Re: [Numpy-discussion] glibc error

2009-01-24 Thread David Cournapeau
Gideon Simpson wrote:
> Rerunning the tests with verbosity, it dies at:
>
> test_single (test_linalg.TestSolve) ... ok
> Ticket #652 ... *** glibc detected *** python: free(): invalid next  
> size (fast): 0x01e284e0 ***
>
> I'm using ATLAS 3.8.2 and lapack 3.2.
>   

Lapack 3.2 may be the problem. There have been interface changes in some
functions related to LU factorization in LAPACK 3.2 - I am not sure that
those are the ones used by eig, but since many people have run the test
suite with numpy 1.2.1 and atlas 3.8.2, I would look at that first.

cheers,

David
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Re: [Numpy-discussion] glibc error

2009-01-24 Thread Gideon Simpson
Rerunning the tests with verbosity, it dies at:

test_single (test_linalg.TestSolve) ... ok
Ticket #652 ... *** glibc detected *** python: free(): invalid next  
size (fast): 0x01e284e0 ***

I'm using ATLAS 3.8.2 and lapack 3.2.  ATLAS and lapack were all built  
with the -m64 flag.
-gideon

On Jan 24, 2009, at 11:37 PM, David Cournapeau wrote:

> Gideon Simpson wrote:
>> Having built an up to date lapack and ATLAS against gcc 4.3.2, I  
>> tried
>> installing numpy 1.2.1 on Python 2.5.4.  When testing I get:
>>
>> Python 2.5.4 (r254:67916, Jan 24 2009, 00:27:20)
>> [GCC 4.3.2] on linux2
>> Type "help", "copyright", "credits" or "license" for more  
>> information.
> import numpy
> numpy.test()
>> Running unit tests for numpy
>> NumPy version 1.2.1
>> NumPy is installed in /usr/local/nonsystem/simpson/lib/python2.5/ 
>> site-
>> packages/numpy
>> Python version 2.5.4 (r254:67916, Jan 24 2009, 00:27:20) [GCC 4.3.2]
>> nose version 0.10.4
>> ..F
>> K
>> 
>> 
>> ***
>>  glibc
>>  detected *** python: free(): invalid next size (fast):
>> 0x1196b550 ***
>>
>
> Can you rerun the test verbosely ?
>
> python -c "import numpy; numpy.test(verbose=10)"
>
> This glibc message is generally a symptom of serious memory  
> corruption -
> which is why only the OS can stop it at that point.
>
> cheers,
>
> David
>
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Re: [Numpy-discussion] glibc error

2009-01-24 Thread David Cournapeau
Hoyt Koepke wrote:
> Not sure what the problem is in your case, but I had the same error a
> while back.  For some reason, ATLAS thought it should be compiled as
> 64 bit but numpy as 32 bit. .  It went away after I passed the -b 32
> flag to configure in ATLAS (I think).  Thus that's one thing to check.
> Also, make sure you're using ATLAS 3.8.x, as I had problems with the
> 3.9 series (don't know if that would be an issue still).
>   

Actually, I would advise using only 3.8.2. Previous versions had bugs
for some core routines used by numpy (at least 3.8.0 did). I am a bit
surprised that a 64 bits-built atlas would be runnable at all in a 32
bits binary - I would expect the link phase to fail if two different
object formats are linked together.

cheers,

David
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Re: [Numpy-discussion] glibc error

2009-01-24 Thread Hoyt Koepke
Not sure what the problem is in your case, but I had the same error a
while back.  For some reason, ATLAS thought it should be compiled as
64 bit but numpy as 32 bit. .  It went away after I passed the -b 32
flag to configure in ATLAS (I think).  Thus that's one thing to check.
Also, make sure you're using ATLAS 3.8.x, as I had problems with the
3.9 series (don't know if that would be an issue still).

--Hoyt

On Sat, Jan 24, 2009 at 8:47 PM, Gideon Simpson
 wrote:
> Having built an up to date lapack and ATLAS against gcc 4.3.2, I tried
> installing numpy 1.2.1 on Python 2.5.4.  When testing I get:
>
> Python 2.5.4 (r254:67916, Jan 24 2009, 00:27:20)
> [GCC 4.3.2] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>  >>> import numpy
>  >>> numpy.test()
> Running unit tests for numpy
> NumPy version 1.2.1
> NumPy is installed in /usr/local/nonsystem/simpson/lib/python2.5/site-
> packages/numpy
> Python version 2.5.4 (r254:67916, Jan 24 2009, 00:27:20) [GCC 4.3.2]
> nose version 0.10.4
> ..F
> K
> 
> 
> ***
>  glibc
>  detected *** python: free(): invalid next size (fast):
> 0x1196b550 ***
>
>
> I then have to kill python to get control again.
> -gideon
>
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-- 


+ Hoyt Koepke
+ University of Washington Department of Statistics
+ http://www.stat.washington.edu/~hoytak/
+ hoy...@gmail.com
++
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Re: [Numpy-discussion] glibc error

2009-01-24 Thread Robert Kern
On Sat, Jan 24, 2009 at 22:47, Gideon Simpson  wrote:
> Having built an up to date lapack and ATLAS against gcc 4.3.2, I tried
> installing numpy 1.2.1 on Python 2.5.4.  When testing I get:

Run numpy.test(verbose=2) in order to have nose print out the name of
the method it is running before actually running it. This will let us
figure out which test is causing the failure.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless
enigma that is made terrible by our own mad attempt to interpret it as
though it had an underlying truth."
  -- Umberto Eco
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Re: [Numpy-discussion] glibc error

2009-01-24 Thread David Cournapeau
Gideon Simpson wrote:
> Having built an up to date lapack and ATLAS against gcc 4.3.2, I tried  
> installing numpy 1.2.1 on Python 2.5.4.  When testing I get:
>
> Python 2.5.4 (r254:67916, Jan 24 2009, 00:27:20)
> [GCC 4.3.2] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>  >>> import numpy
>  >>> numpy.test()
> Running unit tests for numpy
> NumPy version 1.2.1
> NumPy is installed in /usr/local/nonsystem/simpson/lib/python2.5/site- 
> packages/numpy
> Python version 2.5.4 (r254:67916, Jan 24 2009, 00:27:20) [GCC 4.3.2]
> nose version 0.10.4
> ..F
>  
> K 
>  
>  
> ***
>  glibc 
>   detected *** python: free(): invalid next size (fast):  
> 0x1196b550 ***
>   

