Re: [Ifeffit] iXAFS xQuartz
On 10/15/2014 11:00 AM, Gaspard Jean-Pierre wrote: Hi all, On a MacBook under OS X.8.5, I downloaded iXAFS and xQuartz. I start xQuartz. When I try to start iXAFS, it requests X11 that is obviously active, I see it. However iXAFS says : X11 is not installed. I am missing something but I do not know what. I would guess that you are not getting an answer to your question because you are asking about an unsupported, 8-year-old version of the software. If you have some compelling reason to use that particular version, you could search through the archives of this mailing list for some hints on how to address your problem. Not being a Mac owner myself, I surely don't know how to solve it. Another option is to use a recent, supported version of the software: http://bruceravel.github.io/demeter/#mac B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] iXAFS xQuartz
Hi all, On a MacBook under OS X.8.5, I downloaded iXAFS and xQuartz. I start xQuartz. When I try to start iXAFS, it requests X11 that is obviously active, I see it. However iXAFS says : X11 is not installed. I am missing something but I do not know what. Regards JP ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] iXAFS on Mountain Lion
Hi, I had problem launching iXAFS on Mountain Lion after the OS upgrade. It seems the path to X11 might be hard wired in the program. Here is my workaround solution by creating a symbolic link to XQuartz. It might be worth sharing the trick. 1. Install XQuartz 2.7.4 from http://xquartz.macosforge.org/landing/ 2. Launch Terminal.app and issue the following commands: 2.1) cd /Applications/Utilities 2.2) sudo mkdir X11.app 2.3) cd X11.app 2.4) sudo ln -s ../XQuartz.app/Contents 3. Now either double-click on iXAFS.app or command line `open -a ixafs` should work -- Tsu-Chien WENG Stanford Synchrotron Radiation Lightsource 2575 Sand Hill Road, Mail Stop 69 Menlo Park, CA 94025, USA +1-650-926-4107 (office) +1-650-926-4100 (fax) ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] iXAFS
Hi, I am wondering what is the best way to uninstall iXAFS version 2.1.1 for Leopard before installing the new version. Is it sufficient to just drag iXAFS.app to the trash or is there a better way to make sure everything gets removed? Thank you, George ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] iXAFS
That should work fine. Alternately, you the new version should overwrite the old if you drag it to the Applications folder. Sent from my iPhone On Nov 29, 2010, at 9:05 AM, George Sterbinsky georgesterbin...@u.northwestern.edu wrote: Hi, I am wondering what is the best way to uninstall iXAFS version 2.1.1 for Leopard before installing the new version. Is it sufficient to just drag iXAFS.app to the trash or is there a better way to make sure everything gets removed? Thank you, George ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] iXAFS
After downloading the iXAFS3.0.3.dmg from http://cars9.uchicago.edu/ifeffit/Downloads; and installing iXAFS, I find that if I open iXAFS look at about iXAFS, it tells me that I have version 2. Is this just a case of confusing labeling, or has some aspect of my installation gone awry? Thank you, George On Mon, Nov 29, 2010 at 10:37 AM, Jeff Terry ter...@iit.edu wrote: That should work fine. Alternately, you the new version should overwrite the old if you drag it to the Applications folder. Sent from my iPhone On Nov 29, 2010, at 9:05 AM, George Sterbinsky georgesterbin...@u.northwestern.edu wrote: Hi, I am wondering what is the best way to uninstall iXAFS version 2.1.1 for Leopard before installing the new version. Is it sufficient to just drag iXAFS.app to the trash or is there a better way to make sure everything gets removed? Thank you, George ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] iXAFS
