[SciPy-user] error linking to libg2c on 64-bit machine

Giovanni Samaey Giovanni.Samaey at cs.kuleuven.ac.be
Fri Nov 19 04:01:34 CST 2004


Pearu,

thank you so much for your help so far.  I believe I am getting in the 
range of "standard" problems now ;-)

>
>
> But until then, you can force undetecting X11 libraries by setting
>
>   x11_libs = noX11
>
> in [x11] section of site.cfg file. That should give you a change to 
> complete scipy build.

I got scipy built completely (without x11), but the scipy.test() gives 5 
failures and 2 errors, listed below this mail.
I suspect the ATLAS binary atlas atlas3.7.8_Linux_HAMMER64SSE2_2.tgz 
that I downloaded from scipy.org
is the cause, since it is probably not compatible with my system.
System info as required by the INSTALL file is attached in info.txt
However, when I follow the instructions on the scipy webpage for 
building scipy, I get the familiar error that I should
recompile them with -fPIC.  How do I alter the building of ATLAS to take 
care of this?
(Or is there another cause for the error?)

Then concerning x11: I indeed only have .so files.  I have libX11.so.6 
and libX11.so.6.2; so if I could configure something such that they are 
used, also this problem should be solvable. 

Thanks,

Giovanni



---
scipy.test() errors:

======================================================================
ERROR: check_simple_overdet (scipy.linalg.basic.test_basic.test_lstsq)
----------------------------------------------------------------------
Traceback (most recent call last):
  File 
"/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_basic.py", 
line 361, in check_simple_overdet
    x,res,r,s = lstsq(a,b)
  File 
"/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/basic.py", 
line 353, in lstsq
    if rank==n: resids = sum(x[n:]**2)
ArithmeticError: Integer overflow in power.

======================================================================
ERROR: check_simple_sym (scipy.linalg.basic.test_basic.test_solve)
----------------------------------------------------------------------
Traceback (most recent call last):
  File 
"/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_basic.py", 
line 80, in check_simple_sym
    x = solve(a,b,sym_pos=1,lower=lower)
  File 
"/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/basic.py", 
line 123, in solve
    raise LinAlgError, "singular matrix"
LinAlgError: singular matrix

======================================================================
FAIL: check_simple (scipy.linalg.decomp.test_decomp.test_cholesky)
----------------------------------------------------------------------
Traceback (most recent call last):
  File 
"/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_decomp.py", 
line 247, in check_simple
    assert_array_almost_equal(Numeric.dot(Numeric.transpose(c),c),a)
  File 
"/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", 
line 688, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [[-1885965976648932823  7796773222197633577  
-761725725645001531]
 [ 7796773222197633577 -6619736815450336083  789149371...
        Array 2: [[8 2 3]
 [2 9 3]
 [3 3 6]]


======================================================================
FAIL: check_simple (scipy.linalg.basic.test_basic.test_det)
----------------------------------------------------------------------
Traceback (most recent call last):
  File 
"/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_basic.py", 
line 273, in check_simple
    assert_almost_equal(a_det,-2.0)
  File 
"/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", 
line 610, in assert_almost_equal
    assert round(abs(desired - actual),decimal) == 0, msg
AssertionError:
Items are not equal:
DESIRED: -2.0
ACTUAL: -0.0

======================================================================
FAIL: check_simple (scipy.linalg.basic.test_basic.test_inv)
----------------------------------------------------------------------
Traceback (most recent call last):
  File 
"/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_basic.py", 
line 202, in check_simple
    [[1,0],[0,1]])
  File 
"/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", 
line 688, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [[9216616637413720064   -4503599627370496]
 [9207609438158979072   -9007199254740992]]
        Array 2: [[1 0]
 [0 1]]


======================================================================
FAIL: check_simple_exact (scipy.linalg.basic.test_basic.test_lstsq)
----------------------------------------------------------------------
Traceback (most recent call last):
  File 
"/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_basic.py", 
line 356, in check_simple_exact
    assert_array_almost_equal(Numeric.matrixmultiply(a,x),b)
  File 
"/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", 
line 688, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 50.0%):
        Array 1: [0 0]
        Array 2: [1 0]