Can you rerun the test verbosely ?

python -c "import numpy; numpy.test(verbose=10)"

This glibc message is generally a symptom of serious memory corruption -
which is why only the OS can stop it at that point.

cheers,

David

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[Numpy-discussion] glibc error

2009-01-24 Thread Gideon Simpson
Having built an up to date lapack and ATLAS against gcc 4.3.2, I tried  
installing numpy 1.2.1 on Python 2.5.4.  When testing I get:

Python 2.5.4 (r254:67916, Jan 24 2009, 00:27:20)
[GCC 4.3.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
 >>> import numpy
 >>> numpy.test()
Running unit tests for numpy
NumPy version 1.2.1
NumPy is installed in /usr/local/nonsystem/simpson/lib/python2.5/site- 
packages/numpy
Python version 2.5.4 (r254:67916, Jan 24 2009, 00:27:20) [GCC 4.3.2]
nose version 0.10.4
..F
 
K 
 
 
***
 glibc 
  detected *** python: free(): invalid next size (fast):  
0x1196b550 ***


I then have to kill python to get control again.
-gideon

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Re: [Numpy-discussion] Having trouble installing Numpy on OS X

2009-01-24 Thread Michael Abshoff
Robert Kern wrote:
> On Sat, Jan 24, 2009 at 18:31, Nat Wilson  wrote:
>> It throws this out.
>>
>> Python 2.6.1 (r261:67515, Jan 24 2009, 16:08:37)
>> [GCC 4.0.0 20041026 (Apple Computer, Inc. build 4061)] on darwin
>> Type "help", "copyright", "credits" or "license" for more information.
>>  >>> import os
>>  >>> os.urandom(16)
>> '\xe0;n\x8a*\xb4\x08N\x80<\xef\x9b*\x06\x1b\xc4'
>>  >>>
> 
> Well, looking at the C code for random_seed(), I don't see a way for
> it to return NULL without having an exception set (assuming that the
> Python API calls aren't buggy). Except maybe the assert() call in
> there. When you built your Python, are you sure that -DNDEBUG was
> being used?
> 

Well, the gcc used to compiler Python is rather ancient and that gcc 
release by Apple has the reputation to be "buggier than a Florida swamp 
in July" and at least for building Sage it is blacklisted. So I would 
suggest updating gcc by using some more recent XCode and trying again.

Cheers,

Michael
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Re: [Numpy-discussion] Having trouble installing Numpy on OS X

2009-01-24 Thread Robert Kern
On Sat, Jan 24, 2009 at 19:13, Nat Wilson  wrote:
> To be honest, I really don't know. I followed the directions in /Mac/
> README for a framework install.
>
> How would I check this?

Another possibility for tracking down the problem would be to start up
Python under gdb, add a breakpoint for the function random_seed() then
step through. That would help you find out the code path that makes it
return NULL without setting the exception.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless
enigma that is made terrible by our own mad attempt to interpret it as
though it had an underlying truth."
  -- Umberto Eco
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Re: [Numpy-discussion] Having trouble installing Numpy on OS X

2009-01-24 Thread Robert Kern
On Sat, Jan 24, 2009 at 19:13, Nat Wilson  wrote:
> To be honest, I really don't know. I followed the directions in /Mac/
> README for a framework install.
>
> How would I check this?

Rebuild and look at the compiler command lines as they go by.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless
enigma that is made terrible by our own mad attempt to interpret it as
though it had an underlying truth."
  -- Umberto Eco
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Re: [Numpy-discussion] Having trouble installing Numpy on OS X

2009-01-24 Thread Nat Wilson
To be honest, I really don't know. I followed the directions in /Mac/ 
README for a framework install.

How would I check this?

Thanks a lot for sticking with me,

Nat

On Jan 24, 2009, at 7:41 PM, Robert Kern wrote:

> On Sat, Jan 24, 2009 at 18:31, Nat Wilson   
> wrote:
>> It throws this out.
>>
>> Python 2.6.1 (r261:67515, Jan 24 2009, 16:08:37)
>> [GCC 4.0.0 20041026 (Apple Computer, Inc. build 4061)] on darwin
>> Type "help", "copyright", "credits" or "license" for more  
>> information.
> import os
> os.urandom(16)
>> '\xe0;n\x8a*\xb4\x08N\x80<\xef\x9b*\x06\x1b\xc4'
>
>
> Well, looking at the C code for random_seed(), I don't see a way for
> it to return NULL without having an exception set (assuming that the
> Python API calls aren't buggy). Except maybe the assert() call in
> there. When you built your Python, are you sure that -DNDEBUG was
> being used?
>
> -- 
> Robert Kern
>
> "I have come to believe that the whole world is an enigma, a harmless
> enigma that is made terrible by our own mad attempt to interpret it as
> though it had an underlying truth."
>   -- Umberto Eco
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Re: [Numpy-discussion] Having trouble installing Numpy on OS X

2009-01-24 Thread Robert Kern
On Sat, Jan 24, 2009 at 18:31, Nat Wilson  wrote:
> It throws this out.
>
> Python 2.6.1 (r261:67515, Jan 24 2009, 16:08:37)
> [GCC 4.0.0 20041026 (Apple Computer, Inc. build 4061)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>  >>> import os
>  >>> os.urandom(16)
> '\xe0;n\x8a*\xb4\x08N\x80<\xef\x9b*\x06\x1b\xc4'
>  >>>

Well, looking at the C code for random_seed(), I don't see a way for
it to return NULL without having an exception set (assuming that the
Python API calls aren't buggy). Except maybe the assert() call in
there. When you built your Python, are you sure that -DNDEBUG was
being used?

