[SciPy-user] weave problem on ubuntu 8.10

Kristian Hans Sandberg Kristian.Sandberg@Colorado....
Mon Nov 17 10:42:21 CST 2008


That's exactly the problem I wrote about a couple of days ago (with topic "weave/blitz problem"). It's listed as Ticket # 739 in the scipy trac system:

http://www.scipy.org/scipy/scipy/ticket/739 

This seems to happen with g++ version 4.3. As a temporary fix, I installed g++ version 4.2, and then it worked.

I believe this problem will be more common as more people update to newer compilers. 

Kristian

Kristian Sandberg, Ph.D.
 
 Dept. of Applied Mathematics and
 The Boulder Laboratory for 3-D Electron Microscopy of Cells
 University of Colorado at Boulder
 Campus Box 526
 Boulder, CO 80309-0526, USA
 
 Phone: (303) 492 0593 (work)
        (303) 499 4404 (home)
        (303) 547 6290 (cell)
 
 Home page: http://amath.colorado.edu/faculty/sandberg


---- Original message ----
>Date: Mon, 17 Nov 2008 11:18:30 -0500
>From: "Bobby H. Braswell" <rob.braswell@unh.edu>  
>Subject: Re: [SciPy-user] weave problem on ubuntu 8.10  
>To: SciPy Users List <scipy-user@scipy.org>
>
>   Hi, thanks for the reply. Here are the first lines:
>
>   <weave: compiling>
>   In file included from
>   /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/applics.h:400,
>                    from
>   /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/vecexpr.h:32,
>                    from
>   /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/vecpick.cc:16,
>                    from
>   /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/vecpick.h:293,
>                    from
>   /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/vector.h:449,
>                    from
>   /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/tinyvec.h:430,
>                    from
>   /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/array-impl.h:44,
>                    from
>   /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/array.h:32,
>                    from
>   /home/braswell/.python25_compiled/sc_f935818f52299953943b3b48fe3685483.cpp:11:
>   /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/mathfunc.h:
>   In static member function `static long int
>   blitz::_bz_abs<long int>::apply(long int)':
>   /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/mathfunc.h:45:
>   error: `labs' is not a member of `std'
>   In file included from
>   /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/array/funcs.h:29,
>                    from
>   /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/array/newet.h:29,
>                    from
>   /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/array/et.h:27,
>                    from
>   /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/array-impl.h:2515,
>                    from
>   /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/array.h:32,
>                    from
>   /home/braswell/.python25_compiled/sc_f935818f52299953943b3b48fe3685483.cpp:11:
>   /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/funcs.h:
>   In static member function `static int
>   blitz::Fn_abs<int>::apply(int)':
>   /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/funcs.h:509:
>   error: call of overloaded `abs(int&)' is ambiguous
>   /usr/include/c++/4.3/cmath:99: note: candidates are:
>   double std::abs(double)
>   /usr/include/c++/4.3/cmath:103:
>   note:                 float std::abs(float)
>   /usr/include/c++/4.3/cmath:107:
>   note:                 long double std::abs(long
>   double)
>   /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/funcs.h:
>   In static member function `static long int
>   blitz::Fn_abs<long int>::apply(long int)':
>   /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/funcs.h:530:
>   error: `labs' is not a member of `std'
>   /home/braswell/.python25_compiled/sc_f935818f52299953943b3b48fe3685483.cpp:
>   In function `char* find_type(PyObject*)':
>   /home/braswell/.python25_compiled/sc_f935818f52299953943b3b48fe3685483.cpp:35:
>   warning: deprecated conversion from string constant
>   to `char*'
>   ...
>
>   On Mon, 2008-11-17 at 17:08 +0100, So/ren Nielsen
>   wrote:
>
>     Hi Rob,
>
>     What are the first lines of your error message?
>
>     I found the answer to my own question... I just
>     had to add type_converters = converters.blitz
>     under the ext_function.
>
>     On Mon, Nov 17, 2008 at 4:18 PM, Bobby H. Braswell
>     <rob.braswell@unh.edu> wrote:
>
>       Hi-
>
>       By coincidence I am trying to get weave working
>       on a new system, I had previously been using it
>       successfully under OS X with the Fink version of
>       SciPy. I don't want to distract from Soren's
>       question but when I try his simple example (or
>       any of my own) using converters.blitz, I get a
>       very long error message, actually mostly
>       warnings, but it ends like this:
>
>       >>> ravg = weave.inline(code, ['xlen', 'ylen',
>       'test'], type_converters=converters.blitz,
>       compiler = 'gcc')
>       ...hundreds of lines...
