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Fernando Perez | 3 Jun 2004 05:42
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Problem with shared libraries

Hi all,

today I tried to build current CVS scipy on a new Fedora Core 2 system, and 
I'm running into a problem.  I think the gist of it has already been seen by 
Eric here:

http://www.scipy.net/pipermail/scipy-dev/2002-April/000836.html

albeit in a slightly different incarnation.

The symptom is:

In [1]: import linalg
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)

/usr/local/installers/src/scipy/build/lib.linux-i686-2.3/scipy/≤console>

/usr/local/installers/src/scipy/build/lib.linux-i686-2.3/scipy/scipy/linalg/__init__.py
       6 ---------------------
       7
----> 8 """
       9 # Modules to import under the scipy namespace
      10 from scipy_version import scipy_version as __version__

/usr/local/installers/src/scipy/build/lib.linux-i686-2.3/scipy/scipy/linalg/basic.py

/usr/local/installers/src/scipy/build/lib.linux-i686-2.3/scipy/scipy/linalg/lapack.py

ImportError: linalg/clapack.so: undefined symbol: clapack_sgesv
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Robert Kern | 3 Jun 2004 05:52
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Re: Problem with shared libraries

Fernando Perez wrote:

[snip]

> I can't put the libs from the Atlas pack in /usr/local/lib, because this 
> directory is NFS-shared by several clients, all with different 
> architectures (Pentium-3, P-4 wihout HT, P-4 with HT, dual-P4, etc).  So 
> I want the Atlas library set provided by scipy to go into each client's 
> own /usr/lib, leaving /usr/local/lib for things which aren't so 
> cpu-sensitive as Atlas.
> 
> Can anyone suggest a way out of this problem?

How about /usr/lib/atlas ? That's how Debian does it.

> Thanks in advance for any suggestions,
> 
> Fernando

--

-- 
Robert Kern
rkern <at> ucsd.edu

"In the fields of hell where the grass grows high
  Are the graves of dreams allowed to die."
   -- Richard Harter
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Fernando Perez | 3 Jun 2004 06:38
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Re: Problem with shared libraries

Robert Kern wrote:
> Fernando Perez wrote:

>>I can't put the libs from the Atlas pack in /usr/local/lib, because this 
>>directory is NFS-shared by several clients, all with different 
>>architectures (Pentium-3, P-4 wihout HT, P-4 with HT, dual-P4, etc).  So 
>>I want the Atlas library set provided by scipy to go into each client's 
>>own /usr/lib, leaving /usr/local/lib for things which aren't so 
>>cpu-sensitive as Atlas.
>>
>>Can anyone suggest a way out of this problem?
> 
> 
> How about /usr/lib/atlas ? That's how Debian does it.

Beautiful!  Many, many thanks.  I was afraid of putting them anywhere except 
for straight /usr/lib or /usr/local/lib, because I thought the scipy build 
process might not find them.  It turns out that the builder is smart enough to 
find them there, and it all works perfectly.

You've saved me hours of frustration, I owe you one :)

Best,

f
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Fernando Perez | 3 Jun 2004 06:40
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One test failed in current CVS

Hi all,

after Robert's help, I got current CVS to successfully build on a Fedora Core 
2 box, using the scipy ATLAS libs for P4 with HT.  Running the level=10 tests 
gives me a single failure:

======================================================================
FAIL: check_expon (scipy.stats.morestats.test_morestats.test_anderson)
----------------------------------------------------------------------
Traceback (most recent call last):
   File "scipy/stats/tests/test_morestats.py", line 55, in check_expon
     assert_array_less(A, crit[-2:])
   File "scipy_test/testing.py", line 705, in assert_array_less
     assert cond,\
AssertionError:
Arrays are not less-ordered (mismatch 100.0%):
         Array 1: 3.20099820806
         Array 2: [ 1.587               1.9339999999999999]

----------------------------------------------------------------------
Ran 950 tests in 106.527s

FAILED (failures=1)

I figured it was worth reporting it here.

Best,

f
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Prabhu Ramachandran | 4 Jun 2004 13:05
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Citing SciPy

Hi,

I cite SciPy in my Thesis and need to specify the authors and a year.
This is what I have so far:

 <at> Misc{,
  title =     {{SciPy}: Open source scientific tools for {Python}},
  url = "http://www.scipy.org/"
}

The bibliography style I use (natbib) requires a year and author
names.  Any recommendations for these fields?

