Model diagram in the Simbiology freeze and disappear

Dear MatLab,

I am building a PBPK model in Simbiology. The model is quite complex. Whenever I add a new compartment or specie into the model diagram, it froze for a few minutes. Somehow my model diagram never shows up again... How can I solve this problem? Is it a problem of insufficient RAM or CPU power? How can I let my matlab assess more RAM or CPU power than usual?

Link: https://drive.google.com/file/d/1epB8FlTthFvdmblmAmvmohybDsy1mmVn/view?usp=sharing

The link is a video showed my screen record. The first project I opened is the problematic model that has no model diagram. The second is the confirmation that the other project works okay.

[Fulden Buyukozturk]

Hi Jesse,

How large is the model with the issue, for example how many blocks or compartments, species and reactions are there on the diagram?

Is it possible that you share the model? If so, please feel free to contact me directly using my community profile.

Fulden

[Jesse Chao]

Dear Fulden,

Thank you for your reply. Due to some restrictions of sharing research data in my lab, I could not share the file withe you. However, I have the screenshots of parts of my model. It has 15 repeated compartments like the attached photo.

Jesse

[Jesse Chao]

[Manish Mahalwal]

Hi Jessie,

Can you contact MathWorks Technical Support for this issue? As it would be difficult to reproduce the issue at our end without the model. You will be able to safely share this model, without compromising your intellectual property, over secure artifacts or via a webex meeting.

[Prakash Packirisamy]

I am facing the same issue!

Do we have a solution yet or whether will I have to conatct the MathWorks for it?

[Jesse Chao]

Hello Prakash,

I didn’t reach out to the Matlab support team, because I was urgent to get my result at the moment. Instead I used command line to execute my simulation and fitting and it worked fine, but you need to write the code. If you have time, maybe you can contact them as they mentioned in their reply on my post. Hope you could find this helpful. Best

[Massimo Lai]

I've just had a similar problem. I tried to drag a new reaction block within a compartment, the window froze, I decided to save the changes and reload, but the model diagram completely vanished when I reloaded.

Other models in the same project file are unaffected.

The culprit model is quite compact, 3 compartments, twenty or so species, twenty or so reactions. I've been running much larger ones for years on previous versions.

Answer 1

[Jeremy Huard]

(edited: added a more detailed description of the issue)

Dear users,

We were able to reproduce the issue you reported:

• Dragging a model component from the palette can make the diagram appear to freeze. We think low memory conditions aggravated or causes the problem.
• If the user closes the project in this state without saving, the .sbproj file can be loaded including the diagram information. However, all changes made after the last save will be lost.
• If the user hits save in the ‘frozen’ state before the diagram is fully updated, the .sbproj file will be corrupt. However, the backup file with the .bak extension will contain the version prior to the saved, corrupt version. If you are in this case, please make a copy of this file, remove the .bak extension and load it into the Model Builder to recover the last saved version of your diagram.
• If the user tries to load the corrupt .sbproj file, a grey screen will appear in the place of the diagram. If the user hits save again, then the .bak file will be corrupt as well and the customized diagram layout will be lost permanently. Only the diagram information seems to be affected though. So, if you are in this case, you can recover the model information without your customized layout (namely with the default diagram) using the following steps:

1. Load the project in Model Builder
2. Export the model without the diagram to the MATLAB workspace
3. Remove the model without the diagram from the SimBiology Model Builder
4. Import the model back into the SimBiology Model Builder from the MATLAB workspace. The model will come in with the default layout.

We will release a fix in a coming update.

Sorry for the inconvenience this issue may have caused. We hope the information above will minimize the recovery efforts.

Best regards,

Jérémy

[R Andreev]

Had the same problem. Thanks for the suggestions.

[Sameed Ahmed]

My situation was the last case. It worked, thanks!!!

I must say that I am disappointed in how fragile/clunky Simbiology is. In addition to this problem, I've had other similar problems where some simple task/operation would cause a problem in Simbiology (freezing or otherwise). Usually restarting MATLAB fixes the problem.

[Jeremy Huard]

Hi Sameed,

sorry to read this. This problem was fixed in an update for R2020b, R2021a and is fixed in the general release of R2021b.

Can you tell me which version you are currently running?

Also, do you typically install updates within a release? These contain bug fixes only and can be installed easily from within MATLAB.

Concerning issues you might encounter with SimBiology, I strongly encourage you to contact our technical support and describe any step that could help reproduce the issue. These informations and details about the machine you are using will help our development team identify and fix the problem.

Thanks,

Jérémy