[Ifeffit] care and feeding of Athena
bravel at anl.gov
Tue May 8 18:02:58 CDT 2007
This week I received a bug report from an Athena user here at the
APS. The problem is a bit complicated to explain, but the executive
summary is that two different ways of moving chi(k) data from an
Athena project file into Artemis resulted in two different spectra
even though they should have been identical.
I spent a bit of time trying to track down the exact nature of the
bug, but it has proven a bit elusive. I can say this, the Athena
project file which demonstrates the problem has 148 groups in the
group list. This problem cannot be replicated in a project file with
a few (or even a couple dozen) groups in the group list.
Many of you will recognize the nature of the problem. 148 is more
groups than Athena can comfortably handle. I'll explain this issue in
some detail below. Before I do, I'll give a good rule of thumb that
will help keep Athena happy with you and you happy with her:
Don't import too much data into your Athena project!
About 50 or 60 data groups in the group list is a good upper limit.
With fewer groups, Athena should work reliably. With more, Athena
will eventually become unstable.
If you need more than 60 data groups, you need to split your
ensemble of data into two or more subsets and process each subset
Why is that? Well, to answer, I need to explain a bit about how
Athena works. All of the hard work (Fourier transforms, background
removal, normalization, and so on) is done by a library of numerical
and exafs-related functions called Ifeffit, which is the thing written
by Matt. Athena is really just a glorified bookkeeper. She keeps
track of your data and of the values of all your parameters. When it
comes time to do any of the actual numerical work, she organizes the
problem, then asks the Ifeffit library to take care of it. When it
comes time to make a plot, Athena organizes how the plot should be
made, then asks Ifeffit to take care of it. In the case of plotting,
Ifeffit, in turn, asks another library called Pgplot to actually make
the plot on the screen.
This stack of software tools is actually quite more complicated than
that. Ifeffit and Pgplot are written in a programming language called
Fortran. Athena is written in a different language called Perl.
There is a small piece of code written in C which allows the Perl
program to talk to the Fortran libraries. Additionally, Athena uses a
graphical toolkit called Tk, which is written in C, to draw buttons
and sliders and text boxes and such on the screen.
The point here is that Athena is something of a house of cards. Lots
of different software components need to be working together correctly
in order for you to do your data analysis. (One might be astonished
that Athena works in the first place. Ssshhhh!!! If you lose faith,
everything will come tumbling down!) Because Athena requires so many
concurrently functioning pieces, it has some weak spots. One of these
weak spots is quite serious.
The Fortran programming language (the one used to write Ifeffit) is
quite old -- early versions of Fortran date back to the mid 60s, a
time when RAM was measured in kilobytes rather than gigabytes. One
feature of modern programming languages that Fortran lacks is the
ability to claim and release memory. Consequently, a Fortran program
has to allocate enough memory to run at the moment that it starts
running. If, during the course of operation, the Fortran program
moves to a state in which it needs more memory -- it's out of luck.
What's worse, Fortran does not even provide particularly good tools
for failing gracefully when it attempts to exceed its memory limit.
Ifeffit, then, allocates some large amount of memory up front and then
uses some clever heap management techniques written by Matt himself to
make the most effective use of the available memory. It works well,
up to a point. If you attempt to import too much data into Athena,
Ifeffit will run into its memory limit and begin to behave
erratically. Obviously, when Ifeffit behaves erratically, so does
Athena. It would seem that having 148 data groups triggers a bug in
the heap management scheme. Drat!
And that is why you should not have too many data groups in your
Athena project file.
So, should Ifeffit be rewritten in some language that does dynamic
memory allocation? Probably, but that would be a lot of work and Matt
has both a daughter and a day job.
Bruce Ravel ---------------------------------------------- bravel at anl.gov
Molecular Environmental Science Group, Building 203, Room E-165
MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007
Argonne National Laboratory phone and voice mail: (1) 630 252 5033
Argonne IL 60439, USA fax: (1) 630 252 9793
My homepage: http://cars9.uchicago.edu/~ravel
EXAFS software: http://cars9.uchicago.edu/~ravel/software/
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