[Rdkit-devel] seg faults running tests on a mac

[Cyrus H. <cyr...@gm...>]

Hi Greg,

Sorry it's been a while since I first reported my troubles on a Mac. I
continue to have problems on my MacBook Pro, but things seem to work fine
on linux for me.

The problem is that many of the tests fail with a segfault and there
doesn't seem to much information in any of the log files about the problem.
In an effort to figure out what's going on here, I've been trying to run
things under gdb.

If I run the testBV.py test under gdb I see the following:

Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: KERN_INVALID_ADDRESS at address: 0x0000000000000000
0x00000001029e7cb9 in PyInt_FromLong ()
(gdb) bt
#0  0x00000001029e7cb9 in PyInt_FromLong ()
#1  0x0000000102844908 in
boost::python::detail::keywords<1ul>::operator=<int> ()
#2  0x000000010284277a in init_module_rdBase ()
#3  0x0000000102b2f391 in boost::python::handle_exception_impl ()
#4  0x0000000102b303b9 in boost::python::detail::init_module ()
#5  0x00000001000a04ea in _PyImport_LoadDynamicModule ()
#6  0x00000001000a01d2 in import_submodule ()
#7  0x000000010009fd9c in load_next ()
#8  0x000000010009df99 in PyImport_ImportModuleLevel ()
#9  0x0000000100083459 in builtin___import__ ()
#10 0x000000010000e3b6 in PyObject_Call ()
#11 0x000000010008dd9b in PyEval_CallObjectWithKeywords ()
#12 0x000000010008a0b7 in PyEval_EvalFrameEx ()
#13 0x0000000100087df9 in PyEval_EvalCodeEx ()
#14 0x000000010008786f in PyEval_EvalCode ()
#15 0x000000010009ca46 in PyImport_ExecCodeModuleEx ()
#16 0x000000010009f731 in load_source_module ()
#17 0x000000010009f9f2 in load_package ()
#18 0x00000001000a01d2 in import_submodule ()
#19 0x000000010009fd9c in load_next ()
#20 0x000000010009df99 in PyImport_ImportModuleLevel ()
#21 0x0000000100083459 in builtin___import__ ()
#22 0x000000010000e3b6 in PyObject_Call ()
#23 0x000000010008dd9b in PyEval_CallObjectWithKeywords ()
#24 0x000000010008a0b7 in PyEval_EvalFrameEx ()
#25 0x0000000100087df9 in PyEval_EvalCodeEx ()
#26 0x000000010008786f in PyEval_EvalCode ()
#27 0x00000001000a7a2a in run_mod ()
#28 0x00000001000a7acd in PyRun_FileExFlags ()
#29 0x00000001000a766a in PyRun_SimpleFileExFlags ()
#30 0x00000001000b8d6f in Py_Main ()
#31 0x00007fff947ec5c9 in start ()

So it looks to me like things are sort of working for a while, but that
somewhere along the line I'm getting a segfault, which may in turn be
triggered by a problem loading a dylib.

I'm guessing that part of the problem is that there are a lot of moving
parts here:

1. RDKIT -- I'm using the latest git head as of today
2. Python
 a. version 2 or version 3?
   - I'm trying to get things working with python2, but python3 would be
nice at some point
 b. system installed, hombrew, or self-installed?
   - I'm trying to use the homebrew-installed python2. Perhaps this is a
mistake.
3. Python libraries (installed via pip)
4. Homebrew libraries
5. System libraries
6. Environment variables
7. etc...

What a mess...

speaking of environment variables, one thing that might be problematic for
me is that I am trying to use the following environment variables:

export PYTHONPATH=/Users/sly/projects/rdkit/
export RDBASE=/Users/sly/projects/rdkit/
export
DYLD_LIBRARY_PATH=/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources:/Users/sly/projects/rdkit/lib:/usr/local/lib:

If I don't add the system ImageIO path, cmake fails with:

dyld: Symbol not found: __cg_png_create_info_struct
  Referenced from:
/System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
  Expected in: /usr/local/lib/libPng.dylib
 in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO

Adding that to DYLD_LIBRARY_PATH at least gets things to build and has some
tests running.

Happy to provide more info if that will help figure out what's going on
here.

thanks,

Cyrus

p.s. sorry about the duplicate subscription and sending this from
not-my-normal-email account, but I'm having travel-based connectivity
issues.