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Model diagram in the Simbiology freeze and disappear

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Jesse Chao
Jesse Chao on 27 Nov 2020
Commented: R Andreev on 12 May 2021
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?
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.
Massimo Lai
Massimo Lai on 16 Apr 2021
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.

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Accepted Answer

Jeremy Huard
Jeremy Huard on 20 Apr 2021
Edited: Jeremy Huard on 21 Apr 2021
(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,

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