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
Hi Joel, All,
Yes, sorry for that. I'm still learning how to do this. Here's the
latest news (some progress, incomplete):
With Jeff's earlier message I looked into and solved at least one of
the problems: that /Users/Newville/Codes/ifeffit/local/bin/perl
was all over the place and expected. Of course, this worked when I
tested it on my own machine!! I also found an issue with png
support.
I put a 3.0.1 dmg with these changes at
http://cars9.uchicago.edu/~ifeffit/src/iXAFS3.0.1.dmg
I believe this may work on 10.6 systems.
I tried this on a 10.5.7, i386 system (Julie's). The main iXAFS app
runs, but I unfortunately get 'dyld' loading errors for all
executables (including perl and ifeffit). I do not understand this,
as thhe executables are definitely listed as "universal", ut I suspect
it is a x86_64 v i386 issue. If anyone does understand this, please
let me know. FWIW, the machine I'm building on is less than 3 months
old, so I think it's x86_64, but 'arch' and 'uname -p' report i386.
On the build machine, running
arch -x86_64 ifeffit
runs fine.
arch -i386 ifeffit
runs, but Aquaterm does not generate a plot (using PGPLOT_DEV=/XS does
generate a plot with both settings). So my sense is that my box is
really x86_64, but reports i386 and this may be causing trouble on
real i386 machines.
What's stranger is that I also tried this on a very old G4 powerpc,
running 10.5. Here the iXAFS.app does not run, and indeed
the iXAFS executable (iXAFS.app/Contents/MacOS/iXAFS) is indeed i386
only. But, the ifeffit application DOES RUN(!!!) on this machine.
Perl runs too, but it appears I forgot to rebuild Ifeffit.pm for perl
after some change for png support because
perl -e 'use Ifeffit' still complains about png support. This is
fixable. I'll look into making the iXAFS launcher application be
universal.
The python problem is definitely fixable too -- sorry for such poor testing!
If you or Jeff or someone else wants to try this v3.0.1 out, that
would be fine, but there are definitely "known problems". I'll make
a v3.0.2 with the perl and python fixes today. I'll look into the
i386 v x86_64 issues too, but that will take some research...
Cheers,
--Matt
On Mon, Sep 6, 2010 at 7:34 AM, Brugger, Joel (SAM)
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
Hi All, Looks like it works now on intel machines.. I can run ifeffit from the iXAFS shell. The iXAFS app is not universal though, it is Intel only. Nice job Matt. Jeff On Sep 6, 2010, at 10:17 AM, Matt Newville wrote:
Hi Joel, All,
Yes, sorry for that. I'm still learning how to do this. Here's the latest news (some progress, incomplete):
With Jeff's earlier message I looked into and solved at least one of the problems: that /Users/Newville/Codes/ifeffit/local/bin/perl was all over the place and expected. Of course, this worked when I tested it on my own machine!! I also found an issue with png support.
I put a 3.0.1 dmg with these changes at http://cars9.uchicago.edu/~ifeffit/src/iXAFS3.0.1.dmg
I believe this may work on 10.6 systems.
I tried this on a 10.5.7, i386 system (Julie's). The main iXAFS app runs, but I unfortunately get 'dyld' loading errors for all executables (including perl and ifeffit). I do not understand this, as thhe executables are definitely listed as "universal", ut I suspect it is a x86_64 v i386 issue. If anyone does understand this, please let me know. FWIW, the machine I'm building on is less than 3 months old, so I think it's x86_64, but 'arch' and 'uname -p' report i386. On the build machine, running arch -x86_64 ifeffit runs fine. arch -i386 ifeffit runs, but Aquaterm does not generate a plot (using PGPLOT_DEV=/XS does generate a plot with both settings). So my sense is that my box is really x86_64, but reports i386 and this may be causing trouble on real i386 machines.
What's stranger is that I also tried this on a very old G4 powerpc, running 10.5. Here the iXAFS.app does not run, and indeed the iXAFS executable (iXAFS.app/Contents/MacOS/iXAFS) is indeed i386 only. But, the ifeffit application DOES RUN(!!!) on this machine. Perl runs too, but it appears I forgot to rebuild Ifeffit.pm for perl after some change for png support because perl -e 'use Ifeffit' still complains about png support. This is fixable. I'll look into making the iXAFS launcher application be universal.
The python problem is definitely fixable too -- sorry for such poor testing!
If you or Jeff or someone else wants to try this v3.0.1 out, that would be fine, but there are definitely "known problems". I'll make a v3.0.2 with the perl and python fixes today. I'll look into the i386 v x86_64 issues too, but that will take some research...
Cheers,
--Matt
On Mon, Sep 6, 2010 at 7:34 AM, Brugger, Joel (SAM)
wrote: 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
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
participants (3)
-
Brugger, Joel (SAM)
-
Jeff Terry
-
Matt Newville