numpy-discussion — Discussion list for all users of Numerical Python

[Numpy-discussion] Re: Any Numeric or numarray users on this list?

[Nick F. <nv...@MI...>]

> 1) Have you transitioned or started to transition to NumPy (i.e.  
> import
> numpy)?

Yes, I've pretty much decided that numpy is the way to go with my  
young analysis codes, even though it is going to be somewhat painful  
to distribute to my colleagues and among compute nodes in clusters.   
I am saved by the fact that we all work within an NFS space, so I can  
host up-to-date compiles of numpy and scipy without requiring root  
access nor requiring everyone to compile their own.  Of course, I  
will end up giving them a few lines of LD_LIBRARY_PATH to add.

Old codes that used Numeric have all transitioned smoothly to numpy  
in my internal tests.  I may distribute two versions (one Numeric,  
one numpy) for wider distribution outside my clusters, but there may  
be a better way to do this.

> 2) Will you transition within the next 6 months? (if you answered  
> No to #1)
> 3) Please, explain your reason(s) for not making the switch. (if you
> answered No to #2)
> 4) Please provide any suggestions for improving NumPy.

I think NumPy is fantastic.  That said, even the fantastic can  
improve.  I am very happy with numpy as software, so my comments are  
mostly about adoption and accessibility.

I'd really like to see the team getting packages (32 and 64 bit) into  
standard Redhat, Debian, and Fink repositories quickly after a  
release.  I believe Redhat is at numpy 0.9.5 and neither Debian  
(testing) nor Fink have packages in the default repositories.  Having  
to add extra lines to /etc/apt/sources.list (or Redhat equivalent) to  
grab packages from private repositories will dissuade a lot of people  
from adopting numpy.  Many of them are the same people who are unable  
to compile it themselves.  Up-to-date packages also help me with my  
problem in #1 -- an admin will happily yum an rpm for me an all of  
the cluster nodes, but might not be willing to install it from a  
nonstandard source.

I agree that Googlability is very important and easily addressable.   
I'm glad someone brought this up.  Btw, googling "numpy rpm" brings  
up http://pylab.sourceforge.net/, which is some more of Travis's old  
Numeric stuff (labeled as such on the page).

Thanks for the hard work in coding and thanks for keeping a thriving  
discussion list going.

Take care,
Nick

Re: [Numpy-discussion] numpy-0.9.5 build is not clean

[Krishna M. G. <gk...@gm...>]

Dear Andrew,

I forgot to delete the include files from the previous installation,
which I installed manually by copying the include files. Sorry for the
trouble.

Hope this helps someone, if (s)he does the same mistake as mine.

cheers,
Krishna.

On 5/24/06, Krishna Mohan Gundu <gk...@gm...> wrote:
> Dear Andrew,
>
> Thanks for your reply. As I said earlier I deleted the existing numpy
> installation and the build directories. I am more than confidant that
> I did it right. Is there anyway I can prove myself wrong?
>
> I also tried importing umath.so from build directory
> ===
> $ cd numpy-0.9.5/build/lib.linux-x86_64-2.4/numpy/core
> $ ls -l umath.so
> -rwxr-xr-x    1 krishna  users      463541 May 22 17:46 umath.so
> $ python
> Python 2.4.3 (#1, Apr  8 2006, 19:10:42)
> [GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-49)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import umath
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
> RuntimeError: module compiled against version 90500 of C-API but this
> version of numpy is 90504
> >>>
> ===
>
> So something is wrong with the build for sure. Could there be anything
> wrong other than not deleting the build directory?
>
> thanks,
> Krishna.
>
> On 5/24/06, Andrew Straw <str...@as...> wrote:
> > Dear Krishna, it looks like there are some mixed versions of numpy
> > floating around on your system. Before building, remove the "build"
> > directory completely.
> >
> > Krishna Mohan Gundu wrote:
> >
> > > Hi,
> > >
> > > I am trying to build numpy-0.9.5, downloaded from sourceforge download
> > > page, as higher versions are not yet tested for pygsl. The build seems
> > > to be broken. I uninstall existing numpy and start build from scratch
> > > but I get the following errors when I import numpy after install.
> > >
> > > ====
> > >
> > >>>> from numpy import *
> > >>>
> > > import core -> failed: module compiled against version 90504 of C-API
> > > but this version of numpy is 90500
> > > import random -> failed: 'module' object has no attribute 'dtype'
> > > import linalg -> failed: module compiled against version 90504 of
> > > C-API but this version of numpy is 90500
> > > ====
> > >
> > > Any help is appreciated. Am I doing something wrong or is it known
> > > that this build is broken?
> > >
> > > thanks,
> > > Krishna.
> > >
> > >
> > > -------------------------------------------------------
> > > All the advantages of Linux Managed Hosting--Without the Cost and Risk!
> > > Fully trained technicians. The highest number of Red Hat
> > > certifications in
> > > the hosting industry. Fanatical Support. Click to learn more
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> > > _______________________________________________
> > > Numpy-discussion mailing list
> > > Num...@li...
> > > https://lists.sourceforge.net/lists/listinfo/numpy-discussion
> >
> >
> >
>

[Numpy-discussion] Re: cx_freezing numpy problem.

