[Ifeffit] iXAFS3.0.2

Matt Newville newville at cars.uchicago.edu
Wed Sep 8 11:36:06 CDT 2010


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


On Wed, Sep 8, 2010 at 11:09 AM, Brandon Reese <bjreese at gmail.com> wrote:
> 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
>>
>> 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
>> >>
>> >> 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
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>> >>>
>> >>>
>> >>
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