[SciPy-dev] scipy core and atlas on IA64

Jan Braun jan_braun at gmx.net
Fri Dec 9 12:11:02 CST 2005


Hi all, 
 
after many problems with Intel mkl and SGI scs on IA64 we are now 
switching back to atlas. 
Atlas is compiled with its very own (self chosen) options. So it takes 
the Intel compilers and needs libifcore at runtime. 
 
Unfortunately there seems to be no way to get scipy find atlas __and__ 
link libifcore in. This is very similar to problems arising from mkl and 
scs compiles where everything compiles fine and ends with missing 
symbols. Trying to add the missing libs to site.cfg results in the 
equivalent of Step 3 (see below): no atlas/lapack is found at all. 
 
The question is what to do to get scipy compile and link additional libs 
by modifying site.cfg. 
 
The description of the mentioned problems occuring with scipy.distutils 
and site.cfg's follow. My description only covers scipy core from svn. 
 
Thanks, 
  Jan 
----------------------------------------------------------- 
 
Step 1: 
  site.cfg: nothing set (empty) 
  env variable ATLAS to the right directory 
  in scipy core: 
    python setup.py install | tee install.log 
 
Result 1: 
  Setting PTATLAS=ATLAS 
  FOUND: 
    libraries = ['ptf77blas', 'ptcblas', 'atlas'] 
    library_dirs = ['/work/home/jb672983/gcc-python//lib/atlas'] 
    language = c 
    include_dirs = ['/usr/include'] 
 
  everyting compiles fine and is installed 
 
Test 1: at the ipython prompt 
  In [1]: import scipy 
  Importing test to scipy 
  Importing base to scipy 
  Importing basic to scipy 
  Failed to import basic 
  lib/python2.4/site-packages/scipy/lib/lapack_lite.so: undefined symbol:  
for_cpstr 
 
----------------------------------------------------------- 
 
Step 2: relink lapack_lite.so (grep on install.log) 
  /usr/bin/g77 -shared [build...]lapack_litemodule.o \ 
    -L/gcc-python/lib/atlas -L/opt/intel/fc_90/lib -lifcore \ 
    -llapack -lptf77blas -lptcblas -latlas -lg2c -o 
[build...]lapack_lite.so 
  copy lapack_lite.so to site-packages/scipy/lib 
 
Test 2:  at the ipython prompt 
  In [1]: import scipy 
  Importing test to scipy 
  Importing base to scipy 
  Importing basic to scipy 
 
  => everythings ok 
 
----------------------------------------------------------- 
 
Step 3: use results from 1. and 2., add the libifcore to site.cfg 
  site.cfg now includes: 
    [atlas] 
    library_dirs 
= /opt/intel/fc_90/lib:/home/jb672983/gcc-python/lib/atlas 
    atlas_libs = ptf77blas, ptcblas, atlas, ifcore 
 
Result 3: 
 
/work/home/jb672983/src/core-fftw3-atlas/scipy/distutils/system_info.py:1076:
 
UserWarning: 
    Atlas (http://math-atlas.sourceforge.net/) libraries not found. 
    Directories to search for the libraries can be specified in the 
    scipy_distutils/site.cfg file (section [atlas]) or by setting 
    the ATLAS environment variable. 
  warnings.warn(AtlasNotFoundError.__doc__) 
 

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