[Mike R. <mr...@ca...>]

Seems, the problem was that _internal.py was not picked up by Freeze.
Using --include-modules=numpy.core._internal helps.

Mike Rovner wrote:
> Hi,
> 
> I'm trying to package numpy based application but get following TB:
> 
> No scipy-style subpackage 'core' found in 
> /home/mrovner/dev/psgapp/src/gui/lnx32/dvip/numpy. Ignoring: No module 
> named _internal
> Traceback (most recent call last):
>   File "/home/mrovner/src/cx_Freeze-3.0.2/initscripts/Console.py", line 
> 26, in ?
>     exec code in m.__dict__
>   File "dvip.py", line 42, in ?
>   File "dvip.py", line 31, in dvip_gui
>   File "mainui.py", line 1, in ?
>   File "psgdb.pyx", line 162, in psgdb
>   File 
> "/lan/dfm/grp_mm_data1/dev/tools/linux-x86_32/lib/python2.4/site-packages/numpy/__init__.py", 
> line 35, in ?
>     verbose=NUMPY_IMPORT_VERBOSE,postpone=False)
>   File 
> "/lan/dfm/grp_mm_data1/dev/tools/linux-x86_32/lib/python2.4/site-packages/numpy/_import_tools.py", 
> line 173, in __call__
>     self._init_info_modules(packages or None)
>   File 
> "/lan/dfm/grp_mm_data1/dev/tools/linux-x86_32/lib/python2.4/site-packages/numpy/_import_tools.py", 
> line 68, in _init_info_modules
>     exec 'import %s.info as info' % (package_name)
>   File "<string>", line 1, in ?
>   File 
> "/lan/dfm/grp_mm_data1/dev/tools/linux-x86_32/lib/python2.4/site-packages/numpy/lib/__init__.py", 
> line 5, in ?
>     from type_check import *
>   File 
> "/lan/dfm/grp_mm_data1/dev/tools/linux-x86_32/lib/python2.4/site-packages/numpy/lib/type_check.py", 
> line 8, in ?
>     import numpy.core.numeric as _nx
>   File 
> "/lan/dfm/grp_mm_data1/dev/tools/linux-x86_32/lib/python2.4/site-packages/numpy/core/__init__.py", 
> line 6, in ?
>     import umath
>   File "ExtensionLoader.py", line 12, in ?
> AttributeError: 'module' object has no attribute '_ARRAY_API'
> 
> I did freezing with:
> FreezePython --install-dir=lnx32 --include-modules=numpy 
> --include-modules=numpy.core dvip.py
> 
> I'm using Python-2.4.2 numpy-0.9.8 cx_Freeze-3.0.2 on linux. Everything 
> compiled from source.
> 
> Any help appreciated.
> 
> Thanks,
> Mike
> 
> 
> 
> -------------------------------------------------------
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Re: [Numpy-discussion] Any Numeric or numarray users on this list?

[Bruce S. <bso...@gm...>]

Hi,

On 5/30/06, Travis Oliphant <oli...@ie...> wrote:
>
> Please help the developers by responding to a few questions.
>
>
>
> 1) Have you transitioned or started to transition to NumPy (i.e. import
> numpy)?

Yes and No

> 2) Will you transition within the next 6 months? (if you answered No to #1)

Probably for new code only. Having ported numarray code to NumPy there
are too many quirks that need to be found.


> 3) Please, explain your reason(s) for not making the switch. (if you
> answered No to #2)

Hopefully 1.0 will be out by then :-). Also bugs and performance will
at a similar level to numeric and numarray.


> 4) Please provide any suggestions for improving NumPy.

The main one at present is to provide a stable release that can serve
as a reference point for users. This is more a reflection of having a
stable version of numpy for reference rather than having to check the
svn for an appropriate version.

Bruce


> Thanks for your answers.
>
>
> NumPy Developers
>
>
>
>
> -------------------------------------------------------
> All the advantages of Linux Managed Hosting--Without the Cost and Risk!
> Fully trained technicians. The highest number of Red Hat certifications in
> the hosting industry. Fanatical Support. Click to learn more
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> _______________________________________________
> Numpy-discussion mailing list
> Num...@li...
> https://lists.sourceforge.net/lists/listinfo/numpy-discussion
>

Re: [Numpy-discussion] masked arrays

[Philip A. <pa...@eo...>]

 > John Hunter wrote:
 > >I read through the docstring, but didn't see anything better.