FWIW, this is what I use for SWIG and Python:

 <at> Misc{,
  author =    {Guido van Rossum and others},
  title =     {The {Python} programming language},
  year =         {1991--},
  url = "http://www.python.org/"
}

 <at> Misc{,
  author =       {David Beazley and others},
  title =        {{SWIG}: Simplified Wrapper and Interface Generator},
  year =         {1995--},
  url = "http://www.swig.org"
}

Thanks.
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Travis N. Vaught | 4 Jun 2004 18:26

Re: Citing SciPy

Prabhu Ramachandran wrote:

>Hi,
>
>I cite SciPy in my Thesis and need to specify the authors and a year.
>This is what I have so far:
>
> <at> Misc{,
>  title =     {{SciPy}: Open source scientific tools for {Python}},
>  url = "http://www.scipy.org/"
>}
>
>The bibliography style I use (natbib) requires a year and author
>names.  Any recommendations for these fields?
>
>
>FWIW, this is what I use for SWIG and Python:
>
> <at> Misc{,
>  author =    {Guido van Rossum and others},
>  title =     {The {Python} programming language},
>  year =         {1991--},
>  url = "http://www.python.org/"
>}
>
> <at> Misc{,
>  author =       {David Beazley and others},
>  title =        {{SWIG}: Simplified Wrapper and Interface Generator},
>  year =         {1995--},
>  url = "http://www.swig.org"
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Prabhu Ramachandran | 4 Jun 2004 19:15
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Re: Citing SciPy

>>>>> "TNV" == Travis N Vaught <travis <at> enthought.com> writes:

[...]
    TNV>  <at> Misc{,
    TNV>   author = {Eric Jones, Travis Oliphant, Pearu Peterson and
    TNV>   others}, title = {{SciPy}: Open source scientific tools for
    TNV>   {Python}}, year = {2001--}, url = "http://www.scipy.org/"
    TNV> }

    TNV> Granted, I'm no authority, but I noticed nobody else was
    TNV> fielding this one.  Let's consider this the standard if this
    TNV> doesn't incite any negative response, and I'll make an
    TNV> insightful note bout citing SciPy on the scipy.org site ;-)

Thanks!  The entry should then read:

 <at> Misc{,
  author =    {Eric Jones and Travis Oliphant and Pearu Peterson and others},
  title =     {{SciPy}: Open source scientific tools for {Python}},
  year =      {2001--},
  url = "http://www.scipy.org/"
}

The difference being that the author names in BibTeX are separated by
'and' and not ','.

Thanks again!

cheers,
prabhu
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Travis Oliphant | 5 Jun 2004 07:10
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slicing using Index and Mask arrays


I have just added a feature to scipy in CVS

This feature lets

a[a > 3] = 10
a[indexarray] = 3

and so forth  to function.

Currently
a[maskarray]  and a[indexarray]
always return a 1-d array (multidimensional returns not yet supported)

while
a[maskarray] = obj   and a[indexarray]= obj
will keep the shape of a

To enable the new feature you must type (we will do this by default on 
scipy import at some point)

scipy.alter_numeric()

You can get back old numeric behavior using

scipy.restore_numeric()

Please report any bugs you find...

-Travis O.
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Ying-Chieh Liao | 9 Jun 2004 03:33
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any FreeBSD user here ?

I'd like to use SciPy on FreeBSD
I've installed all the dependencies (all from FreeBSD ports collection):
	python 2.3.4
	py-numeric 23.1
	atlas 3.6.0
	fftw 2.1.5
	djbfft 0.76

But when I build scipy, there are many error messages (attached below)
looks like it cannot find the lapack and blas lib
I think maybe because FreeBSD changes it's name ...
        195:-lalapack.1 => /usr/local/lib/libalapack.so.1
        197:-lcblas.1 => /usr/local/lib/libcblas.so.1
        198:-lf77blas.1 => /usr/local/lib/libf77blas.so.1
        200:-lalapack_r.1 => /usr/local/lib/libalapack_r.so.1
        202:-lcblas_r.1 => /usr/local/lib/libcblas_r.so.1
        203:-lf77blas_r.1 => /usr/local/lib/libf77blas_r.so.1
        205:-lptcblas.1 => /usr/local/lib/libptcblas.so.1
        206:-lptf77blas.1 => /usr/local/lib/libptf77blas.so.1

How can I let scipy find these libs ?

lapack_opt_info:                  
atlas_threads_info:               
scipy_distutils.system_info.atlas_threads_info
scipy_core/scipy_distutils/system_info.py:595: UserWarning:
*********************************************************************
    Could not find lapack library within the ATLAS installation.
*********************************************************************
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Fernando Perez | 10 Jun 2004 19:44
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Re: slicing using Index and Mask arrays

Travis Oliphant wrote:
> I have just added a feature to scipy in CVS
> 
> This feature lets
> 
> a[a > 3] = 10
> a[indexarray] = 3
> 
> and so forth  to function.

So far so good!  This is a great addition, this message is just to report that
it works here with current CVS, Numeric 23.1 built with dotblas on, and a
binary ATLAS as supplied by scipy.org:

planck[~]> scipy

IPython profile: scipy

Welcome to the SciPy Scientific Computing Environment.

In [1]: a=arange(10)

In [2]: a[a>3]=9
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)

/home/fperez/≤console>

IndexError: invalid index
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