[Ifeffit] IXAFS3.0.2 and python scripting

[Matt Newville]

Hi Joel and Barb,

Ah, sorry.  I believe you need to do
   . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh

in the shell prior to running python, or add this to your bash .profile file.

It would be better if the setup procedure detected that it was on a
Mac and set the environment up automatically.
I'll work on that (and on the build for10.5).

--Matt


On Thu, Sep 9, 2010 at 9:41 AM, Brugger, Joel (SAM)
<Joel.Brugger at samuseum.sa.gov.au> wrote:
> Dear Matt,
>
> Works great on 10.6 for us too. Thanks a million times, and fingers crossed for finding the error in 10.5 !
>
> We tried the python scripting, but apparently a /Users/Newville still lurks in there.
>
> Running the aps-12p9mLiCl.py  script
>
> 1. #!/usr/bin/python
> 2.
> 3. import math
> 4. import Ifeffit
> 5. iff = Ifeffit.Ifeffit()
>
> gives the following error:
>
> bash-3.2$ python aps-12p9mLiCl.py
>  failed to load ifeffit library  libifeffit.dylib
> /Users/Newville/Codes/ifeffit/local/share/ifeffit:/opt/local/bin:/opt/local/sbin:/opt/pgi/osx86/10.4/bin:/Users/joelb/Public/XDS/XDS-OSX_Intel:/Applications/iXAFS.app/Contents/Resources/local/bin:/opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/X11R6/bin:/usr/local/lib:/Users/joelb/Desktop/FitYK/:/usr/local/lib/:/sw/lib/:/sw/include/readline/:/unix/Molecular Dynamics/moldy-2.16e:/Users/joelb/Public/XDS/XDS-OSX_Intel:/Users/joelb/Desktop/fdmnes:/usr/local/lib:/Users/joelb/Desktop/FitYK/:/usr/local/lib/:/sw/lib/:/sw/include/readline/:/unix/Molecular Dynamics/moldy-2.16e:/Users/joelb/Public/XDS/XDS-OSX_Intel:/Users/joelb/Desktop/fdmnes:/Applications/iXAFS.app/Contents/Resources/local/bin
> Traceback (most recent call last):
>  File "aps-12p9mLiCl.py", line 5, in <module>
>    iff = Ifeffit.Ifeffit()
>  File "/Library/Python/2.6/site-packages/Ifeffit/Ifeffit.py", line 79, in __init__
>    raise ImportError('Cannot load ifeffit library')
> ImportError: Cannot load ifeffit library
>
>
> I tried to add /Applications/iXAFS.app/Contents/Resources/local/lib to PATH (there's a libifeffit.dylib there), but that did not help.
>
> Also notice that my PATH variables have been duplicated. This happens because I still have '. /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh' in my '.profile'. Do I need to keep this? If so, it would be nice to fix iff_init.sh too :-)
>
> Thanks,
>
> Joel + Barb
>
> ________________________________________
>
>
> Today's Topics:
>
>   1. Re: iXAFS3.0.2 (Matt Newville)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 8 Sep 2010 11:36:06 -0500
> From: Matt Newville <newville at cars.uchicago.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] iXAFS3.0.2
> Message-ID:
>        <AANLkTinmG5RGjBwj5eX5yui2JQo_nEP+1JJuMMdWPndh at mail.gmail.com>
> Content-Type: text/plain; charset=windows-1252
>
> Hi Brandon,
>
> Thanks for the report.   I've seen the same errors on the only system
> I have access to running 10.5.something: All the executable programs
> (perl, ifeffit) report the same dyld error.    I thought these
> messages were perhaps because I had built a "universal binary" that
> included x86_64 and i386, so I rebuilt for i386 but not x86_64, hoping
> that would solve the problem.  But it didn't.
>
> I've looked into a little bit more (if anyone knows more, please let
> me know!!), and believe the issue may be solved by adding compiler
> flags of    -mmacosx-version-min=10.5 -isysroot
> /Developer/SDKs/MacOSX10.5u.sdk
> I have not tried this yet, but will try to get this rebuilt in the
> next day or two.
>
> Sorry for the trouble.
>
> FWIW, I still get results I don't understand on PPC, where ifeffit and
> artemis run but hephaestus are artemis do not.... isn't that amazing?
>
> --Matt
>
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