Andrew Straw writes:
 > John, you want c.compressed().

I've also found the old Numeric documentation to be helpful:
http://numeric.scipy.org/numpydoc/numpy-22.html

regards, Phil

Re: [Numpy-discussion] masked arrays

[Andrew S. <str...@as...>]

John, you want c.compressed().

John Hunter wrote:

>I'm a bit of an ma newbie.  I have a 2D masked array R and want to
>extract the non-masked values in the last column.  Below I use logical
>indexing, but I suspect there is a "built-in" way w/ masked arrays.  I
>read through the docstring, but didn't see anything better.
>
>In [66]: c = R[:,-1]
>
>In [67]: m = R.mask[:,-1]
>
>
>In [69]: c[m==0]
>Out[69]:
>array(data =
> [ 0.94202899  0.51839465  0.24080268  0.26198439  0.29877369
> 2.06856187
>  0.91415831  0.64994426  0.96544036  1.11259755  2.53623188
>  0.71571906
>  0.18394649  0.78037904  0.60869565  3.56744705  0.44147157
>  0.07692308
>  0.27090301  0.16610925  0.57068004  0.80267559  0.57636566
>  0.23634337
>  1.9509476   0.50761427  0.09587514  0.45039019  0.14381271
>  0.69007804
>  2.44481605  0.2909699   0.45930881  1.37123746  2.00668896
>  3.1638796
>  1.0735786   1.06800446  0.18952062  1.55964326  1.16833891
>  0.17502787
>  1.16610925  0.85507246  0.42140468  0.04236343  1.01337793
>  0.22853958
>  1.76365663  1.78372352  0.96209588  0.73578595  0.94760312
>  1.59531773
>  0.88963211],
>      mask =
> [False False False False False False False False False False False
> False
> False False False False False False False False False False False
> False
> False False False False False False False False False False False
> False
> False False False False False False False False False False False
> False
> False False False False False False False],
>      fill_value=1e+20)
>
>
>
>
>-------------------------------------------------------
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>https://lists.sourceforge.net/lists/listinfo/numpy-discussion
>  
>

Re: [Numpy-discussion] Suggestions for NumPy

[Christopher B. <Chr...@no...>]

Ed Schofield wrote:
> Improvements for NumPy's web presence:
> http://projects.scipy.org/scipy/numpy/ticket/132

 From that page:

NumPy's web presence could be improved by:

2. Pointing www.numpy.org to numeric.scipy.org instead of the SF page

I don't like this. *numpy is not scipy*. It should have it's own page 
(which would refer to scipy). That page should be something better than 
the raw sourceforge page, however.

A lot of us use numpy without anything else from the scipy project, and 
scipy is still a major pain in the *&&^* to build. Can you even build it 
with gcc 4 yet?


I like the other ideas.

-Chris





-- 
Christopher Barker, Ph.D.
Oceanographer
                                     		
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Chr...@no...

Re: [Numpy-discussion] Any Numeric or numarray users on this list?

[eric <er...@en...>]

>
> Please help the developers by responding to a few questions.
>
>
>
> 1) Have you transitioned or started to transition to NumPy (i.e. 
> import numpy)?
We (Enthought) have started.
>
>
> 2) Will you transition within the next 6 months? (if you answered No 
> to #1)
We have a number of deployed applications that use Numeric heavily.   
Much of our code is now NumPy/Numeric compatible, but it is not well 
tested on NumPy.  That said, a recent large project will be delivered on 
NumPy this summer, and we are releasing an update to a legacy app using 
NumPy in the next month or so.  Pearu, Travis, and the Numeric->NumPy 
conversion scripts have been very helpful in this respect.

It has been (and remains) a big effort to get the ship turned in the 
direction of NumPy, but we're committed to it.  We are very much looking 
forward to using its new features. 
>
>
> 3) Please, explain your reason(s) for not making the switch. (if you 
> answered No to #2)
Just time right now.  We have noticed one major slow down in code, but 
it is a known issue (scalar math).  This was easily fixed with a little 
weave code in the time being (so now we're actually 2-3 times faster 
than the old Numeric code. :-)
>
> 4) Please provide any suggestions for improving NumPy.
No strong opinions here yet as I (sadly) haven't gotten to use it much 
yet.   The scalar math speed hit us once, so others will probably hit it 
as well. 

