Glad you sorted it out!
In principle I think it should be possible to run with the standard
numpy as well.
At least you are up and running now, which is the most important thing :)
Andy
On 10/18/2012 12:23 AM, Andrew Godbehere wrote:
Problem solved.
Brief: sklearn depends on builds of numpy and scipy that link to
atlas. On MacOSX, default builds of numpy and scipy through macports
link to the Accelerate framework, and not to atlas. After forcing the
atlas variants of numpy and scipy, sklearn works fine.
Action: The implication here is that there is a bug in the macports
port file. Specific variants should be listed as dependencies rather
than simply "py27-numpy" and "py27-scipy" in the case of Python 2.7.
Thanks everyone for your help!
Best,
Andrew
On Oct 17, 2012, at 3:53 PM, Andrew Godbehere
<[email protected]
<mailto:[email protected]>> wrote:
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]
<mailto:[email protected]> wrote:
can you try linking against libatlas manually? that should do it.
then i'll to fix the setup.py <http://setup.py/>
Andrew Godbehere <[email protected]
<mailto:[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]
<mailto:[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]
<mailto:[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] <mailto:[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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