JISCMail - CCPNMR Archives

Wayne,

Was talking with Justin this morning and it seems that this problem is  
only cropping up in the pre-compiled versions of analysis.  We also  
run analysis and use updateAll (via a cron job) and our builds are  
doing fine (as of today, 02-10-09).  The only difference between our  
analysis builds is that our were built against the fink python/tcl/tk  
libraries.  Just a few more bits of information for you to mull over  
in diagnosing the problem.

J

On Feb 10, 2009, at 7:58 AM, Wayne Boucher wrote:

> Well my theory doesn't seem to have held out, at least on the Macs  
> here.
> So I put the Tiger (OSX 10.4) pre-compiled 2.0.5.1 Analysis release  
> on a
> Leopard (OSX 10.5) box and did bin/updateAll, and it installed and
> compiled 2.0.6 ok and ran ok.  (Note, when moving up versions,  
> updateAll
> gets the source code release and compiles it.  It does not get the
> pre-compiled OSX release.)  And as a second check I then did a "make
> clean" in the ccpnmr2.0/c directory and then a "make" and it did it  
> ok and
> ran ok.  So this is a puzzle.
>
> Anyway, the first thing worth knowing is if you have Leopard.  Another
> alternative for you is just to download the 2.0.6 pre-compiled  
> release and
> use that (so get it that way rather than via updateAll).  But this C
> compilation is bound to come up at some point in the future, so it's  
> worth
> trying to figure out why it's gone wrong.
>
> Wayne
>
> On Tue, 10 Feb 2009, Wayne Boucher wrote:
>
>> Right, it's a compiler problem.  So the message
>>
>>  ld warning: in /Applications/ccpnmr/python2.5/bin/python2.5, file  
>> is not
>> of required architecture
>>
>> is definitely a problem.  Can you run
>> /Applications/ccpnmr/python2.5/bin/python2.5?  I assume so, since  
>> this was
>> working for you, no?  Which would mean your Mac is happy with the
>> executable but not happy re-compiling against it (or the other stuff
>> there).  Is your Mac Leopard (10.5)?  The code was compiled on  
>> Tiger.  So
>> if the above is correct (namely that Leopard is happy to run Tiger  
>> code
>> but not compile against it) then it looks like I'll have to provide a
>> Leopard pre-compiled release as well as the Tiger one.
>>
>> Wayne
>>
>> On Mon, 9 Feb 2009, Justin Douglas wrote:
>>
>>> Hi Wayne
>>>
>>>> So in the /Applications/ccpnmr/bin/analysis script is the  
>>>> PYTHONPATH set
>>>> to /Applications/ccpnmr/ccpnmr2.0/python?  I guess another thing  
>>>> to check
>>>> is if bin/formatConverter is working.
>>>>
>>>
>>> FormatConverter works.
>>>
>>>
>>>> If those are both ok, then cd into /Applications/ccpnmr/ccpnmr2.0/ 
>>>> c and
>>>> type "make" and see if you get an error (but it might whizz past  
>>>> quickly).
>>>> Now the main change recently to the C code was to try and get the  
>>>> > 2 Gb
>>>> files to work, so perhaps that is causing problems.  But that's  
>>>> just a
>>>> possibility.