Thanks again for all the amazing work on this stuff.  It has already had 
an amazing impact on the community involvement and growth.  From my own 
experience, I understand why others are slow to convert.  Enthought has 
wanted to be an early adopter from the beginning, and we are still not 
there because of the effort involved in conversion and testing along 
with time pressures from other projects.  Still, there is a nice feed 
back loop that happens here.  As scipy/numpy continue to improve (more 
functionality, 64-bit stability, etc.) and more projects convert over, 
there are more reasons for people to update their code to the latest and 
greatest.  My bet is it'll take 2-3 more years for the transition to run 
its course.

see ya,
eric
>
>
>
>
>
> Thanks for your answers.
>
>
> NumPy Developers
>
>
>
>
> -------------------------------------------------------
> All the advantages of Linux Managed Hosting--Without the Cost and Risk!
> Fully trained technicians. The highest number of Red Hat 
> certifications in
> the hosting industry. Fanatical Support. Click to learn more
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> _______________________________________________
> Numpy-discussion mailing list
> Num...@li...
> https://lists.sourceforge.net/lists/listinfo/numpy-discussion
>

Re: [Numpy-discussion] masked arrays

[Pierre GM <pgm...@ma...>]

On Wednesday 31 May 2006 10:25, John Hunter wrote:
> I'm a bit of an ma newbie.  I have a 2D masked array R and want to
> extract the non-masked values in the last column.  Below I use logical
> indexing, but I suspect there is a "built-in" way w/ masked arrays.  I
> read through the docstring, but didn't see anything better.

R[:,-1].compressed() should do the trick. 

[Numpy-discussion] numpy.test(1,10) results in a segfault

[Nils W. <nw...@ia...>]

test_wrap (numpy.core.tests.test_umath.test_special_methods) ... ok
check_types (numpy.core.tests.test_scalarmath.test_types)*** glibc
detected *** free()                           : invalid pointer:
0xb7ab74a0 ***

Program received signal SIGABRT, Aborted.
[Switching to Thread 16384 (LWP 14948)]
0xb7ca51f1 in kill () from /lib/i686/libc.so.6
(gdb) bt
#0  0xb7ca51f1 in kill () from /lib/i686/libc.so.6
#1  0xb7e90401 in pthread_kill () from /lib/i686/libpthread.so.0
#2  0xb7e9044b in raise () from /lib/i686/libpthread.so.0
#3  0xb7ca4f84 in raise () from /lib/i686/libc.so.6
#4  0xb7ca6498 in abort () from /lib/i686/libc.so.6
#5  0xb7cd8cf6 in __libc_message () from /lib/i686/libc.so.6
#6  0xb7cde367 in malloc_printerr () from /lib/i686/libc.so.6
#7  0xb7cdfacf in free () from /lib/i686/libc.so.6
#8  0xb7ae3fc5 in gentype_dealloc (v=0x0) at scalartypes.inc.src:281
#9  0xb7f57bed in PyEval_EvalFrame () from /usr/lib/libpython2.4.so.1.0
#10 0xb7f5ad21 in PyEval_EvalCodeEx () from /usr/lib/libpython2.4.so.1.0
#11 0xb7f58cc5 in PyEval_EvalFrame () from /usr/lib/libpython2.4.so.1.0
#12 0xb7f5ad21 in PyEval_EvalCodeEx () from /usr/lib/libpython2.4.so.1.0
#13 0xb7f1113a in function_call () from /usr/lib/libpython2.4.so.1.0
#14 0xb7ef9c37 in PyObject_Call () from /usr/lib/libpython2.4.so.1.0
#15 0xb7f02edb in instancemethod_call () from /usr/lib/libpython2.4.so.1.0
#16 0xb7ef9c37 in PyObject_Call () from /usr/lib/libpython2.4.so.1.0
---Type <return> to continue, or q <return> to quit---
#17 0xb7f58097 in PyEval_EvalFrame () from /usr/lib/libpython2.4.so.1.0
#18 0xb7f5ad21 in PyEval_EvalCodeEx () from /usr/lib/libpython2.4.so.1.0
#19 0xb7f1113a in function_call () from /usr/lib/libpython2.4.so.1.0
#20 0xb7ef9c37 in PyObject_Call () from /usr/lib/libpython2.4.so.1.0
#21 0xb7f02edb in instancemethod_call () from /usr/lib/libpython2.4.so.1.0
#22 0xb7ef9c37 in PyObject_Call () from /usr/lib/libpython2.4.so.1.0
#23 0xb7f34c2c in slot_tp_call () from /usr/lib/libpython2.4.so.1.0
#24 0xb7ef9c37 in PyObject_Call () from /usr/lib/libpython2.4.so.1.0
#25 0xb7f58097 in PyEval_EvalFrame () from /usr/lib/libpython2.4.so.1.0
#26 0xb7f5ad21 in PyEval_EvalCodeEx () from /usr/lib/libpython2.4.so.1.0
#27 0xb7f1113a in function_call () from /usr/lib/libpython2.4.so.1.0
#28 0xb7ef9c37 in PyObject_Call () from /usr/lib/libpython2.4.so.1.0
#29 0xb7f02edb in instancemethod_call () from /usr/lib/libpython2.4.so.1.0
#30 0xb7ef9c37 in PyObject_Call () from /usr/lib/libpython2.4.so.1.0
#31 0xb7f34c2c in slot_tp_call () from /usr/lib/libpython2.4.so.1.0
#32 0xb7ef9c37 in PyObject_Call () from /usr/lib/libpython2.4.so.1.0
#33 0xb7f58097 in PyEval_EvalFrame () from /usr/lib/libpython2.4.so.1.0
---Type <return> to continue, or q <return> to quit---
#34 0xb7f5a663 in PyEval_EvalFrame () from /usr/lib/libpython2.4.so.1.0
#35 0xb7f5ad21 in PyEval_EvalCodeEx () from /usr/lib/libpython2.4.so.1.0
#36 0xb7f58cc5 in PyEval_EvalFrame () from /usr/lib/libpython2.4.so.1.0
#37 0xb7f5ad21 in PyEval_EvalCodeEx () from /usr/lib/libpython2.4.so.1.0
#38 0xb7f58cc5 in PyEval_EvalFrame () from /usr/lib/libpython2.4.so.1.0
#39 0xb7f5ad21 in PyEval_EvalCodeEx () from /usr/lib/libpython2.4.so.1.0
#40 0xb7f5aff5 in PyEval_EvalCode () from /usr/lib/libpython2.4.so.1.0
#41 0xb7f75778 in run_node () from /usr/lib/libpython2.4.so.1.0
#42 0xb7f77228 in PyRun_InteractiveOneFlags () from
/usr/lib/libpython2.4.so.1.0
#43 0xb7f77396 in PyRun_InteractiveLoopFlags () from
/usr/lib/libpython2.4.so.1.0
#44 0xb7f774a7 in PyRun_AnyFileExFlags () from /usr/lib/libpython2.4.so.1.0
#45 0xb7f7d66a in Py_Main () from /usr/lib/libpython2.4.so.1.0
#46 0x0804871a in main (argc=0, argv=0x0) at ccpython.cc:10

