[SciPy-user] installation problem w/ scipy 0.2: flbas.so has

gvermeul at grenoble.cnrs.fr gvermeul at grenoble.cnrs.fr
Mon Jun 3 16:44:03 CDT 2002


David,

The LAPACK that comes with ATLAS is incomplete, you should merge
it with you Fortran LAPACK into a combined "Fortran/Atlas" LAPACK,
after building the ATLAS libs.

There are instructions how to do this in the Doc directory (README.lib?)
or see http://math-atlas.sourceforge.net/errata.html#completelp

-- Start quote --

Building a complete LAPACK library ATLAS does not provide a full LAPACK library.
However, there is a simple way to get ATLAS to provide its faster LAPACK
routines to a full LAPACK library. ATLAS's internal routines are distinct from
LAPACK's, so it is safe to compile ATLAS's LAPACK routines directly into a
netlib-style LAPACK library. First, download and install the standard LAPACK
library from the LAPACK homepage. Then, in your ATLAS/lib/ARCH directory (where
you should have a liblapack.a), issue the following commands: 
  mkdir tmp
  cd tmp
  ar x ../liblapack.a
  cp <your LAPACK path & lib> ../liblapack.a
  ar r ../liblapack.a *.o
  cd ..
  rm -rf tmp


 Just linking in ATLAS's liblapack.a first will not get you the best LAPACK
performance, mainly because LAPACK's untuned ILAENV will be used instead of
ATLAS's tuned one. So, if you use any LAPACK routine that is not provided by
ATLAS, it is essential that you create this hybrid LAPACK/ATLAS library in order
to get the best performance.

-- End quote --

Gerard

> I built and installed the complete lapack library (AFAIK), rebuilt atlas and
scipy, and
I'm
> still getting errors.  Here's what happens where I try to import scipy:
> 
> [marimont at serenity scipy_distutils]$ python
> Python 2.2 (#1, Dec 24 2001, 15:43:58)
> [GCC 2.96 20000731 (Red Hat Linux 7.1 2.96-98)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>  >>> import scipy
> exceptions.ImportError:
/usr/local/lib/python2.2/site-packages/scipy/linalg/flapack.so:
undefined 
> symbol: sgesdd_
> exceptions.ImportError:
/usr/local/lib/python2.2/site-packages/scipy/linalg/_flinalg.so:
undefined 
> symbol: dlaswp_
> Traceback (most recent call last):
>    File "<stdin>", line 1, in ?
>    File "/usr/local/lib/python2.2/site-packages/scipy/__init__.py", line 42, in ?
>      import special, io, linalg, stats, fftpack
>    File "/usr/local/lib/python2.2/site-packages/scipy/special/__init__.py",
line 325, in ?

