[Ifeffit] iXAFS 3.0.3 for Mac OS X (Brandon Reese)

Matt Newville newville at cars.uchicago.edu
Thu Sep 23 09:22:37 CDT 2010


Hi Joel,

Hmm, I'm not sure what's going on for you.  It definitely works for me:

  mbook:~$ . ~/Desktop/iXAFS.app/Contents/Resources/local/bin/iff_init.sh
  mbook:~$ python
  Python 2.6.5 (r265:79359, Mar 24 2010, 01:32:55)
  [GCC 4.0.1 (Apple Inc. build 5493)] on darwin
  Type "help", "copyright", "credits" or "license" for more information.
  >>> import Ifeffit
  >>> i = Ifeffit.Ifeffit()
  >>> i.ifeffit("show $&build")
   $&build        = 	1.2.12 Copyright (c) 2005 Matt Newville, Univ of Chicago
  0

If I had to guess, I'd look at what DYLD_LIBRARY_PATH is set to.  That
should definitely include the folder that contains libifeffit.dylib,
eg  /Applications/iXAFS.app/Contents/Resources/local/lib

Have you tried to run this from the iXAFS shell from the iXAFS app?
That should definitely set the environment correctly.

Sorry for the trouble,

--Matt

On Thu, Sep 23, 2010 at 1:51 AM, Brugger, Joel (SAM)
<Joel.Brugger at samuseum.sa.gov.au> wrote:
> Hi Brandon,
>
> Did you actually test the python module (i.e. Use python scripting to
> control arthemis?)
>
> On 10.6.4, I’ve obtain the following error:
>
> bash-3.2$ python
>   Python 2.6.1 (r261:67515, Dec 17 2009, 00:59:15)
>   [GCC 4.2.1 (Apple Inc. build 5646)] on darwin
>   Type "help", "copyright", "credits" or "license" for more information.
>>>> import math
>>>> import Ifeffit
>>>> iff = Ifeffit.Ifeffit()
>  failed to load ifeffit library  libifeffit.dylib
> /usr/local/share/ifeffit/:/opt/intel/Compiler/11.1/089/bin/intel64:/opt/local/bin:/opt/local/sbin:/Volumes/iXAFS3.0/iXAFS.app/Contents/Resources/local/bin:/opt/intel/Compiler/11.1/089/bin/intel64:/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/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:/Applications/iXAFS.app/Contents/Resources/local/bin:/Users/joelb/Desktop/Molecular
> Dynamics/nwchem-5.1-MACX-Darwin-gfortran-i386/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:/Users/joelb/Desktop/Molecular
> Dynamics/nwchem-5.1-MACX-Darwin-gfortran-i386/bin/:/Applications/iXAFS.app/Contents/Resources/local/lib:/Applications/iXAFS.app/Contents/Resources/local/bin
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/Library/Python/2.6/site-packages/Ifeffit/Ifeffit.py", line 80, in
> __init__
>     raise ImportError('Cannot load ifeffit library')
> ImportError: Cannot load ifeffit library
>
>
>
> . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh is in my
> .profile and is loaded. Indeed, invoking libifeffit.dylib from the command
> line ‘works’:
>
> bash-3.2$ libifeffit.dylib
> bash: /Applications/iXAFS.app/Contents/Resources/local/lib/libifeffit.dylib:
> cannot execute binary file
>
> bash-3.2$ ls -l libifeffit.dylib
> -rwxr-xr-x  1 joelb  admin  1500676 12 Sep 00:07 libifeffit.dylib
>
> So close!
>
> Godd news last: we did not try python scripting on another machine, but
> IFEFFIT appears to run perfectly on 10.5 now – thanks Matt (champagne cork
> noise).
>
> Joel & Barbara
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