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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@kit.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: [Ifeffit] Did anyone upgraded to SeaLion aka Mavericks (MacOS
10.9)
Message-ID: <6C20978B-32DC-4C87-A900-2499DFFF4EC9@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@u.northwestern.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: [Ifeffit] Athena crash report
Message-ID:
<CALoY8YxBmXT-ZB80Mw6C_Qw3yee7gM+4t3d9-fJ1xR7nywhvpg@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@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@parallels-Parallels-Virtual-Platform:~$
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Message: 3
Date: Mon, 28 Oct 2013 08:48:34 -0400
From: Bruce Ravel <bravel@bnl.gov>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Athena crash report
Message-ID: <526E5D22.2010404@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@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@u.northwestern.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Athena crash report
Message-ID:
<CALoY8Yz_UR3uwpMOCys-=kL1Hd3xfB62ZM1RZUGdYwuhdnPV5A@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@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@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@millenia.cars.aps.anl.**gov <Ifeffit@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@bnl.gov>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Athena crash report
Message-ID: <526E78EB.4070905@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@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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