telFittingStatistics.py WindowsError('exception: access violation reading 0x00007532',)

[mgaldzic]

telFittingStatistics.py issues error, no explanation, here.

this was run: in wdir=r'C:/Users/mgaldzic/Documents/tellurium-files/teplugins/parameter_minimization'

Notice: performing conserved moiety conversion Notice: source document is level 2, version 4, converting tolevel 3, version 1 for Moiety > Conservation Conversion Exception: WindowsError('exception: access violation reading 0x00007532',)

[TotteKarlsson]

I can't reproduce this one. I see something funky with the plotting if it is run twice however. Looking into what that is. Think it has to do with matplotlib..

[mgaldzic]

Update for teplugins-1.0.12 Running telFittingStatistics.py produces [image: Inline image 1]

Error: Problem with column names when creating residual data! Error: Problem with column names when creating residual data! Error: Problem with column names when creating residual data! Error: Prob

On Mon, Mar 31, 2014 at 12:41 PM, Totte Karlsson notifications@github.comwrote:

I can't reproduce this one. I see something funky with the plotting if it is run twice however. Looking into what that is. Think it has to do with matplotlib..

Reply to this email directly or view it on GitHubhttps://github.com/sys-bio/telPlugins/issues/6#issuecomment-39131896 .

[mgaldzic]

screenshot did not come through, here it is again

[TotteKarlsson]

Weird.. I get the following plots

[mgaldzic]

ok, let see I put the latest tellurium installer in dropbox. see tellurium-0.9.5-Python-2.7-win32-superpack-setup.exe

My tests where done on a clean Win7 virtual machine.

I'll try to help to diagnose, but let see if you can reproduce the issue.

On Mon, Mar 31, 2014 at 1:09 PM, Totte Karlsson notifications@github.comwrote:

Weird.. I get the following plots

[image: image]https://cloud.githubusercontent.com/assets/3292436/2572206/3e8a6456-b910-11e3-9e7a-7f2afafac395.png [image: image]https://cloud.githubusercontent.com/assets/3292436/2572208/45480136-b910-11e3-8d8d-5e04ef84c888.png

[image: image]https://cloud.githubusercontent.com/assets/3292436/2572211/4ad4d6ba-b910-11e3-9162-9f8ffd3713ef.png

Reply to this email directly or view it on GitHubhttps://github.com/sys-bio/telPlugins/issues/6#issuecomment-39135051 .

[mgaldzic]

It says it will take 15min to upload

On Mon, Mar 31, 2014 at 1:13 PM, Michal Galdzicki mgaldzic@gmail.comwrote:

ok, let see I put the latest tellurium installer in dropbox. see tellurium-0.9.5-Python-2.7-win32-superpack-setup.exe

My tests where done on a clean Win7 virtual machine.

I'll try to help to diagnose, but let see if you can reproduce the issue.

On Mon, Mar 31, 2014 at 1:09 PM, Totte Karlsson notifications@github.comwrote:

Weird.. I get the following plots

[image: image]https://cloud.githubusercontent.com/assets/3292436/2572206/3e8a6456-b910-11e3-9e7a-7f2afafac395.png [image: image]https://cloud.githubusercontent.com/assets/3292436/2572208/45480136-b910-11e3-8d8d-5e04ef84c888.png

[image: image]https://cloud.githubusercontent.com/assets/3292436/2572211/4ad4d6ba-b910-11e3-9162-9f8ffd3713ef.png

Reply to this email directly or view it on GitHubhttps://github.com/sys-bio/telPlugins/issues/6#issuecomment-39135051 .

[mgaldzic]

in the meantime could you paste the return value of roadrunner.version

On Mon, Mar 31, 2014 at 1:14 PM, Michal Galdzicki mgaldzic@gmail.comwrote:

It says it will take 15min to upload

On Mon, Mar 31, 2014 at 1:13 PM, Michal Galdzicki mgaldzic@gmail.comwrote:

ok, let see I put the latest tellurium installer in dropbox. see tellurium-0.9.5-Python-2.7-win32-superpack-setup.exe

My tests where done on a clean Win7 virtual machine.

I'll try to help to diagnose, but let see if you can reproduce the issue.

On Mon, Mar 31, 2014 at 1:09 PM, Totte Karlsson <notifications@github.com

wrote:

Weird.. I get the following plots

[image: image]https://cloud.githubusercontent.com/assets/3292436/2572206/3e8a6456-b910-11e3-9e7a-7f2afafac395.png [image: image]https://cloud.githubusercontent.com/assets/3292436/2572208/45480136-b910-11e3-8d8d-5e04ef84c888.png

[image: image]https://cloud.githubusercontent.com/assets/3292436/2572211/4ad4d6ba-b910-11e3-9162-9f8ffd3713ef.png

Reply to this email directly or view it on GitHubhttps://github.com/sys-bio/telPlugins/issues/6#issuecomment-39135051 .

[TotteKarlsson]

'1.1.0; Compiler: Microsoft Visual Studio 2012; Date: Mar 29 2014, 13:52:11'

[TotteKarlsson]

I suggest we leave this example out, ship, figure out why the plotting behaves erratic in this example, and add it to next release. What do you think?

[TotteKarlsson]

I installed the superpack and indeed getting the same error as you. So now we have a situation where the example works standalone, i.e. just using the teplugins installer, versus not working in the superpack...