Can someone reproduce the segfault ?

Linux amanda 2.6.11.4-21.12-default #1 Wed May 10 09:38:20 UTC 2006 i686
athlon i386 GNU/Linux
>>> numpy.__version__
'0.9.9.2553'

[Numpy-discussion] masked arrays

[John H. <jdh...@ac...>]

I'm a bit of an ma newbie.  I have a 2D masked array R and want to
extract the non-masked values in the last column.  Below I use logical
indexing, but I suspect there is a "built-in" way w/ masked arrays.  I
read through the docstring, but didn't see anything better.

In [66]: c = R[:,-1]

In [67]: m = R.mask[:,-1]


In [69]: c[m==0]
Out[69]:
array(data =
 [ 0.94202899  0.51839465  0.24080268  0.26198439  0.29877369
 2.06856187
  0.91415831  0.64994426  0.96544036  1.11259755  2.53623188
  0.71571906
  0.18394649  0.78037904  0.60869565  3.56744705  0.44147157
  0.07692308
  0.27090301  0.16610925  0.57068004  0.80267559  0.57636566
  0.23634337
  1.9509476   0.50761427  0.09587514  0.45039019  0.14381271
  0.69007804
  2.44481605  0.2909699   0.45930881  1.37123746  2.00668896
  3.1638796
  1.0735786   1.06800446  0.18952062  1.55964326  1.16833891
  0.17502787
  1.16610925  0.85507246  0.42140468  0.04236343  1.01337793
  0.22853958
  1.76365663  1.78372352  0.96209588  0.73578595  0.94760312
  1.59531773
  0.88963211],
      mask =
 [False False False False False False False False False False False
 False
 False False False False False False False False False False False
 False
 False False False False False False False False False False False
 False
 False False False False False False False False False False False
 False
 False False False False False False False],
      fill_value=1e+20)

Re: [Numpy-discussion] Distutils problem with g95

[Pearu P. <pe...@sc...>]

On Wed, 31 May 2006, James Graham wrote:

> Pearu Peterson wrote:
>> 
>> Could you send me the output of
>>
>>   g95 --version
>> 
>> for reference?
>
> $ g95 --version
>
> G95 (GCC 4.0.3 (g95!) May 22 2006)

Thanks, I have applied the patch with modifications to numpy svn.
Let me know if it fails to work.

