[Numpy-discussion] Problems building NumPy with GotoBLAS

Paul Anton Letnes paul.anton.letnes@gmail....
Tue Mar 22 17:18:09 CDT 2011


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
>
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>
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