>>>>
>>>
>>> When I recompile the code I get the following error message:
>>>
>>> cd memops/global; make
>>> cc -L/Applications/ccpnmr/python2.5/lib -bundle -bundle_loader
>>> /Applications/ccp
>>> nmr/python2.5/bin/python2.5 -o  BlockFile.so utility.o python_util.o
>>> hash_list.o
>>> hash_table.o mem_cache.o mutex.o py_mem_cache.o block_file.o  
>>> shape_file.o
>>> int_a
>>> rray.o py_block_file.o py_shape_file.o
>>> ld warning: in /Applications/ccpnmr/python2.5/bin/python2.5, file  
>>> is not of
>>> requ
>>> ired architecture
>>> Undefined symbols:
>>>  "_PyInt_Type", referenced from:
>>>      _PyInt_Type$non_lazy_ptr in python_util.o
>>>  "_PyTuple_Size", referenced from:
>>>      _get_python_list_size in python_util.o
>>>      _get_python_int_array in python_util.o
>>>      _get_python_int_alloc_array in python_util.o
>>>      _get_python_float_array in python_util.o
>>>      _get_python_float_alloc_array in python_util.o
>>>      _get_python_float_alloc_matrix in python_util.o
>>>      _get_python_float_alloc_cube in python_util.o
>>>      _get_python_double_array in python_util.o
>>>      _get_python_double_alloc_array in python_util.o
>>>      _get_python_double_alloc_matrix in python_util.o
>>>      _set_python_float_matrix in python_util.o
>>>      _set_python_double_matrix in python_util.o
>>>      _set_python_float_cube in python_util.o
>>>  "_PyList_New", referenced from:
>>>      _get_python_int_list in python_util.o
>>>      _get_python_float_list in python_util.o
>>>      _get_python_double_list in python_util.o
>>>      _get_python_float_matrix in python_util.o
>>>      _get_python_float_matrix in python_util.o
>>>      _create_python_float_array in python_util.o
>>>  "_PyFloat_Type", referenced from:
>>>      _PyFloat_Type$non_lazy_ptr in python_util.o
>>>  "_PyInt_FromLong", referenced from:
>>>      _get_python_int_list in python_util.o
>>>  "_PyInt_AsLong", referenced from:
>>>      _get_python_int_array in python_util.o
>>>      _get_python_int_alloc_array in python_util.o
>>>      _get_python_float_array in python_util.o
>>>      _get_python_float_alloc_array in python_util.o
>>>      _get_python_double_array in python_util.o
>>>      _get_python_double_alloc_array in python_util.o
>>>  "_PyErr_Occurred", referenced from:
>>>      _initMemCache in py_mem_cache.o
>>>      _initBlockFile in py_block_file.o
>>>      _initShapeFile in py_shape_file.o
>>>  "_PyList_GetItem", referenced from:
>>>      _get_python_object_by_index in python_util.o
>>>      _get_python_int_array in python_util.o
>>>      _get_python_int_alloc_array in python_util.o
>>>      _get_python_float_array in python_util.o
>>>      _get_python_float_alloc_array in python_util.o
>>>      _get_python_float_alloc_matrix in python_util.o
>>>      _get_python_float_alloc_cube in python_util.o
>>>      _get_python_double_array in python_util.o
>>>      _get_python_double_alloc_array in python_util.o
>>>      _get_python_double_alloc_matrix in python_util.o
>>>      _set_python_float_matrix in python_util.o
>>>      _set_python_double_matrix in python_util.o
>>>      _set_python_float_cube in python_util.o
>>>  "_PyList_SetItem", referenced from:
>>>      _get_python_int_list in python_util.o
>>>      _get_python_float_list in python_util.o
>>>      _get_python_double_list in python_util.o
>>>      _get_python_float_matrix in python_util.o
>>>      _get_python_float_matrix in python_util.o
>>>      _set_python_float_array in python_util.o
>>>      _set_python_double_array in python_util.o
>>>  "_PyFloat_AsDouble", referenced from:
>>>      _get_python_float_array in python_util.o
>>>      _get_python_float_alloc_array in python_util.o
>>>      _get_python_double_array in python_util.o
