[Numpy-discussion] Built Lapack, Atlas from source.... now numpy.linalg.eig() hangs at 100% CPU

Chris Colbert sccolbert@gmail....
Fri Mar 27 22:41:31 CDT 2009


Alright, building numpy against atlas from the repositories works, but this
atlas only contains the single threaded libraries. So i would like to get my
build working completely.

I think the problem has to do with how im making the atlas .so's from the .a
files. I am simply calling the command 'make ptshared' in the atlas lib
directory. The LDFLAGS of that particular makefile is set to '-melf_i386'. I
have no idea what this means, the only thing I know is that LDFLAGS has
something to do with linking, and from what I read on google, the error I am
getting is do to improperly created .so files.

I've attached both makefiles to this message, if anyone could take a look
and see if something obvious is amiss.

Thanks,

Chris

On Fri, Mar 27, 2009 at 10:32 PM, Chris Colbert <sccolbert@gmail.com> wrote:

> Ok, im getting the same error on an install of straight ubuntu 8.10
>
> the guy in this thread got the same error as me, but its not clear how he
> worked it out:
> http://www.mail-archive.com/numpy-discussion@scipy.org/msg13565.html
>
> from googling here:
> http://sources.redhat.com/ml/binutils/2004-12/msg00033.html
>
> it says that the library was not built correctly.
>
> does this mean my atlas .so's (which i built via -> make ptshared) are
> incorrect?
>
> I suppose I could just grab atlas from the repositories, but that would be
> admitting defeat.
>
> Chris
>
>
> On Fri, Mar 27, 2009 at 1:09 PM, Chris Colbert <sccolbert@gmail.com>wrote:
>
>> some other things I might mention, though I doubt they would have an
>> effect:
>>
>> When i built Atlas, I had to force it to use a 32-bit pointer length (I
>> assume this is correct for a 32-bit OS as gcc.stub_64 wasnt found on my
>> system)
>>
>> in numpy's site.cfg I only linked to the pthread .so's. Should I have also
>> linked to the single threaded counterparts in the section above? (I assumed
>> one would be overridden by the other)
>>
>> Other than those, I followed closely the instructions on scipy.org.
>>
>> Chris
>>
>>
>> On Fri, Mar 27, 2009 at 12:57 PM, Chris Colbert <sccolbert@gmail.com>wrote:
>>
>>> this is true. but not nearly as good of a learning experience :)
>>>
>>> I'm a mechanical engineer, so all of this computer science stuff is
>>> really new and interesting to me. So i'm trying my best to get a handle on
>>> exactly what is going on behind the scenes.
>>>
>>> Chris
>>>
>>>
>>> On Fri, Mar 27, 2009 at 12:36 PM, David Cournapeau <
>>> david@ar.media.kyoto-u.ac.jp> wrote:
>>>
>>>> Chris Colbert wrote:
>>>> > forgive my ignorance, but wouldn't installing atlas from the
>>>> > repositories defeat the purpose of installing atlas at all, since the
>>>> > build process optimizes it to your own cpu timings?
>>>>
>>>> Yes and no. Yes, it will be slower than a cutom-build atlas, but it will
>>>> be reasonably faster than blas/lapack. Please also keep in mind that
>>>> this mostly matters for linear algebra and big matrices.
>>>>
>>>> Thinking from another POV: how many 1000x1000 matrices could have you
>>>> inverted while wasting your time on this already :)
>>>>
>>>> cheers,
>>>>
>>>> David
>>>> _______________________________________________
>>>> Numpy-discussion mailing list
>>>> Numpy-discussion@scipy.org
>>>> http://mail.scipy.org/mailman/listinfo/numpy-discussion
>>>>
>>>
>>>
>>
>
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