[Numpy-discussion] build errors

Paul Anton Letnes paul.anton.letnes@gmail....
Thu Oct 6 08:15:58 CDT 2011


You can use the BLAS and LAPACK environment variables.
export BLAS=/path/to/libatlas.so
export LAPACK=/path/to/libatlas.so
python setup.py build ....

I've recently had problems with ATLAS solving equation systems
incorrectly for certain inputs with no adequate explanation.
Re-running the same simulation but linking to Goto2 BLAS/LAPACK
instead solved the problem. Strange, yet worrisome. YMMV!

Cheers
Paul

On Thu, Oct 6, 2011 at 3:05 PM, Miah Wadud Dr (ITCS) <W.Miah@uea.ac.uk> wrote:
> Hi again,
>
> I have built the ATLAS dynamic shared libraries and now need to tell numpy to build against them which are located in a different location to where it expects them. Do you know how I can do that? The command I am using to build numpy is:
>
> python setup.py build --fcompiler=gnu95
>
> but this looks in /usr/lib64/atlas and I need it to look in another location (/gpfs/grace/atlas-3.8.4).
>
> Thanks in advance,
> Regards.
>
>>-----Original Message-----
>>From: numpy-discussion-bounces@scipy.org [mailto:numpy-discussion-
>>bounces@scipy.org] On Behalf Of Miah Wadud Dr (ITCS)
>>Sent: Thursday, October 06, 2011 11:12 AM
>>To: Discussion of Numerical Python
>>Subject: Re: [Numpy-discussion] build errors
>>
>>Hi David,
>>
>>Thanks for your reply. Nope, I didn't build the ATLAS libraries myself and am
>>trying to do that now. However, whenever I try to build the shared libraries
>>using the configure command:
>>
>>[root@cn130 linux]# ../configure -Fa alg -fPIC --prefix=/gpfs/grace/atlas-3.8.4
>>
>>it keeps building the static version. The ATLAS documentation stated that I
>>need to provide the above flags to build the dynamic ones but this doesn't seem
>>to work.
>>
>>Any help will be greatly appreciated. Thanks in advance.
>>
>>Regards,
>>Wadud.
>>
>>>-----Original Message-----
>>>From: numpy-discussion-bounces@scipy.org [mailto:numpy-discussion-
>>>bounces@scipy.org] On Behalf Of David Cournapeau
>>>Sent: Tuesday, October 04, 2011 6:40 PM
>>>To: Discussion of Numerical Python
>>>Subject: Re: [Numpy-discussion] build errors
>>>
>>>On Tue, Oct 4, 2011 at 11:54 AM, Miah Wadud Dr (ITCS) <W.Miah@uea.ac.uk>
>>wrote:
>>>> Hello numpy users,
>>>>
>>>> I am trying to build numpy 1.6.1 and am having problems. It prints the
>>>following error message:
>>>>
>>>> gcc -pthread -shared build/temp.linux-x86_64-
>>>2.4/numpy/core/blasdot/_dotblas.o -L/usr/lib64/atlas -Lbuild/temp.linux-
>>x86_64-
>>>2.4 -lptf77blas -lptcblas -latlas -o build/lib.linux-x86_64-
>>>2.4/numpy/core/_dotblas.so
>>>> /usr/bin/ld: /usr/lib64/atlas/libptcblas.a(cblas_dptgemm.o): relocation
>>>R_X86_64_32 against `a local symbol' can not be used when making a shared
>>>object; recompile with -fPIC
>>>> /usr/lib64/atlas/libptcblas.a: could not read symbols: Bad value
>>>> collect2: ld returned 1 exit status
>>>> /usr/bin/ld: /usr/lib64/atlas/libptcblas.a(cblas_dptgemm.o): relocation
>>>R_X86_64_32 against `a local symbol' can not be used when making a shared
>>>object; recompile with -fPIC
>>>> /usr/lib64/atlas/libptcblas.a: could not read symbols: Bad value
>>>> collect2: ld returned 1 exit status
>>>> error: Command "gcc -pthread -shared build/temp.linux-x86_64-
>>>2.4/numpy/core/blasdot/_dotblas.o -L/usr/lib64/atlas -Lbuild/temp.linux-
>>x86_64-
>>>2.4 -lptf77blas -lptcblas -latlas -o build/lib.linux-x86_64-
>>>2.4/numpy/core/_dotblas.so" failed with exit status 1
>>>
>>>
>>>Did you build Atlas by yourself ? If so, it is most likely not usable
>>>for shared libraries (mandatory for any python extension, including
>>>bumpy). You need to configure atlas with the option "-Fa alg -fPIC".
>>>
>>>David
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>>>NumPy-Discussion mailing list
>>>NumPy-Discussion@scipy.org
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