Hi George, The 'About' screen didn't get changed. I did very little to Jeff and Ken's outer Cocoa layer. I'll try to fix that, but it's probably not worth a new install. The main thing to check is whether Athena is the right version (0.8.061). Like Jeff said, iXAFS 2 and 3 do nothing to the system on install (it uses its own set of perl libraries even), and you should be able to simply delete the App and/or have them running side-by-side. --Matt On Mon, Nov 29, 2010 at 10:52 AM, George Sterbinsky georgesterbin...@u.northwestern.edu wrote: After downloading the iXAFS3.0.3.dmg from http://cars9.uchicago.edu/ifeffit/Downloads; and installing iXAFS, I find that if I open iXAFS look at about iXAFS, it tells me that I have version 2. Is this just a case of confusing labeling, or has some aspect of my installation gone awry? Thank you, George On Mon, Nov 29, 2010 at 10:37 AM, Jeff Terry ter...@iit.edu wrote: That should work fine. Alternately, you the new version should overwrite the old if you drag it to the Applications folder. Sent from my iPhone On Nov 29, 2010, at 9:05 AM, George Sterbinsky georgesterbin...@u.northwestern.edu wrote: Hi, I am wondering what is the best way to uninstall iXAFS version 2.1.1 for Leopard before installing the new version. Is it sufficient to just drag iXAFS.app to the trash or is there a better way to make sure everything gets removed? Thank you, George ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] iXAFS
Probably bad labeling as mine is version 2(2.2). Jeff On Nov 29, 2010, at 10:52 AM, George Sterbinsky wrote: After downloading the iXAFS3.0.3.dmg from http://cars9.uchicago.edu/ifeffit/Downloads; and installing iXAFS, I find that if I open iXAFS look at about iXAFS, it tells me that I have version 2. Is this just a case of confusing labeling, or has some aspect of my installation gone awry? Thank you, George On Mon, Nov 29, 2010 at 10:37 AM, Jeff Terry ter...@iit.edu wrote: That should work fine. Alternately, you the new version should overwrite the old if you drag it to the Applications folder. Sent from my iPhone On Nov 29, 2010, at 9:05 AM, George Sterbinsky georgesterbin...@u.northwestern.edu wrote: Hi, I am wondering what is the best way to uninstall iXAFS version 2.1.1 for Leopard before installing the new version. Is it sufficient to just drag iXAFS.app to the trash or is there a better way to make sure everything gets removed? Thank you, George ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
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 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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Re: [Ifeffit] iXAFS 3.0.3 for Mac OS X (Brandon Reese)
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)
$build= 1.2.12 Copyright (c) 2005 Matt Newville, Univ of Chicago
0
If I had to guess, I'd look at what DYLD_LIBRARY_PATH is set to. That
should definitely include the folder that contains libifeffit.dylib,
eg /Applications/iXAFS.app/Contents/Resources/local/lib
Have you tried to run this from the iXAFS shell from the iXAFS app?
That should definitely set the environment correctly.
Sorry for the trouble,
--Matt
On Thu, Sep 23, 2010 at 1:51 AM, Brugger, Joel (SAM)
joel.brug...@samuseum.sa.gov.au wrote:
Hi Brandon,
Did you actually test the python module (i.e. Use python scripting to
control arthemis?)
On 10.6.4, I’ve obtain the following error:
bash-3.2$ 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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Re: [Ifeffit] iXAFS 3.0.3 for Mac OS X (Brandon Reese)
Hi Joel,
I did not test the python module. I just tested the function of
Artemis/Athena from the iXAFS window and work great. Thanks again for that!
I gave it try from both the iXAFS shell and regular bash terminal and got
this error (I am using 10.5.8)...
bash-3.2$ python
Python 2.5.4 (r254:67917, Dec 23 2008, 14:57:27)
[GCC 4.0.1 (Apple Computer, Inc. build 5363)] on darwin
Type help, copyright, credits or license for more information.
import math
import ifeffit
Traceback (most recent call last):
File stdin, line 1, in module
ImportError: No module named ifeffit
Sorry I can't add much else to this discussion, but I am happy to try things
out if people have ideas.
