Re: [Ifeffit] IXAFS3.0.2 and python scripting

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) 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

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Today's Topics:

  1. Re: iXAFS3.0.2 (Matt Newville)

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Message: 1 Date: Wed, 8 Sep 2010 11:36:06 -0500 From: Matt Newville To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] iXAFS3.0.2 Message-ID:         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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