[Ifeffit] Sudden Difficulty with Importing Data into Athena
George Sterbinsky
GeorgeSterbinsky at u.northwestern.edu
Fri Feb 3 09:28:19 CST 2012
Tony, You ask "are there hidden files I should remove as well that aren't
removed...?" I do find a "Perl" folder in my "Library" folder. I'm not sure
if this was installed by iXAFS or affects iXAFS...
George
On Thu, Feb 2, 2012 at 8:18 PM, Tony Kelly <tkelly72 at gmail.com> wrote:
> This will make me seem pretty dense, but I'm still trying to figure
> out how to reply to specific threads in the list-serve from my gmail,
> and I keep seeming to create new threads... for which I wholeheartedly
> apologize if it's becoming annoying. But I really do thank everyone
> for their help and patience thus far.
>
> What I've attempted since earlier today:
> 1. Completely reinstalling from older versions and newer versions of
> IFEFFIT onto the Mac. Didn't work.
> 2. I went to two other Macs, did a clean install of the newest iXAFS
> software and it worked fine... which can only mean something really
> crazy is going on with the Mac I am trying to use for my work. I'd
> like to mention again that I was able to import data just fine last
> night, and it was only this morning that things started breaking.
> 3. I've reinstalled X11 and XQuartz.
> 4. I've checked the data files on the other Mac machines (and Dr.
> Zając checked them) and the files were fine.
> 5. I attempted to run from the command line and found some errors
> that weren't there at one time.
> 6. I then checked my version of perl, and it is version 5
>
> bash-3.2$ perl -v
>
> This is perl, v5.10.0 built for darwin-thread-multi-2level
> (with 2 registered patches, see perl -V for more detail)
>
> 6. Something that MAY shed light on the situation... when I open
> iXAFS from the Application menu in the Dock (I'll try attaching an
> image), it seems that iXAFS is "broken" or not installing correctly.
> However, I can then open iXAFS up in the FINDER window, it looks
> "okay" and can be opened... it just doesn't function correctly. What
> I don't understand is why a clean install doesn't fit the problem...
> are there hidden files I should remove as well that aren't removed
> when I uninstall iXAFS from the application directory with (rm -rf ) ?
>
> 7. George mentions that his build is different than my own, so now I
> am looking at my structure (modified for more pleasant viewing), but
> the directory does seem to exist.:
>
> bash-3.2$ ls /Applications/iXAFS.app/
> Contents
>
> ls /Applications/iXAFS.app/Contents/
> Info.plist MacOS PkgInfo Resources
>
> ls /Applications/iXAFS.app/Contents/Resources/
> Artemis.icns Athena.icns English.lproj
> Hephaestus.icns Horae iXAFS Shell.icns
> iXAFS Shell.sh iXAFS.icns
>
> ls /Applications/iXAFS.app/Contents/Resources/Horae/bin/
> Aquaterm.app atoms crc32
> feffit
> ifeffit libpng-config perlindex
> tkpod
> artemis autobk diffkk
> findatp
> ifeffit_shell.pl libpng12-config rdaj
> athena chartex feff6
> hephaestus ixafs-env lsprj
> tkmore
>
>
> Tony Kelly, M.Sc.
> DTRA PhD Student
> Air Force Institute of Technology
> Nuclear Physics and Engineering
>
>
>
> On Thu, Feb 2, 2012 at 5:15 PM,
> <ifeffit-request at millenia.cars.aps.anl.gov> wrote:
> > Send Ifeffit mailing list submissions to
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> >
> >
> > Today's Topics:
> >
> > 1. Re: Sudden Difficulty with Importing Data into Athena
> > (Dr. Dariusz A. Zaj?c)
> > 2. Sudden Difficulty with Importing Data into Athena (Tony Kelly)
> > 3. Re: Sudden Difficulty with Importing Data into Athena
> > (Bruce Ravel)
> > 4. Re: Sudden Difficulty with Importing Data into Athena (Tony Kelly)
> > 5. Re: Sudden Difficulty with Importing Data into Athena
> > (Dr. Dariusz A. Zaj?c)
> > 6. Re: Sudden Difficulty with Importing Data into Athena
> > (Dr. Dariusz A. Zaj?c)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Thu, 02 Feb 2012 19:07:32 +0100
> > From: "Dr. Dariusz A. Zaj?c" <kicaj at ifj.edu.pl>
> > To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> > Subject: Re: [Ifeffit] Sudden Difficulty with Importing Data into
> > Athena
> > Message-ID: <4F2AD0E4.3010107 at ifj.edu.pl>
> > Content-Type: text/plain; charset=UTF-8; format=flowed
> >
> > check the data, if at the end of files are some zeros or strange
> > numbers or even empty line(maybe). That what you described can be
> > exactly caused by problem with the data in file, eg. injection during
> > measurements
> >
> > W dniu 12-02-02 18:22, Tony Kelly pisze:
> >> Hopefully this is not long winded, but I want to be as detailed with
> >> the problem as I can be. In the past, I have never had difficulty
> >> importing data into Athena, given it was formatted properly. It was
> >> working as recently as last night, but suddenly I have a problem
> >> today.
