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

David Marimont marimont at nxpdata.com
Mon Jun 3 13:44:32 CDT 2002


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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