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 <tkell...@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-requ...@millenia.cars.aps.anl.gov> wrote: > > Send Ifeffit mailing list submissions to > > ifeffit@millenia.cars.aps.anl.gov > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > or, via email, send a message with subject or body 'help' to > > ifeffit-requ...@millenia.cars.aps.anl.gov > > > > You can reach the person managing the list at > > ifeffit-ow...@millenia.cars.aps.anl.gov > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Ifeffit digest..." > > > > > > 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" <ki...@ifj.edu.pl> > > To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Sudden Difficulty with Importing Data into > > Athena > > Message-ID: <4f2ad0e4.3010...@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@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 <tkell...@gmail.com> > > To: ifeffit@millenia.cars.aps.anl.gov > > Subject: [Ifeffit] Sudden Difficulty with Importing Data into Athena > > Message-ID: > > < > caooxqkmugzwk-0wxduipd9_vfh3iodgy+wbf0xwlzddvjmn...@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 <bra...@bnl.gov> > > To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Sudden Difficulty with Importing Data into > > Athena > > Message-ID: <201202021327.38153.bra...@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 ------------------------------------ bra...@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 <tkell...@gmail.com> > > To: ifeffit@millenia.cars.aps.anl.gov > > Subject: Re: [Ifeffit] Sudden Difficulty with Importing Data into > > Athena > > Message-ID: > > < > caooxqkp72uoa-8z_nkcprdx1+td4_cwswdyirbmtxb3dvyj...@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" <ki...@ifj.edu.pl> > > To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Sudden Difficulty with Importing Data into > > Athena > > Message-ID: <4f2aea7c.8070...@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@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" <ki...@ifj.edu.pl> > > To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Sudden Difficulty with Importing Data into > > Athena > > Message-ID: <4f2b0b14.2070...@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@millenia.cars.aps.anl.gov > >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > > > > > > ------------------------------ > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit@millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > End of Ifeffit Digest, Vol 108, Issue 3 > > *************************************** > > _______________________________________________ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >
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