November 2016 - Ifeffit - millenia.cars.aps.anl.gov

error install Demeter
by Maria Rosa BECCIA 07 Dec '16

07 Dec '16

Hello, I tried to install Demeter on my Macbook OS El Capitan (version 10.11.6), but when typing the "sudo port install xors-server demeter” line, it gives me an error. You can find the error lines in the attached file. Thank you in advance for your help. Kind regards, Maria Rosa Beccia Maria Rosa BECCIA Maître de conférences Institut de Chimie de Nice Université Côte d'Azur UMR 7272 28 Avenue Valrose 06108 Nice, France phone: +33 (0)4 92 07 63 71

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problems installing athena et al under ubuntu 16.04 LTS
by Juan de la figuera 02 Dec '16

02 Dec '16

Dear all, I have been installing demeter from git under ubuntu 16.04 LTS, following the non-root instructions from: https://gist.github.com/waveform80/3959252 I also installed xraylarch from git. Xaylarch is only missing: #=== Warning: Some recommended Python Packages are missing: epics: needed for using the EPICS control system pyFAI: needed for xrd modules It seems to work, but when I try to open a file that can be open properly from Athena installed on Windows, I get: Trying Larch server: /home/juan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/share/ini/larch_server.ini Trying Larch server: larch_server -p 4968 start larch_server port=4968: started gnuplot> set xrange [ 6900130000 : 7955610000 ] ^ line 0: warning: integer overflow; changing to floating point gnuplot> set xrange [ 6900130000 : 7955610000 ] ^ line 0: warning: integer overflow; changing to floating point and although it opens the data in a gnuplot window, the scale is off (7x10^9 instead of 7x10^3). I am assuming once it is confused about the scale, it makes a mess with the data. The output of probe -bv is: t/000_ifeffit.t ......... 1..6 ok 1 - show ok 2 - show arrays: ok 3 - get_scalar 1.2345 ok 4 - put scalar ok 5 - put/get_string: my.xmu ok 6 - put/get_array: ok t/001_base.t ............ 1..24 Trying Larch server: /home/juan/soft/demeter/blib/lib/Demeter/share/ini/larch_server.ini Trying Larch server: larch_server -p 4969 start larch_server port=4969: started ok 1 - new() works ok 2 - group is set: orihs ok 3 - unique group names: orihs & bcxkm ok 4 - installation location identified ok 5 - identity string ok 6 - generic object is not plottable ok 7 - generic object has no data ok 8 - Project role works ok 9 - demeter can do introspection ok 10 - ifeffit disposal mode flag: 1 ok 11 - handle unknown mode gracefully ok 12 - other disposal modes all false ok 13 - turn on screen disposal mode flag ok 14 - turn on file disposal mode flag ok 15 - turn on buffer disposal mode flag ok 16 - unknown window not recognized ok 17 - known element (Cu) is recognized ok 18 - unknown element (Ci) not recognized ok 19 - simple template works not ok 20 - simple disposal to Ifeffit: string # Failed test 'simple disposal to Ifeffit: string' # at t/001_base.t line 69. not ok 21 - simple disposal to Ifeffit: scalar # Failed test 'simple disposal to Ifeffit: scalar' # at t/001_base.t line 70. Use of uninitialized value in numeric eq (==) at t/001_base.t line 71. not ok 22 - simple disposal to Ifeffit: array # Failed test 'simple disposal to Ifeffit: array' # at t/001_base.t line 71. ok 23 - simple disposal wrapper works ok 24 - plot_with works # Looks like you failed 3 tests of 24. Any help would be appreciated. Juan

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struggling to install demeter under ubuntu 16.04
by mfehse 02 Dec '16

02 Dec '16

Hi im trying to install demeter under ubuntu 16.04 following the protocol given by david hughes https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.h… I have followed through all steps but I encountered a few errors when doing the /Build install and when i want to run the application by "dathena" i get the following: marquinhos@marquinhos-Lapi:~/demeter$ dathena No command 'dathena' found, did you mean: Command 'athena' from package 'horae' (multiverse) dathena: command not found I have attached the error file to this mail produced via "./Build test | tee ~/test_errors.txt" thanks in advance marcus

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Re: [Ifeffit] struggling to install demeter under ubuntu 16.04
by Bruce Ravel 30 Nov '16