Brandon
On Thu, Sep 23, 2010 at 12:51 AM, Brugger, Joel (SAM)
joel.brug...@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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http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
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Re: [Ifeffit] iXAFS 3.0.3 for Mac OS X
Hi Matt, Just got around to trying out the new iXAFS 3.0.3 build on my 10.5 (Intel) Mac. Interestingly enough the app ran fine for me without doing anything with the Pyhton module you linked. Although I had the old beta version of iXAFS installed and have attempted at least one source build, so I suspect that had something to do with it. I haven't been using Unix systems for long, and am bit clunky with such things. Thanks for all the hard work in building these packages for us!! Brandon On Sun, Sep 19, 2010 at 11:46 AM, Matt Newville newvi...@cars.uchicago.eduwrote: Hi All, OK, sorry for the delay, but I think that http://cars9.uchicago.edu/~ifeffit/src/iXAFS3.0.3.dmghttp://cars9.uchicago.edu/%7Eifeffit/src/iXAFS3.0.3.dmg should now work well for both Mac OS X 10.6 and 10.5. That is, all the applications launch for me on a 10.6.5 machine and a 10.5.8 machine, and seem to work as expected. I'll try this on a PowerPC machine within the next couple days. I didn't include the Python module in this installer (I forgot), but put it at http://cars9.uchicago.edu/~ifeffit/src/IfeffitPython-2.0.1.tar.gzhttp://cars9.uchicago.edu/%7Eifeffit/src/IfeffitPython-2.0.1.tar.gz This *should* work now, but then I thought the last one was going to work too. It might be best to run this through the Ifeffit Shell, or to be extra careful in setting the environment to source the //iXAFS.app/Contents/Resources/local/bin/iff_init.sh As always, any feedback on what works and what doesn't would be greatly appreciated. Cheers, --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] iXAFS 3.0.3 for Mac OS X
Hi All, OK, sorry for the delay, but I think that http://cars9.uchicago.edu/~ifeffit/src/iXAFS3.0.3.dmg should now work well for both Mac OS X 10.6 and 10.5. That is, all the applications launch for me on a 10.6.5 machine and a 10.5.8 machine, and seem to work as expected. I'll try this on a PowerPC machine within the next couple days. I didn't include the Python module in this installer (I forgot), but put it at http://cars9.uchicago.edu/~ifeffit/src/IfeffitPython-2.0.1.tar.gz This *should* work now, but then I thought the last one was going to work too. It might be best to run this through the Ifeffit Shell, or to be extra careful in setting the environment to source the //iXAFS.app/Contents/Resources/local/bin/iff_init.sh As always, any feedback on what works and what doesn't would be greatly appreciated. Cheers, --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] iXAFS for Mac OS X
Hi Folks, With help from Ken McIvor and Jeff Terry, I've built a new version of iXAFS for Mac OS X. This version should be considered experimental, but for the brave and/or foolhardy please try it out and let us know how it works. This version offers the latest versions of Athena, Artemis, and Hephaestus, and the latest version of Ifeffit.It is meant to be universal (for x86_64, i386, and ppc), though I have not fully tested this. The download is fairly large (~74Mb), mostly because it includes a full distribution of Perl built right in (so it doesn't interfere with the system Perl). It also provides a complete Unix shell-like environment that can be used for those who need it. For example, a python module is included that can be installed. The disk image is at http://car9.uchicago.edu/~ifeffit/src/iXAFS3.0.dmg This should be able to be installed by dragging the iXAFS application to any folder. To use the Unix shell, you'd put . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh in your .profile or from a bash Terminal command prompt (assuming you installed to /Applications/). To install the Python module, first run iff_init.sh above, then copy and unpack /Applications/iXAFS.app/Contents/Resources/local/extras/IfeffitPython-2.0.0.tar.gz and run 'python setup.py install'. Again, this should be considered a beta release. Please be willing to look for and report problems. Cheers, --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] iXAFS for Mac OS X