>>>      _get_python_double_alloc_array in python_util.o
>>>  "__Py_NoneStruct", referenced from:
>>>      __Py_NoneStruct$non_lazy_ptr in py_mem_cache.o
>>>      __Py_NoneStruct$non_lazy_ptr in py_block_file.o
>>>      __Py_NoneStruct$non_lazy_ptr in py_shape_file.o
>>>  "_PyTuple_Type", referenced from:
>>>      _PyTuple_Type$non_lazy_ptr in python_util.o
>>>  "_PyObject_Init", referenced from:
>>>      _init_Py_Mem_cache in py_mem_cache.o
>>>      _init_Py_Block_file in py_block_file.o
>>>      _init_Py_Shape_block_file in py_block_file.o
>>>      _init_Py_Shape_file in py_shape_file.o
>>>  "_PyType_IsSubtype", referenced from:
>>>      _get_python_list_size in python_util.o
>>>      _get_python_list_size in python_util.o
>>>      _get_python_object_by_index in python_util.o
>>>      _get_python_object_by_index in python_util.o
>>>      _get_python_object_by_index in python_util.o
>>>      _get_python_int_array in python_util.o
>>>      _get_python_int_array in python_util.o
>>>      _get_python_int_array in python_util.o
>>>      _get_python_int_alloc_array in python_util.o
>>>      _get_python_int_alloc_array in python_util.o
>>>      _get_python_int_alloc_array in python_util.o
>>>      _get_python_float_array in python_util.o
>>>      _get_python_float_array in python_util.o
>>>      _get_python_float_array in python_util.o
>>>      _get_python_float_array in python_util.o
>>>      _get_python_float_array in python_util.o
>>>      _get_python_float_alloc_array in python_util.o
>>>      _get_python_float_alloc_array in python_util.o
>>>      _get_python_float_alloc_array in python_util.o
>>>      _get_python_float_alloc_array in python_util.o
>>>      _get_python_float_alloc_array in python_util.o
>>>      _get_python_float_alloc_matrix in python_util.o
>>>      _get_python_float_alloc_matrix in python_util.o
>>>      _get_python_float_alloc_cube in python_util.o
>>>      _get_python_float_alloc_cube in python_util.o
>>>      _get_python_double_array in python_util.o
>>>      _get_python_double_array in python_util.o
>>>      _get_python_double_array in python_util.o
>>>      _get_python_double_array in python_util.o
>>>      _get_python_double_array in python_util.o
>>>      _get_python_double_alloc_array in python_util.o
>>>      _get_python_double_alloc_array in python_util.o
>>>      _get_python_double_alloc_array in python_util.o
>>>      _get_python_double_alloc_array in python_util.o
>>>      _get_python_double_alloc_array in python_util.o
>>>      _get_python_double_alloc_matrix in python_util.o
>>>      _get_python_double_alloc_matrix in python_util.o
>>>      _set_python_float_array in python_util.o
>>>      _set_python_double_array in python_util.o
>>>      _set_python_float_matrix in python_util.o
>>>      _set_python_float_matrix in python_util.o
>>>      _set_python_double_matrix in python_util.o
>>>      _set_python_double_matrix in python_util.o
>>>      _set_python_float_cube in python_util.o
>>>      _set_python_float_cube in python_util.o
>>>  "_Py_BuildValue", referenced from:
>>>      _havePeak in py_block_file.o
>>>      _maxValue in py_block_file.o
>>>      _minValue in py_block_file.o
>>>      _getValue in py_block_file.o
>>>      _getPointValue in py_block_file.o
>>>      _getattr_py_block_file in py_block_file.o
>>>      _compareSlices in py_block_file.o
>>>      _getattr_py_shape_file in py_shape_file.o
>>>      _getattr_py_shape_file in py_shape_file.o
>>>  "_Py_FatalError", referenced from:
>>>      _initMemCache in py_mem_cache.o
>>>      _initBlockFile in py_block_file.o
>>>      _initShapeFile in py_shape_file.o
>>>  "_PyTuple_GetItem", referenced from:
>>>      _get_python_object_by_index in python_util.o
>>>      _get_python_int_array in python_util.o
