[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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