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless
enigma that is made terrible by our own mad attempt to interpret it as
though it had an underlying truth."
  -- Umberto Eco
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Re: [Numpy-discussion] Having trouble installing Numpy on OS X

2009-01-24 Thread Nat Wilson
It throws this out.

Python 2.6.1 (r261:67515, Jan 24 2009, 16:08:37)
[GCC 4.0.0 20041026 (Apple Computer, Inc. build 4061)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
 >>> import os
 >>> os.urandom(16)
'\xe0;n\x8a*\xb4\x08N\x80<\xef\x9b*\x06\x1b\xc4'
 >>>

Nat

On Jan 24, 2009, at 7:12 PM, Robert Kern wrote:

> On Sat, Jan 24, 2009 at 17:58, Nat Wilson   
> wrote:
>> Ah, no, I can't import it.
>>
>> What does this mean? As far as I know, I built Python as instructed.
>
> I'm not sure. Can you show me what os.urandom(16) gives you?
>
> -- 
> Robert Kern
>
> "I have come to believe that the whole world is an enigma, a harmless
> enigma that is made terrible by our own mad attempt to interpret it as
> though it had an underlying truth."
>   -- Umberto Eco
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Re: [Numpy-discussion] Having trouble installing Numpy on OS X

2009-01-24 Thread Robert Kern
On Sat, Jan 24, 2009 at 17:58, Nat Wilson  wrote:
> Ah, no, I can't import it.
>
> What does this mean? As far as I know, I built Python as instructed.

I'm not sure. Can you show me what os.urandom(16) gives you?

-- 
Robert Kern

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enigma that is made terrible by our own mad attempt to interpret it as
though it had an underlying truth."
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Re: [Numpy-discussion] Having trouble installing Numpy on OS X

2009-01-24 Thread Nat Wilson
Ah, no, I can't import it.

What does this mean? As far as I know, I built Python as instructed.


Python 2.6.1 (r261:67515, Jan 24 2009, 16:08:37)
[GCC 4.0.0 20041026 (Apple Computer, Inc. build 4061)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
 >>> from random import Random as _Random
Traceback (most recent call last):
   File "", line 1, in 
   File "/Library/Frameworks/Python.framework/Versions/2.6/lib/ 
python2.6/random.py", line 871, in 
 _inst = Random()
   File "/Library/Frameworks/Python.framework/Versions/2.6/lib/ 
python2.6/random.py", line 96, in __init__
 self.seed(x)
   File "/Library/Frameworks/Python.framework/Versions/2.6/lib/ 
python2.6/random.py", line 115, in seed
 super(Random, self).seed(a)
SystemError: error return without exception set

Nat


On Jan 24, 2009, at 6:09 PM, Robert Kern wrote:

> On Sat, Jan 24, 2009 at 12:34, Nat Wilson   
> wrote:
>> Would anyone be willing to help me interpret an error while trying to
>> build and install Numpy? I've searched around, and haven't seen this
>> elsewhere.
>
>>   File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
>> python2.6/tempfile.py", line 34, in 
>> from random import Random as _Random
>>   File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
>> python2.6/random.py", line 871, in 
>> _inst = Random()
>>   File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
>> python2.6/random.py", line 96, in __init__
>> self.seed(x)
>>   File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
>> python2.6/random.py", line 115, in seed
>> super(Random, self).seed(a)
>> SystemError: error return without exception set
>>
>> Any ideas?
>
> It looks unrelated to numpy. Can you import the random module in other
> situations?
>
> -- 
> Robert Kern
>
> "I have come to believe that the whole world is an enigma, a harmless
> enigma that is made terrible by our own mad attempt to interpret it as
> though it had an underlying truth."
>   -- Umberto Eco
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Re: [Numpy-discussion] numpy and the ACML

2009-01-24 Thread Gideon Simpson
That's not working for me.  Any thoughts on how to troubleshoot it?
-gideon

On Jan 24, 2009, at 6:18 PM, George Nurser wrote:

> I did manage to get it working.
> I remember that both libcblas.a (or a link to it) and libacml.so had
> to be in the same directory.
>
> Also I had to comment out lines 399-400 of setup.py:
> # if ('NO_ATLAS_INFO',1) in  
> blas_info.get('define_macros',[]):
> # return None # dotblas needs ATLAS, Fortran compiled
> blas will not be sufficient
>
> In my site.cfg I have
> [blas]
> blas_libs = cblas, acml
> library_dirs = /noc/users/agn/ext/AMD64/acml/ifort64/lib
> include_dirs =  /noc/users/agn/ext/AMD64/acml/ifort64/include
>
> [lapack]
> language = f77
> lapack_libs = acml
> library_dirs = /noc/users/agn/ext/AMD64/acml/ifort64/lib
> include_dirs = /noc/users/agn/ext/AMD64/acml/ifort64/include
>
> Both libcblas.a (or a link to it) and libacml.so  are in
> /noc/users/agn/ext/AMD64/acml/ifort64/lib
>
> HTH. George.
>
> 2009/1/24 Gideon Simpson :
>> I've tried building CBLAS, which seems to run properly by itself, but
>> numpy is still having difficulty.  I've got the following in my
>> site.cfg:
>>
>> [blas_opt]
>> library_dirs = /usr/local/nonsystem/simpson/CBLAS/lib/LINUX:/usr/ 
>> local/
>> nonsystem/simpson/acml4.2.0/gfortran64/lib
>> include_dirs = /usr/local/nonsystem/simpson/CBLAS/include:/usr/local/
>> nonsystem/simpson/acml4.2.0/gfortran64/include
>> libraries = cblas, acml
>>
>> [lapack_opt]
>> library_dirs = /usr/local/nonsystem/simpson/CBLAS/lib/LINUX:/usr/ 
>> local/
>> nonsystem/simpson/acml4.2.0/gfortran64/lib
>> include_dirs = /usr/local/nonsystem/simpson/CBLAS/include:/usr/local/
>> nonsystem/simpson/acml4.2.0/gfortran64/include
>> libraries = cblas, acml
>>
>> I also created a symbolic link in /usr/local/nonsystem/simpson/CBLAS/
>> lib/LINUX, from cblas_LINUX.a to libcblas.a.
>>
>>
>> Is there an easier way to check if numpy is locating the libs other
>> than doing python setup.py build, and looking at the output?
>> -gideon
>>
>> On Jan 24, 2009, at 4:05 PM, Pauli Virtanen wrote:
>>
>>> Sat, 24 Jan 2009 15:26:17 -0500, Gideon Simpson wrote:
>>>
 Nadav-