> >>
> >> 1. I open Athena
> >> 2. I go to File->Open Files
> >> 3. I click on the data file to bring me to the window where I choose
> >> Energy, Numerator, Denominator for the data and any reference spectra,
> >> etc
> >> 4. I choose the Energy, Numerator and Denominator
> >>
> >> This is when the first moment of "oddness" happens... I don't get a
> >> plot. Normally, I would get a plot of the spectra I am about to
> >> import to know if I selected the correct columns with the correct sign
> >> (and whether a Log is needed).
> >>
> >> 5. Confused, I continue anyway and import my choices.
> >> 6. I then get the following error from Athena:
> >>
> >> The following problems were found for group "Fe.060"
> >> 1 : The edge energy is unset
> >> 2 : The kmin for the forward transfer is negative (-2)
> >> You should fix these values before continuing analysis of these data.
> >>
> >> Note 1: I was trying with some old data that I have analyzed in the
> >> past from Athena through Artemis and know to be okay for analysis.
> >> Note 2: I then tried studying some MnO spectra by importing that data
> >> taken during the 2011 XAFS Summer School in Chicago taken from APS. I
> >> know these text files to work, as we looked at them AT the summer
> >> school.
> >> Note 3: As a last resort, I tried downloading the Fe example from the
> >> Athena website (as you can see above from Fe.060), but it can't even
> >> read this in.
> >> Note 4: Athena CAN open old projects where the data was already
> >> imported without problems... it just seems I can't start a new project
> >> and import data into it successfully. I have tried searching all
> >> through the internet for anyone who had the error above or my
> >> difficulties to no avail. I have tried making sure the line breaks
> >> were correct by resaving data into new files through textwrangler and
> >> even going through vim in a terminal, to no avail.
> >> Note 5: As a last resort, I reinstalled iXAFS, but this hasn't fixed
> >> the problem.
> >>
> >> Anyone have any suggestions? Am I suddenly forgetting a step in the
> >> data import process?
> >>
> >> Thanks,
> >>
> >> Tony Kelly
> >> Air Force Institute of Technology
> >> Nuclear Physics and Engineering
> >> _______________________________________________
> >> Ifeffit mailing list
> >> Ifeffit at millenia.cars.aps.anl.gov
> >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >>
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Thu, 2 Feb 2012 13:18:14 -0500
> > From: Tony Kelly <tkelly72 at gmail.com>
> > To: ifeffit at millenia.cars.aps.anl.gov
> > Subject: [Ifeffit] Sudden Difficulty with Importing Data into Athena
> > Message-ID:
> > <
> CAOOxQkMUGzwk-0wxDuipd9_VFh3iodgY+WBF0xwLzddvJMNfZA at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > Hi Bruce,
> >
> > Thank you for the quick reply. I tried uninstalling and reinstalling
> > twice, though I suppose I could try a different version. I have also
> > made sure that my x11/xquartz software was up to date, though I have
> > not changed or added software or updates between the last time it
> > worked and now.
> >
> > It literally worked last night, then it no longer worked this morning.
> >
> > I've never had antivirus software on my macs, but I could download one
> > and do a scan to see what that gives me.
> >
> > If I find a clear solution to what may have happened, I'll be sure to
> > reply again to share the answer.
> >
> > Tony Kelly
> > Air Force Institute of Technology
> > Nuclear Physics and Engineering
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Thu, 2 Feb 2012 13:27:37 -0500
> > From: Bruce Ravel <bravel at bnl.gov>
> > To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> > Subject: Re: [Ifeffit] Sudden Difficulty with Importing Data into
> > Athena
> > Message-ID: <201202021327.38153.bravel at bnl.gov>
> > Content-Type: Text/Plain; charset="iso-8859-1"
> >
> > On Thursday, February 02, 2012 01:18:14 pm Tony Kelly wrote:
> >> Thank you for the quick reply. I tried uninstalling and reinstalling
> >> twice, though I suppose I could try a different version. I have also
> >> made sure that my x11/xquartz software was up to date, though I have
> >> not changed or added software or updates between the last time it
> >> worked and now.
