[SciPy-User] problems configuring scipy (0.8.0) from numpy (1.5.0) in a itanium cluster

Miguel Pan Fidalgo mpan@cesga...
Mon Sep 27 07:54:18 CDT 2010


Technical information
++++++++++++++++++++++

$ python -c 'import sys;print sys.version'
2.4.2 (#1, Apr 13 2007, 16:14:04) 
[GCC 4.1.0 (SUSE Linux)]

$ module load numpy/1.5.0 
$ module list 
Currently Loaded Modulefiles:
  1) icc/11.1.056        3) mkl/10.2.2          5) nose/0.11.2         7) 
numpy/1.5.0
  2) ifort/11.1.056      4) fftw/3.2.2          6) SuiteSparse/3.4.0
$ python -c 'import numpy;print numpy.__version__' 
1.5.0

$  uname -a 
Linux cn002 2.6.16.53-0.8_SFS2.3_0-default #1 SMP Mon Nov 5 14:15:47 CET 2007 
ia64 ia64 ia64 GNU/Linux


numpy-1.5.0
+++++++++++++++++

I have installed numpy-1.5.0 in our Itanium cluster. This is my site.cfg file: 

$ cat /opt/cesga/numpy-1.5.0/src_numpy-1.5.0/site.cfg
[DEFAULT]
library_dirs = 
/opt/cesga/fftw-3.2.2/lib:/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/lib/64:/opt/cesga/SuiteSparse-3.4.0/lib  
include_dirs = 
/opt/cesga/fftw-3.2.2/include:/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/include:/opt/cesga/SuiteSparse-3.4.0/include 

# UMFPACK
# -------
[amd]
amd_libs = amd

[umfpack]
umfpack_libs = umfpack

# FFT libraries
# -------------
[fftw]
libraries = fftw3

# MKL
# ----
[mkl]
library_dirs = /opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/lib/64  
lapack_libs = mkl_lapack
mkl_libs = mkl_solver_lp64, mkl_intel_lp64, mkl_intel_thread, mkl_i2p, 
mkl_core

These are the hacks: 

$ diff system_info.py.original system_info.py
818c818
<     _lib_mkl = ['mkl','vml','guide']
---
>     _lib_mkl = ['mkl','mkl_lapack','guide']


$ diff intelccompiler.py.original intelccompiler.py
28a29
>           cc_exe=cc_exe + ' -liomp5 -lpthread -fPIC' 


scipy-0.8.0
+++++++++++++++

When I try to install scipy-0.8.0, the configuration process fails: 

$ tar zxvf scipy-0.8.0.tar.gz 
$ mv scipy-0.8.0 src
$ cp -va run.sh src/
$ cd src/
$ cat run.sh 
#!/bin/bash

module load numpy/1.5.0

python setup.py config_fc --fcompiler=intele 

#install --prefix=/sfs/home/cesga/mpan/scipy-0.8.0 

$ ./run.sh 
Warning: No configuration returned, assuming unavailable.blas_opt_info:
blas_mkl_info:
  FOUND:
    libraries = ['mkl_solver_lp64', 'mkl_intel_lp64', 'mkl_intel_thread', 
'mkl_i2p', 'mkl_core', 'pthread']
    library_dirs = ['/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/lib/64']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/opt/cesga/fftw-3.2.2/include', 
'/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/include', 
'/opt/cesga/SuiteSparse-3.4.0/include']

  FOUND:
    libraries = ['mkl_solver_lp64', 'mkl_intel_lp64', 'mkl_intel_thread', 
'mkl_i2p', 'mkl_core', 'pthread']
    library_dirs = ['/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/lib/64']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/opt/cesga/fftw-3.2.2/include', 
'/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/include', 
'/opt/cesga/SuiteSparse-3.4.0/include']

lapack_opt_info:
lapack_mkl_info:
mkl_info:
  FOUND:
    libraries = ['mkl_solver_lp64', 'mkl_intel_lp64', 'mkl_intel_thread', 
'mkl_i2p', 'mkl_core', 'pthread']
    library_dirs = ['/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/lib/64']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/opt/cesga/fftw-3.2.2/include', 
'/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/include', 
'/opt/cesga/SuiteSparse-3.4.0/include']

