[SciPy-user] weave problem on ubuntu 8.10
Kristian Hans Sandberg
Kristian.Sandberg at Colorado.EDU
Mon Nov 17 11:42:21 EST 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 at unh.edu>
>Subject: Re: [SciPy-user] weave problem on ubuntu 8.10
>To: SciPy Users List <scipy-user at 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 at 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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