[Ifeffit] Ifeffit Digest, Vol 128, Issue 22

Kyler Carroll kyler.carroll at gmail.com
Wed Oct 30 20:31:01 CDT 2013


Hi Stefan,

I had help from Tsu-Chein Weng (tsuchien at slac.stanford.edu) with this issue
and his solution worked for me. Basically I had to unistall both iXAFS and
XQuartz and reinstall and do a similar trick in terminal. Hope this helps!

1. Drag /Applications/iXAFS.app into the trash bin
2. Download iXAFS3.0.3.dmg and install the package
3. Drage /Applications/XQuartz.app and /opt/X11 into the trash bin
4. Download XQuartz-2.7.4.dmg and install the package
5. Launch Terminal.app
5.1 cd /Applications/Utilities
 5.2 sudo rm -fr X11.app
5.3 sudo mkdir X11.app
 5.4 cd X11.app
5.5 sudo ln -s ../XQuartz.app/Contents
 5.6 open -a X11
5.7 open -a ixafs


Thank you,

Kyler J. Carroll, Ph.D.
Research Scientist
Chemical Engineering
Massachusetts Institute of Technology,





On Mon, Oct 28, 2013 at 10:47 AM, <ifeffit-request at millenia.cars.aps.anl.gov
> wrote:

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> Today's Topics:
>
>    1. Did anyone upgraded to SeaLion aka Mavericks (MacOS 10.9)
>       (Mangold, Stefan)
>    2. Athena crash report (George Sterbinsky)
>    3. Re: Athena crash report (Bruce Ravel)
>    4. Re: Athena crash report (George Sterbinsky)
>    5. Re: Athena crash report (Bruce Ravel)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 27 Oct 2013 18:00:28 +0100
> From: "Mangold, Stefan" <stefan.mangold at kit.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: [Ifeffit] Did anyone upgraded to SeaLion aka Mavericks (MacOS
>         10.9)
> Message-ID: <6C20978B-32DC-4C87-A900-2499DFFF4EC9 at kit.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear all,
>
> one question to the early adopter. Did anyone tried ifeffit already on
> Mavericks? Is there any known issue beside the X11/Quartz issue? I have it
> installed ifeffit on MoutainLion with the know trick to "emulate" the old
> X11 (was on the mailing list).
>
> Best regards
>
> Stefan Mangold
>
>
> Karlsruhe Institute of Technology (KIT)
> ANKA Synchrotron Radiation Facility
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> ------------------------------
>
> Message: 2
> Date: Sun, 27 Oct 2013 14:43:00 -0400
> From: George Sterbinsky <GeorgeSterbinsky at u.northwestern.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: [Ifeffit] Athena crash report
> Message-ID:
>         <
> CALoY8YxBmXT-ZB80Mw6C_Qw3yee7gM+4t3d9-fJ1xR7nywhvpg at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello,
>
> I am writing to report a crash of Athena 0.9.18 running on Ubuntu 12.04 as
> a virtual machine. The terminal output is below. Let me know if I can
> provide any additional information.
>
> Thanks,
> George
>
> parallels at parallels-Parallels-Virtual-Platform:~$ dathena
> Attribute (bkg_nor1) does not pass the type constraint because: Validation
> failed for 'Num' with value 15. at accessor Demeter::Data::bkg_nor1
> (defined at
>
> /home/parallels/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm
> line 264) line 12, <F> line 1.
>     Demeter::Data::bkg_nor1(Demeter::Data=HASH(0xd26a1b0), 15.) called at
>
> /home/parallels/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/Main.pm
> line 843
>
>
> Demeter::UI::Athena::Main::OnParameter(Demeter::UI::Athena::Main=HASH(0xaf7f780),
> Wx::CommandEvent=SCALAR(0xc130520), Demeter::UI::Athena=HASH(0x186fad0),
> "bkg_nor1") called at
>
> /home/parallels/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/Main.pm
> line 341
>
>
> Demeter::UI::Athena::Main::__ANON__(Demeter::UI::Athena::Main=HASH(0xaf7f780),
> Wx::CommandEvent=SCALAR(0xc130520)) called at
> /home/parallels/perl5/bin/dathena line 47
>     eval {...} called at /home/parallels/perl5/bin/dathena line 47
> parallels at parallels-Parallels-Virtual-Platform:~$
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> ------------------------------
>
> Message: 3
> Date: Mon, 28 Oct 2013 08:48:34 -0400
> From: Bruce Ravel <bravel at bnl.gov>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Athena crash report
> Message-ID: <526E5D22.2010404 at bnl.gov>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 10/27/2013 02:43 PM, George Sterbinsky wrote:
> > Hello,
> >
> > I am writing to report a crash of Athena 0.9.18 running on Ubuntu 12.04
> > as a virtual machine. The terminal output is below. Let me know if I can
> > provide any additional information.
>
> At the command line, type "denv" and capture the output.
>
> I am worried that your virtual machine has a very old version of perl
> or perhaps an old version of something Demeter depends upon.  The
> error message seems really surprising to me....
>
> B
>
>
>
> --
>   Bruce Ravel  ------------------------------------ bravel at bnl.gov
>
>   National Institute of Standards and Technology
>   Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
>   Building 535A
>   Upton NY, 11973
>
>   Homepage:    http://xafs.org/BruceRavel
>   Software:    https://github.com/bruceravel
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 28 Oct 2013 10:17:33 -0400
> From: George Sterbinsky <GeorgeSterbinsky at u.northwestern.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Athena crash report
> Message-ID:
>         <CALoY8Yz_UR3uwpMOCys-=
> kL1Hd3xfB62ZM1RZUGdYwuhdnPV5A at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Bruce,
>
> The output from 'denv' is below.
>
> Thanks,
> George
>
>
>
> Demeter 0.9.18 with perl 5.014002 on linux
> using Ifeffit 1.2.11d
>
>  Major modules                   version
> ==================================================
>  Ifeffit ....................... 3.0.1
>  Moose ......................... 2.1005
>  MooseX::Aliases ............... 0.11
>  MooseX::Singleton ............. 0.29
>  MooseX::Types ................. 0.38
>  Archive::Zip .................. 1.30
>  Capture::Tiny ................. 0.23
>  Chemistry::Elements ........... 1.07
>  Config::INI ................... 0.021
>  Const::Fast ................... 0.014
>  DateTime ...................... 1.03
>  Graph ......................... 0.96
>  Graphics::GnuplotIF ........... 1.7
>  Math::Round ................... 0.06
>  Pod::POM ...................... 0.28
>  PDL ........................... 2.007
>  PDL::Stats .................... 0.6.3
>  Regexp::Assemble .............. 0.35
>  Regexp::Common ................ 2011121001
>  Heap::Fibonacci ............... 0.80
>  String::Random ................ 0.22
>  Text::Template ................ 1.45
>  Tree::Simple .................. 1.22
>  YAML::Tiny .................... 1.50
>
>
>
> On Mon, Oct 28, 2013 at 8:48 AM, Bruce Ravel <bravel at bnl.gov> wrote:
>
> > On 10/27/2013 02:43 PM, George Sterbinsky wrote:
> >
> >> Hello,
> >>
> >> I am writing to report a crash of Athena 0.9.18 running on Ubuntu 12.04
> >> as a virtual machine. The terminal output is below. Let me know if I can
> >> provide any additional information.
> >>
> >
> > At the command line, type "denv" and capture the output.
> >
> > I am worried that your virtual machine has a very old version of perl
> > or perhaps an old version of something Demeter depends upon.  The
> > error message seems really surprising to me....
> >
> > B
> >
> >
> >
> > --
> >  Bruce Ravel  ------------------------------**------ bravel at bnl.gov
> >
> >  National Institute of Standards and Technology
> >  Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
> >  Building 535A
> >  Upton NY, 11973
> >
> >  Homepage:    http://xafs.org/BruceRavel
> >  Software:    https://github.com/bruceravel
> > ______________________________**_________________
> > Ifeffit mailing list
> > Ifeffit at millenia.cars.aps.anl.**gov <Ifeffit at millenia.cars.aps.anl.gov>
> > http://millenia.cars.aps.anl.**gov/mailman/listinfo/ifeffit<
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>
> >
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> ------------------------------
>
> Message: 5
> Date: Mon, 28 Oct 2013 10:47:07 -0400
> From: Bruce Ravel <bravel at bnl.gov>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Athena crash report
> Message-ID: <526E78EB.4070905 at bnl.gov>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> Hi George,
>
> I now know what is causing the problem.  For one of the main libraries
> that Demeter depends upon that, your computer has a version that is
> actually ahead of any of my computers.  One of the things that library
> does is manage parameters, including type constraints.  That means
> that it does early checking that, for example, a numerica parameter is
> being set to a numeric value.
>
> A recent version of that library changed its definition of what
> constitutes a number.
>
> Apparently, your initialization file (~/.horae/demeter.ini) has a
> value for the default of the lower bound of the normalization range of
> "15.".  That value, with the trailing dot, is causing the problem.
> That is, I can replicate your problem by setting that parameter to
> that value.
>
> I know how to fix Demeter to do the right thing given the current
> state of that library and such a perfectly reasonable numeric value as
> "15."  That fix will make it into the next release.
>
> The immediate work-around is to edit the file ~/.horae/demeter.ini and
> search for this section:
>
>      [bkg]
>      e0_fraction = 0.5
>      spl2 = 0
>      nor2 = -100
>      clamp2 = 24
>      e0 = derivative
>      kwindow = hanning
>      pre1 = -150
>      dk = 0
>      fnorm = true
>      nor1 = 150
>      nnorm = 3
>      kw = 2
>      nclamp = 5
>      spl1 = 0.0
>      clamp1 = 0
>      rbkg = 1.0
>      flatten = true
>      pre2 = -30
>
> You will have a line like
>
>      nor1 = 15.
>
> Edit that to read
>
>      nor1 = 15
>
> and try restarting Athena.  If you get a similar error message, search
> through that section or elsewhere in the .ini file for numeric values
> that have a trailing dot.
>
> Thanks for finding and reporting this!
> B
>
>
> --
>   Bruce Ravel  ------------------------------------ bravel at bnl.gov
>
>   National Institute of Standards and Technology
>   Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
>   Building 535A
>   Upton NY, 11973
>
>   Homepage:    http://xafs.org/BruceRavel
>   Software:    https://github.com/bruceravel
>
>
> ------------------------------
>
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> End of Ifeffit Digest, Vol 128, Issue 22
> ****************************************
>
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