Hi All, If you have been using the iXAFS Shell for command line access, note that it is currently not working in this version. Jeff On Sep 3, 2010, at 10:08 PM, Matt Newville wrote: Hi Folks, With help from Ken McIvor and Jeff Terry, I've built a new version of iXAFS for Mac OS X. This version should be considered experimental, but for the brave and/or foolhardy please try it out and let us know how it works. This version offers the latest versions of Athena, Artemis, and Hephaestus, and the latest version of Ifeffit.It is meant to be universal (for x86_64, i386, and ppc), though I have not fully tested this. The download is fairly large (~74Mb), mostly because it includes a full distribution of Perl built right in (so it doesn't interfere with the system Perl). It also provides a complete Unix shell-like environment that can be used for those who need it. For example, a python module is included that can be installed. The disk image is at http://car9.uchicago.edu/~ifeffit/src/iXAFS3.0.dmg This should be able to be installed by dragging the iXAFS application to any folder. To use the Unix shell, you'd put . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh in your .profile or from a bash Terminal command prompt (assuming you installed to /Applications/). To install the Python module, first run iff_init.sh above, then copy and unpack /Applications/iXAFS.app/Contents/Resources/local/extras/IfeffitPython-2.0.0.tar.gz and run 'python setup.py install'. Again, this should be considered a beta release. Please be willing to look for and report problems. Cheers, --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] iXAFS for OS X 10.6
Hi Jeff, Hello from a sunny and warm Japan. I would love to upgrade to snow leopard... but ixafs is a must have for me hence I am still at 10.5. Would it be possible to test whatever version you have ready on my mac? So long as I can select a file from X11 and fit stuff, any functional problems with the pretty front end are something I can live with. Please let me know if I can help. Cheers, Paul On Jan 14, 2010, at 1:26 PM, Jeff Terry wrote: Hi All, We have a beta version of iXAFS for Snow Leopard (OS X 10.6). Please email me if you would like to test this version. We hope to have a full release shortly, but would like to have a small group look for major issues for a short time. Thanks, Jeff ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] iXAFS for OS X 10.6
Hi Jeff, (A somewhat belated) happy new year. I was at the APS recently and it so happened that Bruce was using sector 20 right before me. I was curious about the version of ixafs for snow leopard and if there was any way that I might be of some help to you (Bruce mentioned your surgery). I also noticed your note (just now) on the ifeffit list about wanting to run a beta. I would be glad to help out in this regard (I have been postponing the upgrade to snow leopard up to this point as ixafs is a must have for me. Thanks for your efforts. Sincerely, Paul ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Ifeffit/iXAFS won't launch in OS 10.6 (Snow Leopard)
Paul, Thanks for the information! Jeff and I are hoping to have the opportunity to work on a fix sooner rather than later. From the sound of things we may be able to avoid Heroic Measures. The hope is to slip by with something like wrapper scripts for athena et alia that invoke the correct version of Perl, as opposed to migrating to a full- blow ppc/x86 32-/64-bit build. Ken On Sep 13, 2009, at 11:37 PM, Paul Fons wrote: The problem with iXAFS is that it is attempting to run a 32 bit version of perl contained within the application in a 64 bit process. The new version of perl that ships with Snow Leopard is 5.10.0. I pasted the error message from the ixafs shell below. The solution would seem to be to repackage the perl libraries in 5.10.0 and use 64 bit binaries for the Intel compiler. I have the Intel compiler as well so if you need help, please drop me a line. Note Perl 5.8 is included with Snow Leopard as well and can be invoked by changing the defaults of the system, but this is probably a bad thing to do as it will change the perl application for all programs and will undoubtably cause more problems in the long run than it will solve. Cheers, Paul p.s. lines below are from perl and iXAFS under Snow Leopard (10.6.1) $perl --version This is perl, v5.10.0 built for darwin-thread-multi-2level (with 2 registered patches, see perl -V for more detail) Copyright 1987-2007, Larry Wall athena Can't load '/Applications/iXAFS.app/Contents/Resources/Horae/lib/ perl5/ site_perl/5.8.6/darwin-thread-multi-2level/auto/Tk/Event/Event.bundle' for module Tk::Event: /Applications/iXAFS.app/Contents/Resources/ Horae/ lib/perl5/site_perl/5.8.6/darwin-thread-multi-2level/auto/Tk/Event/ Event.bundle: no appropriate 64-bit architecture (see man perl for running in 32-bit mode) at /System/Library/Perl/5.10.0/darwin-thread- multi-2level/XSLoader.pm line 67. at /Applications/iXAFS.app/Contents/Resources/Horae/lib/perl5/ site_perl/5.8.6/darwin-thread-multi-2level/Tk/Event.pm line 10 Compilation failed in require at /Applications/iXAFS.app/Contents/ Resources/Horae/lib/perl5/site_perl/5.8.6/darwin-thread-multi-2level/ Tk.pm line 13. BEGIN failed--compilation aborted at /Applications/iXAFS.app/Contents/ Resources/Horae/lib/perl5/site_perl/5.8.6/darwin-thread-multi-2level/ Tk.pm line 13. Compilation failed in require at /Applications/iXAFS.app/Contents/ Resources/Horae/bin/athena line 64. BEGIN failed--compilation aborted at /Applications/iXAFS.app/Contents/ Resources/Horae/bin/athena line 64. Undefined subroutine Tk::Event::CleanupGlue called at /Applications/ iXAFS.app/Contents/Resources/Horae/lib/perl5/site_perl/5.8.6/darwin- thread-multi-2level/Tk/Event.pm line 3. END failed--call queue aborted at /Applications/iXAFS.app/Contents/ Resources/Horae/bin/athena line 64. ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Ifeffit/iXAFS won't launch in OS 10.6 (Snow Leopard)
The problem with iXAFS is that it is attempting to run a 32 bit version of perl contained within the application in a 64 bit process. The new version of perl that ships with Snow Leopard is 5.10.0. I pasted the error message from the ixafs shell below. The solution would seem to be to repackage the perl libraries in 5.10.0 and use 64 bit binaries for the Intel compiler. I have the Intel compiler as well so if you need help, please drop me a line. Note Perl 5.8 is included with Snow Leopard as well and can be invoked by changing the defaults of the system, but this is probably a bad thing to do as it will change the perl application for all programs and will undoubtably cause more problems in the long run than it will solve. Cheers, Paul p.s. lines below are from perl and iXAFS under Snow Leopard (10.6.1) $perl --version This is perl, v5.10.0 built for darwin-thread-multi-2level (with 2 registered patches, see perl -V for more detail) Copyright 1987-2007, Larry Wall athena Can't load '/Applications/iXAFS.app/Contents/Resources/Horae/lib/perl5/ site_perl/5.8.6/darwin-thread-multi-2level/auto/Tk/Event/Event.bundle' for module Tk::Event: /Applications/iXAFS.app/Contents/Resources/Horae/ lib/perl5/site_perl/5.8.6/darwin-thread-multi-2level/auto/Tk/Event/ Event.bundle: no appropriate 64-bit architecture (see man perl for running in 32-bit mode) at /System/Library/Perl/5.10.0/darwin-thread- multi-2level/XSLoader.pm line 67. at /Applications/iXAFS.app/Contents/Resources/Horae/lib/perl5/ site_perl/5.8.6/darwin-thread-multi-2level/Tk/Event.pm line 10 Compilation failed in require at /Applications/iXAFS.app/Contents/ Resources/Horae/lib/perl5/site_perl/5.8.6/darwin-thread-multi-2level/ Tk.pm line 13. BEGIN failed--compilation aborted at /Applications/iXAFS.app/Contents/ Resources/Horae/lib/perl5/site_perl/5.8.6/darwin-thread-multi-2level/ Tk.pm line 13. Compilation failed in require at /Applications/iXAFS.app/Contents/ Resources/Horae/bin/athena line 64. BEGIN failed--compilation aborted at /Applications/iXAFS.app/Contents/ Resources/Horae/bin/athena line 64. Undefined subroutine Tk::Event::CleanupGlue called at /Applications/ iXAFS.app/Contents/Resources/Horae/lib/perl5/site_perl/5.8.6/darwin- thread-multi-2level/Tk/Event.pm line 3. END failed--call queue aborted at /Applications/iXAFS.app/Contents/ Resources/Horae/bin/athena line 64. ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Ifeffit/iXAFS won't launch in OS 10.6 (Snow Leopard)
Hi All, We will take a look at this when we get a 10.6 machine. Jeff On Sep 8, 2009, at 4:11 PM, Joel Kelly wrote: Hello, I recently upgraded to OS 10.6 (snow leopard) on my intel Mac. It comes with version 2.3.4 of X11. Now, I can't seem to run any of the Horae GUI applications! I've tried launching Athena from iXAFS or from the stand alone IFEFFIT suite. When I run iXAFS, the normal launch window with Athena, Artemis, Hephaestus and the iXAFS shell appears. Clicking on the Athena, Artemis, and icons Hephaestus causes X11 to launch with an xterm window, but Aquaterm does not load. However, the iXAFS shell seems to load, though I'm not experienced enough with the shell to know if it's fine or not. Upon launching the Athena standalone program from IFEFFIT (downloaded here: http://cars9.uchicago.edu/~ifeffit/src/Ifeffit-1.2.10-Mac10.4_Intel_horae066.dmg) , clicking on X11 graphics launches xterm but not Aquaterm, and clicking on Aquaterm closes the program. Not sure if this is a Snow Leopard related problem or not- there has been a new version of X11 released (2.4) that is unsupported in OS 10.6, and unfortunately it doesn't seem to allow me to install a previous 2.3.2 version. Looks like I'll have to downgrade back to Leopard, these cat names are getting confusing. Has anyone experienced anything similar, or have any insight on how to fix the problem? Best regards, Joel Kelly University of Alberta ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] IXAFS for Mac OSX - Problem launching Artemis
