[SciPy-user] scipy.test() from trunk segfaults

Scott Beardsley scott@cse.ucdavis....
Fri Feb 8 17:45:11 CST 2008


Scott Beardsley wrote:

> * If atlas library is not found by numpy/distutils/system_info.py,
>    then scipy uses fblas instead of cblas.

FYI, atlas is found in numpy's system_info.py but I do get the following 
message:

$ python numpy/distutils/system_info.py

<snip>

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: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall 
-Wstrict-prototypes -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/share/apps/ATLAS-3.8.0/lib -llapack 
-lptf77blas -lptcblas -latlas -o _configtest
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `e_wsfe'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `z_abs'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `c_sqrt'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `z_exp'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `c_exp'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `do_fio'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `z_sqrt'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `s_cat'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `c_abs'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `s_wsfe'
collect2: ld returned 1 exit status
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `e_wsfe'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `z_abs'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `c_sqrt'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `z_exp'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `c_exp'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `do_fio'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `z_sqrt'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `s_cat'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `c_abs'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `s_wsfe'
collect2: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
Status: 255
Output:
   FOUND:
     libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
     library_dirs = ['/share/apps/ATLAS-3.8.0/lib']
     language = f77
     define_macros = [('NO_ATLAS_INFO', 2)]

<snip>

The above source will compile if I add -lg2c and -lm to the compilation 
command. Is there a way to add this to the site.cfg so it compiles 
_configtest.c successfully? I'm guessing it is failing because it thinks 
lapack is incomplete.

BTW, the INSTALL.txt mentions doing the following:

5) ATLAS version, the locations of atlas and lapack libraries, building
    information if any. If you have ATLAS version 3.3.6 or newer, then
    give the output of the last command in
    ::

      cd scipy/Lib/linalg
      python setup_atlas_version.py build_ext --inplace --force
      python -c 'import atlas_version'


But it looks to be out-of-date because I don't have a Lib directory in 
<trunk>/scipy/. I found a couple setup_atlas_version.py scripts but they 
don't seem to like the above commands.

Scott


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