>>>      _get_python_int_alloc_array in python_util.o
>>>      _get_python_float_array in python_util.o
>>>      _get_python_float_alloc_array in python_util.o
>>>      _get_python_float_alloc_matrix in python_util.o
>>>      _get_python_float_alloc_cube in python_util.o
>>>      _get_python_double_array in python_util.o
>>>      _get_python_double_alloc_array in python_util.o
>>>      _get_python_double_alloc_matrix in python_util.o
>>>      _set_python_float_matrix in python_util.o
>>>      _set_python_double_matrix in python_util.o
>>>      _set_python_float_cube in python_util.o
>>>  "_PyObject_Free", referenced from:
>>>      _delete_py_mem_cache in py_mem_cache.o
>>>      _delete_py_block_file in py_block_file.o
>>>      _delete_py_shape_file in py_shape_file.o
>>>  "_PyList_Size", referenced from:
>>>      _get_python_list_size in python_util.o
>>>      _get_python_int_array in python_util.o
>>>      _get_python_int_alloc_array in python_util.o
>>>      _get_python_float_array in python_util.o
>>>      _get_python_float_alloc_array in python_util.o
>>>      _get_python_float_alloc_matrix in python_util.o
>>>      _get_python_float_alloc_cube in python_util.o
>>>      _get_python_double_array in python_util.o
>>>      _get_python_double_alloc_array in python_util.o
>>>      _get_python_double_alloc_matrix in python_util.o
>>>      _set_python_float_array in python_util.o
>>>      _set_python_double_array in python_util.o
>>>      _set_python_float_matrix in python_util.o
>>>      _set_python_double_matrix in python_util.o
>>>      _set_python_float_cube in python_util.o
>>>  "_PyType_Type", referenced from:
>>>      _Mem_cache_type in py_mem_cache.o
>>>      _Shape_block_file_type in py_block_file.o
>>>      _Block_file_type in py_block_file.o
>>>      _Shape_file_type in py_shape_file.o
>>>  "_PyErr_NewException", referenced from:
>>>      _initMemCache in py_mem_cache.o
>>>      _initBlockFile in py_block_file.o
>>>      _initShapeFile in py_shape_file.o
>>>  "_PyFloat_FromDouble", referenced from:
>>>      _get_python_float_list in python_util.o
>>>      _get_python_double_list in python_util.o
>>>      _get_python_float_matrix in python_util.o
>>>      _set_python_float_array in python_util.o
>>>      _set_python_double_array in python_util.o
>>>  "_PyArg_ParseTuple", referenced from:
>>>      _resize in py_mem_cache.o
>>>      _init_Py_Mem_cache in py_mem_cache.o
>>>      _maxValue in py_block_file.o
>>>      _minValue in py_block_file.o
>>>      _getValue in py_block_file.o
>>>      _getPointValue in py_block_file.o
>>>      _getValues in py_block_file.o
>>>      _setValue in py_block_file.o
>>>      _setValues in py_block_file.o
>>>      _save in py_block_file.o
>>>      _planeProduct in py_block_file.o
>>>      _planeProduct in py_block_file.o
>>>      _init_Py_Block_file in py_block_file.o
>>>      _init_Py_Shape_block_file in py_block_file.o
>>>      _compareSlices in py_block_file.o
>>>      _setComponentAmplitude in py_shape_file.o
>>>      _setShapeData in py_shape_file.o
>>>      _init_Py_Shape_file in py_shape_file.o
>>>  "_Py_FindMethod", referenced from:
>>>      _getattr_py_mem_cache in py_mem_cache.o
>>>      _getattr_py_block_file in py_block_file.o
>>>      _getattr_py_shape_file in py_shape_file.o
>>>  "_PyErr_SetString", referenced from:
>>>      _resize in py_mem_cache.o
>>>      _resize in py_mem_cache.o
>>>      _init_Py_Mem_cache in py_mem_cache.o
>>>      _init_Py_Mem_cache in py_mem_cache.o
>>>      _init_Py_Mem_cache in py_mem_cache.o
>>>      _openFile in py_block_file.o
>>>      _havePeak in py_block_file.o
>>>      _havePeak in py_block_file.o
>>>      _havePeak in py_block_file.o
>>>      _havePeak in py_block_file.o
>>>      _maxValue in py_block_file.o
>>>      _maxValue in py_block_file.o
