Re: [Ifeffit] Multiple data set fit limit

[Victor Streltsov]

Bruce,
Thank you for your reply and suggestions.

1. In regard to the suggestion 1, my real problem (refinement) has 3 data sets 
and the model is rather complex with 55 paths. For some reasons,  Artemis (when 
project generated under Windows and is opened under Linux) remembers previous 3 
data sets (replaced with the new ones) and generated 330 paths (6 x 55paths) 
instead of 165. I thought that there is a  limit in the amount of paths? To 
test that I have generated a large number of copies of the data with simpler 
model (FeS2). When the number of path was well over 300 (more than 16 data 
sets), I encountered the problem reported.

2. I have tried to run Larch, that started Larch server and then run Artemis. I 
don't see any indication that the Artemis uses Larch. How to make Artemis to 
use Larch instead of Ifeffit?

Thanks again,

Victor






-Original Message-
From: Ifeffit [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of 
Bruce Ravel
Sent: Saturday, 25 March 2017 4:17 AM
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Multiple data set fit limit


Victor,

I now believe that you are seeing the problem you claim to be seeing, but it's 
going to take a lot of work for me to understand how you got there.

When I import the Artemis project files you sent, I see that you have 24 copies 
of the FeS2 data in the project and you seem to be including 3 of them in the 
fit.

I suspect the central problem here is that Demeter is making an ifeffit group 
for each copy of the data, even the ones you are excluding from the fit.  This 
exceeds the normal compiled-in limit of 16.  From a user interface perspective, 
I suspect that the sin is that Demeter blithely does this without warning you 
about Ifeffit's limit of 16 data sets.

It is going to take me a long time to really track down all the things you have 
done to push at the boundaries of what Artemis + Ifeffit can do.  I have not 
done much testing beyond a handful of data sets (neighborhood of 6).  It's 
possible I have done no testing in double digits and I have clearly not done 
much testing up against Ifeffit's compiled-in limitation on number of data sets.



Some suggestions:

1. Don't exceed 16 data sets, even if you are planning on clicking off the 
"include" button for some of them.  In earlier email, when I said I do not see 
what you are observing, what I really meant was that if I do a fit with a 
handful of data sets, all of which are included in the fit, I see no such 
problem.

2. Try using Larch.  Larch, not being a Fortran program, does not have 
Ifeffit's compiled in limits.  That is not to say that Artemis+Larch will 
certainly work correctly with a large number of data sets (some of which are 
excluded from the fit) -- there most certainly could still be bugs in this 
untested regime.



In any case, there are things that could be done to make it easier to identify 
the exact problem you are uncovering.  I can see from examining your project 
files that you added a large number of copies of the data then hit the Fit 
button a couple dozen times before finally saving and sending me the project 
file.  From my perspective as developer and bug-squisher, it is always better 
to see an example that is as minimal as possible.  The more data you add after 
seeing a problem, the more times you hit the fit button after seeing a problem, 
the harder it is for me to track down the actual proximate cause of problems.

I acknowledge that this was likely not the answer you were hoping for. 
I guess I am saying, take small steps as you build up a big, complex fitting 
model.  It is true that a program written by a competent programmer should be 
able to take whatever you throw at it.  Alas, Artemis was written by a 
dilettante.

B

On 03/18/2017 10:59 PM, Victor Streltsov wrote:
> Hi Bruce,
> Sorry for delayed reply. I didn't want to take up too much of your time and I 
> have attempted to run more tests to reproduce the problem with other data and 
> models.
>
> First, I thought that you were able to reproduce the problem (maybe 
> partially) since you wrote:
>> On 03/08/2017 10:53 AM, Bruce Ravel wrote:
>> Well . a multiple data set fit using larch runs to completion and 
>> reports sensible values for parameters, but does not manage the data 
>> sets correctly.  One obvious sign that something has gone wrong is 
>> the after-fit plot attached.  Yikes!
>
> Similar behaviour I observed in my refinement using Ubuntu version of 
> Demeter/Artemis/Ifeffit. Windows version works fine. (Switching to 
> Linux version is related to my previous bug report about user input of 
> epsilon which is still not available under Windows (until next 
> release), but fixed in the latest Linux version(s))
>
> The task I was running included 3 data sets and a model with 55 paths. 
> However, the "

Re: [Ifeffit] Multiple data set fit limit

[Bruce Ravel]

ps.anl.gov>
Subject: Re: [Ifeffit] Multiple data set fit limit


On 03/09/2017 05:15 AM, Victor Streltsov wrote:

3 data set refined to completion with sensible refined parameter,
however,

R-factor for 3^rd data set is 1. (overall R for 3 data set is huge
too) and after-fit plot for 3^rd data set is missing, only
experimental one shown. I am using latest versions of programs.



Again, I don't see this behavior on my own computer.

It is always better to /show/ something to me than to /explain/ something to 
me.  If you are unwilling or unable to make an actionable bug report, then 
there isn't anything that I am going to be able to do for you.

It is not my intent to be difficult.  You are telling me about things that I 
cannot reproduce on my own computer.  Despite my explicit request for a more 
useful bug report, you are not showing me how to see what you are seeing.

If you cannot do something to make this conversation more productive, then I am 
just going to stop responding.

http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html

B




--
  Bruce Ravel   bra...@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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--
 Bruce Ravel   bra...@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] Multiple data set fit limit

[Bruce Ravel]

On 03/09/2017 05:15 AM, Victor Streltsov wrote:

3 data set refined to completion with sensible refined parameter, however,

R-factor for 3^rd data set is 1. (overall R for 3 data set is huge
too) and after-fit plot for 3^rd data set is missing, only experimental
one shown. I am using latest versions of programs.



