[Numpy-discussion] Trying out Numeric3

Michiel Jan Laurens de Hoon mdehoon at ims.u-tokyo.ac.jp
Thu Mar 17 22:02:32 CST 2005

First of all, thanks to the Numerical Python developers for releasing version 
23.8 of Numerical Python. It compiles out of the box and avoids the blas/lapack 
compilation problems in earlier versions, which makes my life as a developer a 
lot easier. Thanks!

Travis Oliphant wrote:
> I wanted to let people who may be waiting, that now is a good time to 
>  help with numeric3.  The CVS version builds (although I"m sure there are 
>  still bugs), but more eyes could help me track them down.  
>  Currently, all that remains for the arrayobject is to implement the 
>  newly defined methods (really it"s just a re-organization and 
>  re-inspection of the code in multiarraymodule.c to call it using methods). 

I downloaded Numeric3 today and installed it. The compilation and installation 
run fine. There are still some warnings from the compiler here and there, but I 
guess they will be fixed some other time.

During compilation, I noticed that some test program is run, presumably for 
configuration. The test program is compiled by a different compiler as the one 
used in the build process. Note that "python setup.py config" is available in 
the standard distutils, so it may be better to use that instead of a 
self-defined configuration tool. For one thing, it'll make sure that the 
compiler used for configuration is the same as the one used for compilation.

To use Numeric3, I did "from ndarray import *". I guess for the final version, 
this will be "from Numeric import *"?

When using ndarray, I got a core dump using "zeros":

$ python
Python 2.5a0 (#1, Mar  2 2005, 12:15:06)
[GCC 3.3.3] on cygwin
Type "help", "copyright", "credits" or "license" for more information.
 >>> from ndarray import *
 >>> zeros(5)
creating data 0xa0c03d0 associated with 0xa0d52c0
array([0.0, 0.0, 0.0, 0.0, 0.0], 'd')
Segmentation fault (core dumped)

With Python 2.4, the segmentation fault occurs slightly later:
$ python2.4
Python 2.4 (#1, Dec  5 2004, 20:47:03)
[GCC 3.3.3] on cygwin
Type "help", "copyright", "credits" or "license" for more information.
 >>> from ndarray import *
 >>> zeros(5)
creating data 0xa0a07f8 associated with 0xa0d6230
array([0.0, 0.0, 0.0, 0.0, 0.0], 'd')
 >>> ^D
freeing 0xa0a07f8 associated with array 0xa0d6230
freeing 0xa123b88 associated with array 0xa0d6230
Segmentation fault (core dumped)

Finally, I tried to compile a C extension module that uses Numerical Python (by 
replacing #include <Numeric/arrayobject.h> by #include <ndarray/arrayobject.h>):
$ python setup.py build
running build
running build_py
running build_ext
building 'Pycluster.cluster' extension
gcc -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -Isrc -Iranli
b/src -I/usr/local/include/python2.5 -c python/clustermodule.c -o build/temp.cyg
In file included from python/clustermodule.c:2:
/usr/local/include/python2.5/ndarray/arrayobject.h:76: warning: redefinition of
/usr/include/sys/types.h:85: warning: `ushort' previously declared here
/usr/local/include/python2.5/ndarray/arrayobject.h:77: warning: redefinition of
/usr/include/sys/types.h:86: warning: `uint' previously declared here

These two warnings are probably not so serious, but it would be better to get 
rid of them anyway.

python/clustermodule.c: In function `parse_data':
python/clustermodule.c:38: warning: passing arg 1 of pointer to function from in
compatible pointer type

The offending line 38 is:

     { PyArrayObject* av = (PyArrayObject*) PyArray_Cast(*array, PyArray_DOUBLE);

where array is a PyArrayObject**.

Another warning was that PyArrayObject's "dimensions" doesn't seem to be an int 
array any more.

Finally, when linking I get an undefined reference to _PyArray_API.


Michiel de Hoon, Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
Tokyo 108-8639

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