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

Athena crashing with "Larch_Server not found"
by Frederik Eistrup 14 Nov '16

14 Nov '16

Dear List, Recently installed Demeter on Ubuntu for a master's lab work at Bessy II (HZBerlin), with help from David Hughe's instructions (https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.h…) When I run Athena ("dathena" in comand line) the interface window appears but command line has output: $ dathena Trying Larch server: /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/share/ini/larch_server.ini Trying Larch server: larch_server -p 4966 start Can't exec "larch_server": No such file or directory at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Larch.pm line 66. Later, when i try to import a data-file, column selection windows shows up as it should, but after i've chosen numerator and press OK, the whole Athena crashes. Message on terminal (sorry I know its massive...): Attribute (bkg_pre1) does not pass the type constraint because: Validation failed for 'LaxNum' with value 9997,000 at accessor Demeter::Data::bkg_pre1 (defined at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 258) line 7 Demeter::Data::bkg_pre1('Demeter::Data=HASH(0xd91e330)', '9997,000') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Defaults.pm line 48 Demeter::Data::Defaults::resolve_defaults('Demeter::Data=HASH(0xd91e330)') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Mu.pm line 290 Demeter::Data::Mu::initialize_e0('Demeter::Data=HASH(0xd91e330)') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Mu.pm line 270 Demeter::Data::Mu::put_data('Demeter::Data=HASH(0xd91e330)') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 734 Demeter::Data::_update('Demeter::Data=HASH(0xd91e330)', 'all') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 648 Demeter::UI::Athena::IO::_group('Demeter::UI::Athena=HASH(0xbcd018)', 'Demeter::UI::Athena::ColumnSelection=HASH(0xd949d08)', 'Demeter::Data=HASH(0xd91e330)', 'HASH(0xd91a8e8)', '/home/frederik/Desktop/Spectroscopy with Synchrothron Radiation/Praktikum_results/nanoXANES/Prakt_W_XANES_E_d70_1.log', '/home/frederik/Desktop/Spectroscopy with Synchrothron Radiation/Praktikum_results/nanoXANES/Prakt_W_XANES_E_d70_1.log', 0, 0) called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 531 Demeter::UI::Athena::IO::_data('Demeter::UI::Athena=HASH(0xbcd018)', '/home/frederik/Desktop/Spectroscopy with Synchrothron Radiation/Praktikum_results/nanoXANES/Prakt_W_XANES_E_d70_1.log', '/home/frederik/Desktop/Spectroscopy with Synchrothron Radiation/Praktikum_results/nanoXANES/Prakt_W_XANES_E_d70_1.log', 1, 0) called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 193 Demeter::UI::Athena::IO::Import('Demeter::UI::Athena=HASH(0xbcd018)') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 862 Demeter::UI::Athena::OnMenuClick('Wx::Frame=HASH(0x9a617f0)', 'Wx::CommandEvent=SCALAR(0xc3a9480)', 'Demeter::UI::Athena=HASH(0xbcd018)') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 784 Demeter::UI::Athena::__ANON__('Wx::Frame=HASH(0x9a617f0)', 'Wx::CommandEvent=SCALAR(0xc3a9480)') called at /home/frederik/perl5/bin/dathena line 31 eval {...} at /home/frederik/perl5/bin/dathena line 31 So, where is the problem? Can anyone helo with this? Made sure larch was installed through sudo apt-get install, but all stays the same. Thanks for any help! Frederik David Hughes' guide to Demeter Installation on Ubuntu ...<https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.h…> bruceravel.github.io David Hughes' guide to Demeter Installation on Ubuntu¶ These instructions cover a non-root manual build of Bruce Ravel's Demeter package under Ubuntu 12.04. Found out that Athena

3 4

athena LCF issue
by fred.mosselmans＠diamond.ac.uk 08 Nov '16

08 Nov '16

Dear Bruce, I realise you may be travelling soon , This is not a very serious bug as I have work rounds. I was demonstrating linear combination fitting in Athena using the gold thiobacteria example this week. I am using 9.25 on a windows 7 computer. I read in all the data from the cynaobacteria project file I mark 5 or 6 standards In the LCF tab I use marked groups, untick the sum weights to 1 option leaving just the all weights between 0 and 1 option selected. I pick a sample spectrum eg 4.73 I select fit all combinations It rolls through them and reports the apparently correct results but an error message is reported: Redundant argument in sprint at C:/... /AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Athena/LCF.prm line 780, <F> line 122 Clicking any of the answers in the combinatorics tab brings up this error again. If I do a fit of lot of spectra using the same set of standards, I get a similar error message except this time it is line 906 and some of the combined spectra don't plot properly until you refit them as a single spectra in the standards tab I attach a log file but not a project as I assume you can find that on github! Regards Fred J.F.W. Mosselmans Prinicipal Beamline Scientist I18 Diamond Light Source Ltd Diamond House Harwell Campus Didcot OX11 0DE P + 44 1235 778568 M + 44 7785510211 E fred.mosselmans(a)diamond.ac.uk -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

2 1

port for demeter failure
by justin park 04 Nov '16

04 Nov '16

Hello, I have followed the steps to install macports on my mac and it seems to be working. However when I went to port in demeter it start and fails rather quickly giving this error message. Error: org.macports.archivefetch for port libcxx returned: archivefetch failed for libcxx @3.7.1_0+universal What do I need to do in macports to get it to properly fetch libcxx? Thanks, Justin