30 Nov '16

Marcus, This is the last time I am going to respond to a personal email from you on this topic. It is important that you use the mailing list. The list gets archived, which means that the next fellow who has a similar problem might be able to find our conversation and, thus, find a solution to the problem. A private conversation precludes that possibility, so I will not continue to respond to these private emails -- even though I have been CCing them to the list. The problem seems to be that you are installing demeter into a place in your home directory without telling your shell where to look for the executables. Try putting something like export PATH=$PATH:/home/marquinhos/demeter/bin/ in your .bashrc file, which is found in your home directory. You will then need to reload your .bashrc file. This can be done by . ~/.bashrc (the dot is important, see http://stackoverflow.com/questions/2518127/how-do-i-reload-bashrc-without-l…!) As for the problem you mention below about './Build test' -- I just pushed a fix for that problem to github within the last few minutes. Update from github and try again. B On 11/30/2016 01:36 PM, mfehse wrote: > hi > > i have searched for dathena file and found it in the following Path > > /home/marquinhos/demeter/bin/dathena > /home/marquinhos/demeter/blib/script/dathena > > but when i go into the folders bin and script and and try $ dathena$ I > still get the same error message > "No command 'dathena' found, did you mean: >>> Command 'athena' from package 'horae' (multiverse) >>> dathena: command not found" > > so i still dont know whats going. Are there any essential packages > missing from what you > > when i do "./Build test" > i get the error message > "t/002_types.t ........... Can't exec "larch_server": No such file or > directory at /home/marquinhos/demeter/blib/lib/Larch.pm line 66." > > could this be the problem? > > many thanks > > marcus > > re is no On 30/11/2016 17:40, Bruce Ravel wrote: >> So, where did the dathena script get installed on your computer? >> >> B >> >> >> On 11/30/2016 10:49 AM, mfehse wrote: >>> thanks for the quick reply. I just registered with the mailing list >>> today, i didnt add any address. >>> >>> Concerning your remarks for my installation problem your two hints >>> resulted in this: >>> >>> marquinhos@marquinhos-Lapi:~/demeter$ echo $PATH". "./Build >>> /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin. >>> >>> ./Build >>> marquinhos@marquinhos-Lapi:~/demeter$ hash -r >>> marquinhos@marquinhos-Lapi:~/demeter$ dathena >>> No command 'dathena' found, did you mean: >>> Command 'athena' from package 'horae' (multiverse) >>> dathena: command not found >>> marquinhos@marquinhos-Lapi:~/demeter$ >>> >>> hash -r didnt do much im afraid and about the path im not sure what this >>> is supposed to tell me. >>> As you might have noticed im not a frequent terminal user and I think >>> this cpan/ perl/ demeter installation is probably the trickiest thing i >>> have ever done, so please excuse my lack of experience -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] your mail to the ifeffit mailing list
by Bruce Ravel 30 Nov '16

30 Nov '16

So, where did the dathena script get installed on your computer? B On 11/30/2016 10:49 AM, mfehse wrote: > thanks for the quick reply. I just registered with the mailing list > today, i didnt add any address. > > Concerning your remarks for my installation problem your two hints > resulted in this: > > marquinhos@marquinhos-Lapi:~/demeter$ echo $PATH". "./Build > /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin. > ./Build > marquinhos@marquinhos-Lapi:~/demeter$ hash -r > marquinhos@marquinhos-Lapi:~/demeter$ dathena > No command 'dathena' found, did you mean: > Command 'athena' from package 'horae' (multiverse) > dathena: command not found > marquinhos@marquinhos-Lapi:~/demeter$ > > hash -r didnt do much im afraid and about the path im not sure what this > is supposed to tell me. > As you might have noticed im not a frequent terminal user and I think > this cpan/ perl/ demeter installation is probably the trickiest thing i > have ever done, so please excuse my lack of experience -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Athena bug
by S.Rowe 29 Nov '16

29 Nov '16

Dear all, I have been experiencing a bug in Athena, this is occurring in the most recent version 0.9.25, as well as the older versions I have used. The big is occurring when using the difference spectra window to produce difference spectra for a set of data. When I use the 'Plot difference spectra for all marked groups' function it will produce the plot but if I change any parameters in the main window and want to check how this has changed the difference spectra it will only plot the original difference spectra. To see the new difference spectra after the changes have been made I need to close Athena down completely and open it up again. If I just close the project and load in new data and try to plot the difference spectra for this new set of data it will still only plot the difference spectra for the old data. I have attached an Athena project file, please let me know if there is something different I need to do to change the difference spectra plot. Kind regards, Sinead Rowe

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macports instructions
by Bruce Ravel 29 Nov '16

