer points here
eb 7f 00 00 20 3d 90 f2 eb 7f 00 00 03 00 00 00 00 00 00 00 94 81 8c 07 01 00 00 00 52 06 39 d4
^

Use of the sanitizers is described at https://docs.python.org/devguide/clang.html.

Also according to the thread at http://lists.cs.uiuc.edu/pipermail/cfe-dev/2013-August/031191.html, the issue detected for Scripted Animation may be a false positive.

[Jack Howarth]

The first issue at pymol startup backtraces in lldb as...

(lldb) bt
thread #1: tid = 0x25e6a8, 0x0000000102804577 _cmd.soOVLexicon_GetFromCString(_OVLexicon*, char const*) [inlined] _GetCStringHash(str=0x00000001037a8ba5) at OVLexicon.cpp:106, queue = 'com.apple.main-thread', stop reason = breakpoint 1.1 * frame #0: 0x0000000102804577 _cmd.soOVLexicon_GetFromCString(_OVLexicon, char const*) [inlined] _GetCStringHash(str=0x00000001037a8ba5) at OVLexicon.cpp:106
frame #1: 0x0000000102804577 _cmd.soOVLexicon_GetFromCString(uk=0x0000000100628220, str=0x00000001037a8ba5) + 23 at OVLexicon.cpp:252 frame #2: 0x00000001034f7a62 _cmd.soPyMOL_InitAPI(I=0x0000000101057600) + 1042 at PyMOL.cpp:292
frame #3: 0x00000001034f7137 _cmd.soPyMOL_Start(I=0x0000000101057600) + 215 at PyMOL.cpp:2116 frame #4: 0x00000001034e521d _cmd.somain_common() [inlined] MainInit(G=<unavailable>) + 129 at main.cpp:1038
frame #5: 0x00000001034e519c _cmd.somain_common() [inlined] launch(own_the_options=<unavailable>) + 2529 at main.cpp:1633 frame #6: 0x00000001034e47bb _cmd.somain_common() + 59 at main.cpp:1731
frame #7: 0x00000001034e748c _cmd.somain_shared(block_input_hook=<unavailable>) + 108 at main.cpp:1718 frame #8: 0x00000001034c5baa _cmd.soCmdRunPyMOL(self=<unavailable>, args=<unavailable>) + 90 at Cmd.cpp:4553
frame #9: 0x00000001000b00f8 libpython2.7.dylibPyEval_EvalFrameEx + 19480 frame #10: 0x00000001000ab1d2 libpython2.7.dylibPyEval_EvalCodeEx + 1538
frame #11: 0x00000001000b2cb5 libpython2.7.dylibfast_function + 117 frame #12: 0x00000001000aeda1 libpython2.7.dylibPyEval_EvalFrameEx + 14529
frame #13: 0x00000001000ab1d2 libpython2.7.dylibPyEval_EvalCodeEx + 1538 frame #14: 0x00000001000aabc6 libpython2.7.dylibPyEval_EvalCode + 54
frame #15: 0x00000001000d4aa4 libpython2.7.dylibPyRun_FileExFlags + 164 frame #16: 0x00000001000d4621 libpython2.7.dylibPyRun_SimpleFileExFlags + 769
frame #17: 0x00000001000e8378 libpython2.7.dylibPy_Main + 3096 frame #18: 0x00007fff9050f5c9 libdyld.dylibstart + 1
frame #19: 0x00007fff9050f5c9 libdyld.dylib`start + 1
(lldb)

and seems to be occurring in the call to...

LEX(string);

[Thomas Holder]

1) and 2) are hash functions, they are expected to overflow.