>>>      _maxValue in py_block_file.o
>>>      _maxValue in py_block_file.o
>>>      _minValue in py_block_file.o
>>>      _minValue in py_block_file.o
>>>      _minValue in py_block_file.o
>>>      _minValue in py_block_file.o
>>>      _getValue in py_block_file.o
>>>      _getValue in py_block_file.o
>>>      _getValue in py_block_file.o
>>>      _getPointValue in py_block_file.o
>>>      _getPointValue in py_block_file.o
>>>      _getPointValue in py_block_file.o
>>>      _getValues in py_block_file.o
>>>      _getValues in py_block_file.o
>>>      _getValues in py_block_file.o
>>>      _getValues in py_block_file.o
>>>      _getValues in py_block_file.o
>>>      _setValue in py_block_file.o
>>>      _setValue in py_block_file.o
>>>      _setValue in py_block_file.o
>>>      _setValues in py_block_file.o
>>>      _setValues in py_block_file.o
>>>      _setValues in py_block_file.o
>>>      _setValues in py_block_file.o
>>>      _setValues in py_block_file.o
>>>      _save in py_block_file.o
>>>      _save in py_block_file.o
>>>      _check in py_block_file.o
>>>      _planeProduct in py_block_file.o
>>>      _planeProduct in py_block_file.o
>>>      _planeProduct in py_block_file.o
>>>      _planeProduct in py_block_file.o
>>>      _planeProduct in py_block_file.o
>>>      _planeProduct in py_block_file.o
>>>      _planeProduct in py_block_file.o
>>>      _planeProduct in py_block_file.o
>>>      _init_Py_Block_file in py_block_file.o
>>>      _init_Py_Block_file in py_block_file.o
>>>      _init_Py_Block_file in py_block_file.o
>>>      _init_Py_Block_file in py_block_file.o
>>>      _init_Py_Block_file in py_block_file.o
>>>      _init_Py_Block_file in py_block_file.o
>>>      _init_Py_Block_file in py_block_file.o
>>>      _init_Py_Shape_block_file in py_block_file.o
>>>      _init_Py_Shape_block_file in py_block_file.o
>>>      _init_Py_Shape_block_file in py_block_file.o
>>>      _init_Py_Shape_block_file in py_block_file.o
>>>      _init_Py_Shape_block_file in py_block_file.o
>>>      _init_Py_Shape_block_file in py_block_file.o
>>>      _init_Py_Shape_block_file in py_block_file.o
>>>      _compareSlices in py_block_file.o
>>>      _compareSlices in py_block_file.o
>>>      _compareSlices in py_block_file.o
>>>      _compareSlices in py_block_file.o
>>>      _compareSlices in py_block_file.o
>>>      _compareSlices in py_block_file.o
>>>      _setComponentAmplitude in py_shape_file.o
>>>      _setComponentAmplitude in py_shape_file.o
>>>      _setShapeData in py_shape_file.o
>>>      _setShapeData in py_shape_file.o
>>>      _setShapeData in py_shape_file.o
>>>      _init_Py_Shape_file in py_shape_file.o
>>>      _init_Py_Shape_file in py_shape_file.o
>>>      _init_Py_Shape_file in py_shape_file.o
>>>      _init_Py_Shape_file in py_shape_file.o
>>>  "_PyList_Type", referenced from:
>>>      _PyList_Type$non_lazy_ptr in python_util.o
>>>  "_Py_InitModule4", referenced from:
>>>      _initMemCache in py_mem_cache.o
>>>      _initBlockFile in py_block_file.o
>>>      _initShapeFile in py_shape_file.o
>>>  "_PyObject_Malloc", referenced from:
>>>      _init_Py_Mem_cache in py_mem_cache.o
>>>      _init_Py_Block_file in py_block_file.o
>>>      _init_Py_Shape_block_file in py_block_file.o
>>>      _init_Py_Shape_file in py_shape_file.o
>>>  "_PyArg_ParseTupleAndKeywords", referenced from:
>>>      _havePeak in py_block_file.o
>>>  "_PyModule_AddObject", referenced from:
>>>      _initMemCache in py_mem_cache.o
>>>      _initBlockFile in py_block_file.o
>>>      _initShapeFile in py_shape_file.o
>>> ld: symbol(s) not found
>>> collect2: ld returned 1 exit status
>>> make[1]: *** [BlockFile.so] Error 1
>>> make: *** [global] Error 2
>>>
>>> Thanks,
>>>
>>> Justin
>>>
>>