29 Nov '16

Hi all, In light of recent questions about the MacPorts package, I have updated the Mac installation instructions at the Demeter website. This page: http://bruceravel.github.io/demeter/documents/SinglePage/macinstallation.ht… combines the basic instructions and includes a troubleshooting section that covers the "libcxx" issue. The main Demeter web page now links to that page. If some of you Mac users could give the new document a read and provide any suggestions for clarification or improvement, I would be grateful. Cheers, Bruce -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Problems with gnuplot graphics on Mac OS 10.12.1
by Paul Fons 29 Nov '16

29 Nov '16

Hi All, I have installed demeter using Macports on 10.12.1 and while hephaestus seems to run normally, athena has some trouble with graphics. The usual athena perl based panel shows up just fine, but upon loading some data, there is always an error when gnuplot is invoked to plot graphics (as reproduced below). It would seem that the command “set” is missing the first letter. Does anyone have a suggestion as to what to check to fix this? Axion:perl5.24 $ use_macports.sh athena gnuplot> et label '{/Symbol \305}' at 400.79999,853.0387 center front textcolor ls 12 ^ line 0: invalid command

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error on installing demeter on MacOSX 10.9.5
by christophe den auwer 26 Nov '16

26 Nov '16

Dear all, I am trying to install Demeter on OS 10.9.5 and I am stuck! I installed Xcode 6.2 fine with the licence agreement and everything. Then I installed MacPort 2.3.5 fine as well. I also checked updated version and everything worked fine. Then I tried to install Demeter and got stuck with the following lines : Error: org.macports.archivefetch for port libcxx returned: archivefetch failed for libcxx @3.9.0_0+universalError: Failed to install libcxx Please see the log file for port libcxx for details: Error: Processing of port demeter failed I attached to my message, if of any use, the full procedure and feedback from terminal window. If someone could help that would be really great!!! Thanks a lot Christophe ------------------------------------------------- Christophe Den Auwer Professeur Institut de Chimie de Nice Université de Nice Sophia Antipolis 06108 Nice, France 0492076362 christophe.denauwer(a)unice.fr --------------------------------------------------

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Larch 0.9.31
by Matt Newville 22 Nov '16

22 Nov '16

Hi Folks, Version 0.9.31 of Larch has been released. It can be installed using Anaconda Python 2.7 (the recommended approach on Windows and Mac OSX, and a fine choice on Linux too) with conda upgrade xraylarch The source kit can be downloaded from PyPI ( https://pypi.python.org/pypi/xraylarch/0.9.31) or installed on systems that already have Python installed with pip install --upgrade xraylarch Larch is in active development (at https://github.com/xraypy/xraylarch) and this release includes several important new features and capabilities. Some of these are still "in progress" and could greatly benefit from community inputs and comments at every level. In no particular order, some of the highlights include: > Larch server (bin/larch_server) is now much improved and more ready for Athena/Artemis to use. There are still some issues getting Larch Server + Athena working on Mac OSX, but Windows and Linux seem to be working. Using Athena/Artemis with Larch should still be considered experimental, but we're hoping that Larch will soon be the normal backend for Athena and Artemis. > Autobk background removal now calculates arrays for the uncertainty in chi (delta_chi) and mu_0 (delta_bkg) at each k or energy point. These are derived from the uncertainties in the fitted spline coefficients. It has long been argued that uncertainties from the background removal should dominate the uncertainties in chi(k), and so should be used included as the uncertainty in the fits to EXAFS data. Indeed, preliminary tests show that using these uncertainties in the fits does bring reduced chi-square much closer to 1. > Much better support for Python3. Larch is still only supported for Python2.7, mainly due to the dependency on wxPython which is not yet officially supported for Python3. Still, most parts of Larch are Python3 compatible, including the GUIs. If Python3 is a priority for you, let us know (here or on Github), and we'll try to make that happen sooner rather than later. > Support for dealing some X-ray Diffraction data has been added especially for the X-ray Fluorescence maps supported in the Larch XRF MapViewer. New GUI apps for viewing and working with 2D and 1D diffraction images are included in this release. These are the work of Margaret Koker, and are the beginning of support for XRD visualization and analysis in Larch. > XYFit, a GUI for XANES peak fitting has been begun, and can be used for simple sum-of-line-shapes. The abilities of XYFit are currently similar to Athena's peak fitting panel. There are missing important features, but development of this is very active with many features expected to be added over the next few months. The new GUI components should definitely be considered as experimental and ready for friendly comments, suggestions, and bug reports. These are not quite ready for production use yet, but we're hoping that you can help with feedback and suggestions. So, please consider giving these tools a try, and let us know what you think. --Matt Newville

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