Re: [Ifeffit] iXAFS 3.0.3 for Mac OS X (Brandon Reese)
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 "", line 1, in
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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[Ifeffit] iXAFS & python scripting
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
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 $PATH
/Applications/iXAFS.app/Contents/Resources/local/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin
--
Message: 4
Date: Thu, 9 Sep 2010 10:12:09 -0500
From: Matt Newville
To: XAFS Analysis using Ifeffit
Cc: "barbara.etschm...@adelaide.edu.au"
Subject: Re: [Ifeffit] IXAFS3.0.2 and python scripting
Message-ID:
Content-Type: text/plain; charset=ISO-8859-1
Hi Joel and Barb,
Ah, sorry. I believe you need to do
. /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh
in the shell prior to running python, or add this to your bash .profile file.
It would be better if the setup procedure detected that it was on a
Mac and set the environment up automatically.
I'll work on that (and on the build for10.5).
--Matt
> Works great on 10.6 for us too. Thanks a million times, and fingers crossed
> for finding the error in 10.5 !
>
> We tried the python scripting, but apparently a /Users/Newville still lurks
> in there.
>
> Running the aps-12p9mLiCl.py ?script
>
> 1. #!/usr/bin/python
> 2.
> 3. import math
> 4. import Ifeffit
> 5. iff = Ifeffit.Ifeffit()
>
> gives the following error:
>
> bash-3.2$ 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
> ? ?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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[Ifeffit] IXAFS3.0.2 and python scripting
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
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
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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[Ifeffit] iXAFS3.0 - not much luck so far
Hi Matt, Not much luck with iXAFS3.0 so far. Under 10.5.8 (two macbooks), iXAFS crashes at startup. Under 10.6.4 (macbook pro), IXAFS opens, but clicking on athena/Artemis/Hephaestus only opens an X11 terminal. I think that somehow the installer expects perl to live in /Users/Newville/: $ pwd /Applications/iXAFS.app/Contents/Resources/local/bin b$ artemis -bash: /Applications/iXAFS.app/Contents/Resources/local/bin/artemis: /Users/Newville/Codes/ifeffit/local//bin/perl: bad interpreter: No such file or directory $ I also tried to install python, but something must be wrong with setup.py since files are copied to /Users/Newville. I now have such an inhabitant on my HD thanks to sudo, but even then the install failed. See details below. Hope it’s nothing traumatic! Thanks, JOEL JoelMacBook-Silver:IfeffitPython-2.0.0 joelb$ python setup.py install running install running build running build_py creating build creating build/lib creating build/lib/Ifeffit copying lib/__init__.py -> build/lib/Ifeffit copying lib/Ifeffit.py -> build/lib/Ifeffit copying lib/ifeffit_config.py -> build/lib/Ifeffit copying lib/shell.py -> build/lib/Ifeffit running install_lib creating /Library/Python/2.6/site-packages/Ifeffit copying build/lib/Ifeffit/__init__.py -> /Library/Python/2.6/site-packages/Ifeffit copying build/lib/Ifeffit/Ifeffit.py -> /Library/Python/2.6/site-packages/Ifeffit copying build/lib/Ifeffit/ifeffit_config.py -> /Library/Python/2.6/site-packages/Ifeffit copying build/lib/Ifeffit/shell.py -> /Library/Python/2.6/site-packages/Ifeffit byte-compiling /Library/Python/2.6/site-packages/Ifeffit/__init__.py to __init__.pyc byte-compiling /Library/Python/2.6/site-packages/Ifeffit/Ifeffit.py to Ifeffit.pyc byte-compiling /Library/Python/2.6/site-packages/Ifeffit/ifeffit_config.py to ifeffit_config.pyc byte-compiling /Library/Python/2.6/site-packages/Ifeffit/shell.py to shell.pyc running install_data creating /Users/Newville error: could not create '/Users/Newville': Permission denied Running as SUDO: JoelMacBook-Silver:IfeffitPython-2.0.0 joelb$ sudo python setup.py install Password: running install running build running build_py running install_lib running install_data creating /Users/Newville creating /Users/Newville/Codes creating /Users/Newville/Codes/ifeffit creating /Users/Newville/Codes/ifeffit/local creating /Users/Newville/Codes/ifeffit/local/bin error: can't copy 'ifeffit_shell.py': doesn't exist or not a regular file ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] PYTHON scripting on MacOS & XP (Joel Brugger)
Hi Matt, Thanks for the update. We had trouble getting the XP version to work. We're running Win XP under parallels on the Mac. Ifeffit (1.2.11), python (2.5) and the wrapper installed successfully. The ifeffit.py shell (in the python/scripts directory) does not recognise any python commands. And opening python in the ifeffit directory - it does not recognise ifeffit in the "import ifeffit" command. What are we doing wrong? Thanks, Joel & Barbara ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] PYTHON scripting on MacOS & XP
We used python scripting in 2005 (Win XP). However trying to get back into it we ran into trouble: - We're now using MacOS X, but could not find a python wrapper in the current iXAFS or IFEFFIT installs; is python scripting supported on the mac at all? - We then tried to get back to the PC version, only to discover that the wrapper also seems to be absent from the latest install. Can you please help us to get going again with python scripting? If this option is not supported anymore, can you recommend an alternative? Thanks, Joel & Barbara ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
