From fperez at colorado.edu  Wed Jun  2 23:42:00 2004
From: fperez at colorado.edu (Fernando Perez)
Date: Wed, 02 Jun 2004 21:42:00 -0600
Subject: [SciPy-dev] Problem with shared libraries
Message-ID: <40BE9E08.1080508@colorado.edu>

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


And I think I know why it's happening:  I installed the ATLAS binaries from 
scipy.org on my system, putting them in /usr/lib, _including_ the modified 
lapack/blas libraries.  However, in /usr/lib Fedora also provides shared 
libraries (.so) for lapack and blas.  I guess that the build is getting 
confused, picking up the shared libraries at build time.

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?

Thanks in advance for any suggestions,

Fernando



From rkern at ucsd.edu  Wed Jun  2 23:52:25 2004
From: rkern at ucsd.edu (Robert Kern)
Date: Wed, 02 Jun 2004 20:52:25 -0700
Subject: [SciPy-dev] Problem with shared libraries
In-Reply-To: <40BE9E08.1080508@colorado.edu>
References: <40BE9E08.1080508@colorado.edu>
Message-ID: <40BEA079.10909@ucsd.edu>

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



From fperez at colorado.edu  Thu Jun  3 00:38:34 2004
From: fperez at colorado.edu (Fernando Perez)
Date: Wed, 02 Jun 2004 22:38:34 -0600
Subject: [SciPy-dev] Problem with shared libraries
In-Reply-To: <40BEA079.10909@ucsd.edu>
References: <40BE9E08.1080508@colorado.edu> <40BEA079.10909@ucsd.edu>
Message-ID: <40BEAB4A.7060305@colorado.edu>

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



From fperez at colorado.edu  Thu Jun  3 00:40:32 2004
From: fperez at colorado.edu (Fernando Perez)
Date: Wed, 02 Jun 2004 22:40:32 -0600
Subject: [SciPy-dev] One test failed in current CVS
Message-ID: <40BEABC0.9010004@colorado.edu>

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



From prabhu at aero.iitm.ernet.in  Fri Jun  4 07:05:17 2004
From: prabhu at aero.iitm.ernet.in (Prabhu Ramachandran)
Date: Fri, 4 Jun 2004 16:35:17 +0530
Subject: [SciPy-dev] Citing SciPy
Message-ID: <16576.22381.284792.148146@monster.linux.in>

Hi,

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

@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:

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

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


Thanks.
prabhu



From travis at enthought.com  Fri Jun  4 12:26:16 2004
From: travis at enthought.com (Travis N. Vaught)
Date: Fri, 04 Jun 2004 11:26:16 -0500
Subject: [SciPy-dev] Citing SciPy
In-Reply-To: <16576.22381.284792.148146@monster.linux.in>
References: <16576.22381.284792.148146@monster.linux.in>
Message-ID: <40C0A2A8.4090400@enthought.com>

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:
>
>@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:
>
>@Misc{,
>  author =    {Guido van Rossum and others},
>  title =     {The {Python} programming language},
>  year =         {1991--},
>  url = "http://www.python.org/"
>}
>
>@Misc{,
>  author =       {David Beazley and others},
>  title =        {{SWIG}: Simplified Wrapper and Interface Generator},
>  year =         {1995--},
>  url = "http://www.swig.org"
>}
>
>
>Thanks.
>prabhu
>
>_______________________________________________
>Scipy-dev mailing list
>Scipy-dev at scipy.net
>http://www.scipy.net/mailman/listinfo/scipy-dev
>  
>
Taking guidance from the Maintainers page 
(http://www.scipy.org/development/maintainers.html) I would explicitly 
list Eric, Travis O., and Pearu with 'and others' as above.  For a date, 
I think 2001-- should do it, e.g.:

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


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

Regards,

Travis



From prabhu at aero.iitm.ernet.in  Fri Jun  4 13:15:38 2004
From: prabhu at aero.iitm.ernet.in (Prabhu Ramachandran)
Date: Fri, 4 Jun 2004 22:45:38 +0530
Subject: [SciPy-dev] Citing SciPy
In-Reply-To: <40C0A2A8.4090400@enthought.com>
References: <16576.22381.284792.148146@monster.linux.in>
	<40C0A2A8.4090400@enthought.com>
Message-ID: <16576.44602.645696.648312@monster.linux.in>

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

[...]
    TNV> @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:

@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



From oliphant at ee.byu.edu  Sat Jun  5 01:10:04 2004
From: oliphant at ee.byu.edu (Travis Oliphant)
Date: Fri, 04 Jun 2004 23:10:04 -0600
Subject: [SciPy-dev] slicing using Index and Mask arrays 
Message-ID: <40C155AC.2020000@ee.byu.edu>


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.








