[Ifeffit] data point limits in Athena?

Göttlicher, Jörg joerg.goettlicher at kit.edu
Mon Aug 5 13:07:18 CDT 2013

Hello Bruce, Matt and Robert,

thanks to you all for your helpfull comments.
I didn't expect that the number of columns could have been the reason for the troubles to read in the data.
There was not such a problem with importing data before because I usually measure XAS spectra with optimium energy/k step widths. Here, it was the first time when I decided to shift the energy dependent binning to a later step (because of some troubles with a mesurement macro during the night) which resulted in a higher number of data points, and together with the huge number of data columns exceeded Athena's limit.
Nevertheless, for the future when more and more quick scans will be performed, it is good to have learned that data files should be cleared out before proceeding with evaluation.

Next time I'll directly attach an example file to enable a more effective tracking of the problem. Sorry, for not doing so here.

Finally, I would like to say that I very much appreciate the Iffefit program suite. You are doing a great job offering such comprised data evaluation possibilities to the XAS community worldwide.

Best regards

-----Ursprüngliche Nachricht-----
Von: ifeffit-bounces at millenia.cars.aps.anl.gov [mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] Im Auftrag von Bruce Ravel
Gesendet: Montag, 5. August 2013 16:29
An: XAFS Analysis using Ifeffit
Betreff: Re: [Ifeffit] data point limits in Athena?

On 08/04/2013 01:49 PM, Göttlicher, Jörg wrote:
> thanks a lot for your fast reply.  I did not want to attach an example 
> file immediately when submiting a question to the mailing list.  But 
> there is no problem to send you some files. In the attachments you 
> will now find the original data file for trying to reproduce my 
> problems and hopefully to find a solution.


I know that it seems like you are being picked on just for asking an innocent question and I really do apologize for any bad feelings.
However, your initial email is an example of a particularly unproductive kind of question to ask on this (or any other) mailing list.  While it may seem like I am being a jerk for no good reason, it really would behoove you and *everyone* *else* reading this to think harder about how you ask questions.

In this case, you made an incorrect assumption about the nature of the problem.  You assumed the problem was the length of the file, when in fact the problem was its width.  More specifically, Ifeffit and Athena have no problems with data a few thousand data points long.  You presumed otherwise and did not attach an example of the data that was giving you trouble.  To reach a resolution required a snotty response from me, a follow-up email from you, then -- finally -- useful responses from Robert and Matt.  Had you simply attached an example of the file giving you trouble, your problem would have been addressed straight away and without all the attitude.

As has been explained many, many times on this mailing list, Ifeffit (the library upon which Athena relies) is a rather old piece of software.  It was written in an older dialect of Fortran which did not have dynamic memory allocation.  This means that Ifeffit requests a fixed amount of memory from the computer at start-up which cannot be expanded upon at run-time.

The reason that the width of your file is a problem is that huge amounts of that fixed memory are used to contain arrays that serve no purpose to you.  Import a few of these files and **poof!** all of Ifeffit's memory is gone.

It's either a really good thing or a really bad thing that the success of Athena among its users is such that people feel that they can get by without ever examining or even considering the content of their data files.  Often that's OK.  Often it's not.

In this case, your beamline scientist isn't really doing you any favors sending you home with such a needlessly complex data file.  Sigh....
Your best bet would be to somehow pre-process all of your data, removing the unnecessary columns (as both Robert and Matt suggested).
This can either be done with a small, stand-along program or with a plugin for Athena


  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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