[Ifeffit] iXAFS & python scripting

[Brugger, Joel (SAM)]

Hi Matt,

Actually we did run . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh (I was just wondering if it was still required).

Hopefully the following output will be clearer than my prose. Line 5 in "iff = Ifeffit.Ifeffit()". The problem seems to be access to "/Users/Newville/Codes/ifeffit/local/share/ifeffit" while running Ifeffit.Ifeffit().

Thanks!

Joel + Barb


Last login: Fri Sep 10 08:14:26 on ttys004
JoelMacBook-Silver:~ joelb$ echo $PATH
/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin

JoelMacBook-Silver:~ joelb$ . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh

JoelMacBook-Silver:~ joelb$ echo $PATH
/Applications/iXAFS.app/Contents/Resources/local/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin

JoelMacBook-Silver:~ joelb$ cd /Users/joelb/data_ifeffit/APS-April08-Pascal/python 

JoelMacBook-Silver:python joelb$ python aps-12p9mLiCl.py 
 failed to load ifeffit library  libifeffit.dylib
/Users/Newville/Codes/ifeffit/local/share/ifeffit:/Applications/iXAFS.app/Contents/Resources/local/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/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

JoelMacBook-Silver:python joelb$ echo $PATH
/Applications/iXAFS.app/Contents/Resources/local/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin










________________________________________
------------------------------

Message: 4
Date: Thu, 9 Sep 2010 10:12:09 -0500
From: Matt Newville <newville at cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Cc: "barbara.etschmann at adelaide.edu.au"
        <barbara.etschmann at adelaide.edu.au>
Subject: Re: [Ifeffit] IXAFS3.0.2 and python scripting
Message-ID:
        <AANLkTikYLAwnRcwZWNK+yBL0Byp7NgxNJ=Zrn_v3V56M at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

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

> 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
>