>      import orthogonal
>    File "/usr/local/lib/python2.2/site-packages/scipy/special/orthogonal.py",
line 59, in
?
>      from scipy.linalg import eig
>    File "/usr/local/lib/python2.2/site-packages/scipy/linalg/__init__.py",
line 40, in ?
>      from basic import *
>    File "/usr/local/lib/python2.2/site-packages/scipy/linalg/basic.py", line
17, in ?
>      import calc_lwork
> ImportError:
/usr/local/lib/python2.2/site-packages/scipy/linalg/calc_lwork.so: undefined
symbol: 
> ieeeck_
>  >>>
> 
> I noticed in the install file with the scipy distribution that I should
include all sorts
> of version info when I ask for help -- it's below.  The only strange thing I
noticed is
that
> when I build scipy, it only listed the atlas libraries as found, not the blas
or lapack
ones,
> but when I ask for system_info, the blas and lapack ones are listed.  Does
that mean that
scipy
> isn't using the atlas versions?
> 
>    David
> 
> [root at serenity root]# python -c 'import os,sys;print os.name,sys.platform'
> posix linux2
> [root at serenity root]# uname -a
> Linux serenity 2.4.13 #1 SMP Fri Dec 21 20:53:17 PST 2001 i686 unknown
> [root at serenity root]# gcc -v
> Reading specs from /usr/lib/gcc-lib/i386-redhat-linux/2.96/specs
> gcc version 2.96 20000731 (Red Hat Linux 7.1 2.96-98)
> [root at serenity root]# g77 --version
> GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.1 2.96-98)
> Copyright (C) 1997 Free Software Foundation, Inc.
> For more version information on components of the GNU Fortran
> compilation system, especially useful when reporting bugs,
> type the command `g77 --verbose'.
> 
> GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
> You may redistribute copies of GNU Fortran
> under the terms of the GNU General Public License.
> For more information about these matters, see the file named COPYING
> or type the command `info -f g77 Copying'.
> [root at serenity root]# python -c 'import sys;print sys.version'
> 2.2 (#1, Dec 24 2001, 15:43:58)
> [GCC 2.96 20000731 (Red Hat Linux 7.1 2.96-98)]
> [root at serenity root]# python -c 'import Numeric;print Numeric.__version__'
> 21.0
> [root at serenity root]# f2py -v
> 2.13.175-1250
> [root at serenity root]# python scipy_distutils/system_info.py
> python: can't open file 'scipy_distutils/system_info.py'
> [root at serenity root]# cd /usr/local/lib/python2.2/site-packages/
> [root at serenity site-packages]# python scipy_distutils/system_info.py
> atlas_info:
>    FOUND:
>      libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
>      library_dirs = ['/usr/local/lib']
> 
> blas_info:
>    FOUND:
>      libraries = ['blas']
>      library_dirs = ['/usr/lib']
> 
> fftw_info:
>    FOUND:
>      libraries = ['fftw', 'rfftw', 'fftw_threads', 'rfftw_threads', 'sfftw',
'srfftw', 
> 'sfftw_threads', 'srfftw_threads']
>      library_dirs = ['/usr/local/lib']
>      define_macros = [('SCIPY_FFTW_H', 1), ('SCIPY_SFFTW_H', 1)]
>      include_dirs = ['/usr/local/include']
> 
> lapack_info:
>    FOUND:
>      libraries = ['lapack']
>      library_dirs = ['/usr/local/lib']
> 
> x11_info:
>    FOUND:
>      libraries = ['X11']
>      library_dirs = ['/usr/X11R6/lib']
>      include_dirs = ['/usr/X11R6/include']
> 
> [root at serenity site-packages]# python scipy_distutils/command/build_flib.py
> command: f77 -V -c /tmp/__dummy.f -o /tmp/__dummy.o
> 256 f77: invalid version number format
> command: f77 -version
> 256 f77: unrecognized option `-version'
> /usr/lib/gcc-lib/i386-redhat-linux/2.96/libg2c.a(main.o): In function `main':
> main.o(.text+0x2a): undefined reference to `MAIN__'
> collect2: ld returned 1 exit status
> command: f90 -V
> 32512 sh: f90: command not found
> command: ifc -FI -V -c /tmp/__dummy.f -o /tmp/__dummy.o
> 32512 sh: ifc: command not found
> command: efc -FI -V -c /tmp/__dummy.f -o /tmp/__dummy.o
> 32512 sh: efc: command not found
> command: f95 -V
> 32512 sh: f95: command not found
> command: fort -V
> 32512 sh: fort: command not found
> command: DF /what
> 32512 sh: DF: command not found
> command: g77 --version
> 0 GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.1 2.96-98)
> Copyright (C) 1997 Free Software Foundation, Inc.
> For more version information on components of the GNU Fortran
> compilation system, especially useful when reporting bugs,
> type the command `g77 --verbose'.
> 
> GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
> You may redistribute copies of GNU Fortran
> under the terms of the GNU General Public License.
> For more information about these matters, see the file named COPYING
> or type the command `info -f g77 Copying'.
> command: vf90 -v
> 32512 sh: vf90: command not found
> command: f90 +version
> 32512 sh: f90: command not found
> command: g77 --version
> 0 GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.1 2.96-98)
> Copyright (C) 1997 Free Software Foundation, Inc.
> For more version information on components of the GNU Fortran
> compilation system, especially useful when reporting bugs,
> type the command `g77 --verbose'.
> 
> GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
> You may redistribute copies of GNU Fortran
> under the terms of the GNU General Public License.
> For more information about these matters, see the file named COPYING
> or type the command `info -f g77 Copying'.
> command: F -V
> 32512 sh: F: command not found
> command: g77 --version
> 0 GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.1 2.96-98)
> Copyright (C) 1997 Free Software Foundation, Inc.
> For more version information on components of the GNU Fortran
> compilation system, especially useful when reporting bugs,
> type the command `g77 --verbose'.
> 
> GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
> You may redistribute copies of GNU Fortran
> under the terms of the GNU General Public License.
> For more information about these matters, see the file named COPYING
> or type the command `info -f g77 Copying'.
> Gnu 0.5.26
> 
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> SciPy-user mailing list
> SciPy-user at scipy.net
> http://www.scipy.net/mailman/listinfo/scipy-user
> 


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