  FOUND:
    libraries = ['mkl_lapack', 'mkl_solver_lp64', 'mkl_intel_lp64', 
'mkl_intel_thread', 'mkl_i2p', 'mkl_core', 'pthread']
    library_dirs = ['/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/lib/64']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/opt/cesga/fftw-3.2.2/include', 
'/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/include', 
'/opt/cesga/SuiteSparse-3.4.0/include']

  FOUND:
    libraries = ['mkl_lapack', 'mkl_solver_lp64', 'mkl_intel_lp64', 
'mkl_intel_thread', 'mkl_i2p', 'mkl_core', 'pthread']
    library_dirs = ['/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/lib/64']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/opt/cesga/fftw-3.2.2/include', 
'/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/include', 
'/opt/cesga/SuiteSparse-3.4.0/include']

umfpack_info:
  libraries umfpack not found in /opt/cesga/fftw-3.2.2/lib
  libraries umfpack not found in 
/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/lib/64
amd_info:
  libraries amd not found in /opt/cesga/fftw-3.2.2/lib
  libraries amd not found in 
/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/lib/64
  FOUND:
    libraries = ['amd']
    library_dirs = ['/opt/cesga/SuiteSparse-3.4.0/lib']
    swig_opts = ['-I/opt/cesga/SuiteSparse-3.4.0/include']
    define_macros = [('SCIPY_AMD_H', None)]
    include_dirs = ['/opt/cesga/SuiteSparse-3.4.0/include']

  FOUND:
    libraries = ['umfpack', 'amd']
    library_dirs = ['/opt/cesga/SuiteSparse-3.4.0/lib']
    swig_opts = ['-I/opt/cesga/SuiteSparse-3.4.0/include', '-
I/opt/cesga/SuiteSparse-3.4.0/include']
    define_macros = [('SCIPY_UMFPACK_H', None), ('SCIPY_AMD_H', None)]
    include_dirs = ['/opt/cesga/SuiteSparse-3.4.0/include']

running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler 
options

the warning (first line) implies that BLAS primitives have to be recompiled. 
At the end the installation ends properly... this is not the point, but scipy 
doesn't use MKL BLAS primitives. 

BUT according to numpy... blas_mkl and blas_opt should be the same (like 
lapack_mkl and lapack_opt): 

$ module load numpy/1.5.0 
$ python 
Python 2.4.2 (#1, Apr 13 2007, 16:14:04) 
[GCC 4.1.0 (SUSE Linux)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from numpy.distutils.system_info import get_info
>>> get_info('blas_mkl')
{'libraries': ['mkl_solver_lp64', 'mkl_intel_lp64', 'mkl_intel_thread', 
'mkl_i2p', 'mkl_core', 'pthread'], 'library_dirs': 
['/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/lib/64'], 'define_macros': 
[('SCIPY_MKL_H', None)], 'include_dirs': ['/opt/cesga/fftw-3.2.2/include', 
'/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/include', 
'/opt/cesga/SuiteSparse-3.4.0/include']}
>>> get_info('blas_opt')
{'libraries': ['mkl_solver_lp64', 'mkl_intel_lp64', 'mkl_intel_thread', 
'mkl_i2p', 'mkl_core', 'pthread'], 'library_dirs': 
['/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/lib/64'], 'define_macros': 
[('SCIPY_MKL_H', None)], 'include_dirs': ['/opt/cesga/fftw-3.2.2/include', 
'/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/include', 
'/opt/cesga/SuiteSparse-3.4.0/include']}
>>> 

There is no need to recompile BLAS!!!!

any idea or suggestion ? 
WHAT I'm doing wrong ?

-- 

Atentamente,

Miguel Pan Fidalgo (Applications Technician)
mail: mpan at cesga.es
web: http://www.cesga.es
Avda. de Vigo s/n 15705, Santiago de Compostela
Telf.: +34 981 569810 - Fax: 981 594616
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