 That doesn't quite seem to work for me.  I added:

 [blas_opt]
 library_dirs = /usr/local/nonsystem/simpson/acml4.2.0/gfortran64/ 
 lib
 include_dirs = /usr/local/nonsystem/simpson/acml4.2.0/gfortran64/
 include
 libraries = acml

 [lapack_opt]
 library_dirs = /usr/local/nonsystem/simpson/acml4.2.0/gfortran64/ 
 lib
 include_dirs = /usr/local/nonsystem/simpson/acml4.2.0/gfortran64/
 include
 libraries = acml

 to my site.cfg with no luck.  Somewhere else, people indicated that
 the
 ACML lacked a CBLAS which was necessary to make this work.
>>>
>>> Yep, IIRC you needed also CBLAS. (I think I got Numpy & Scipy linked
>>> against ACML at some point, but it's been a while and I've forgotten
>>> details...) There's a CBLAS here:
>>>
>>>  http://www.netlib.org/blas/blast-forum/cblas.tgz
>>>
>>> So, I think you need to compile it & link it with ACML, and add it  
>>> in
>>> site.cfg with ACML libs.
>>>
>>> --
>>> Pauli Virtanen
>>>
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>>
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Re: [Numpy-discussion] Bug with mafromtxt

2009-01-24 Thread Ryan May
Pierre GM wrote:
> Ryan,
> Thanks for reporting. An idea would be to force the dtype of the  
> masked column to the largest dtype of the other columns (in your  
> example, that would be int). I'll try to see how easily it can be done  
> early next week. Meanwhile, you can always give an explicit dtype at  
> creation.

Ok, thanks.  I've dug a little further, and it seems like the problem is that a
column of all missing values ends up as a column of all None's.  When you create
a (masked) array from a list of None's, you end up with an object array.  On one
hand I'd love for things to behave differently in this case, but on the other I
understand why things work this way.

Ryan

> 
> On Jan 24, 2009, at 5:58 PM, Ryan May wrote:
> 
>> Pierre,
>>
>> I've found what I consider to be a bug in the new mafromtxt (though  
>> apparently it
>> existed in earlier versions as well).  If you have an entire column  
>> of data in a
>> file that contains only masked data, and try to get mafromtxt to  
>> automatically
>> choose the dtype, the dtype gets selected to be object type.  In  
>> this case, I'd
>> think the better behavior would be float, but I'm not sure how hard  
>> it would be
>> to make this the case.  Here's a test case:
>>
>> import numpy as np
>> from StringIO import StringIO
>> s = StringIO('1 2 3\n4 5 6\n')
>> a = np.mafromtxt(s, missing='2,5', dtype=None)
>> print a.dtype
>>
>> Ryan
>>
>> -- 
>> Ryan May
>> Graduate Research Assistant
>> School of Meteorology
>> University of Oklahoma
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> 
> ___
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-- 
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School of Meteorology
University of Oklahoma
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Re: [Numpy-discussion] numpy and the ACML

2009-01-24 Thread George Nurser
I did manage to get it working.
I remember that both libcblas.a (or a link to it) and libacml.so had
to be in the same directory.

Also I had to comment out lines 399-400 of setup.py:
# if ('NO_ATLAS_INFO',1) in blas_info.get('define_macros',[]):
# return None # dotblas needs ATLAS, Fortran compiled
blas will not be sufficient

In my site.cfg I have
[blas]
blas_libs = cblas, acml
library_dirs = /noc/users/agn/ext/AMD64/acml/ifort64/lib
include_dirs =  /noc/users/agn/ext/AMD64/acml/ifort64/include

[lapack]
language = f77
lapack_libs = acml
library_dirs = /noc/users/agn/ext/AMD64/acml/ifort64/lib
include_dirs = /noc/users/agn/ext/AMD64/acml/ifort64/include

Both libcblas.a (or a link to it) and libacml.so  are in
/noc/users/agn/ext/AMD64/acml/ifort64/lib

HTH. George.

2009/1/24 Gideon Simpson :
> I've tried building CBLAS, which seems to run properly by itself, but
> numpy is still having difficulty.  I've got the following in my
> site.cfg:
>
> [blas_opt]
> library_dirs = /usr/local/nonsystem/simpson/CBLAS/lib/LINUX:/usr/local/
> nonsystem/simpson/acml4.2.0/gfortran64/lib
> include_dirs = /usr/local/nonsystem/simpson/CBLAS/include:/usr/local/
> nonsystem/simpson/acml4.2.0/gfortran64/include
> libraries = cblas, acml
>
> [lapack_opt]
> library_dirs = /usr/local/nonsystem/simpson/CBLAS/lib/LINUX:/usr/local/
> nonsystem/simpson/acml4.2.0/gfortran64/lib
> include_dirs = /usr/local/nonsystem/simpson/CBLAS/include:/usr/local/
> nonsystem/simpson/acml4.2.0/gfortran64/include
> libraries = cblas, acml
>
> I also created a symbolic link in /usr/local/nonsystem/simpson/CBLAS/
> lib/LINUX, from cblas_LINUX.a to libcblas.a.
>
>
> Is there an easier way to check if numpy is locating the libs other
> than doing python setup.py build, and looking at the output?
> -gideon
>
> On Jan 24, 2009, at 4:05 PM, Pauli Virtanen wrote:
>
>> Sat, 24 Jan 2009 15:26:17 -0500, Gideon Simpson wrote:
>>
>>> Nadav-
>>>
>>> That doesn't quite seem to work for me.  I added:
>>>
>>> [blas_opt]
>>> library_dirs = /usr/local/nonsystem/simpson/acml4.2.0/gfortran64/lib
>>> include_dirs = /usr/local/nonsystem/simpson/acml4.2.0/gfortran64/
>>> include
>>> libraries = acml
>>>
>>> [lapack_opt]
>>> library_dirs = /usr/local/nonsystem/simpson/acml4.2.0/gfortran64/lib
>>> include_dirs = /usr/local/nonsystem/simpson/acml4.2.0/gfortran64/
>>> include
>>> libraries = acml
>>>
>>> to my site.cfg with no luck.  Somewhere else, people indicated that
>>> the
>>> ACML lacked a CBLAS which was necessary to make this work.
>>
>> Yep, IIRC you needed also CBLAS. (I think I got Numpy & Scipy linked
>> against ACML at some point, but it's been a while and I've forgotten
>> details...) There's a CBLAS here:
>>
>>   http://www.netlib.org/blas/blast-forum/cblas.tgz
>>
>> So, I think you need to compile it & link it with ACML, and add it in
>> site.cfg with ACML libs.
>>
>> --
>> Pauli Virtanen
>>
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Re: [Numpy-discussion] Bug with mafromtxt

