CopasiUI quit unexpectedly.

[Konstantia Georgouli]

Hi,

I am sending you this email because I would like to ask you a question. I am trying to import a big SBML model (33.7 MB) into CopasiIUI and CopasiUI is crashing. I tried to import the SBML file from CopasiSE and save as a .cps file:

~/copasi/bin/CopasiSE -i test.xml -s test_init.cps

but when I tried  to open the .cps file  with CopasiUI, CopasiUI is crashing again. Is there any way to tackle this problem?

I am looking forward to hearing from you.

Thank you.

Kind regards,
Konstantia

[Frank Bergmann]

I'm sorry you are having that issue. You might try a different version of COPASI. Otherwise, i can just invite you to send me the model and i can convert it for you (and figure out why copasi was crashing for you). 

best

Frank

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[Konstantia Georgouli]

Dear Frank,

Thank you very much for your answer. I am using the COPASI 4.30 (Build 240). Can you tell me a different version of COPASI that it could work for this problem? I have tried a smaller version of this file with less species and reactions and it worked  perfectly.  I am attaching the model as you suggested. 

Could you see the model and tell me what is wrong with this file and how can I import this file ? Apart from this file, I have also to import a much bigger file than this.

I am looking forward to hearing from you.

Thank you.

Kind regards,

Konstantia

[Hoops, Stefan (sh9cq)]

Hello Kantantia,

I was able to load the file in COPASI 4.30 (Build 240) under Linux.
What is your OS and how much memory do you have. I suspect you are
running out of memory.

Thanks,
Stefan

--
Stefan Hoops, Ph.D.
Research Associate Professor
Biocomplexity Institute & Initiative
University of Virginia
995 Research Park Boulevard
Charlottesville, VA 22911

Phone: +1 540 570 1301
Email: sho...@virginia.edu

[Konstantia Georgouli]

Hi Stefan,

Thank you very much for your help. I am running CopasiUI on a Mac with 32GB memory. I have access to a linux machine with more memory where

 I have installed the COPASI but I cannot use the CopasiUI on that machine to set the task parameters (time course).

Is it possible to do that through the command line (CopasiSE)?

Thanks,

Konstantia

[Hoops, Stefan (sh9cq)]

Hello Konstantia,

32GB is more than sufficient. I am on a Linux machine with 24GB and the
load succeeded. This means the issue is somewhere else. Unfortunately I
do not have access to a Mac but Frank might be able to verify and solve
your issue.

Thanks,
Stefan

[Hoops, Stefan (sh9cq)]

Just in case that it is the import here is a link the COPASI file:

https://drive.google.com/file/d/1QuUm-GGev1XQuPXQeplaCxGwghpmb1Yc/view?usp=sharing

Thanks,
Stefan

[Konstantia Georgouli]

Dear Stefan,

Thank you very much for your help. I will wait for Frank's reply .

I have tried to open the file that you sent with CopasiUI  and CopasiUI is crashing again.

What about my second question? Is it possible to set the task parameters (time course) through the command line (CopasiSE)?

Thanks,

Konstantia

[sven....@gmail.com]

I just tested on  my Mac (Catalina, 8GB), and the SBML file loads and simulates with Build 228, but not with 240.

Sven

[Frank Bergmann]

I'm in a meeting this week, so sorry for the slow reply. i can confirm, that the 240 release does indeed crash upon import of the file on WIndows x64. I'm looking into why that happens and will report back here. Once i find out the reason. I can confirm that loading the file worked fine in release 4.28 . 

best

Frank

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[Konstantia Georgouli]

Hi all,

Thank you very much for your help. I managed to load and simulate this SBML file with Build 228. 

Kind regards,

Konstantia