[SciPy-Dev] suitesparse vs scipy

Jack Howarth howarth@bromo.med.uc....
Mon Aug 29 09:55:21 CDT 2011


On Mon, Aug 29, 2011 at 09:02:35AM -0400, Jack Howarth wrote:
> 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

These missing symbols seem to exist in libcholmod.a which isn't being added to the linkage.
Any idea of the correct way to fix this for the newer suitesparse?

> 
> 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
> > 
> > _______________________________________________
> > SciPy-Dev mailing list
> > SciPy-Dev@scipy.org
> > http://mail.scipy.org/mailman/listinfo/scipy-dev
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