2009-01-24 Thread Pierre GM
Ryan,
Thanks for reporting. An idea would be to force the dtype of the  
masked column to the largest dtype of the other columns (in your  
example, that would be int). I'll try to see how easily it can be done  
early next week. Meanwhile, you can always give an explicit dtype at  
creation.

On Jan 24, 2009, at 5:58 PM, Ryan May wrote:

> Pierre,
>
> I've found what I consider to be a bug in the new mafromtxt (though  
> apparently it
> existed in earlier versions as well).  If you have an entire column  
> of data in a
> file that contains only masked data, and try to get mafromtxt to  
> automatically
> choose the dtype, the dtype gets selected to be object type.  In  
> this case, I'd
> think the better behavior would be float, but I'm not sure how hard  
> it would be
> to make this the case.  Here's a test case:
>
> import numpy as np
> from StringIO import StringIO
> s = StringIO('1 2 3\n4 5 6\n')
> a = np.mafromtxt(s, missing='2,5', dtype=None)
> print a.dtype
>
> Ryan
>
> -- 
> Ryan May
> Graduate Research Assistant
> School of Meteorology
> University of Oklahoma
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Re: [Numpy-discussion] Having trouble installing Numpy on OS X

2009-01-24 Thread Robert Kern
On Sat, Jan 24, 2009 at 12:34, Nat Wilson  wrote:
> Would anyone be willing to help me interpret an error while trying to
> build and install Numpy? I've searched around, and haven't seen this
> elsewhere.

>   File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
> python2.6/tempfile.py", line 34, in 
> from random import Random as _Random
>   File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
> python2.6/random.py", line 871, in 
> _inst = Random()
>   File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
> python2.6/random.py", line 96, in __init__
> self.seed(x)
>   File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
> python2.6/random.py", line 115, in seed
> super(Random, self).seed(a)
> SystemError: error return without exception set
>
> Any ideas?

It looks unrelated to numpy. Can you import the random module in other
situations?

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless
enigma that is made terrible by our own mad attempt to interpret it as
though it had an underlying truth."
  -- Umberto Eco
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[Numpy-discussion] Bug with mafromtxt

2009-01-24 Thread Ryan May
Pierre,

I've found what I consider to be a bug in the new mafromtxt (though apparently 
it
existed in earlier versions as well).  If you have an entire column of data in a
file that contains only masked data, and try to get mafromtxt to automatically
choose the dtype, the dtype gets selected to be object type.  In this case, I'd
think the better behavior would be float, but I'm not sure how hard it would be
to make this the case.  Here's a test case:

import numpy as np
from StringIO import StringIO
s = StringIO('1 2 3\n4 5 6\n')
a = np.mafromtxt(s, missing='2,5', dtype=None)
print a.dtype

Ryan

-- 
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Graduate Research Assistant
School of Meteorology
University of Oklahoma
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Re: [Numpy-discussion] numpy and the ACML

2009-01-24 Thread Gideon Simpson
I've tried building CBLAS, which seems to run properly by itself, but  
numpy is still having difficulty.  I've got the following in my  
site.cfg:

[blas_opt]
library_dirs = /usr/local/nonsystem/simpson/CBLAS/lib/LINUX:/usr/local/ 
nonsystem/simpson/acml4.2.0/gfortran64/lib
include_dirs = /usr/local/nonsystem/simpson/CBLAS/include:/usr/local/ 
nonsystem/simpson/acml4.2.0/gfortran64/include
libraries = cblas, acml

[lapack_opt]
library_dirs = /usr/local/nonsystem/simpson/CBLAS/lib/LINUX:/usr/local/ 
nonsystem/simpson/acml4.2.0/gfortran64/lib
include_dirs = /usr/local/nonsystem/simpson/CBLAS/include:/usr/local/ 
nonsystem/simpson/acml4.2.0/gfortran64/include
libraries = cblas, acml

I also created a symbolic link in /usr/local/nonsystem/simpson/CBLAS/ 
lib/LINUX, from cblas_LINUX.a to libcblas.a.