Pearu

[Numpy-discussion] Re: Any Numeric or numarray users on this list?

[RayS <ra...@bl...>]

At 08:10 PM 5/30/2006, you wrote:
>1) Have you transitioned or started to transition to NumPy (i.e. import
>numpy)?

only by following the threads here, so far
no download yet

>2) Will you transition within the next 6 months? (if you answered No to #1)

yes, on this next project (assuming the small array, <2048, 
performance compares to Numeric

>3) Please, explain your reason(s) for not making the switch. (if you
>answered No to #2)

if no, it is because most projects involve small bin number FFTs and 
correlations

>4) Please provide any suggestions for improving NumPy.

24 bit signed integer type, for the new class of ADCs coming out (or 
at least the ability to cast efficiently to Float32)

a GPU back-end option for FFT ;-)

Thanks, it's all good,
Ray

Re: [Numpy-discussion] Distutils problem with g95

[James G. <jg...@ca...>]

Pearu Peterson wrote:
> 
> 
> On Wed, 31 May 2006, James Graham wrote:
> 
>> numpy.distutils seems to have difficulties detecting the current 
>> version of the g95 compiler. I believe this is because the output of 
>> `g95 --version` has changed. The patch below seems to correct the 
>> problem (i.e. it now works with the latest g95) but my regexp foo is 
>> very weak so it may not be correct/optimal.
> 
> Could you send me the output of
> 
>   g95 --version
> 
> for reference?

$ g95 --version

G95 (GCC 4.0.3 (g95!) May 22 2006)
Copyright (C) 2002-2005 Free Software Foundation, Inc.

G95 comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of G95
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING

-- 
"You see stars that clear have been dead for years
But the idea just lives on..." -- Bright Eyes

Re: [Numpy-discussion] Distutils problem with g95

[Pearu P. <pe...@sc...>]

On Wed, 31 May 2006, James Graham wrote:

> numpy.distutils seems to have difficulties detecting the current version of 
> the g95 compiler. I believe this is because the output of `g95 --version` has 
> changed. The patch below seems to correct the problem (i.e. it now works with 
> the latest g95) but my regexp foo is very weak so it may not be 
> correct/optimal.

Could you send me the output of

   g95 --version

for reference?

Thanks,
Pearu

Re: [Numpy-discussion] Any Numeric or numarray users on this list?

[Gary S. <st...@nm...>]

Numeric user since somewhere near "the beginning" (~1996-7?).

> 1) Have you transitioned or started to transition to NumPy (i.e. import 
> numpy)?

No. Just dabbling so far.

> 2) Will you transition within the next 6 months? (if you answered No to #1)

Depends.

> 3) Please, explain your reason(s) for not making the switch. (if you answered 
> No to #2)

(i) Numpy out-of-the-box build failed on my linux boxes, and I will need 
to upgrade linux and Windoze simultaneously. (ii) So far, Numeric is still 
working for me. (iii) Time ... I also have ~200k lines of code to convert. 
(iv) Like others, I guess I'm waiting for NumPy 1.0 to take a stab.

> 4) Please provide any suggestions for improving NumPy.

From what I've tried/tested so far on Windoze, Numpy looks awesome. Thanks 
Travis! And the rest of the development team! (Now, if I could only truly 
understand and remember all the new indexing options ... esp. a[tuple] vs. 
a[array] .....)

Gary

[Numpy-discussion] Distutils problem with g95

[James G. <jg...@ca...>]

numpy.distutils seems to have difficulties detecting the current version of the 
g95 compiler. I believe this is because the output of `g95 --version` has 
changed. The patch below seems to correct the problem (i.e. it now works with 
the latest g95) but my regexp foo is very weak so it may not be correct/optimal.

--- /usr/lib64/python2.3/site-packages/numpy/distutils/fcompiler/g95.py 
2006-01-06 21:29:40.000000000 +0000
+++ /home/jgraham/lib64/python/numpy/distutils/fcompiler/g95.py	2006-05-26 
12:49:50.000000000 +0100
@@ -9,7 +9,7 @@
  class G95FCompiler(FCompiler):

      compiler_type = 'g95'
-    version_pattern = r'G95.*\(experimental\) \(g95!\) (?P<version>.*)\).*'
+    version_pattern = r'G95.*(?:\(experimental\))? \(g95!\) (?P<version>.*)\).*'

      executables = {
          'version_cmd'  : ["g95", "--version"],

-- 
"You see stars that clear have been dead for years
But the idea just lives on..." -- Bright Eyes

