[SciPy-Dev] suitesparse vs scipy

Jack Howarth howarth@bromo.med.uc....
Mon Aug 29 08:02:35 CDT 2011


On Mon, Aug 29, 2011 at 08:36:42AM +0000, Pauli Virtanen wrote:
> Sun, 28 Aug 2011 19:26:04 -0400, Jack Howarth wrote:
> 
> > I've asked this question before without any responses. What are the
> > supported versions of suitesparse for use with scipy? The current scipy
> > 0.9.0 release doesn't appear to be fully compatible with suitesparse
> > 3.6.1 and causes testsuite failures in scipy.
> 
> Can you paste the test failures you see? 
> 
> Scipy does not use suitesparse except for the optional UMFPACK wrapper,
> which many people do not use. Suitesparse is still at 3.4.0 in
> Debian/Ubuntu, and I suppose newer ones have not been tested.

Pauli,
   My mistake. This isn't a testsuite failure but rather a build failure on
x86_64-apple-darwin11...

building 'scipy.sparse.linalg.dsolve.umfpack.__umfpack' extension
compiling C sources
C compiler: gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include

creating build/temp.macosx-10.7-x86_64-2.6/build/src.macosx-10.7-x86_64-2.6/scipy/sparse/linalg/dsolve
creating build/temp.macosx-10.7-x86_64-2.6/build/src.macosx-10.7-x86_64-2.6/scipy/sparse/linalg/dsolve/umfpack
compile options: '-DNO_ATLAS_INFO=3 -I/sw/lib/python2.6/site-packages/numpy/core/include -I/sw/include/python2.6 -c'
extra options: '-msse3 -I/System/Library/Frameworks/vecLib.framework/Headers'
gcc: build/src.macosx-10.7-x86_64-2.6/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c
build/src.macosx-10.7-x86_64-2.6/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c:2351:23: warning: explicitly assigning a variable of type 'int' to itself [-Wself-assign]
                  res = SWIG_AddCast(res);
                  ~~~ ^              ~~~
build/src.macosx-10.7-x86_64-2.6/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c:2354:23: warning: explicitly assigning a variable of type 'int' to itself [-Wself-assign]
                  res = SWIG_AddCast(res);                  
                  ~~~ ^              ~~~
build/src.macosx-10.7-x86_64-2.6/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c:6941:14: warning: explicitly assigning a variable of type 'void *' to itself [-Wself-assign]
  clientdata = clientdata;
  ~~~~~~~~~~ ^ ~~~~~~~~~~
3 warnings generated.
gcc -L/sw/lib -bundle -L/sw/lib/python2.6/config -lpython2.6 -I/sw/include build/temp.macosx-10.7-x86_64-2.6/build/src.macosx-10.7-x86_64-2.6/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.o -L/opt/local/lib -Lbuild/temp.macosx-10.7-x86_64-2.6 -lumfpack -lamd -o build/lib.macosx-10.7-x86_64-2.6/scipy/sparse/linalg/dsolve/umfpack/__umfpack.so -Wl,-framework -Wl,Accelerate
Undefined symbols for architecture x86_64:
  "_cholmod_start", referenced from:
      _umf_i_cholmod in libumfpack.a(umf_i_cholmod.o)
  "_cholmod_transpose", referenced from:
      _umf_i_cholmod in libumfpack.a(umf_i_cholmod.o)
  "_cholmod_analyze", referenced from:
      _umf_i_cholmod in libumfpack.a(umf_i_cholmod.o)
  "_cholmod_free_sparse", referenced from:
      _umf_i_cholmod in libumfpack.a(umf_i_cholmod.o)
  "_cholmod_free_factor", referenced from:
      _umf_i_cholmod in libumfpack.a(umf_i_cholmod.o)
  "_cholmod_print_common", referenced from:
      _umf_i_cholmod in libumfpack.a(umf_i_cholmod.o)
  "_cholmod_finish", referenced from:
      _umf_i_cholmod in libumfpack.a(umf_i_cholmod.o)
  "_cholmod_l_start", referenced from:
      _umf_l_cholmod in libumfpack.a(umf_l_cholmod.o)
  "_cholmod_l_transpose", referenced from:
      _umf_l_cholmod in libumfpack.a(umf_l_cholmod.o)
  "_cholmod_l_analyze", referenced from:
      _umf_l_cholmod in libumfpack.a(umf_l_cholmod.o)
  "_cholmod_l_free_sparse", referenced from:
      _umf_l_cholmod in libumfpack.a(umf_l_cholmod.o)
  "_cholmod_l_free_factor", referenced from:
      _umf_l_cholmod in libumfpack.a(umf_l_cholmod.o)
  "_cholmod_l_print_common", referenced from:
      _umf_l_cholmod in libumfpack.a(umf_l_cholmod.o)
  "_cholmod_l_finish", referenced from:
      _umf_l_cholmod in libumfpack.a(umf_l_cholmod.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
Undefined symbols for architecture x86_64:
  "_cholmod_start", referenced from:
      _umf_i_cholmod in libumfpack.a(umf_i_cholmod.o)
  "_cholmod_transpose", referenced from:
      _umf_i_cholmod in libumfpack.a(umf_i_cholmod.o)
  "_cholmod_analyze", referenced from:
      _umf_i_cholmod in libumfpack.a(umf_i_cholmod.o)
  "_cholmod_free_sparse", referenced from:
      _umf_i_cholmod in libumfpack.a(umf_i_cholmod.o)
  "_cholmod_free_factor", referenced from:
      _umf_i_cholmod in libumfpack.a(umf_i_cholmod.o)
  "_cholmod_print_common", referenced from:
      _umf_i_cholmod in libumfpack.a(umf_i_cholmod.o)
  "_cholmod_finish", referenced from:
      _umf_i_cholmod in libumfpack.a(umf_i_cholmod.o)
  "_cholmod_l_start", referenced from:
      _umf_l_cholmod in libumfpack.a(umf_l_cholmod.o)
  "_cholmod_l_transpose", referenced from:
      _umf_l_cholmod in libumfpack.a(umf_l_cholmod.o)
  "_cholmod_l_analyze", referenced from:
      _umf_l_cholmod in libumfpack.a(umf_l_cholmod.o)
  "_cholmod_l_free_sparse", referenced from:
      _umf_l_cholmod in libumfpack.a(umf_l_cholmod.o)
  "_cholmod_l_free_factor", referenced from:
      _umf_l_cholmod in libumfpack.a(umf_l_cholmod.o)
  "_cholmod_l_print_common", referenced from:
      _umf_l_cholmod in libumfpack.a(umf_l_cholmod.o)
  "_cholmod_l_finish", referenced from:
      _umf_l_cholmod in libumfpack.a(umf_l_cholmod.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: Command "gcc -L/sw/lib -bundle -L/sw/lib/python2.6/config -lpython2.6 -I/sw/include build/temp.macosx-10.7-x86_64-2.6/build/src.macosx-10.7-x86_64-2.6/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.o -L/opt/local/lib -Lbuild/temp.macosx-10.7-x86_64-2.6 -lumfpack -lamd -o build/lib.macosx-10.7-x86_64-2.6/scipy/sparse/linalg/dsolve/umfpack/__umfpack.so -Wl,-framework -Wl,Accelerate" failed with exit status 1

The initial output from setup.py in scipy 0.9 is...

#!/bin/sh -ev
 unset LDFLAGS
 /sw/bin/python2.6 setup.py build --fcompiler=gnu95
Warning: No configuration returned, assuming unavailable.blas_opt_info:
  FOUND:
    extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
    define_macros = [('NO_ATLAS_INFO', 3)]
    extra_compile_args = ['-msse3', '-I/System/Library/Frameworks/vecLib.framework/Headers']

non-existing path in 'scipy/io': 'docs'
lapack_opt_info:
  FOUND:
    extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
    define_macros = [('NO_ATLAS_INFO', 3)]
    extra_compile_args = ['-msse3']

umfpack_info:
  libraries umfpack not found in /usr/local/lib
  libraries umfpack not found in /usr/lib
amd_info:
  libraries amd not found in /usr/local/lib
  libraries amd not found in /usr/lib
  FOUND:
    libraries = ['amd']
    library_dirs = ['/opt/local/lib']

  FOUND:
    libraries = ['umfpack', 'amd']
    library_dirs = ['/opt/local/lib']

running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building py_modules sources
creating build
creating build/src.macosx-10.7-x86_64-2.6
creating build/src.macosx-10.7-x86_64-2.6/scipy
building library "dfftpack" sources
building library "fftpack" sources
building library "linpack_lite" sources
building library "mach" sources
building library "quadpack" sources
building library "odepack" sources
building library "dop" sources
building library "fitpack" sources
building library "odrpack" sources
building library "minpack" sources
building library "rootfind" sources
building library "superlu_src" sources
building library "arpack" sources
building library "qhull" sources
building library "sc_c_misc" sources
building library "sc_cephes" sources
building library "sc_mach" sources
building library "sc_toms" sources
building library "sc_amos" sources
building library "sc_cdf" sources
building library "sc_specfun" sources
building library "statlib" sources
building extension "scipy.cluster._vq" sources
building extension "scipy.cluster._hierarchy_wrap" sources
building extension "scipy.fftpack._fftpack" sources
creating build/src.macosx-10.7-x86_64-2.6/scipy/fftpack
creating build/src.macosx-10.7-x86_64-2.6/scipy/fftpack/src
conv_template:> build/src.macosx-10.7-x86_64-2.6/scipy/fftpack/src/dct.c
f2py options: []
f2py: scipy/fftpack/fftpack.pyf
Reading fortran codes...
	Reading file 'scipy/fftpack/fftpack.pyf' (format:free)
Line #86 in scipy/fftpack/fftpack.pyf:"       /* Single precision version */"
	crackline:2: No pattern for line

> 
> -- 
> Pauli Virtanen
> 
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