[SciPy-user] blas/lapack issue on a freebsd box...

Robert Kern robert.kern at gmail.com
Wed Dec 6 11:52:15 CST 2006


fred wrote:
> compiling '_configtest.c':
> 
> /* This file is generated from numpy_distutils/system_info.py */
> void ATL_buildinfo(void);
> int main(void) {
>   ATL_buildinfo();
>   return 0;
> }
> C compiler: cc -fno-strict-aliasing -DNDEBUG -O2 -fno-strict-aliasing -pipe -D__wchar_t=wchar_t -DTHREAD_STACK_SIZE=0x20000 -fPIC
> 
> compile options: '-c'
> cc: _configtest.c
> cc _configtest.o -L/usr/local/lib -llapack -lblas -o _configtest
> _configtest.o(.text+0x18): In function `main':
> : undefined reference to `ATL_buildinfo'
> /usr/local/lib/liblapack.so: undefined reference to `log'
> /usr/local/lib/liblapack.so: undefined reference to `sqrt'
> /usr/local/lib/liblapack.so: undefined reference to `e_wsfe'
> /usr/local/lib/liblapack.so: undefined reference to `z_abs'
> /usr/local/lib/liblapack.so: undefined reference to `c_sqrt'
> /usr/local/lib/liblapack.so: undefined reference to `s_cmp'
> /usr/local/lib/liblapack.so: undefined reference to `z_exp'
> /usr/local/lib/liblapack.so: undefined reference to `cos'
> /usr/local/lib/liblapack.so: undefined reference to `c_exp'
> /usr/local/lib/liblapack.so: undefined reference to `pow'
> /usr/local/lib/liblapack.so: undefined reference to `log10'
> /usr/local/lib/liblapack.so: undefined reference to `do_fio'
> /usr/local/lib/liblapack.so: undefined reference to `z_sqrt'
> /usr/local/lib/liblapack.so: undefined reference to `s_cat'
> /usr/local/lib/liblapack.so: undefined reference to `s_stop'
> /usr/local/lib/liblapack.so: undefined reference to `c_abs'
> /usr/local/lib/liblapack.so: undefined reference to `s_wsfe'
> /usr/local/lib/liblapack.so: undefined reference to `s_copy'
> _configtest.o(.text+0x18): In function `main':
> : undefined reference to `ATL_buildinfo'
> /usr/local/lib/liblapack.so: undefined reference to `log'
> /usr/local/lib/liblapack.so: undefined reference to `sqrt'
> /usr/local/lib/liblapack.so: undefined reference to `e_wsfe'
> /usr/local/lib/liblapack.so: undefined reference to `z_abs'
> /usr/local/lib/liblapack.so: undefined reference to `c_sqrt'
> /usr/local/lib/liblapack.so: undefined reference to `s_cmp'
> /usr/local/lib/liblapack.so: undefined reference to `z_exp'
> /usr/local/lib/liblapack.so: undefined reference to `cos'
> /usr/local/lib/liblapack.so: undefined reference to `c_exp'
> /usr/local/lib/liblapack.so: undefined reference to `pow'
> /usr/local/lib/liblapack.so: undefined reference to `log10'
> /usr/local/lib/liblapack.so: undefined reference to `do_fio'
> /usr/local/lib/liblapack.so: undefined reference to `z_sqrt'
> /usr/local/lib/liblapack.so: undefined reference to `s_cat'
> /usr/local/lib/liblapack.so: undefined reference to `s_stop'
> /usr/local/lib/liblapack.so: undefined reference to `c_abs'
> /usr/local/lib/liblapack.so: undefined reference to `s_wsfe'
> /usr/local/lib/liblapack.so: undefined reference to `s_copy'
> failure.
> removing: _configtest.c _configtest.o
> Status: 255
> Output: 
>   FOUND:
>     libraries = ['lapack', 'blas']
>     library_dirs = ['/usr/local/lib']
>     language = c
>     define_macros = [('NO_ATLAS_INFO', 2)]
>     include_dirs = ['/usr/local/include']

This is part of your problem. Do you have a site.cfg file? If so, please post it.

You ought to have sections that look like these:


[DEFAULT]
library_dirs=/usr/local/lib
include_dirs=/usr/local/include

[blas_opt]
libraries=f77blas, cblas, atlas

[lapack_opt]
libraries=lapack, f77blas, cblas, atlas


Possibly, you might also need to add g2c to the end of the libraries= lines.

Now, those libraries lists are from what I normally see installed from ATLAS.
Given that I've never seen libalapack_r.so.1 before, it's possible that ATLAS
gets build strangely on your machine. Please also give us a list of the
libraries that ATLAS installs. Also tell us where you got
/usr/local/lib/liblapack.so and /usr/local/lib/libblas.so .

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


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