From ijliao at csie.nctu.edu.tw  Tue Jun  8 21:33:16 2004
From: ijliao at csie.nctu.edu.tw (Ying-Chieh Liao)
Date: Wed, 9 Jun 2004 09:33:16 +0800
Subject: [SciPy-dev] any FreeBSD user here ?
Message-ID: <20040609013316.GA93849@freebsd.csie.nctu.edu.tw>

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.
*********************************************************************
                                  
  warnings.warn(message)          
  FOUND:                          
    libraries = ['ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/usr/local/lib']
    language = c                  
    define_macros = [('ATLAS_WITHOUT_LAPACK', None)]
    include_dirs = ['/usr/local/include']
                                  
running build_src                 
building extension "atlas_version" sources
  adding 'build/src/atlas_version_0x1f56736.c' to sources.
running build_ext                 
customize UnixCCompiler           
customize UnixCCompiler using build_ext
lapack_info:                      
  NOT AVAILABLE                   
                                  
scipy_core/scipy_distutils/system_info.py:916: UserWarning:
    Lapack (http://www.netlib.org/lapack/) libraries not found.
    Directories to search for the libraries can be specified in the
    scipy_distutils/site.cfg file (section [lapack]) or by setting
    the LAPACK environment variable.
  warnings.warn(LapackNotFoundError.__doc__)
lapack_src_info:                  
  NOT AVAILABLE                   
                                  
scipy_core/scipy_distutils/system_info.py:919: UserWarning:
    Lapack (http://www.netlib.org/lapack/) sources not found.
    Directories to search for the sources can be specified in the
    scipy_distutils/site.cfg file (section [lapack_src]) or by setting
    the LAPACK_SRC environment variable.
  warnings.warn(LapackSrcNotFoundError.__doc__)
  NOT AVAILABLE                   
                                  
Traceback (most recent call last):
  File "setup.py", line 110, in ? 
    setup_package(ignore_packages)
  File "setup.py", line 83, in setup_package
    ignore_packages = ignore_packages)
  File "scipy_core/scipy_distutils/misc_util.py", line 459, in get_subpackages
    config = setup_module.configuration(*args)
  File "/tmp/py-scipy/work/SciPy_complete-0.3/Lib/linalg/setup_linalg.py", line 40, in configuration
    raise NotFoundError,'no lapack/blas resources found'
scipy_distutils.system_info.NotFoundError: no lapack/blas resources found
-- 
Pi seconds is a nanocentury.
					--- Tom Duff
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From Fernando.Perez at colorado.edu  Thu Jun 10 13:44:06 2004
From: Fernando.Perez at colorado.edu (Fernando Perez)
Date: Thu, 10 Jun 2004 11:44:06 -0600
Subject: [SciPy-dev] slicing using Index and Mask arrays
In-Reply-To: <40C155AC.2020000@ee.byu.edu>
References: <40C155AC.2020000@ee.byu.edu>
Message-ID: <40C89DE6.4040105@colorado.edu>

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

In [3]: scipy.alter_numeric()

In [4]: a[a>3]=9

In [5]: a
Out[5]: NumPy array, format: long
[0 1 2 3 9 9 9 9 9 9]

In [6]: scipy.restore_numeric()

In [7]: a[a>3]=9
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)

/home/fperez/<console>

IndexError: invalid index


I'll enable the alter_numeric() from now on permanently for me.

Many thanks!

f.



From arnd.baecker at web.de  Thu Jun 17 05:14:58 2004
From: arnd.baecker at web.de (Arnd Baecker)
Date: Thu, 17 Jun 2004 11:14:58 +0200 (CEST)
Subject: [SciPy-dev] interest in xplt bug reports?
Message-ID: <Pine.LNX.4.51.0406171113210.31344@ptpcp2.phy.tu-dresden.de>

Dear all,

I would like to know if there is any interest in
bug reports concerning scipy.xplt?
During the last months a couple of issues/features/bugs
and differences between linux/windows
were found by the students of our computational physics
course with python/Numeric/scipy.
The xplt issues caused the largest amount
of complaints (shortly followed by documentation ;-).

