[Ifeffit] iXAFS3.0.2

Wed Sep 8 11:09:08 CDT 2010

Hi Matt,

Thanks for all of the work building a new iXAFS, it is much appreciated.  I
am running an intel machine with 10.5.8.  I just installed iXAFS 3.0.2 and
the application launches but when I click on one of the apps X11 starts but
I get an error that perl quit unexpectedly.  In the problem report I get a
Dyld error message: unknown required load command 0x80000022.  The iXAFS
shell does launch.  I tried 'arch -i386 ifeffit' and got the same dyld error
message.  For kicks I also tried 'arch -x86_64 ifeffit' and got the error
'arch: posix_spawnp: ifeffit: Bad CPU type in executable'.  Let me know if
there is any other information that I can provide you with.

Thanks again
Brandon

On Tue, Sep 7, 2010 at 2:15 PM, Matt Newville <newville at cars.uchicago.edu>wrote:

> Hi All,
>
> OK, I put a next attempt for a Mac distribution at
>    http://cars9.uchicago.edu/~ifeffit/src/iXAFS3.0.2.dmg<http://cars9.uchicago.edu/%7Eifeffit/src/iXAFS3.0.2.dmg>
>
> which should have some improvements.  I believe this should work on
> 10.6 without issue -- I tested it on one other system at work, and
> everything launched without trouble.    The Python module should now
> install well.
>
> With earlier attempts, I still had problems with a 10.5 machine, and
> suspected something wrong with i386 v x86_64.   So I rebuilt
> everything (including perl) to be for i386 and ppc architectures, but
> not x86_64.     In fact, I noticed some Aquaterm-related issues that
> also seemed x86_64 v i386, and went back to using (and including in
> the distribution) the standard issue Aquaterm1.0.1 that has i386 and
> ppc binaries, but not x86_64.   Thus, iXAFS3.0.2 has no x86_64
> binaries. For one thing, this makes the image "only" 60Mb.
>
> I could not find suitable 10.5 or PowerPC machines at work, but will
> test later today.
>
> For PPC, the iXAFS launcher application is now universal, and runs on
> PPC (G4) machine.  With an earlier incarnation (when x86_64 was still
> included)  I could run the Ifeffit shell and Athena.  Unfortunately,
> both Artemis and Hephaestus failed to load with
>   dyld: lazy symbol binding failed: Symbol not found: ___gcc_gmul
>   Referenced from: ....local/bin/perl
>   Expected in: /usr/lib/libSystem.B.dylib
>
> Hephaestus showed a splash screen, Artemis did not.  I grepped out all
> the 'use' statements from Hephaestus, and these can all be loaded.  In
> addition, all '*.bundle" files (Perl's binaries) claim to be universal
> binaries (including ppc).     I don't really know what to make of
> this, but will try again with the latest build.
>
> Any feedback on what works and what doesn't would be greatly appreciated.
>
> Cheers,
>
> --Matt
>
> On Mon, Sep 6, 2010 at 11:06 AM, Jeff Terry <terryj at iit.edu> wrote:
> > 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<http://cars9.uchicago.edu/%7Eifeffit/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)
> >> <Joel.Brugger at samuseum.sa.gov.au> 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
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> _______________________________________________
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> >>> Ifeffit at millenia.cars.aps.anl.gov
> >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >>>
> >>>
> >>
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