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Requesting sensitivities for algebraic equations breaks simulation #2102

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dilpath opened this issue May 22, 2023 · 1 comment · May be fixed by #2101
Open

Requesting sensitivities for algebraic equations breaks simulation #2102

dilpath opened this issue May 22, 2023 · 1 comment · May be fixed by #2101
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bug DAE related to differential algebraic equations

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@dilpath
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dilpath commented May 22, 2023

What did you expect to happen?
Sensitivities to be computed

What has happened instead?
rdata.x and rdata.sx are zero matrices

To Reproduce
Compile a model with algebraic expressions, e.g. SBML semantic test case 00039, simulate with and without computation of forward sensitivities.

sbml_file = "tests/sbml-test-suite/cases/semantic/00039/00039-sbml-l3v2.xml"

from pathlib import Path
model_name = "m00039"
model_dir = Path("amici_models") / model_name
model_dir.mkdir(parents=True, exist_ok=True)

import amici
import numpy as np

sbml_importer = amici.SbmlImporter(sbml_file)    
sbml_importer.sbml2amici(    
    model_name,    
    output_dir=model_dir,    
    generate_sensitivity_code=True,    
)    

model_module = amici.import_model_module(model_name, model_dir)
model = model_module.getModel()
solver = model.getSolver()

model.setTimepoints(np.linspace(0, 8, 51))
solver.setMaxSteps(int(1e6))

solver.setSensitivityOrder(amici.SensitivityOrder.first)
solver.setSensitivityMethod(amici.SensitivityMethod.forward)

rdata = amici.runAmiciSimulation(model, solver)
print(rdata.x) 
print(rdata.sx)

AMICI version and system environment

  • OS and version: Ubuntu 22.04
  • AMICI interface: Python
  • AMICI version: latest develop branch
  • Additional information: GCC 10.4.0, Python 3.10.6
@dilpath dilpath added the new Newly created label May 22, 2023
@dweindl dweindl linked a pull request May 23, 2023 that will close this issue
Sensitivities for AlgebraicRule models #2101
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@dweindl
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dweindl commented May 23, 2023

I agree that this is not the desired behavior. In case of errors, x and sx (and others) should be NaN. It seems there is a call to ReturnData::invalidate missing. Since rdata.status is AMICI_ERROR, it wouldn't consider this high priority, and would rather have the root cause fixed via #2101. (Volunteers?)

@dweindl dweindl added bug and removed new Newly created labels May 23, 2023
dilpath added a commit that referenced this issue May 23, 2023
@dilpath
temp skip DAEs (#2102); skip models with no parameters
4351ca1
@dweindl dweindl added the DAE related to differential algebraic equations label Apr 21, 2024
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Sensitivities for AlgebraicRule models AMICI-dev/AMICI
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@dweindl @dilpath