If there is sufficient interest, we have some money
for a student who could compile a list of problems
(with short examples).

As xplt derives from pygist, should we better address
the questions to the pygist people and
hope that any fixes will get incorporated into scipy.xplt
at some point?
If so, whom should we contact (Michiel de Hoon?)?

Best,

Arnd



From oliphant at ee.byu.edu  Thu Jun 17 15:06:53 2004
From: oliphant at ee.byu.edu (Travis Oliphant)
Date: Thu, 17 Jun 2004 13:06:53 -0600
Subject: [SciPy-dev] interest in xplt bug reports?
In-Reply-To: <Pine.LNX.4.51.0406171113210.31344@ptpcp2.phy.tu-dresden.de>
References: <Pine.LNX.4.51.0406171113210.31344@ptpcp2.phy.tu-dresden.de>
Message-ID: <40D1EBCD.4010002@ee.byu.edu>

Arnd Baecker wrote:

>Dear all,
>
>I would like to know if there is any interest in
>bug reports concerning scipy.xplt?
>During the last months a couple of issues/features/bugs
>and differences between linux/windows
>were found by the students of our computational physics
>course with python/Numeric/scipy.
>The xplt issues caused the largest amount
>of complaints (shortly followed by documentation ;-).
>
>If there is sufficient interest, we have some money
>for a student who could compile a list of problems
>(with short examples).
>  
>
This feedback would be useful.  

>As xplt derives from pygist, should we better address
>the questions to the pygist people and
>hope that any fixes will get incorporated into scipy.xplt
>at some point?
>  
>
We have already made some changes to scipy.xplt but ideally any fixes 
would go to both places.

-Travis O.








From mcseem at antigrain.com  Sun Jun 20 14:20:18 2004
From: mcseem at antigrain.com (Maxim Shemanarev)
Date: Sun, 20 Jun 2004 14:20:18 -0400
Subject: [SciPy-dev] Hello
Message-ID: <003701c456f3$3e134b30$0c01a8c0@mcseemxp>

Hello All,

I'm Maxim Shemanarev and I will work on the new graphic back-end in Kiva.
It's based on my Anti-Grain Geometry (http://antigrain.com). I can perfectly
do the C++ part of the job, and Eric and I have lots of new ideas, but I
also will need to do some job in Python and SWIG. I'm still not very good in
those things, so, please forgive me possible stupid questions. I will
gratefully appreciate your help. Currently I'm working on improving
alpha-blending in AGG (very basic things), so it will be a while before I
ask you of some help.

Thank you in advance.

McSeem



From Giovanni.Samaey at cs.kuleuven.ac.be  Fri Jun 25 10:07:21 2004
From: Giovanni.Samaey at cs.kuleuven.ac.be (Giovanni Samaey)
Date: Fri, 25 Jun 2004 16:07:21 +0200
Subject: [SciPy-dev] installation problems with SciPy
Message-ID: <40DC3199.40505@cs.kuleuven.ac.be>

Hi,

I seem to have some problems installing SciPy.
I installed SciPy from the latest (?) source that I downloaded following
the instructions at
  http://www.scipy.org/documentation/buildscipy.txt

I took advantage of the fact that ATLAS is already installed here under
/usr/lib/3dnow.  I don't have
root access to my system.

The test() routine runs, but gives 15 errors of the type
======================================================================
ERROR: check_sh_legendre (scipy.special.basic.test_basic.test_sh_legendre)
----------------------------------------------------------------------
Traceback (most recent call last):
   File
"/home/giovanni/bin/lib/python2.3/site-packages/scipy/special/tests/test_basic.py", 

line 1806, in check_sh_legendre
     Ps1 = sh_legendre(1)
   File
"/home/giovanni/bin/lib/python2.3/site-packages/scipy/special/orthogonal.py", 

line 593, in sh_legendre
     x,w,mu0 = ps_roots(n,mu=1)
   File
"/home/giovanni/bin/lib/python2.3/site-packages/scipy/special/orthogonal.py", 

line 584, in ps_roots
     return js_roots(n,1.0,1.0,mu=mu)
   File
"/home/giovanni/bin/lib/python2.3/site-packages/scipy/special/orthogonal.py", 

line 205, in js_roots
     val = gen_roots_and_weights(n,an_Js,sbn_Js,mu0)
   File
"/home/giovanni/bin/lib/python2.3/site-packages/scipy/special/orthogonal.py", 

line 121, in gen_roots_and_weights
     eig = get_eig_func()
   File
"/home/giovanni/bin/lib/python2.3/site-packages/scipy/special/orthogonal.py", 

line 91, in get_eig_func
     eig = scipy.linalg.eig
AttributeError: 'module' object has no attribute 'eig'

