[Ifeffit] Sudden Difficulty with Importing Data into Athena
Tony Kelly
tkelly72 at gmail.com
Thu Feb 2 19:18:27 CST 2012
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:
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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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