[mgaldzic]

ok I made some progress Config.setValue(Config.SIMULATEOPTIONS_STRUCTURED_RESULT, True) gives the following:

so the introduction of the conf file with

LOADSBMLOPTIONS_CONSERVED_MOIETIES : True SIMULATEOPTIONS_STRUCTURED_RESULT : False

is to blame. Herbert wanted the SIMULATEOPTIONS_STRUCTURED_RESULT as False for a long time. Is there anyway the plot command can change so that it expects this option?

BTW I have matplotlib.version '1.3.1' shipped with tellurium

[mgaldzic]

oh i see, these three plots are generated on top of each other if you just run through the the whole file at one time... so this config flag is indeed the issue

[TotteKarlsson]

OK. After going trough examples using the super pack I conclude that the new roadrunner flags, options etc is breaking some of the examples. We need to figure out what options, flags etc that need to be set.. I don't think this is ready to be released. There been too many changes in roadrunner

[TotteKarlsson]

Actually, I believe there there is something in the super pack setup. Is the 'superpack' configuring roadrunner?

[hsauro]

The roadrunner plot command expect structured arrays but all other matplot lib commands expect non-structured. It is more likely that people will get upset if matplotlib doesn't work. In any case the roadrunner plot command could be changed to accept unstructured arrays because the legend that it builds could be obtained from the selectionlist which is what I do in plotWithLegend method.

Herbert

On 3/31/2014 1:38 PM, Michal Galdzicki wrote:

ok I made some progress Config.setValue(Config.SIMULATEOPTIONS_STRUCTURED_RESULT, True) gives the following:

image https://cloud.githubusercontent.com/assets/406285/2572434/7b707d62-b913-11e3-8c0f-dd271dcac6f4.png

so the introduction of the conf file with

LOADSBMLOPTIONS_CONSERVED_MOIETIES : True
SIMULATEOPTIONS_STRUCTURED_RESULT : False

is to blame. Herbert wanted the SIMULATEOPTIONS_STRUCTURED_RESULT as False for a long time. Is there anyway the plot command can change so that it expects this option?

BTW I have matplotlib.version '1.3.1' shipped with tellurium

— Reply to this email directly or view it on GitHub https://github.com/sys-bio/telPlugins/issues/6#issuecomment-39138624.

Herbert M. Sauro, PhD Associate Professor Department of Bioengineering

University of Washington William H. Foege Building Box 355061, Seattle, WA 98195-5061 206.685.2119 (tel), 206.685.3300 (shared fax)

http://www.sys-bio.org; http://blog.analogmachine.org New Text Book: Enzyme Kinetics for Systems Biology Order at Amazon: http://tinyurl.com/3w4b9al

[hsauro]

In tellurium I recommend not to use the roadrunner plot command as it will cause problems down the line as people wonder why matplotlib won't work. In the startup file we could override the plot command with a warning message and recommend people use plotWithLegend instead.

Herbert

On 3/31/2014 1:43 PM, Michal Galdzicki wrote:

oh i see, these three plots are generated on top of each other if you just run through the the whole file at one time... so this config flag is indeed the issue

— Reply to this email directly or view it on GitHub https://github.com/sys-bio/telPlugins/issues/6#issuecomment-39139215.

Herbert M. Sauro, PhD Associate Professor Department of Bioengineering

University of Washington William H. Foege Building Box 355061, Seattle, WA 98195-5061 206.685.2119 (tel), 206.685.3300 (shared fax)

http://www.sys-bio.org; http://blog.analogmachine.org New Text Book: Enzyme Kinetics for Systems Biology Order at Amazon: http://tinyurl.com/3w4b9al

[TotteKarlsson]

OK, here is the latest. If I completely remove the config file, for python roadrunner, the examples works, including the statistics one. If you can confirm that, then getting it together is a matter of having a proper roadrunner config file. Right now, no config file (I just renamed it to .bak) seem to be the proper choice

[mgaldzic]

Herbert and Totte, I don't think this fix is all that difficult. We're currently talking about this specific example.

The results here are returned from the plugin, expecting the roadrunner style output, but we're now working with the new config.

There are 3 plots in this file, the first one gets its values in this line: https://github.com/sys-bio/telPlugins/blob/master/examples/python/parameter_minimization/telFittingStatistics.py#L58

residuals = lmPlugin.Residuals.toNumpy

Does one of you know how to change this line or the next to get proper plotting working using matplotlib?

Otherwise, the simplest hack/solution is to set the following flag at the top of this file.

from roadrunner import Config Config.setValue(Config.SIMULATEOPTIONS_STRUCTURED_RESULT, True)

[TotteKarlsson]

There are other examples needing the same settings. I'll add it and check the examples. Then I'll create a new build for you

[TotteKarlsson]

I did not see these problems because I have not been using a config file.

[mgaldzic]

ok.. sounds like a plan.

I see toNumpy in the examples below, but they all seem to work. Only parameter_minimization/telFittingStatistics.py threw an error.

grep -r toNumpy *

telLevenbergMarquardt.py telMonteCarlo.py telNelderMead.py

[TotteKarlsson]

OK.. 1.0.13 is in the drop box with modified examples The example of chisquare of two parameters needed changing options too.

[mgaldzic]

it works, this closes the issue