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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