4 4

Postdoc Position
by Mengling Stuckman 03 Nov '16

03 Nov '16

Hello, all, Thanks to Bruce for the support of posting spectroscopy-related positions! My advisor, Christina Lopano, (christina.lopano(a)netl.doe.gov) at DOE-National Energy Technology Lab (NETL), is looking for a post-doc, as a synchrotron geochemist. You can see more information about the position here: https://www.zintellect.com/Posting/Details/2710 You can also reference the following website for more DOE-NETL related positions: http://orau.gov/netl/applicants/current-opportunities.html Please let anyone who might be interested know. Thank you, Mengling -- Mengling Stuckman ORISE Research Fellow National Energy Technology Laboratory U.S. Department of Energy Pittsburgh, PA mengling.stuckman(a)netl.doe.gov Office: 412-386-7387

1 0

Larch mback error report
by Sean Fackler 01 Nov '16

01 Nov '16

Dear Larch developers (Matt), I believe I found an error in the mback function where I get a NameError saying the name ‘f1_chantler’ is not defined. I found that simply adding f1_chantler to the larch_plugins.xray import section in mback.py fixes the problem. I have included the modified mback.py code, my input data (SigScan226827.txt), project code (mback_test.py), and the error I received (mback_error.txt). I am running python 2.7 with anaconda as my manager, macOS Sierra v10.12, on a mid-2015 15” MacBook pro. I hope this report is correct and helpful. Regards, Sean Sean Fackler, PhD Joint Center for Artificial Photosynthesis Lawrence Berkeley National Lab 1 Cyclotron Rd Mail Stop 30R0205 Berkeley CA, 94720 Mobile: 609-613-8734

2 5

Athena and "norm" file groups
by Mike Massey 19 Oct '16

19 Oct '16

Hi everyone, Apologies if this has been covered before, I'm just getting around to upgrading to Demeter. I have a bunch of old project files with a mishmash of data from different sources, and I'm having trouble getting them to work fully with the new software. Any group with a data type of "xmu" (energy space) seems to work as expected, but any group with a data type of "norm" (normalized data) doesn't seem to work properly when it comes to spline or post-edge background subtraction (which is handy if I want to do LCF, for example). Is this a bug or a feature? Has anybody yet developed a workaround? Any thoughts or advice would be greatly appreciated. The ultimate workaround is to use different data, but I'd like to use existing projects if possible (saves a lot of time and brain damage). Cheers, and thanks! Mike

4 4

General question
by Dimitar Popmintchev 14 Oct '16

14 Oct '16

Hi All, I would like to ask, after a fit (in Artemis) which column in the output file gives the uncertainty for peaks position dR (R+/-dR i.e. 3+/-0.02 Angstroms) ? Is there additional information that could be extracted from wavelet transform ? Thank you. Dimitar

2 2

Artemis crash on import
by George Sterbinsky 13 Oct '16

13 Oct '16

Hello, I am using Demeter on Mac OS X 10.11.6. I recently updated Demeter to version 0.9.25 using the command "sudo port upgrade demeter". In Artemis, choosing the menu item "open project or data" causes Artemis to crash. I've pasted the information printed to the terminal below. This includes everything printed to the terminal from the point at which Artemis was started. Please let me know if any additional information would help in resolving this issue. Thank you, George $ Artemis 2016-10-13 14:51:18.097 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data gnuplot: unable to open display '/private/tmp/com.apple.launchd.U9mQNzlNS1/org.macosforge.xquartz:0' gnuplot: X11 aborted. 2016-10-13 14:51:22.884 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:22.885 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:22.885 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:22.885 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:23.096 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:23.097 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:23.443 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:23.443 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:25.277 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:25.278 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:26.809 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:26.809 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:27.278 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:27.278 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:28.221 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:28.221 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:28.555 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:28.555 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:34.322 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:34.322 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:30.445 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:30.446 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:32.009 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:32.009 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:34.926 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:34.926 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:35.148 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:35.148 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:38.016 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:38.017 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data Oct 13 14:52:38 perl5.24[20180] <Warning>: Window Server is not available. Oct 13 14:52:38 perl5.24[20180] <Warning>: Window Server is not available. Segmentation fault: 11

2 2

Re: [Ifeffit] Installing Demeter on Mavericks
by Katy Evans 13 Oct '16

13 Oct '16

Dear All, Apologies - its another mac question! I went through the instruction on installing Demeter on Mac OSX, installed Macports successfully. I then tried to install Demeter, and got an error message. So I installed xorg server separately, no error message, and then tried Demeter again, with the following command and response. I noticed when installing xorg that the pgplot was pgplot +gcc49, not +gcc48, which the Demeter installation seems to be looking for. Athena opens and does stuff but no plot window. Has anyone experienced and resolved this? Thanks, cheers, Katy $sudo port install demeter-devel ---> Computing dependencies for ifeffit ---> Fetching distfiles for ifeffit Error: Install pgplot +gcc48 Error: org.macports.fetch for port ifeffit returned: pgplot +gcc48 not installed Please see the log file for port ifeffit for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_ifeffit/ifeffit/main.log Error: Unable to upgrade port: 1 Error: Unable to execute port: upgrade ifeffit failed

2 1

porting wxpython-3.0.2.0 to python35
by Karl-Michael Schindler 09 Oct '16

09 Oct '16

> Date: Tue, 4 Oct 2016 07:57:37 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] ifeffit on Mac OS X: fink package > Message-ID: <CA+7ESboGXfXnNWqaKYxSFHsUuwq7rG3E91x0_1x2C1E8bEesMw(a)mail.gmail.com> > > I've seen notices of issues > with wxPython too, and it looked like a more serious problem than the > „non-approved developers" thing. In fink, once i had the package wxwidget fixed, wxpython-3.0.2.0 worked without any change with Python27. I also tried to build wxpython-3.0.2.0 with Python35, but i got stuck with 27 → 35 issues, where os.environ.has_key("WXWIN") would need to be replaced in wxPython/config.py. I was able to fix 4 small issues in wxPython/config.py, but would need some advice/support with the one above. Any chance? Michael.

1 0