----------------------------------------------------------------------

Moreover, functions from the packages "integrate" and "linalg" are
simply not found...

I generated the information that is requested by the INSTALL.text file;
it is attached to this mail...

The command
$ python scipy_core/scipy_distutils/command/build_flib.py
could not be executed because for some reason "build_flib.py" is not
present; maybe the info in attachment
might tell why?

If these problems could be solved, I would be thrilled, because SciPy
really looks to a promising tool.
Thanks already in advance,


Best,

Giovanni


-- 
Giovanni Samaey		 	http://www.cs.kuleuven.ac.be/~giovanni/
Katholieke Universiteit Leuven 	      email: giovanni at cs.kuleuven.ac.be
Departement Computerwetenschappen                  phone: +32-16-327081
Celestijnenlaan 200A, B-3001 Heverlee, Belgium       fax: +32-16-327996
Office: A04.36



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From pearu at scipy.org  Fri Jun 25 11:03:22 2004
From: pearu at scipy.org (Pearu Peterson)
Date: Fri, 25 Jun 2004 10:03:22 -0500 (CDT)
Subject: [SciPy-dev] installation problems with SciPy
In-Reply-To: <40DC3199.40505@cs.kuleuven.ac.be>
References: <40DC3199.40505@cs.kuleuven.ac.be>
Message-ID: <Pine.LNX.4.58.0406250955510.25309@scipy.org>



On Fri, 25 Jun 2004, Giovanni Samaey wrote:

> Hi,
> 
> I seem to have some problems installing SciPy.
> I installed SciPy from the latest (?) source that I downloaded following
> the instructions at
>   http://www.scipy.org/documentation/buildscipy.txt
> 
> I took advantage of the fact that ATLAS is already installed here under
> /usr/lib/3dnow.  I don't have root access to my system.

> I generated the information that is requested by the INSTALL.text file;
> it is attached to this mail...

Thanks for the information. We should concentrate to the following error
in system_info.py output:

blas_opt_info:
running build_src
building extension "atlas_version" sources
  adding 'build/src/atlas_version_0x8bd9e760.c' to sources.
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
Command: /home/giovanni/bin/bin/python -c "import
imp;imp.load_dynamic(\"atlas_version\",\"atlas_version.so\")"
Status: 1
Output: Traceback (most recent call last):
  File "<string>", line 1, in ?
ImportError: libatlas.so.2: cannot open shared object file: No such file 
or directory

Where is this file libatlas.so.2 in your system? You may need to add
its directory path to /etc/ld.so.conf file (and run ldconfig). Since
you don't have root access then add the directory path to

  LD_LIBRARY_PATH

environment variable and see if atlas_version works then.


> The command
> $ python scipy_core/scipy_distutils/command/build_flib.py
> could not be executed because for some reason "build_flib.py" is not
> present; maybe the info in attachment might tell why?

That is ok. build_flib.py is not existing anymore, its functionality has 
been replaced by *fcompiler.py files.

Pearu



From Giovanni.Samaey at cs.kuleuven.ac.be  Fri Jun 25 11:47:21 2004
From: Giovanni.Samaey at cs.kuleuven.ac.be (Giovanni Samaey)
Date: Fri, 25 Jun 2004 17:47:21 +0200
Subject: [SciPy-dev] installation problems with SciPy
Message-ID: <40DC4909.30600@cs.kuleuven.ac.be>

Thank you for the help.  Putting /usr/lib/3dnow in LD_LIBRARY_PATH made 
the tests run better.