> >
> > I have to ask the obvious questions ... :)
> >
> >> It literally worked last night, then it no longer worked this morning.
> >>
> >> I've never had antivirus software on my macs, but I could download one
> >> and do a scan to see what that gives me.
> >
> > I am not suggesting that. I was suspicious that AV software had
> > deleted something as a false positive.
> >
> > You might have mentioned in your original email that you were using
> > the Mac. In this case, I don't see yet how it matters, but it
> > certainly is awfully big omission.
> >
> >> If I find a clear solution to what may have happened, I'll be sure to
> >> reply again to share the answer.
> >
> > Try opening a terminal and running athena from the command line. The
> > advantage of this is that you will get to see whatever error messages
> > get issued when Athena runs into her problems.
> >
> > Also Darek's suggestion of checking to make sure the input data has not
> > been somehow corrupted is a good one.
> >
> > B
> >
> > --
> >
> > Bruce Ravel ------------------------------------ bravel at bnl.gov
> >
> > National Institute of Standards and Technology
> > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
> > Building 535A
> > Upton NY, 11973
> >
> > My homepage: http://xafs.org/BruceRavel
> > EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Thu, 2 Feb 2012 14:23:07 -0500
> > From: Tony Kelly <tkelly72 at gmail.com>
> > To: ifeffit at millenia.cars.aps.anl.gov
> > Subject: Re: [Ifeffit] Sudden Difficulty with Importing Data into
> > Athena
> > Message-ID:
> > <
> CAOOxQkP72UoA-8Z_NkcPRDX1+tD4_CwsWdyiRBMtXb3DvYJoeg at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > 1. I made sure to check the data files for strange behavior,
> > definitely a good idea. I know when I use other software such as
> > ROOT, file structure and pat names can become problems. This didn't
> > fix the problem, however :-/
> >
> > 2. I then ran Athena from the command line as was suggested, and it
> > seems that there is a major problem there:
> >
> > bash-3.2$ athena
> > Can't load
> '/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle'
> > for module Ifeffit:
> >
> dlopen(/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle,
> > 1): Library not loaded: libifeffit.so
> > Referenced from:
> >
> /Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle
> > Reason: image not found at
> >
> /Applications/iXAFS.app/Contents/Resources/local/lib/perl5/5.12.1/darwin-multi-2level/DynaLoader.pm
> > line 204.
> > at /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67
> > Compilation failed in require at
> > /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67.
> > BEGIN failed--compilation aborted at
> > /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67.
> >
> >
> > 3. Then I became more curious and attempted ifeffit itself:
> >
> > bash-3.2$ ifeffit
> > dyld: Library not loaded: libpgplot.dylib
> > Referenced from:
> /Applications/iXAFS.app/Contents/Resources/Horae/bin/ifeffit
> > Reason: image not found
> > Trace/BPT trap
> >
> >
> > I am using Max OSX 10.6.8.
> > Intel Core i5.
> >
> > Any other Mac users out there have ideas?
> >
> > Thanks much,
> >
> > Tony Kelly
> > Air Force Institute of Technology
> > Nuclear Physics and Engineering
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Thu, 02 Feb 2012 20:56:44 +0100
> > From: "Dr. Dariusz A. Zaj?c" <kicaj at ifj.edu.pl>
> > To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> > Subject: Re: [Ifeffit] Sudden Difficulty with Importing Data into
> > Athena
> > Message-ID: <4F2AEA7C.8070400 at ifj.edu.pl>
> > Content-Type: text/plain; charset=UTF-8; format=flowed
> >
> > can you send me this file you can not open?
> >
> > W dniu 12-02-02 20:23, Tony Kelly pisze:
> >> 1. I made sure to check the data files for strange behavior,
> >> definitely a good idea. I know when I use other software such as
> >> ROOT, file structure and pat names can become problems. This didn't
> >> fix the problem, however :-/
> >>
> >> 2. I then ran Athena from the command line as was suggested, and it
> >> seems that there is a major problem there:
> >>
> >> bash-3.2$ athena
> >> Can't load
> '/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle'
> >> for module Ifeffit:
> >>
> dlopen(/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle,
> >> 1): Library not loaded: libifeffit.so
> >> Referenced from:
> >>
> /Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle
> >> Reason: image not found at
> >>
> /Applications/iXAFS.app/Contents/Resources/local/lib/perl5/5.12.1/darwin-multi-2level/DynaLoader.pm
> >> line 204.