Hello, For months, I have been happily using IXAFS for Mac OSX - excellent program! I am now having problems launching Artemis. An Aquaterm graphics window opens, but the actual Artemis program does not. If I keep trying, periodically Artemis appears as if it will launch, but the message about cleaning up extra sessions comes up, and whether I clean up or keep the sessions and/or close the Aquaterm windows beforehand, the Artemis program quits without opening. The only unusual action today was that I was working with several Athena windows opened at once, but had quit all Athena sessions before trying to launch Artemis. I tried downloading and re- installing X11 1.1.3 - XFree86 4.4.0 from http://mrcat.iit.edu, restarted the computer, etc., but to no avail. Athena seems to run fine. Even after re-installing and restarting, I sometimes receive the multiple sessions cleanup message, so perhaps I need to delete certain files before cleanly re-installing IXAFS. I did remove (trashed) IXAFS from the Applications folder before re-installing. I'm using a Mac Pro Dual Core Intel with Mac OSX version 10.4.11 X11 version 1.1.3 I appreciate any suggestions for fixing this problem, or a lead to a previous posting if this problem has already been discussed here. Dean DEAN HESTERBERG Professor Dept. of Soil Science College of Agriculture and Life Sciences Box 7619 3235 Williams Hall NC State University Raleigh, NC 27695-7619 voice: (919) 513-3035 fax: (919) 515-2167 email: [EMAIL PROTECTED] Hi All, iXAFS version 2 for Mac OS X 10.4 and above has been released as a beta version. We have tested this version on ppc and intel macs running OS X 10.4 and 10.5. You must have Apple's version of X11 installed in order to use iXAFS. Ken McIvor put in yeoman's work to build the full ifeffit, horea suite as a universal binary. He packaged it as a single drag and drop installation within iXAFS. Ken wanted to post this message but had an illness in the family. Hopefully, we can all thank Ken for his work to get this built in a manner that should work on all modern Macs. A link to download this version of iXAFS can be found at the MRCAT website: http://mrcat.iit.edu We forgot to put in the documentation that the iXAFS shell allows you to run any of the programs from the command line ifeffit, feff6, etc. Jeff ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] iXAFS 2 beta 1 released
Hi Jeff, This is great news. I downloaded the beta version, and got the error message Apple's X11 for Mac OSX is not installed So, I downloaded the latest update for X11 from Apple's website from this page: http://www.apple.com/downloads/macosx/apple/macosx_updates/x11update2006113.html And when I tried to install it, an alert message came this system doesn't need this update. So, now I'm baffled, and truly don't know where to go from here. How would I check my system (OSX 10.4.11) for the X11 already installed? Any advice will be very much appreciated. Thanks, Hind Hind A. Al-Abadleh, Ph.D. Assistant Professor Chemistry Department, Wilfrid Laurier University Science Building 3020F 75 University Ave. W. Waterloo, Ontario N2L 3C5 Canada Ph.: (519) 884-0710 ext. 2873 Fax: (519) 746-0677 URL: http://www.wlu.ca/science/chemistry/halabadleh/ [EMAIL PROTECTED] 12/07/07 12:15 AM Hi All, iXAFS version 2 for Mac OS X 10.4 and above has been released as a beta version. We have tested this version on ppc and intel macs running OS X 10.4 and 10.5. You must have Apple's version of X11 installed in order to use iXAFS. Ken McIvor put in yeoman's work to build the full ifeffit, horea suite as a universal binary. He packaged it as a single drag and drop installation within iXAFS. Ken wanted to post this message but had an illness in the family. Hopefully, we can all thank Ken for his work to get this built in a manner that should work on all modern Macs. A link to download this version of iXAFS can be found at the MRCAT website: http://mrcat.iit.edu We forgot to put in the documentation that the iXAFS shell allows you to run any of the programs from the command line ifeffit, feff6, etc. Jeff ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] iXAFS 2 beta 1 released