Is there an easier way to check if numpy is locating the libs other  
than doing python setup.py build, and looking at the output?
-gideon

On Jan 24, 2009, at 4:05 PM, Pauli Virtanen wrote:

> Sat, 24 Jan 2009 15:26:17 -0500, Gideon Simpson wrote:
>
>> Nadav-
>>
>> That doesn't quite seem to work for me.  I added:
>>
>> [blas_opt]
>> library_dirs = /usr/local/nonsystem/simpson/acml4.2.0/gfortran64/lib
>> include_dirs = /usr/local/nonsystem/simpson/acml4.2.0/gfortran64/ 
>> include
>> libraries = acml
>>
>> [lapack_opt]
>> library_dirs = /usr/local/nonsystem/simpson/acml4.2.0/gfortran64/lib
>> include_dirs = /usr/local/nonsystem/simpson/acml4.2.0/gfortran64/ 
>> include
>> libraries = acml
>>
>> to my site.cfg with no luck.  Somewhere else, people indicated that  
>> the
>> ACML lacked a CBLAS which was necessary to make this work.
>
> Yep, IIRC you needed also CBLAS. (I think I got Numpy & Scipy linked
> against ACML at some point, but it's been a while and I've forgotten
> details...) There's a CBLAS here:
>
>   http://www.netlib.org/blas/blast-forum/cblas.tgz
>
> So, I think you need to compile it & link it with ACML, and add it in
> site.cfg with ACML libs.
>
> -- 
> Pauli Virtanen
>
> ___
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Re: [Numpy-discussion] Having trouble installing Numpy on OS X

2009-01-24 Thread Jeff Whitaker
Nat Wilson wrote:
> Would anyone be willing to help me interpret an error while trying to  
> build and install Numpy? I've searched around, and haven't seen this  
> elsewhere.
>
> I've been running into this wall for about half the day now. I've  
> tried reinstalling Python, using numpy 1.2.0 and 1.2.1.
>
> I have Python 2.6.1, running on OS X 10.4.11, with a G4 PPC processor.
>
> Here's the print out:
>
> Ganymede:~/Desktop/numpy-1.2.1 username$ python setup.py build
> Running from numpy source directory.
> Traceback (most recent call last):
>File "setup.py", line 96, in 
>  setup_package()
>File "setup.py", line 68, in setup_package
>  from numpy.distutils.core import setup
>File "/Users/username/Desktop/numpy/numpy/distutils/__init__.py",  
> line 6, in 
>File "/Users/username/Desktop/numpy/numpy/distutils/ccompiler.py",  
> line 11, in 
>File "/Users/username/Desktop/numpy/numpy/distutils/log.py", line  
> 7, in 
>File "/Users/username/Desktop/numpy/numpy/distutils/misc_util.py",  
> line 8, in 
>File "/Library/Frameworks/Python.framework/Versions/2.6/lib/ 
> python2.6/tempfile.py", line 34, in 
>  from random import Random as _Random
>File "/Library/Frameworks/Python.framework/Versions/2.6/lib/ 
> python2.6/random.py", line 871, in 
>  _inst = Random()
>File "/Library/Frameworks/Python.framework/Versions/2.6/lib/ 
> python2.6/random.py", line 96, in __init__
>  self.seed(x)
>File "/Library/Frameworks/Python.framework/Versions/2.6/lib/ 
> python2.6/random.py", line 115, in seed
>  super(Random, self).seed(a)
> SystemError: error return without exception set
>
> Any ideas?
> I've had numpy/scipy installed in the past, but recently had to wipe  
> everything and start from scratch. Everything should be pretty clean  
> right now. Am I missing something obvious?
>
> Thanks,
> NJW
>   

Nat:

numpy 1.2.x doesn't work with python 2.6.  You'll either need to revert 
to python 2.5 or get the latest svn numpy (which still may have some 
python 2.6 glitches).

-Jeff
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Re: [Numpy-discussion] Having trouble installing Numpy on OS X

2009-01-24 Thread Jeff Whitaker
Nat Wilson wrote:
> Would anyone be willing to help me interpret an error while trying to  
> build and install Numpy? I've searched around, and haven't seen this  
> elsewhere.
>
> I've been running into this wall for about half the day now. I've  
> tried reinstalling Python, using numpy 1.2.0 and 1.2.1.
>
> I have Python 2.6.1, running on OS X 10.4.11, with a G4 PPC processor.
>
> Here's the print out:
>
> Ganymede:~/Desktop/numpy-1.2.1 username$ python setup.py build
> Running from numpy source directory.
> Traceback (most recent call last):
>File "setup.py", line 96, in 
>  setup_package()
>File "setup.py", line 68, in setup_package
>  from numpy.distutils.core import setup
>File "/Users/username/Desktop/numpy/numpy/distutils/__init__.py",  
> line 6, in 
>File "/Users/username/Desktop/numpy/numpy/distutils/ccompiler.py",  
> line 11, in 
>File "/Users/username/Desktop/numpy/numpy/distutils/log.py", line  
> 7, in 
>File "/Users/username/Desktop/numpy/numpy/distutils/misc_util.py",  
> line 8, in 
>File "/Library/Frameworks/Python.framework/Versions/2.6/lib/ 
> python2.6/tempfile.py", line 34, in 
>  from random import Random as _Random
>File "/Library/Frameworks/Python.framework/Versions/2.6/lib/ 
> python2.6/random.py", line 871, in 
>  _inst = Random()
>File "/Library/Frameworks/Python.framework/Versions/2.6/lib/ 
> python2.6/random.py", line 96, in __init__
>  self.seed(x)
>File "/Library/Frameworks/Python.framework/Versions/2.6/lib/ 
> python2.6/random.py", line 115, in seed
>  super(Random, self).seed(a)
> SystemError: error return without exception set
>
> Any ideas?
> I've had numpy/scipy installed in the past, but recently had to wipe  
> everything and start from scratch. Everything should be pretty clean  
> right now. Am I missing something obvious?
>
> Thanks,
> NJW
>
>   
numpy 1.2 doesn't work with python 2.6.  You'll either need to revert to 
python 2.5 or get the latest svn numpy (which still may have some python 
2.6 glitches).

-Jeff

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Re: [Numpy-discussion] Having trouble installing Numpy on OS X

2009-01-24 Thread Nat Wilson
I had not, but that doesn't seem to make any difference. By the way,  
I'm using gfortran 4.2.3 as I do this.


Nat

On Jan 24, 2009, at 4:38 PM, John Gleeson wrote:



On 2009-01-24, at 11:34 AM, Nat Wilson wrote:


Would anyone be willing to help me interpret an error while trying to
build and install Numpy? I've searched around, and haven't seen this
elsewhere.

I've been running into this wall for about half the day now. I've
tried reinstalling Python, using numpy 1.2.0 and 1.2.1.