[Numpy-discussion] test_scalarmath.py", line 63

[Nils W. <nw...@ia...>]

>>> numpy.__version__
'0.9.9.2553'


 numpy.test(1,10) results in
======================================================================
FAIL: check_types (numpy.core.tests.test_scalarmath.test_types)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/usr/lib64/python2.4/site-packages/numpy/core/tests/test_scalarmath.py",
line 63, in check_types
    assert val.dtype.num == typeconv[k,l] and \
AssertionError: error with (0,7)

----------------------------------------------------------------------
Ran 368 tests in 0.479s

FAILED (failures=1)

Nils

Re: [Numpy-discussion] Suggestions for NumPy

[Ed S. <sch...@ft...>]

On 31/05/2006, at 4:53 AM, Travis Oliphant wrote:

> Please help the developers by responding to a few questions.

I've ported my code to NumPy.  But I have some suggestions for  
improving NumPy.  I've now entered them as these tickets:

Improvements for NumPy's web presence:
http://projects.scipy.org/scipy/numpy/ticket/132

Squeeze behaviour for 1d and 0d arrays:
http://projects.scipy.org/scipy/numpy/ticket/133

Array creation from sequences:
http://projects.scipy.org/scipy/numpy/ticket/134


-- Ed

Re: [Numpy-discussion] Any Numeric or numarray users on this list?

[Francesc A. <fa...@ca...>]

Hi Travis,

Here you have the answers for PyTables project (www.pytables.org).

A Dimecres 31 Maig 2006 04:53, Travis Oliphant va escriure:
> 1) Have you transitioned or started to transition to NumPy (i.e. import
> numpy)?

Not yet, although suport for it is in-place through the use of the array=20
protocol.

> 2) Will you transition within the next 6 months? (if you answered No to #=
1)

We don't know, but other projects in our radar make us to think that we wil=
l=20
not be able to do that in this timeframe.

> 3) Please, explain your reason(s) for not making the switch. (if you
> answered No to #2)

As I said before, it is mainly a matter of priorities. Also, numarray works=
=20
very well for PyTables usage, and besides, NumPy 1.0 is not yet there.

> 4) Please provide any suggestions for improving NumPy.

You are already doing a *great* work. Perhaps pushing numexpr in NumPy woul=
d=20
be nice. Also working in introducing a simple array class in Python core an=
d=20
using the array protocol to access the data would be very good.

Cheers,

=2D-=20
>0,0<   Francesc Altet =A0 =A0 http://www.carabos.com/
V   V   C=E1rabos Coop. V. =A0=A0Enjoy Data
 "-"

Re: [Numpy-discussion] Any Numeric or numarray users on this list?

[Pujo A. <aj...@gm...>]

On 5/31/06, Travis Oliphant <oli...@ie...> wrote:
>
>
> Please help the developers by responding to a few questions.
>
> I'm a Numeric user.
>
> 1) Have you transitioned or started to transition to NumPy (i.e. import
> numpy)?
> No
>
>
> 2) Will you transition within the next 6 months? (if you answered No to
> #1)
> No
>
>
>
> 3) Please, explain your reason(s) for not making the switch. (if you
> answered No to #2)
> Numeric is ok and the conversion somehow make my unittest fail.....



4) Please provide any suggestions for improving NumPy.
> I think the conversion between Numpy and numeric should be
> compatible......
>
>
>
>
> Thanks for your answers.
>
>
> NumPy Developers
>
>
>
>
> -------------------------------------------------------
> All the advantages of Linux Managed Hosting--Without the Cost and Risk!
> Fully trained technicians. The highest number of Red Hat certifications in
> the hosting industry. Fanatical Support. Click to learn more
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=107521&bid=248729&dat=121642
> _______________________________________________
> Numpy-discussion mailing list
> Num...@li...
> https://lists.sourceforge.net/lists/listinfo/numpy-discussion
>

Re: [Numpy-discussion] Any Numeric or numarray users on this list?

[<rba...@fr...>]

Le Mercredi 31 Mai 2006 04:53, Travis Oliphant a =E9crit :
> Please help the developers by responding to a few questions.
>
>

I am a numarray user

>
> 1) Have you transitioned or started to transition to NumPy (i.e. import
> numpy)?

no

I tried to install numpy but the installation failed.

>
> 2) Will you transition within the next 6 months? (if you answered No to=
 #1)
>

no,=20

(hm, but if numarray will be prohibited, ...)

>
> 3) Please, explain your reason(s) for not making the switch. (if you
> answered No to #2)
>

numarray works and works fine (from version number 0.8 to 1.5)

>
>
>
> 4) Please provide any suggestions for improving NumPy.
>
>
>
>
>
> Thanks for your answers.
>
>
> NumPy Developers
>
>

--=20
Ren=E9 Bastian
http://www.musiques-rb.org
http://pythoneon.musiques-rb.org

Re: [Numpy-discussion] when does numpy create temporaries ?

