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

Graeme O'Keefe graeme.okeefe@petnm.unimelb.edu...
Wed Mar 21 01:52:37 CDT 2007


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
>>
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>>
>
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