Re: [Ifeffit] iXAFS3.0.2

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 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 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 wrote:

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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:

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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:

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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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