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

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

Following up on my own message...

I noticed that the python executable and python libraries found by cmake
don't match. cmake finds the homebrew installed python binary, but the
system installed libraries.

If I remove the homebrew python I can at least get the tests to pass (but
run into problems with various other missing python packages).  A step in
the right direction.

On Sat, May 16, 2015 at 10:11 AM, Cyrus Harmon <cyr...@gm...>
wrote:

> 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.
>
>