======================================================================
FAIL: check_simple (scipy.linalg.basic.test_basic.test_solve)
----------------------------------------------------------------------
Traceback (most recent call last):
  File 
"/data/home/giovanni/lib/python2.3/site-packages/scipy/linalg/tests/test_basic.py", 
line 74, in check_simple
    assert_array_almost_equal(Numeric.matrixmultiply(a,x),b)
  File 
"/data/home/giovanni/lib/python2.3/site-packages/scipy_test/testing.py", 
line 688, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [[             nan              nan]
 [             nan              nan]]
        Array 2: [[1 0]
 [0 1]]


----------------------------------------------------------------------
Ran 984 tests in 1.679s

-------------- next part --------------
------
os.name='posix'
------
sys.platform='linux2'
------
sys.version:
2.3.4 (#7, Nov  8 2004, 11:58:49) 
[GCC 3.3.2 (Debian)]
------
sys.prefix:
/data/home/giovanni
------
sys.path=':/data/home/giovanni/lib/python23.zip:/data/home/giovanni/lib/python2.3:/data/home/giovanni/lib/python2.3/plat-linux2:/data/home/giovanni/lib/python2.3/lib-tk:/data/home/giovanni/lib/python2.3/lib-dynload:/data/home/giovanni/lib/python2.3/site-packages:/data/home/giovanni/lib/python2.3/site-packages/Numeric'
------
Found Numeric version '23.3' in /data/home/giovanni/lib/python2.3/site-packages/Numeric/Numeric.pyc
Found numarray version '1.1' in /data/home/giovanni/lib/python2.3/site-packages/numarray/__init__.pyc
Found f2py2e version '2.39.235_1693' in /data/home/giovanni/lib/python2.3/site-packages/f2py2e/f2py2e.pyc
Found scipy_distutils version '0.3.3_33.560' in '/data/home/giovanni/lib/python2.3/site-packages/scipy_distutils/__init__.pyc'
------
Importing scipy_distutils.command.build_flib ... error: No module named build_flib
------
Checking availability of supported Fortran compilers:
error: local variable 'build_flib' referenced before assignment
------
Importing scipy_distutils.fcompiler ... ok
------
Checking availability of supported Fortran compilers:
customize CompaqFCompiler
customize AbsoftFCompiler
Could not locate executable ifort
Could not locate executable efort
Could not locate executable efc
Could not locate executable ifort
customize IntelFCompiler
Could not locate executable f77
customize GnuFCompiler
customize SunFCompiler
customize VastFCompiler
customize GnuFCompiler
customize IbmFCompiler
customize LaheyFCompiler
customize IntelVisualFCompiler
customize IntelItaniumFCompiler
customize PGroupFCompiler
customize CompaqVisualFCompiler
customize MipsFCompiler
customize HPUXFCompiler
customize IntelItaniumVisualFCompiler
customize NAGFCompiler
List of available Fortran compilers:
  --fcompiler=gnu    GNU Fortran Compiler (3.3.2)
  --fcompiler=intel  Intel Fortran Compiler for 32-bit apps (7.1)
List of unavailable Fortran compilers:
  --fcompiler=absoft   Absoft Corp Fortran Compiler
  --fcompiler=compaq   Compaq Fortran Compiler
  --fcompiler=compaqv  DIGITAL|Compaq Visual Fortran Compiler
  --fcompiler=hpux     HP Fortran 90 Compiler
  --fcompiler=ibm      IBM XL Fortran Compiler
  --fcompiler=intele   Intel Fortran Compiler for Itanium apps
  --fcompiler=intelev  Intel Visual Fortran Compiler for Itanium apps
  --fcompiler=intelv   Intel Visual Fortran Compiler for 32-bit apps
  --fcompiler=lahey    Lahey/Fujitsu Fortran 95 Compiler
  --fcompiler=mips     MIPSpro Fortran Compiler
  --fcompiler=nag      NAGWare Fortran 95 Compiler
  --fcompiler=pg       Portland Group Fortran Compiler
  --fcompiler=sun      Sun|Forte Fortran 95 Compiler
  --fcompiler=vast     Pacific-Sierra Research Fortran 90 Compiler
List of unimplemented Fortran compilers:
  --fcompiler=f  Fortran Company/NAG F Compiler
For compiler details, run 'config_fc --verbose' setup command.
------
Importing scipy_distutils.command.cpuinfo ... error: No module named cpuinfo
Importing scipy_distutils.cpuinfo ... ok
------
CPU information: getNCPUs has_3dnow has_3dnowext has_mmx has_sse has_sse2 is_64bit is_AMD is_Opteron ------
ATLAS version 3.7.8 built by pearu on Thu Sep 30 23:29:06 EEST 2004:
   UNAME    : Linux opt 2.6.3-gentoo-r2 #1 SMP Sat Aug 28 12:40:32 EEST 2004 x86_64 AMD Opteron(tm) Processor 244 AuthenticAMD GNU/Linux
   INSTFLG  : 
   MMDEF    : /usr/local/src/ATLAS-3.7.8/CONFIG/ARCHS/HAMMER64SSE2/gcc/gemm
   ARCHDEF  : /usr/local/src/ATLAS-3.7.8/CONFIG/ARCHS/HAMMER64SSE2/gcc/misc
   F2CDEFS  : -DAdd_ -DStringSunStyle
   CACHEEDGE: 917504
   F77      : /usr/x86_64-pc-linux-gnu/gcc-bin/3.3/g77, version GNU Fortran (GCC) 3.3.4 20040623 (Gentoo Linux 3.3.4-r1, ssp-3.3.2-2, pie-8.7.6)
   F77FLAGS : -fomit-frame-pointer -O -m64 -fno-second-underscore -fPIC
   CC       : /usr/bin/gcc, version gcc (GCC) 3.3.4 20040623 (Gentoo Linux 3.3.4-r1, ssp-3.3.2-2, pie-8.7.6)
   CC FLAGS : -fomit-frame-pointer -O -mfpmath=387 -m64 -fPIC
   MCC      : /usr/bin/gcc, version gcc (GCC) 3.3.4 20040623 (Gentoo Linux 3.3.4-r1, ssp-3.3.2-2, pie-8.7.6)
   MCCFLAGS : -fomit-frame-pointer -O -mfpmath=387 -m64 -fPIC
_pkg_config_info:
Could not locate executable pkg-config
File not found: pkg-config. Cannot determine None info.
  NOT AVAILABLE