The state has progressed:

Running scipy.test() now gives no errors (on all levels).  The only 
things that go "wrong" now is
two warnings. I don't know if they are worth bothering about:

****************************************************************
WARNING: cblas module is empty
-----------
See scipy/INSTALL.txt for troubleshooting.
Notes:
* If atlas library is not found by scipy/system_info.py,
  then scipy uses fblas instead of cblas.
****************************************************************
****************************************************************
WARNING: clapack module is empty
-----------
See scipy/INSTALL.txt for troubleshooting.
Notes:
* If atlas library is not found by scipy/system_info.py,
  then scipy uses flapack instead of clapack.
****************************************************************

However, import atlas_version still gives an error.  I don't know if I 
should care?

bash-2.05a$ python -c 'import atlas_version'
Traceback (most recent call last):
  File "<string>", line 1, in ?
ImportError: ./atlas_version.so: undefined symbol: ATL_buildinfo

Best, and thanks already!  I would never have found this LD_LIBRARY_PATH 
stuff.

Giovanni

-- 
Giovanni Samaey		 	http://www.cs.kuleuven.ac.be/~giovanni/ 
Katholieke Universiteit Leuven 	      email: giovanni at cs.kuleuven.ac.be 
Departement Computerwetenschappen                  phone: +32-16-327081
Celestijnenlaan 200A, B-3001 Heverlee, Belgium       fax: +32-16-327996
Office: A04.36




From pearu at scipy.org  Fri Jun 25 12:06:53 2004
From: pearu at scipy.org (Pearu Peterson)
Date: Fri, 25 Jun 2004 11:06:53 -0500 (CDT)
Subject: [SciPy-dev] installation problems with SciPy
In-Reply-To: <40DC4909.30600@cs.kuleuven.ac.be>
References: <40DC4909.30600@cs.kuleuven.ac.be>
Message-ID: <Pine.LNX.4.58.0406251104200.25309@scipy.org>



On Fri, 25 Jun 2004, Giovanni Samaey wrote:

> Thank you for the help.  Putting /usr/lib/3dnow in LD_LIBRARY_PATH made 
> the tests run better.
> 
> The state has progressed:
> 
> Running scipy.test() now gives no errors (on all levels).  The only 
> things that go "wrong" now is
> two warnings. I don't know if they are worth bothering about:
> 
> ****************************************************************
> WARNING: cblas module is empty
> -----------
> See scipy/INSTALL.txt for troubleshooting.
> Notes:
> * If atlas library is not found by scipy/system_info.py,
>   then scipy uses fblas instead of cblas.
> ****************************************************************

What is the (blas/lapack/atlas related) output of `python system_info.py` 
now that you have changed LD_LIBRARY_PATH? Try adding also 
/usr/lib/3dnow/atlas to LD_LIBRARY_PATH. E.g. set

  LD_LIBRARY_PATH=/usr/lib/3dnow/atlas:/usr/lib/3dnow

Pearu



From Giovanni.Samaey at cs.kuleuven.ac.be  Fri Jun 25 12:31:06 2004
From: Giovanni.Samaey at cs.kuleuven.ac.be (Giovanni Samaey)
Date: Fri, 25 Jun 2004 18:31:06 +0200
Subject: [SciPy-dev] installation problems with SciPy
Message-ID: <40DC534A.6020909@cs.kuleuven.ac.be>

Hi,

just changing LD_LIBRARY_PATH did not make a difference.

I tried reinstalling scipy with the LD_LIBRARY_PATH set, and somehow
this installation crashed with the following final lines:

building extension "scipy.io.numpyio" sources
building extension "scipy.linalg.fblas" sources
generating fblas interface
20
error: build/src/atlas321/fblas.pyf: No such file or directory

Now I am confused again... How did I break this?

Giovanni

-- 
Giovanni Samaey		 	http://www.cs.kuleuven.ac.be/~giovanni/ 
Katholieke Universiteit Leuven 	      email: giovanni at cs.kuleuven.ac.be 
Departement Computerwetenschappen                  phone: +32-16-327081
Celestijnenlaan 200A, B-3001 Heverlee, Belgium       fax: +32-16-327996
Office: A04.36




From pearu at scipy.org  Fri Jun 25 12:52:35 2004
From: pearu at scipy.org (Pearu Peterson)
Date: Fri, 25 Jun 2004 11:52:35 -0500 (CDT)
Subject: [SciPy-dev] installation problems with SciPy
In-Reply-To: <40DC534A.6020909@cs.kuleuven.ac.be>
References: <40DC534A.6020909@cs.kuleuven.ac.be>
Message-ID: <Pine.LNX.4.58.0406251147270.25309@scipy.org>



