On 11/25/06, Werner Hoch <werner.ho@gmx.de> wrote:
Hi David,
On Saturday 25 November 2006 03:57, David Strozzi wrote:
> There's a small problem with the linear algebra library BLAS and
> LAPACK in opensuse. These are Fortran libraries. I (and others)
> have trouble using the libraries with SciPy (python scientific
> computing package). The problem seems to be that different Fortran
> compilers use different symbol names for some output routines. When
> one compiles scipy, there are some Fortran routines that get
> compiled, I think with g77 by default (maybe not). You can compile
> and install scipy, but when you try importing it in python you get an
> error of undefined symbol _gfortran_st_write in the LAPACK library.
Can you provide a small python script that shows the bug?
Can you give some more information about your used SuSE Version and
architecture?
My system - opensuse 10.1 on an amd athlon64. I've updated several packages.
Also, I should warn you that I've compiled python 2.5 and numpy 1.0 myself, and am not using the opensuse rpm's. It may be that my setup is sufficiently non-standard that you shouldn't waste time on this!
As for a python example, start up python and type "from scipy import *". This should load all the modules, functions, etc in scipy. Here's what I get:
Python 2.5 (r25:51908, Sep 30 2006, 14:06:47)
[GCC 4.1.0 (SUSE Linux)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from scipy import *
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python2.5/site-packages/scipy/signal/__init__.py", line 9, in <modu le>
from bsplines import *
File "/usr/local/lib/python2.5/site-packages/scipy/signal/bsplines.py", line 3, in <modu le>
import scipy.special
File "/usr/local/lib/python2.5/site-packages/scipy/special/__init__.py", line 10, in <mo dule>
import orthogonal
File "/usr/local/lib/python2.5/site-packages/scipy/special/orthogonal.py", line 67, in < module>
from scipy.linalg import eig
File "/usr/local/lib/python2.5/site-packages/scipy/linalg/__init__.py", line 8, in <modu le>
from basic import *
File "/usr/local/lib/python2.5/site-packages/scipy/linalg/basic.py", line 17, in <module >
from lapack import get_lapack_funcs
File "/usr/local/lib/python2.5/site-packages/scipy/linalg/lapack.py", line 17, in <modul e>
from scipy.linalg import flapack
ImportError: /usr/lib64/libblas.so.3: undefined symbol: _gfortran_st_write
>>>
> I have the most recent blas and lapack opensuse builds (940). The
> official suse-type webpage I got these from say they were compiled
> with egcs, which is a. wrong (egcs merged back into gcc a long time
> ago) and b. ill-defined (since g77 and gfortran are both part of
> gcc).
Which package exactly are you using? One of those:
http://software.opensuse.org/download/science/SUSE_Linux_10.1/x86_64/
> As you search the web, you see that it's part of the lore that
> "Suse's BLAS is buggy, you have to compile yourself." Not good for
> Suse!
Please provide URL's it's much easier to track them.
> While I'm on it, it's not clear what implementation of BLAS opensuse
> uses. My guess is it's the reference implementation from lapack's
> page on netlib, which is not optimized. Better ones exist, like
> gotoBLAS. Maybe that can be made a suse package?
http://www.tacc.utexas.edu/resources/software/#blas
The package is not accessable from that page without login. Is there a
public place to get it?
I don't know of one. The page you give is the right place to go to download. Seems academic users can d/l the source free, but commercial people should contact someone. Don't know where opensuse falls; maybe we can ask.
> At the least it would help if it were spelled out exactly which
> Fortran compiler was used to make opensuse's blas. If they can be
> compiled to allow multiple Fortran compilers to play nicely with
> them, even better.
??