agg2_info:
( src_dirs = .:/usr/local/src:/data/home/giovanni/src )
  NOT AVAILABLE

atlas_blas_info:
( library_dirs = /data/home/giovanni/lib:/usr/local/lib:/usr/lib )
  NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
( library_dirs = /data/home/giovanni/lib:/usr/local/lib:/usr/lib )
  NOT AVAILABLE

atlas_info:
( library_dirs = /data/home/giovanni/lib:/usr/local/lib:/usr/lib )
system_info.atlas_info
  NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
( library_dirs = /data/home/giovanni/lib:/usr/local/lib:/usr/lib )
system_info.atlas_threads_info
  NOT AVAILABLE

blas_info:
( library_dirs = /data/home/giovanni/lib:/usr/local/lib:/usr/lib )
  NOT AVAILABLE

blas_opt_info:
blas_src_info:
  NOT AVAILABLE

  NOT AVAILABLE

boost_python_info:
( src_dirs = .:/usr/local/src:/data/home/giovanni/src )
  NOT AVAILABLE

dfftw_info:
( library_dirs = /data/home/giovanni/lib:/usr/local/lib:/usr/lib )
( include_dirs = /usr/local/include:/usr/include:/data/home/giovanni/include )
  NOT AVAILABLE

dfftw_threads_info:
( library_dirs = /data/home/giovanni/lib:/usr/local/lib:/usr/lib )
( include_dirs = /usr/local/include:/usr/include:/data/home/giovanni/include )
  NOT AVAILABLE

djbfft_info:
( library_dirs = /data/home/giovanni/lib:/usr/local/lib:/usr/lib )
( include_dirs = /usr/local/include:/usr/include:/data/home/giovanni/include )
  NOT AVAILABLE