On Fri, 25 Jun 2004, Giovanni Samaey wrote:

> just changing LD_LIBRARY_PATH did not make a difference.
> 
> I tried reinstalling scipy with the LD_LIBRARY_PATH set, and somehow
> this installation crashed with the following final lines:
> 
> building extension "scipy.io.numpyio" sources
> building extension "scipy.linalg.fblas" sources
> generating fblas interface
> 20
> error: build/src/atlas321/fblas.pyf: No such file or directory
> 
> Now I am confused again... How did I break this?

Did you remove build directory before reinstalling scipy?
If not then do that and rerun scipy build/install commands.

Sometimes building ATLAS yourself or using prebuilt ATLAS libraries from

  http://www.scipy.org/download/atlasbinaries/

is easier than trying to use system provided ATLAS, especially when the 
system is oldish and you don't have enough permissions to fix the system.

HTH,
Pearu



From Giovanni.Samaey at cs.kuleuven.ac.be  Fri Jun 25 13:10:49 2004
From: Giovanni.Samaey at cs.kuleuven.ac.be (Giovanni Samaey)
Date: Fri, 25 Jun 2004 19:10:49 +0200
Subject: [SciPy-dev] installation problems with SciPy
In-Reply-To: <Pine.LNX.4.58.0406251147270.25309@scipy.org>
References: <40DC534A.6020909@cs.kuleuven.ac.be>
	<Pine.LNX.4.58.0406251147270.25309@scipy.org>
Message-ID: <40DC5C99.5070501@cs.kuleuven.ac.be>

Pearu Peterson wrote:

>On Fri, 25 Jun 2004, Giovanni Samaey wrote:
>
>  
>
>>just changing LD_LIBRARY_PATH did not make a difference.
>>
>>I tried reinstalling scipy with the LD_LIBRARY_PATH set, and somehow
>>this installation crashed with the following final lines:
>>
>>building extension "scipy.io.numpyio" sources
>>building extension "scipy.linalg.fblas" sources
>>generating fblas interface
>>20
>>error: build/src/atlas321/fblas.pyf: No such file or directory
>>
>>Now I am confused again... How did I break this?
>>    
>>
>
>Did you remove build directory before reinstalling scipy?
>  
>
I did.  Apparently the problem was indeed that the atlas installation on 
our systems
is outdated.  (Like almost all other software that is managed by the 
system group ;-) )

Installing the atlas binary in some directory dir/ and pointing both 
LD_LIBRARY_PATH
and ATLAS environment variables to dir/ worked.  Now everything runs 
smoothly!

(I tried installing the binary myself before but this didn't work.  This 
will probably also
have been due to not setting LD_LIBRARY_PATH.)

Now the output of python -c 'import atlas_version' is

ATLAS version 3.6.0 built by pearu on Sun Apr 11 01:13:26 EEST 2004:
   UNAME    : Linux p4.home.net 2.6.0-p4.10 #1 SMP Fri Jan 2 13:37:10 
EET 2004 i686 GNU/Linux
   INSTFLG  :
   MMDEF    : /home/pearu/src/ATLAS/CONFIG/ARCHS/P4SSE2/gcc/gemm
   ARCHDEF  : /home/pearu/src/ATLAS/CONFIG/ARCHS/P4SSE2/gcc/misc
   F2CDEFS  : -DAdd_ -DStringSunStyle
   CACHEEDGE: 1048576
   F77      : /home/pearu/bin/g77, version GNU Fortran (GCC) 3.3.3 
(Debian 20040314)
   F77FLAGS : -fomit-frame-pointer -O -fno-second-underscore
   CC       : /home/pearu/bin/gcc, version gcc-3.3 (GCC) 3.3.3 (Debian 
20040314)
   CC FLAGS : -fomit-frame-pointer -O3 -funroll-all-loops
   MCC      : /home/pearu/bin/gcc, version gcc-3.3 (GCC) 3.3.3 (Debian 
20040314)
   MCCFLAGS : -fomit-frame-pointer -O

which looks like it is what it was supposed to be...

Thanks for the patient help!  I would never have done this on my own!

Bye,

Giovanni