[Arnd B. <arn...@we...>]

On Tue, 30 May 2006, Simon Burton wrote:

> Consider these two operations:
>
> >>> a=numpy.empty( 1024 )
> >>> b=numpy.empty( 1024 )
> >>> a[1:] = b[:-1]
> >>> a[1:] = a[:-1]
> >>>
>
> It seems that in the second operation
> we need to copy the view a[:-1]
> but in the first operation we don't need
> to copy b[:-1].
>
> How does numpy detect this, or does it
> always copy the source when assigning to a slice ?
>
> I've poked around the (numpy) code a bit and
> tried some benchmarks, but it's still not so
> clear to me.

Hi,

not being able to give an answer to this question,
I would like to emphasize that this can be a very important issue:
Firstly, I don't know how to monitor the memory usage
*during* the execution of a line of code.
(Putting numpy.testing.memusage() before and after
that line does not help, if I remember things correctly).

With Numeric I ran into a memory problem with the code appended below.
It turned out, that internally a copy had been made
which for huge arrays brought my system into swapping.
(numpy behaves the same as Numeric. Moreover,  it
seems to consume around 8.5 MB more memory than Numeric?!)

So I strongly agree that it would be nice to know in advance
when temporaries are created.
In addition it would be good to be able to debug memory allocation.
(For example, with f2py there is the option
-DF2PY_REPORT_ON_ARRAY_COPY=1
Note that this only works when generating the wrapper library,
i.e., there is no switch to turn this on or off afterwards,
at least as far as I know).

Best, Arnd



##########################################################
from Numeric import *
#from numpy import *
import os

pid=os.getpid()
print "Process id: ",pid

N=200
NB=30             # number of wavefunctions
NT=20             # time steps
print "Expected size of `wfk`      (in KB):", N*N*NB*8/1024.0
print "Expected size of `time_arr` (in KB):", N*N*NT*16/1024.0

wfk=zeros( (N,N,NB),Float)
phase=ones(NB,Complex)
time_arr=zeros( (N,N,NT),Complex)

print "press enter and watch the memory"
raw_input("(eg. with pmap %d | grep total)" % (pid)  )

# this one does a full copy of wfk, because it is complex !!!
#while 1:
#    for tn in range(NT):
#        time_arr[:,:,tn]+=dot(wfk, phase)
#
#
# memory usage: varies around:
# - 38524K/57276K with Numeric
# - 46980K/66360K with numpy

while 1:
    for tn in range(NT):
        time_arr[:,:,tn]+=dot(wfk, phase.real)+1j*dot(wfk, phase.imag)
#
# memory usage: varies around:
# -  38524K/40412K with Numeric
# -  46984K/47616K with numpy

################################################################

Re: [Numpy-discussion] Any Numeric or numarray users on this list?

[Jens <je...@fy...>]

We use Numeric for our "Atomic Simulation Environment" and for a Density
Functional Theory code:

http://wiki.fysik.dtu.dk/ASE
http://wiki.fysik.dtu.dk/gridcode

> 1) Have you transitioned or started to transition to NumPy (i.e. import
> numpy)?

No.

> 2) Will you transition within the next 6 months? (if you answered No to
> #1)

Yes.  Only problem is that ASE relies on Konrad Hinsen's
Scientific.IO.NetCDF module which is still a Numeric thing.  I saw
recently that this module has been converted to numpy and put in
SciPy/sandbox.  What is the future of this module?

> 4) Please provide any suggestions for improving NumPy.

Can't think of anything!

Jens J=F8rgen Mortensen

Re: [Numpy-discussion] Any Numeric or numarray users on this list?

[Rob H. <ro...@ho...>]

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Travis Oliphant wrote:

Numeric user since 1998. Writing commercial application software for
control of machines. The machine is sold with the application software,
closed source.

| 1) Have you transitioned or started to transition to NumPy (i.e. import
| numpy)?

No

| 2) Will you transition within the next 6 months? (if you answered No
to #1)

Maybe.

| 3) Please, explain your reason(s) for not making the switch. (if you
| answered No to #2)

We are by now late adopters of everything. Everything else we use (we
use about 30 non-GPL opensource packages in our development environment,
some of which are using Numeric themselves) will need to migrate as
well. Our own code is interspersed with Numeric calls, and amounts to
about 200k lines...

Rob

- --
Rob W.W. Hooft  ||  ro...@ho...  ||  http://www.hooft.net/people/rob/
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