I have Python 2.6.1, running on OS X 10.4.11, with a G4 PPC  
processor.




Have you tried setting the environment variable

MACOSX_DEPLOYMENT_TARGET=10.4

before building?
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Re: [Numpy-discussion] Having trouble installing Numpy on OS X

2009-01-24 Thread John Gleeson

On 2009-01-24, at 11:34 AM, Nat Wilson wrote:

> Would anyone be willing to help me interpret an error while trying to
> build and install Numpy? I've searched around, and haven't seen this
> elsewhere.
>
> I've been running into this wall for about half the day now. I've
> tried reinstalling Python, using numpy 1.2.0 and 1.2.1.
>
> I have Python 2.6.1, running on OS X 10.4.11, with a G4 PPC processor.
>

Have you tried setting the environment variable

MACOSX_DEPLOYMENT_TARGET=10.4

before building?
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Re: [Numpy-discussion] numpy and the ACML

2009-01-24 Thread Pauli Virtanen
Sat, 24 Jan 2009 15:26:17 -0500, Gideon Simpson wrote:

> Nadav-
> 
> That doesn't quite seem to work for me.  I added:
> 
> [blas_opt]
> library_dirs = /usr/local/nonsystem/simpson/acml4.2.0/gfortran64/lib
> include_dirs = /usr/local/nonsystem/simpson/acml4.2.0/gfortran64/include
> libraries = acml
> 
> [lapack_opt]
> library_dirs = /usr/local/nonsystem/simpson/acml4.2.0/gfortran64/lib
> include_dirs = /usr/local/nonsystem/simpson/acml4.2.0/gfortran64/include
> libraries = acml
> 
> to my site.cfg with no luck.  Somewhere else, people indicated that the
> ACML lacked a CBLAS which was necessary to make this work.

Yep, IIRC you needed also CBLAS. (I think I got Numpy & Scipy linked 
against ACML at some point, but it's been a while and I've forgotten 
details...) There's a CBLAS here:

http://www.netlib.org/blas/blast-forum/cblas.tgz

So, I think you need to compile it & link it with ACML, and add it in 
site.cfg with ACML libs.

-- 
Pauli Virtanen

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[Numpy-discussion] whohas command

2009-01-24 Thread Ondrej Certik
Hi,

I just discovered a new whohas command in Debian, that can show a
package in virtually all important distributions (Arch, Debian,
Fedora, Gentoo, openSUSE, Slackware (and
linuxpackages.net), Source  Mage,  Ubuntu, FreeBSD, NetBSD, OpenBSD,
Fink and MacPorts distributions).

So for example SymPy is in a lot of them already:

$ whohas sympy
Archpython-sympy-git  20090121-1
unsupported http://aur.archlinux.org/packages.php?ID=23341
MacPortspy-sympy  0.5.15

http://trac.macports.org/browser/trunk/dports/python/py-sympy/Portfile
MacPortspy25-sympy0.6.3

http://trac.macports.org/browser/trunk/dports/python/py25-sympy/Portfile
FreeBSD py25-sympy0.6.3
math
http://www.freebsd.org/cgi/pds.cgi?ports/math/py25-sympy
NetBSD  py-sympy  0.5.15
mathhttp://pkgsrc.se/math/py-sympy
Ubuntu  python-sympy  0.4.2-1
universehttp://packages.ubuntu.com/gutsy/python-sympy
Ubuntu  python-sympy  0.5.8-1
universehttp://packages.ubuntu.com/hardy/python-sympy
Ubuntu  python-sympy  0.5.15-1~hardy1
universe
http://packages.ubuntu.com/hardy-backports/python-sympy
Ubuntu  python-sympy  0.5.15-1
universehttp://packages.ubuntu.com/intrepid/python-sympy
Ubuntu  python-sympy  0.6.3-1
universehttp://packages.ubuntu.com/jaunty/python-sympy
Debian  python-sympy  0.6.1-1
testing http://packages.debian.org/lenny/python-sympy
Finksympy-py240.5.6-1
http://pdb.finkproject.org/pdb/package.php/sympy-py24
Finksympy-py250.5.6-1
http://pdb.finkproject.org/pdb/package.php/sympy-py25
Gentoo  sympy 0.6.3
http://gentoo-portage.com/dev-python/sympy
Gentoo  sympy 0.6.2
http://gentoo-portage.com/dev-python/sympy
openSUSEpython-sympy  0.6.3
science
http://packages.opensuse-community.org/packageinfo.jsp?checksum=a2258d3deaee5f411456f22ea1ab6bb7ec95e12c&distro=openSUSE_111



It's also interesting to click on the links to get to the pages of
sympy for each distribution. And numpy:

$ whohas numpy
Archpython-numexpr1.1.1-1
unsupported http://aur.archlinux.org/packages.php?ID=23380
Archpython-numpy  1.2.1-3
community   http://aur.archlinux.org/packages.php?ID=8497
Archscikits-audiolab-svn  1491-1
unsupported http://aur.archlinux.org/packages.php?ID=21018
FreeBSD py25-numpy1.2.1,1
math
http://www.freebsd.org/cgi/pds.cgi?ports/math/py25-numpy
FreeBSD py25-symeig   1.4_1
math
http://www.freebsd.org/cgi/pds.cgi?ports/math/py25-symeig
NetBSD  py-numpy  1.1.0
wip http://pkgsrc.se/wip/py-numpy
NetBSD  py-numpy  1.1.0
mathhttp://pkgsrc.se/math/py-numpy
Ubuntu  python-numpy  1:1.0.1-8ubuntu1
universehttp://packages.ubuntu.com/feisty/python-numpy
Ubuntu  python-numpy  1:1.0.3-1ubuntu2
universehttp://packages.ubuntu.com/gutsy/python-numpy
Ubuntu  python-numpy  1:1.0.4-6ubuntu3
universehttp://packages.ubuntu.com/hardy/python-numpy
Ubuntu  python-numpy  1:1.1.1-1
http://packages.ubuntu.com/intrepid/python-numpy
Ubuntu  python-numpy  1:1.1.1-2ubuntu1
http://packages.ubuntu.com/jaunty/python-numpy
Ubuntu  python-numpy-dbg  1:1.0.1-8ubuntu1
universehttp://packages.ubuntu.com/feisty/python-numpy-dbg
Ubuntu  python-numpy-dbg  1:1.0.3-1ubuntu2
universehttp://packages.ubuntu.com/gutsy/python-numpy-dbg
Ubuntu  python-numpy-dbg  1:1.0.4-6ubuntu3
universehttp://packages.ubuntu.com/hardy/python-numpy-dbg
Ubuntu  python-numpy-dbg  1:1.1.1-1
http://packages.ubuntu.com/intrepid/python-numpy-dbg
Ubuntu  python-numpy-dbg  1:1.1.1-2ubuntu1
http://packages.ubuntu.com/jaunty/python-numpy-dbg
Ubuntu  python-numpy-dev  1:1.0.1-8ubuntu1
universehttp://packages.ubuntu.com/feisty/python-numpy-dev
Ubuntu  python-numpy-dev  1:1.0.3-1ubuntu2
universehttp://packages.ubuntu.com/gutsy/python-numpy-dev
Ubuntu  python-numpy-dev
http://packages.ubuntu.com/hardy/python-numpy-dev
Ubuntu  python-numpy-doc  1:1.0.1-8ubuntu1
universehttp://packages.ubuntu.com/feisty/python-numpy-doc
Ubuntu  python-numpy-doc  1:1.0.3-1ubuntu2
universehttp://packages.ubuntu.com/gutsy/python-numpy-doc
Ubuntu  python-numpy-doc  1:1.0.4-6ubuntu3
universehttp://packages.ubuntu.com/hardy/python-numpy-doc
Ubuntu  python-numpy-doc  1:1.1.1-1
http://pac

Re: [Numpy-discussion] numpy and the ACML

2009-01-24 Thread Gideon Simpson
Nadav-

That doesn't quite seem to work for me.  I added:

[blas_opt]
library_dirs = /usr/local/nonsystem/simpson/acml4.2.0/gfortran64/lib
include_dirs = /usr/local/nonsystem/simpson/acml4.2.0/gfortran64/include
libraries = acml

[lapack_opt]
library_dirs = /usr/local/nonsystem/simpson/acml4.2.0/gfortran64/lib
include_dirs = /usr/local/nonsystem/simpson/acml4.2.0/gfortran64/include
libraries = acml

to my site.cfg with no luck.  Somewhere else, people indicated that  
the ACML lacked a CBLAS which was necessary to make this work.
-gideon

On Jan 24, 2009, at 3:08 PM, Nadav Horesh wrote:

> You have setup.cfg:
> * set add the directory where acml libraries reside to the library  
> dir path list
> * add acmllibraries under blas and lapack sections
>
>  Nadav
>
>
> -הודעה מקורית-
> מאת: numpy-discussion-boun...@scipy.org בשם Gideon Simpson
> נשלח: ש 24-ינואר-09 18:21
> אל: Discussion of Numerical Python
> נושא: [Numpy-discussion] numpy and the ACML
>
> Does anyone have a guide on how to get numpy to use the ACML as its
> blas/lapack backend?
>
> -gideon
>
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Re: [Numpy-discussion] numpy and the ACML

2009-01-24 Thread Nadav Horesh
You have setup.cfg:
* set add the directory where acml libraries reside to the library dir path list
* add acmllibraries under blas and lapack sections

  Nadav


-הודעה מקורית-
מאת: numpy-discussion-boun...@scipy.org בשם Gideon Simpson
נשלח: ש 24-ינואר-09 18:21
אל: Discussion of Numerical Python
נושא: [Numpy-discussion] numpy and the ACML
 
Does anyone have a guide on how to get numpy to use the ACML as its  
blas/lapack backend?

-gideon

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[Numpy-discussion] Having trouble installing Numpy on OS X

2009-01-24 Thread Nat Wilson
Would anyone be willing to help me interpret an error while trying to  
build and install Numpy? I've searched around, and haven't seen this  
elsewhere.

I've been running into this wall for about half the day now. I've  
tried reinstalling Python, using numpy 1.2.0 and 1.2.1.

I have Python 2.6.1, running on OS X 10.4.11, with a G4 PPC processor.

Here's the print out:

Ganymede:~/Desktop/numpy-1.2.1 username$ python setup.py build
Running from numpy source directory.
Traceback (most recent call last):
   File "setup.py", line 96, in 
 setup_package()
   File "setup.py", line 68, in setup_package
 from numpy.distutils.core import setup
   File "/Users/username/Desktop/numpy/numpy/distutils/__init__.py",  
line 6, in 
   File "/Users/username/Desktop/numpy/numpy/distutils/ccompiler.py",  
line 11, in 
   File "/Users/username/Desktop/numpy/numpy/distutils/log.py", line  
7, in 
   File "/Users/username/Desktop/numpy/numpy/distutils/misc_util.py",  
line 8, in 
   File "/Library/Frameworks/Python.framework/Versions/2.6/lib/ 
python2.6/tempfile.py", line 34, in 
 from random import Random as _Random
   File "/Library/Frameworks/Python.framework/Versions/2.6/lib/ 
python2.6/random.py", line 871, in 
 _inst = Random()
   File "/Library/Frameworks/Python.framework/Versions/2.6/lib/ 
python2.6/random.py", line 96, in __init__
 self.seed(x)
   File "/Library/Frameworks/Python.framework/Versions/2.6/lib/ 
python2.6/random.py", line 115, in seed
 super(Random, self).seed(a)
SystemError: error return without exception set

Any ideas?
I've had numpy/scipy installed in the past, but recently had to wipe  
everything and start from scratch. Everything should be pretty clean  
right now. Am I missing something obvious?

Thanks,
NJW
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[Numpy-discussion] numpy and the ACML

2009-01-24 Thread Gideon Simpson
Does anyone have a guide on how to get numpy to use the ACML as its  
blas/lapack backend?

-gideon

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