[SciPy-User] leastsq and cython

Gregor Thalhammer Gregor.Thalhammer@i-med.ac...
Mon Sep 27 08:50:15 CDT 2010


  Am 26.09.2010 00:45, schrieb Till Stensitzki:
> Warren Weckesser<warren.weckesser<at>  enthought.com>  writes:
>
>>
>>      On 9/25/10 4:27 PM, Charles R Harris wrote:
>>
>>        On Sat, Sep 25, 2010 at 3:03 PM, David Baddeley<david_baddeley<at>
> yahoo.com.au>
>>          wrote:
>>            I've,  run into a similar problem, it's due to the fact that
>>            native methods (ie
>>            ones loaded from c libraries) are not quite the same as pure
>>            python function
>>            objects&  don't possess all the nice attributes. It's been
>>            a while, but I seem
>>            to remember that this error crops up when leastsq is trying to
>>            print some form
>>            of status message with the function name in it. I've
>>            circumvented the problem by
>>            making a thin python wrapper function which just calls my c
>>            method. This works,
>>            but is not ideal, as you introduce additional function call
>>            overhead. If anyone
>>            out there knows of a better solution I'd also be interested.
>>
>>
>>
>>            Maybe it shouldn't try to print the function name? The context
>>            of the message might be enough.
>>
>>
>>
>>
>>      The function 'check_func' in minpack.py uses the attribute
>>      'func_name' in an error message.  I'm tweaking 'check_func' now so
>>      that it first checks for the 'func_name' attribute before trying to
>>      use it.
>>      Any suggestions for incorporating a cython or ctypes function into a
>>      test, so I can include tests of the change?
>>      Warren
>>
>>
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> Hmm, i tried to change my check_func too, but it seems the error stems also from
> c/fortran code. While cython function don't have the func_name attribute, the
> have the __name__  attribute, maybe it help. While we are at it, i have some
> questions about leastsq:
>
> 1. it seems to use always the double precision versions of lmdif, is there a way
> to change it? I am using cuda for the calculation of my function values, so no
> double precision for me. Another reason for using the single precision are
> memory concerns, as i am fitting around 70 000 data points with 600 parameters,
> so the size of jacobian is quite big.
I had a similar problem with analyzing images - millions of data points. 
I ended up in implementing the Levenberg-Marquardt-algorithm (on which 
leastsq is based) in pure Python, so I could use single precision 
arithmetic. I can send you the code.

> 2. does it use the same blas/lapack liberays as numpy?
lmdif uses its own implementation of the QR factorization, which is very 
memory efficient, but slower than state-of-the-art (multithreaded) 
lapack implementations.
In my case I could achieve a large speed improvement by directly solving 
the normal equations instead of using the QR factorization (I know, this 
is less accurate and typically not recommended in literature).

> 3. does it copy the Jacobian every time, or is there a way to write directly to
> the right memory?
Don't know how much of copying takes place, but copying is not the 
limiting the performance.
Gregor
> thanks for the fast answers and help,
> Till
>
>
>
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-- 
Dr. Gregor Thalhammer
Sektion für Biomedizinische Physik
Medizinische Universität Innsbruck
Müllerstr. 44
A-6020 Innsbruck
+43 512 9003 70875



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