fftw_info:
( library_dirs = /data/home/giovanni/lib:/usr/local/lib:/usr/lib )
( include_dirs = /usr/local/include:/usr/include:/data/home/giovanni/include )
  NOT AVAILABLE

fftw_threads_info:
( library_dirs = /data/home/giovanni/lib:/usr/local/lib:/usr/lib )
( include_dirs = /usr/local/include:/usr/include:/data/home/giovanni/include )
  NOT AVAILABLE

freetype2_info:
Could not locate executable pkg-config
File not found: pkg-config. Cannot determine freetype2 info.
  NOT AVAILABLE

gdk_2_info:
Could not locate executable pkg-config
File not found: pkg-config. Cannot determine gdk_2 info.
  NOT AVAILABLE

gdk_info:
Could not locate executable pkg-config
File not found: pkg-config. Cannot determine gdk info.
  NOT AVAILABLE

gdk_pixbuf_2_info:
Could not locate executable pkg-config
File not found: pkg-config. Cannot determine gdk_pixbuf_2 info.
  NOT AVAILABLE

gdk_pixbuf_xlib_2_info:
Could not locate executable pkg-config
File not found: pkg-config. Cannot determine gdk_pixbuf_xlib_2 info.
  NOT AVAILABLE

gdk_x11_2_info:
Could not locate executable pkg-config
File not found: pkg-config. Cannot determine gdk_x11_2 info.
  NOT AVAILABLE

gtkp_2_info:
Could not locate executable pkg-config
File not found: pkg-config. Cannot determine gtkp_2 info.
  NOT AVAILABLE

gtkp_x11_2_info:
Could not locate executable pkg-config
File not found: pkg-config. Cannot determine gtkp_x11_2 info.
  NOT AVAILABLE

lapack_atlas_info:
( library_dirs = /data/home/giovanni/lib:/usr/local/lib:/usr/lib )
system_info.lapack_atlas_info
  NOT AVAILABLE

lapack_atlas_threads_info:
Setting PTATLAS=ATLAS
( library_dirs = /data/home/giovanni/lib:/usr/local/lib:/usr/lib )
system_info.lapack_atlas_threads_info
  NOT AVAILABLE

lapack_info:
( library_dirs = /data/home/giovanni/lib:/usr/local/lib:/usr/lib )
  NOT AVAILABLE

lapack_opt_info:
lapack_src_info:
  NOT AVAILABLE

  NOT AVAILABLE

numarray_info:
( include_dirs = /data/home/giovanni/include/python2.3 )
( paths: /data/home/giovanni/include/python2.3/numarray/arrayobject.h )
( library_dirs =  )
  FOUND:
    define_macros = [('NUMARRAY_VERSION', '"\\"1.1\\""')]
    include_dirs = ['/data/home/giovanni/include/python2.3']

numpy_info:
( include_dirs = /data/home/giovanni/include/python2.3 )
( paths: /data/home/giovanni/include/python2.3/Numeric/arrayobject.h )
( library_dirs = /apps/prod/local64/lib64/ )
( paths: /apps/prod/local64/lib64/libg2c.so )
  FOUND:
    libraries = ['g2c']
    library_dirs = ['/apps/prod/local64/lib64/']
    define_macros = [('NUMERIC_VERSION', '"\\"23.3\\""')]
    include_dirs = ['/data/home/giovanni/include/python2.3']

sfftw_info:
( library_dirs = /data/home/giovanni/lib:/usr/local/lib:/usr/lib )
( include_dirs = /usr/local/include:/usr/include:/data/home/giovanni/include )
  NOT AVAILABLE

sfftw_threads_info:
( library_dirs = /data/home/giovanni/lib:/usr/local/lib:/usr/lib )
( include_dirs = /usr/local/include:/usr/include:/data/home/giovanni/include )
  NOT AVAILABLE

wx_info:
Could not locate executable wx-config
File not found: wx-config. Cannot determine wx info.
  NOT AVAILABLE

x11_info:
( library_dirs = /usr/X11R6/lib:/usr/lib )
( include_dirs = /usr/X11R6/include:/usr/include )
  NOT AVAILABLE

xft_info:
Could not locate executable pkg-config
File not found: pkg-config. Cannot determine xft info.
  NOT AVAILABLE



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