> >> at /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67
> >> Compilation failed in require at
> >> /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67.
> >> BEGIN failed--compilation aborted at
> >> /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67.
> >>
> >>
> >> 3. Then I became more curious and attempted ifeffit itself:
> >>
> >> bash-3.2$ ifeffit
> >> dyld: Library not loaded: libpgplot.dylib
> >> Referenced from:
> /Applications/iXAFS.app/Contents/Resources/Horae/bin/ifeffit
> >> Reason: image not found
> >> Trace/BPT trap
> >>
> >>
> >> I am using Max OSX 10.6.8.
> >> Intel Core i5.
> >>
> >> Any other Mac users out there have ideas?
> >>
> >> Thanks much,
> >>
> >> Tony Kelly
> >> Air Force Institute of Technology
> >> Nuclear Physics and Engineering
> >> _______________________________________________
> >> Ifeffit mailing list
> >> Ifeffit at millenia.cars.aps.anl.gov
> >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >>
> >
> >
> > ------------------------------
> >
> > Message: 6
> > Date: Thu, 02 Feb 2012 23:15:48 +0100
> > From: "Dr. Dariusz A. Zaj?c" <kicaj at ifj.edu.pl>
> > To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> > Subject: Re: [Ifeffit] Sudden Difficulty with Importing Data into
> > Athena
> > Message-ID: <4F2B0B14.2070807 at ifj.edu.pl>
> > Content-Type: text/plain; charset=UTF-8; format=flowed
> >
> > Hmm,
> > under Win XP I had no problems to open files, together with the
> > reference. For Tony's data as well as downloaded from internet's one.
> > I'm just thinking - this maybe is some problem with the settings in open
> > window, or with compilation of Athena.
> > About second case I have not to much to say,
> > About first - maybe some option for opening file and processing data? I
> > tried to see each counter separately and I had no problems, also with
> > negate function...
> > any ideas?
> > darek
> >
> > W dniu 12-02-02 20:23, Tony Kelly pisze:
> >> 1. I made sure to check the data files for strange behavior,
> >> definitely a good idea. I know when I use other software such as
> >> ROOT, file structure and pat names can become problems. This didn't
> >> fix the problem, however :-/
> >>
> >> 2. I then ran Athena from the command line as was suggested, and it
> >> seems that there is a major problem there:
> >>
> >> bash-3.2$ athena
> >> Can't load
> '/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle'
> >> for module Ifeffit:
> >>
> dlopen(/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle,
> >> 1): Library not loaded: libifeffit.so
> >> Referenced from:
> >>
> /Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle
> >> Reason: image not found at
> >>
> /Applications/iXAFS.app/Contents/Resources/local/lib/perl5/5.12.1/darwin-multi-2level/DynaLoader.pm
> >> line 204.
> >> at /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67
> >> Compilation failed in require at
> >> /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67.
> >> BEGIN failed--compilation aborted at
> >> /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67.
> >>
> >>
> >> 3. Then I became more curious and attempted ifeffit itself:
> >>
> >> bash-3.2$ ifeffit
> >> dyld: Library not loaded: libpgplot.dylib
> >> Referenced from:
> /Applications/iXAFS.app/Contents/Resources/Horae/bin/ifeffit
> >> Reason: image not found
> >> Trace/BPT trap
> >>
> >>
> >> I am using Max OSX 10.6.8.
> >> Intel Core i5.
> >>
> >> Any other Mac users out there have ideas?
> >>
> >> Thanks much,
> >>
> >> Tony Kelly
> >> Air Force Institute of Technology
> >> Nuclear Physics and Engineering
> >> _______________________________________________
> >> Ifeffit mailing list
> >> Ifeffit at millenia.cars.aps.anl.gov
> >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >>
> >
> >
> > ------------------------------
> >
> > _______________________________________________
> > Ifeffit mailing list
> > Ifeffit at millenia.cars.aps.anl.gov
> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >
> >
> > End of Ifeffit Digest, Vol 108, Issue 3
> > ***************************************
>
> _______________________________________________
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