Hind, X11 would be in /Applications/Utilities/ You should install X11 off of your 10.4 DVD and then apply the update. Jeff On Dec 7, 2007, at 5:42 AM, Hind Al-Abadleh wrote: Hi Jeff, This is great news. I downloaded the beta version, and got the error message Apple's X11 for Mac OSX is not installed So, I downloaded the latest update for X11 from Apple's website from this page: http://www.apple.com/downloads/macosx/apple/macosx_updates/x11update2006113.html And when I tried to install it, an alert message came this system doesn't need this update. So, now I'm baffled, and truly don't know where to go from here. How would I check my system (OSX 10.4.11) for the X11 already installed? Any advice will be very much appreciated. Thanks, Hind Hind A. Al-Abadleh, Ph.D. Assistant Professor Chemistry Department, Wilfrid Laurier University Science Building 3020F 75 University Ave. W. Waterloo, Ontario N2L 3C5 Canada Ph.: (519) 884-0710 ext. 2873 Fax: (519) 746-0677 URL: http://www.wlu.ca/science/chemistry/halabadleh/ [EMAIL PROTECTED] 12/07/07 12:15 AM Hi All, iXAFS version 2 for Mac OS X 10.4 and above has been released as a beta version. We have tested this version on ppc and intel macs running OS X 10.4 and 10.5. You must have Apple's version of X11 installed in order to use iXAFS. Ken McIvor put in yeoman's work to build the full ifeffit, horea suite as a universal binary. He packaged it as a single drag and drop installation within iXAFS. Ken wanted to post this message but had an illness in the family. Hopefully, we can all thank Ken for his work to get this built in a manner that should work on all modern Macs. A link to download this version of iXAFS can be found at the MRCAT website: http://mrcat.iit.edu We forgot to put in the documentation that the iXAFS shell allows you to run any of the programs from the command line ifeffit, feff6, etc. Jeff ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] iXAFS 2 beta 1 released
Thanks Jeff and Matt for your timely reply. The software runs just fine now. Hind Hind A. Al-Abadleh, Ph.D. Assistant Professor Chemistry Department, Wilfrid Laurier University Science Building 3020F 75 University Ave. W. Waterloo, Ontario N2L 3C5 Canada Ph.: (519) 884-0710 ext. 2873 Fax: (519) 746-0677 URL: http://www.wlu.ca/science/chemistry/halabadleh/ [EMAIL PROTECTED] 12/07/07 9:11 am Hind, X11 would be in /Applications/Utilities/ You should install X11 off of your 10.4 DVD and then apply the update. Jeff On Dec 7, 2007, at 5:42 AM, Hind Al-Abadleh wrote: Hi Jeff, This is great news. I downloaded the beta version, and got the error message Apple's X11 for Mac OSX is not installed So, I downloaded the latest update for X11 from Apple's website from this page: http://www.apple.com/downloads/macosx/apple/macosx_updates/x11update2006113.html And when I tried to install it, an alert message came this system doesn't need this update. So, now I'm baffled, and truly don't know where to go from here. How would I check my system (OSX 10.4.11) for the X11 already installed? Any advice will be very much appreciated. Thanks, Hind Hind A. Al-Abadleh, Ph.D. Assistant Professor Chemistry Department, Wilfrid Laurier University Science Building 3020F 75 University Ave. W. Waterloo, Ontario N2L 3C5 Canada Ph.: (519) 884-0710 ext. 2873 Fax: (519) 746-0677 URL: http://www.wlu.ca/science/chemistry/halabadleh/ [EMAIL PROTECTED] 12/07/07 12:15 AM Hi All, iXAFS version 2 for Mac OS X 10.4 and above has been released as a beta version. We have tested this version on ppc and intel macs running OS X 10.4 and 10.5. You must have Apple's version of X11 installed in order to use iXAFS. Ken McIvor put in yeoman's work to build the full ifeffit, horea suite as a universal binary. He packaged it as a single drag and drop installation within iXAFS. Ken wanted to post this message but had an illness in the family. Hopefully, we can all thank Ken for his work to get this built in a manner that should work on all modern Macs. A link to download this version of iXAFS can be found at the MRCAT website: http://mrcat.iit.edu We forgot to put in the documentation that the iXAFS shell allows you to run any of the programs from the command line ifeffit, feff6, etc. Jeff Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] iXAFS 2 beta 1 released
Hi All, iXAFS version 2 for Mac OS X 10.4 and above has been released as a beta version. We have tested this version on ppc and intel macs running OS X 10.4 and 10.5. You must have Apple's version of X11 installed in order to use iXAFS. Ken McIvor put in yeoman's work to build the full ifeffit, horea suite as a universal binary. He packaged it as a single drag and drop installation within iXAFS. Ken wanted to post this message but had an illness in the family. Hopefully, we can all thank Ken for his work to get this built in a manner that should work on all modern Macs. A link to download this version of iXAFS can be found at the MRCAT website: http://mrcat.iit.edu We forgot to put in the documentation that the iXAFS shell allows you to run any of the programs from the command line ifeffit, feff6, etc. Jeff ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
