cluster and amici

[chloweckel]

Dear all,

I used PyPesto and Petab for a parameter estimation problem. Everything works except when I simulate on a cluster on a specific node. I get this kind of error:

extension in the same location has already been imported, but the file was modified on disk.
Imported at 2025-10-13T15:21:40.193079
Modified at 2025-10-13T15:22:00.
Import the module with a different name or restart the Python kernel.
I don't know why, because it works when I am on another node of the cluster.
My code is as follows:

filename = './config.yaml'
petab_yaml = filename
petab_problem = petab.Problem.from_yaml(petab_yaml)
importer = pypesto.petab.PetabImporter.from_yaml(petab_yaml)
problem = importer.create_problem()

Thank you very much for your help !

[dweindl]

Hi, I am guessing that this happens because some AMICI model is compiled by several processes in parallel in the same directory, overwriting each others output. Could that be the case? problem = importer.create_problem() should initially be called only by a single process, until model compilation finished. Afterwards, it's safe to call it from other processes.

[chloweckel]

I have the impression that it creates the "amici_models" file and then modifies it. That finally explains why I get the "files were modified on the disk" error. However, I have tried different things:

• running these lines in another .py file and then loading them.
• sending the amici files already compiled and then just loading the files.
  However, I always get this kind of error.
  Thanks a lot!

[dweindl]

Can you share a complete script that reproduces this issue, including how you invoke it?