How exactly would I link this manually? My sense is that I'd need to edit the
setup.py script. Is there another way?
Thanks,
Andrew
On Oct 17, 2012, at 2:01 PM, [email protected] wrote:
> can you try linking against libatlas manually? that should do it. then i'll
> to fix the setup.py
>
>
>
> Andrew Godbehere <[email protected]> schrieb:
> Hi Andy,
>
> I found _ATL_drotg defined in /opt/local/lib/libatlas.a.
> _ATL_drotg is listed as an undefined reference in libcblas.a, libf77blas.a,
> and libptcblas.a.
>
> That said, I'm mystified as to why these symbols cannot be located. Does this
> hint at a potential problem in linking?
>
> Thanks again,
> Andrew
>
> On Oct 16, 2012, at 3:26 PM, Andrew Godbehere
> <[email protected]> wrote:
>
>> Also, for some reason, scikit-learn tries to build for posix on my system,
>> rather than mac osx.
>>
>> On Oct 16, 2012, at 3:07 PM, Andrew Godbehere
>> <[email protected]> wrote:
>>
>>> Hi Andy,
>>>
>>> I was suspicious of clang, I'd rather this build with gcc. I'll look into
>>> changing that.
>>>
>>>
>>> Here's the output from distutils on blas_opt:
>>> {'extra_link_args': ['-Wl,-framework', '-Wl,Accelerate'],
>>> 'extra_compile_args': ['-msse3',
>>> '-I/System/Library/Frameworks/vecLib.framework/Headers'], 'define_macros':
>>> [('NO_ATLAS_INFO', 3)]}
>>>
>>> Do you see anything suspicious there?
>>>
>>> I'm trying to find _ATL_drotg, but I'm first having trouble locating the
>>> appropriate .so files on my system. I'll have more info once I track them
>>> down. I'll check cblas and atlas.
>>>
>>> Thanks for the help!
>>>
>>> Best,
>>> Andrew
>>>
>>> On Oct 16, 2012, at 1:11 PM, Andreas Mueller <[email protected]>
>>> wrote:
>>>
>>>> Hi Andrew.
>>>> Let's see if we can get to the bottom of this.
>>>> I'm really no expert here.
>>>>
>>>> On 10/16/2012 09:01 PM, Andrew Godbehere wrote:
>>>>> otools (as opposed to ldd) on arrayfuncs.so yields:
>>>>> (1) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
>>>>> version 169.3.0)
>>>>> (2)
>>>>> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
>>>>> (compatibility version 1.0.0, current version 4.0.0)
>>>>>
>>>>> I'm hoping this isn't an issue with OSX Accelerate.
>>>>>
>>>>> arrayfuncs.so was built as follows:
>>>>>
>>>>> /usr/bin/clang -bundle -undefined dynamic_lookup -L/opt/local/lib
>>>>> build/temp.macosx-10.8-x86_64-2.7/sklearn/utils/arrayfuncs.o
>>>>> -Lbuild/temp.macosx-10.8-x86_64-2.7 -lcblas -lm -o
>>>>> sklearn/utils/arrayfuncs.so -Wl,-framework -Wl,Accelerate
>>>>>
>>>> Err. Has any one tried building with clang yet? But I guess that's not the
>>>> problem ;)
>>>> I would have expected some atlas linker flags.
>>>> Do you by any chance know where
>>>> _ATL_drotg is defined? I have drotg from cblas and it is defined in
>>>> cblas.so. So I would guess some linker flag is missing.
>>>>
>>>> Also, could you please run:
>>>>
>>>> from numpy.distutils.system_info import get_info; print
>>>> get_info('blas_opt', 0)
>>>>
>>>> This should tell us what numpy things are good compiler flags.
>>>>
>>>> Andy
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