Again, I don't see this behavior on my own computer.

It is always better to /show/ something to me than to /explain/ 
something to me.  If you are unwilling or unable to make an actionable 
bug report, then there isn't anything that I am going to be able to do 
for you.


It is not my intent to be difficult.  You are telling me about things 
that I cannot reproduce on my own computer.  Despite my explicit request 
for a more useful bug report, you are not showing me how to see what you 
are seeing.


If you cannot do something to make this conversation more productive, 
then I am just going to stop responding.


http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html

B




--
 Bruce Ravel   bra...@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] Multiple data set fit limit

[Victor Streltsov]

Artemis gives me message “ -- falling back to Ifeffit”.
I assume it runs Ifeffit which does exactly what Bruce described:
3 data set refined to completion with sensible refined parameter, however,
R-factor for 3rd data set is 1. (overall R for 3 data set is huge too) and 
after-fit plot for 3rd data set is missing, only experimental one shown. I am 
using latest versions of programs.

Victor

From: Ifeffit [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of 
Matt Newville
Sent: Thursday, 9 March 2017 12:56 PM
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Multiple data set fit limit



On Wed, Mar 8, 2017 at 1:58 PM, Bruce Ravel 
<bra...@bnl.gov<mailto:bra...@bnl.gov>> wrote:
On 03/08/2017 10:53 AM, Bruce Ravel wrote:


Well . a multiple data set fit using larch runs to completion and
reports sensible values for parameters, but does not manage the data
sets correctly.  One obvious sign that something has gone wrong is the
after-fit plot attached.  Yikes!

This turned out to be a few Larch syntax problems.  I just checked a fix into 
github.

As far as I know, the head of github has an Artemis that works for single and 
multiple data set fits with Larch or Ifeffit.

Awesome!

--Matt
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Re: [Ifeffit] Multiple data set fit limit

[Matt Newville]

On Wed, Mar 8, 2017 at 1:58 PM, Bruce Ravel  wrote:

> On 03/08/2017 10:53 AM, Bruce Ravel wrote:
>
>>
>>>
>> Well . a multiple data set fit using larch runs to completion and
>> reports sensible values for parameters, but does not manage the data
>> sets correctly.  One obvious sign that something has gone wrong is the
>> after-fit plot attached.  Yikes!
>>
>
> This turned out to be a few Larch syntax problems.  I just checked a fix
> into github.
>
> As far as I know, the head of github has an Artemis that works for single
> and multiple data set fits with Larch or Ifeffit.
>
>
Awesome!

--Matt
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Re: [Ifeffit] Multiple data set fit limit

[Bruce Ravel]

On 03/08/2017 10:53 AM, Bruce Ravel wrote:




Well . a multiple data set fit using larch runs to completion and
reports sensible values for parameters, but does not manage the data
sets correctly.  One obvious sign that something has gone wrong is the
after-fit plot attached.  Yikes!


This turned out to be a few Larch syntax problems.  I just checked a fix 
into github.


As far as I know, the head of github has an Artemis that works for 
single and multiple data set fits with Larch or Ifeffit.


B

--
 Bruce Ravel   bra...@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] Multiple data set fit limit

[Bruce Ravel]

On 03/08/2017 09:37 AM, Bruce Ravel wrote:

On 03/08/2017 09:31 AM, Matt Newville wrote:

Can Artemis use Larch?

Yes.
B



Well . a multiple data set fit using larch runs to completion and 
reports sensible values for parameters, but does not manage the data 
sets correctly.  One obvious sign that something has gone wrong is the 
after-fit plot attached.  Yikes!


Shouldn't be too hard to fix.  A single data set fit with larch or any 
fit with ifeffit works as I expect.


B


--
 Bruce Ravel   bra...@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] Multiple data set fit limit

[Matt Newville]

On Wed, Mar 8, 2017 at 8:37 AM, Bruce Ravel  wrote:

> On 03/08/2017 09:31 AM, Matt Newville wrote:
>
>> Can Artemis use Larch?
>>
> Yes.


Great. I think that would be a good option for Victor, since the limit on
the number of datasets is removed and essentially limited only by available
RAM.

--Matt
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Re: [Ifeffit] Multiple data set fit limit

[Bruce Ravel]

On 03/08/2017 09:31 AM, Matt Newville wrote:

Can Artemis use Larch?

Yes.
B

--
 Bruce Ravel   bra...@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] Multiple data set fit limit

[Matt Newville]

On Wed, Mar 8, 2017 at 8:09 AM, Bruce Ravel  wrote:

> On 03/08/2017 03:46 AM, Victor Streltsov wrote:
>
>> The Linux latest version of Artemis limits multiple data set fit to 2
>> data sets.
>>
>> The input takes any number of data sets but 2 sets is used in the fit
>> only.
>>
>> I’ve tried latest available windows version it uses more than 2 in fit
>> (e.g. I used 3).
>>
>>
> That does not seem to be true.  I just ran a three-data-set fit on my
> Ubuntu 16.04 machine.
>
> If you need to me to do something, you will need to submit a more
> informative bug report.
>
>
Can Artemis use Larch?

--Matt
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Re: [Ifeffit] Multiple data set fit limit

[Bruce Ravel]

On 03/08/2017 03:46 AM, Victor Streltsov wrote:

The Linux latest version of Artemis limits multiple data set fit to 2
data sets.

The input takes any number of data sets but 2 sets is used in the fit only.

I’ve tried latest available windows version it uses more than 2 in fit
(e.g. I used 3).



That does not seem to be true.  I just ran a three-data-set fit on my 
Ubuntu 16.04 machine.


If you need to me to do something, you will need to submit a more 
informative bug report.


B

--
 Bruce Ravel   bra...@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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