[SciPy-dev] confidence intervals on multi-parameter minimisation

Graeme O'Keefe graeme.okeefe@petnm.unimelb.edu...
Wed Mar 21 18:40:33 CDT 2007


Found my ppc compile problem with -lcc_dynamic.

Probably known by OS-X users here, but just in case.

The issue is: need to use g77 with gcc3.3 but gfortran with gcc4.x

http://nxg.me.uk/note/2004/restFP/

You can download gfortran-ppc-bin.tar.gz from here
http://www.macresearch.org/xcode_gfortran_contest_winner_damien_bobillot

Or the xcode plugin here.
http://www.macresearch.org/xcode_gfortran_plugin_update


regards,

Graeme

On 21/03/2007, at 5:52 PM, Graeme O'Keefe wrote:

> I'm back.
>
> Just compiled the numpy/scipy scv's on OS-X intel, no changes
> required to gnu.py
>
> Builds fine and import scipy.odr is okay.
>
> My old scipy.optimize code works fine.
>
> So, I clearly have a problem with shared libraries to sort out on my
> ppc workstation.
>
> Sorry to bother people.
>
> regards,
>
> Graeme
>
>
>
> On 21/03/2007, at 5:36 PM, Graeme O'Keefe wrote:
>
>> I should have mentioned, I currently have scipy.__version__ =
>> 0.5.2.dev2095 ppc.
>>
>> I retrieved numpy/scipy from svn (1.0.2.dev3583, 0.5.2.dev2850)
>>
>> I completed the build for numpy/scipy
>>
>> but first I had to remove "-lcc_dynamic" from lib/python2.4/site-
>> packages/numpy/distutils/fcompiler/gnu.py, otherwise I got:
>>
>> /usr/bin/ld: can't locate file for: -lcc_dynamic
>> collect2: ld returned 1 exit status
>> /usr/bin/ld: can't locate file for: -lcc_dynamic
>> collect2: ld returned 1 exit status
>> error: Command "/opt/local/bin/g77 -g -Wall -undefined dynamic_lookup
>> -bundle build/temp.darwin-8.9.0-Power_Macintosh-2.4/build/
>> src.darwin-8.9.0-Power_Macintosh-2.4/Lib/fftpack/_fftpackmodule.o
>> build/temp.darwin-8.9.0-Power_Macintosh-2.4/Lib/fftpack/src/zfft.o
>> build/temp.darwin-8.9.0-Power_Macintosh-2.4/Lib/fftpack/src/drfft.o
>> build/temp.darwin-8.9.0-Power_Macintosh-2.4/Lib/fftpack/src/zrfft.o
>> build/temp.darwin-8.9.0-Power_Macintosh-2.4/Lib/fftpack/src/zfftnd.o
>> build/temp.darwin-8.9.0-Power_Macintosh-2.4/build/src.darwin-8.9.0-
>> Power_Macintosh-2.4/fortranobject.o -L/opt/local/lib -L/opt/local/
>> bin/../lib/gcc/powerpc-apple-darwin7.9.0/3.4.4 -Lbuild/
>> temp.darwin-8.9.0-Power_Macintosh-2.4 -ldfftpack -lfftw3 -lg2c -
>> lcc_dynamic -o build/lib.darwin-8.9.0-Power_Macintosh-2.4/scipy/
>> fftpack/_fftpack.so" failed with exit status 1
>>
>> Removing -cc_dynamic fixed that, something I've come across before,
>> but then when I finished and installed the build, I got the  
>> following:
>>
>>>>> import scipy
>>>>> import scipy.optimize
>> Traceback (most recent call last):
>>    File "<stdin>", line 1, in ?
>>    File "/Library/Frameworks/Python.framework/Versions/2.4/lib/
>> python2.4/site-packages/scipy/optimize/__init__.py", line 7, in ?
>>      from optimize import *
>>    File "/Library/Frameworks/Python.framework/Versions/2.4/lib/
>> python2.4/site-packages/scipy/optimize/optimize.py", line 26, in ?
>>      import linesearch
>>    File "/Library/Frameworks/Python.framework/Versions/2.4/lib/
>> python2.4/site-packages/scipy/optimize/linesearch.py", line 3, in ?
>>      import minpack2
>> ImportError: Failure linking new module: /Library/Frameworks/
>> Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/
>> optimize/minpack2.so: Symbol not found: _sprintf$LDBLStub
>>    Referenced from: /Library/Frameworks/Python.framework/Versions/ 
>> 2.4/
>> lib/python2.4/site-packages/scipy/optimize/minpack2.so
>>    Expected in: dynamic lookup
>>
>>>>> import scipy.odr
>> Traceback (most recent call last):
>>    File "<stdin>", line 1, in ?
>>    File "/Library/Frameworks/Python.framework/Versions/2.4/lib/
>> python2.4/site-packages/scipy/odr/__init__.py", line 11, in ?
>>      import odrpack
>>    File "/Library/Frameworks/Python.framework/Versions/2.4/lib/
>> python2.4/site-packages/scipy/odr/odrpack.py", line 103, in ?
>>      from scipy.odr import __odrpack
>> ImportError: Failure linking new module: /Library/Frameworks/
>> Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/odr/
>> __odrpack.so: Symbol not found: _printf$LDBLStub
>>    Referenced from: /Library/Frameworks/Python.framework/Versions/ 
>> 2.4/
>> lib/python2.4/site-packages/scipy/odr/__odrpack.so
>>    Expected in: dynamic lookup
>>
>>>>>
>>
>> I have /opt/local/lib in DYLD_LIBRARY_PATH, LD_LIBRARY_PATH.
>>
>> gcc --version
>> powerpc-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 (Apple Computer, Inc.
>> build 5363)
>>
>> So I am now stumped, can anyone advise?
>>
>> regards,
>>
>> Graeme
>>
>>
>>
>> On 21/03/2007, at 4:16 PM, Graeme O'Keefe wrote:
>>
>>>
>>> I have been using fmin_l_bfgs_b to perform bounded non-linear multi-
>>> parameter estimation.
>>>
>>> Is there a way to determine the confidence intervals on the  
>>> resultant
>>> parameter estimates.
>>>
>>> I've seen reference to scipy.odr as a better alternative to
>>> scipy.optimize and have checked out the latest svn and currently
>>> trying to build (OS X 10.4.9) which is always fun.
>>>
>>> However, I can't find any documentation on what scipy.odr is.
>>>
>>> Can someone point me somewhere.
>>>
>>> regards,
>>>
>>> Graeme
>>>
>>> _______________________________________________
>>> Scipy-dev mailing list
>>> Scipy-dev@scipy.org
>>> http://projects.scipy.org/mailman/listinfo/scipy-dev
>>>
>>
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