>       Traceback (most recent call last):
>         File "<stdin>", line 2, in <module>
>         File
>       "/usr/lib/python2.5/site-packages/scipy/weave/inline_tools.py",
>       line 339, in inline
>           **kw)
>         File
>       "/usr/lib/python2.5/site-packages/scipy/weave/inline_tools.py",
>       line 447, in compile_function
>           verbose=verbose, **kw)
>         File
>       "/usr/lib/python2.5/site-packages/scipy/weave/ext_tools.py",
>       line 365, in compile
>           verbose = verbose, **kw)
>         File
>       "/usr/lib/python2.5/site-packages/scipy/weave/build_tools.py",
>       line 269, in build_extension
>           setup(name = module_name, ext_modules =
>       [ext],verbose=verb)
>         File
>       "/usr/lib/python2.5/site-packages/numpy/distutils/core.py",
>       line 184, in setup
>           return old_setup(**new_attr)
>         File "/usr/lib/python2.5/distutils/core.py",
>       line 168, in setup
>           raise SystemExit, "error: " + str(msg)
>       scipy.weave.build_tools.CompileError: error:
>       Command "g++ -pthread -fno-strict-aliasing
>       -DNDEBUG -g -fwrapv -O2 -fPIC
>       -I/usr/lib/python2.5/site-packages/scipy/weave
>       -I/usr/lib/python2.5/site-packages/scipy/weave/scxx
>       -I/usr/lib/python2.5/site-packages/scipy/weave/blitz
>       -I/usr/lib/python2.5/site-packages/numpy/core/include
>       -I/usr/include/python2.5 -c
>       /home/braswell/.python25_compiled/sc_f8b4f30889557b51310ac43eda9472b30.cpp
>       -o
>       /tmp/braswell/python25_intermediate/compiler_a9bbef2f14d61f7aa8f0ba6e068e18c2/home/braswell/.python25_compiled/sc_f8b4f30889557b51310ac43eda9472b30.o"
>       failed with exit status 1
>
>       Sorry if this is more of a compiler/Ubuntu
>       problem, I'm not sure about that. I'd be
>       grateful to hear from someone who has had or not
>       had problems with Weave on Ubuntu 8.10.
>
>       Thanks very much,
>       Rob
>
>       On Mon, 2008-11-17 at 15:40 +0100, So/ren
>       Nielsen wrote:
>
>         Can anyone explain why this fails? This piece
>         of code runs perfectly using weave.inline and
>         type_converters = blitz..
>
>         Obviously it can't handle 2D arrays anymore.
>         It's just a stupid example to illustrate that.
>
>         Thanks,
>         Soren
>
>         CODE :
>         ------------------------------------------------------------------------------------------------
>         mod = ext_tools.ext_module('ravg_ext')
>
>         test = zeros((5,5))
>         xlen = 5
>         ylen = 5
>            
>         code = """
>                  int x, y;
>
>                  for( x = 0; x < xlen; x++)
>                  {
>                         for( y = 0; y < ylen; y++)
>                         {
>                             test(x,y) = 2;
>                         }
>                  }
>
>                 """
>          
>         ravg = ext_tools.ext_function('ravg', code,
>         ['xlen', 'ylen', 'test'])   
>         mod.add_function(ravg)
>         mod.compile(compiler = 'gcc')
>
>         RESULT:
>         ------------------------------------------------------------------------------------------------
>         C:\Temp\ravg_ext.cpp: In function `PyObject*
>         ravg(PyObject*, PyObject*, PyObject*)':
>         C:\Temp\ravg_ext.cpp:654: error: `test' cannot
>         be used as a function
>         C:\Temp\ravg_ext.cpp:641: warning: unused
>         variable 'Ntest'
>         C:\Temp\ravg_ext.cpp:642: warning: unused
>         variable 'Stest'
>         C:\Temp\ravg_ext.cpp:643: warning: unused
>         variable 'Dtest'
>
>         Traceback (most recent call last):
>           File "C:\Temp\ravg_extension.py", line 132,
>         in ?
>             build_ravg_extension()
>           File "C:\Temp\ravg_extension.py", line 125,
>         in build_ravg_extension
>             mod.compile(compiler = 'gcc')
>           File
>         "C:\Python24\Lib\site-packages\scipy\weave\ext_tools.py",
>         line 365, in compile
>             verbose = verbose, **kw)
>           File
>         "C:\Python24\Lib\site-packages\scipy\weave\build_tools.py",
>         line 269, in build_extension
>             setup(name = module_name, ext_modules =
>         [ext],verbose=verb)
>           File
>         "C:\Python24\Lib\site-packages\numpy\distutils\core.py",
>         line 184, in setup
>             return old_setup(**new_attr)
>           File "C:\Python24\Lib\distutils\core.py",
>         line 166, in setup
>             raise SystemExit, "error: " + str(msg)
>         CompileError: error: Command "g++ -mno-cygwin
>         -O2 -Wall
>         -IC:\Python24\lib\site-packages\scipy\weave
>         -IC:\Python24\lib\site-packages\scipy\weave\scxx
>         -IC:\Python24\lib\site-packages\numpy\core\include
>         -IC:\Python24\include -IC:\Python24\PC -c
>         C:\Temp\ravg_ext.cpp -o
>         c:\docume~1\ssn\locals~1\temp\ssn\python24_intermediate\compiler_894ad5ed761bb51736c6d2b7872dc212\Releas
>
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