Hi Cyrus,
I'm glad you were able to find something that works. If I had to guess, I
would say that the root cause of all of this was the homebrew version of
python confusing things.
-greg
On Sat, May 16, 2015 at 7:27 PM, Cyrus Harmon <cyrushar...@gmail.com> wrote:
> Ok, I think I've solved (or at least worked around) my python woes. The
> following seems to do the trick:
>
> export RDBASE=/Users/sly/projects/rdkit
> export PYTHONPATH=/usr/local/:${RDBASE}:
> export
> DYLD_LIBRARY_PATH=/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources:${RDBASE}/lib:/usr/local/lib:
>
> # running cmake:
> cmake \
> -D PYTHON_EXECUTABLE=/usr/local/bin/python \
> -D
> PYTHON_INCLUDE_DIR=/usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Headers
> \
> -D
> PYTHON_LIBRARY=/usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib
> \
> ..
>
> # build it
> make -j4
>
> # install
> make install
>
> # test
> ctest
>
>
>
> Now onto the next problem...
>
>
> On Sat, May 16, 2015 at 3:20 PM, Cyrus Harmon <cyrushar...@gmail.com>
> wrote:
>
>> 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 <cyrushar...@gmail.com>
>> 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.
>>>
>>>
>>
>>
>
>
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