[Numpy-discussion] Problems building NumPy with GotoBLAS

Giuseppe Aprea giuseppe.aprea@gmail....
Mon Mar 28 11:34:17 CDT 2011


Dear Paul Anton,

thanks a lot for your suggestion. I was also successful with

[blas]
libraries = blas
library_dirs = $PREFIX/gotoblas2/lib
[lapack]
libraries = lapack
library_dirs = $PREFIX/gotoblas2/lib

but I had compile clapack as a shared library and place a symbolic link
ln -s $PREFIX/gotoblas2/lib/libgoto2.so $PREFIX/gotoblas2/lib/libblas.so

I think your solution works better (the only difference is that I had to
define LAPACK variable before installing numpy to avoid that warning about
an optimized lapack lib missing), but what about source dirs? do you also
set BLAS_SRC and LAPACK_SRC? how?

cheers



On Tue, Mar 22, 2011 at 11:18 PM, Paul Anton Letnes <
paul.anton.letnes@gmail.com> wrote:

> I'm no expert, but I just pulled off the scipy+numpy+GotoBLAS2
> installation. From what I gather, the Makefile for libgoto2 downloads and
> compiles the generic lapack from netlib. It also wraps lapack into
> libgoto2.so/.a. I believe the idea is as long as the BLAS implementation
> is fast(TM), the lapack performance will be good.
>
> To wit*, what I did was to tell numpy where libgoto2 was:
> env BLAS=/path/to/libgoto2.so python setup.py install
> Scipy also wants the path to lapack, which is wrapped inside libgoto2:
> env BLAS=/path/to/libgoto2.so LAPACK=/path/to/libgoto2.so python setup.py
> install
> Afterwards, I added the path to LD_LIBRARY_PATH. This was on a linux
> cluster, if that matters. At any rate, I can testify that it was not a big
> job to get numpy and scipy working with goto blas.
>
> Good luck,
> Paul.
>
> *) I have notes on this on a different computer, but not available right
> now.
>
>
> On Tue, Mar 22, 2011 at 10:13 AM, Giuseppe Aprea <giuseppe.aprea@gmail.com
> > wrote:
>
>> Hi all,
>>
>> I wonder if Peter finally got Gotoblas working with numpy. I am trying
>> with gotoblas 1.13 installed in the same way:
>>
>> $ ls -R
>> .:
>> include  lib
>>
>> ./include:
>> goto
>>
>> ./include/goto:
>> blaswrap.h  cblas.h  clapack.h  f2c.h
>>
>> ./lib:
>> libgoto2.a  libgoto2_nehalemp-r1.13.a  libgoto2_nehalemp-r1.13.so libgoto2.so
>>
>> and numpy 1.5.1 with this site.cfg
>>
>> [DEFAULT]
>> library_dirs =
>> /usr/local/gcc/4.5.2/gcc/lib64:/usr/local/gcc/4.5.2/gcc/lib:/usr/local/gcc/4.5.2/gcc/lib32:/usr/local/gcc/4.5.2/gotoblas2/1.13/lib:/usr/local/gcc/4.5.2/suiteSparse/3.6.0/lib:/usr/local/gcc/4.5.2/fftw/3.2.2/lib
>> include_dirs =
>> /usr/local/gcc/4.5.2/gcc/include:/usr/local/gcc/4.5.2/gotoblas2/1.13/include/goto:/usr/local/gcc/4.5.2/suiteSparse/3.6.0/include:/usr/local/gcc/4.5.2/fftw/3.2.2/include
>> search_static_first = 1
>> [blas_opt]
>> libraries = goto2
>> language = fortran
>> [lapack_opt]
>> libraries = goto2
>> language = fortran
>> [amd]
>> amd_libs = amd
>> [umfpack]
>> umfpack_libs = umfpack
>> [fftw]
>> libraries = fftw3
>>
>> (I also tried without "_opt" and "language = fortran"); I used goto2 for
>> lapack because I read lapack should be included in libgoto (anyway things do
>> not change using "lapack"). I am quite sure the system is not using my
>> goto-lapack stuff since every time I buid i get:
>>
>> building extension "numpy.numarray._capi" sources
>> building extension "numpy.fft.fftpack_lite" sources
>> building extension "numpy.linalg.lapack_lite" sources
>> creating build/src.linux-x86_64-2.7/numpy/linalg
>> *### Warning:  Using unoptimized lapack ###*
>> *  adding 'numpy/linalg/lapack_litemodule.c' to sources.*
>>   adding 'numpy/linalg/python_xerbla.c' to sources.
>>   adding 'numpy/linalg/zlapack_lite.c' to sources.
>>   adding 'numpy/linalg/dlapack_lite.c' to sources.
>>   adding 'numpy/linalg/blas_lite.c' to sources.
>>   adding 'numpy/linalg/dlamch.c' to sources.
>>   adding 'numpy/linalg/f2c_lite.c' to sources.
>> building extension "numpy.random.mtrand" sources
>> creating build/src.linux-x86_64-2.7/numpy/random
>> C compiler: /usr/local/gcc/4.5.2//gcc/bin/gcc -DNDEBUG -g -fwrapv -O3
>> -Wall -Wstrict-prototypes -O1 -pthread -fPIC -march=native -mtune=native
>> -I/usr/local/gcc/4.5.2//gcc/include
>> -I/usr/local/gcc/4.5.2//suiteSparse/3.6.0/include
>> -I/usr/local/gcc/4.5.2//fftw/3.2.2/include -fPIC
>>
>> during numpy installation (which ends successfully). Moreover I cannot see
>> any -lgoto2 as I would have expected.
>> Incidentally, I cannot see -lamd, -lumfpack, -lfftw3 (or any reference
>> to amd, umfpack, fftw3) neither, although there seems to be something to
>> handle them in system_info.py. The failure is so complete that I must have
>> done some big mistake but I can't correct my site.cfg even after searching
>> the internet. This seems to be one of the major discussion about this topic
>> so I am asking here for some help, please.
>> Is the problem related with site.cfg or with gotoblas2 installation? Is it
>> true that gotoblas2 hosts a full lapack inside?
>>
>> thank you very much!
>>
>> giuseppe
>>
>> _______________________________________________
>> NumPy-Discussion mailing list
>> NumPy-Discussion@scipy.org
>> http://mail.scipy.org/mailman/listinfo/numpy-discussion
>>
>>
>
> _______________________________________________
> NumPy-Discussion mailing list
> NumPy-Discussion@scipy.org
> http://mail.scipy.org/mailman/listinfo/numpy-discussion
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.scipy.org/pipermail/numpy-discussion/attachments/20110328/1f9d35de/attachment.html 


More information about the NumPy-Discussion mailing list