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Error when running simulation batch #1016

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PavelBal opened this issue Jul 15, 2022 · 11 comments
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Error when running simulation batch #1016

PavelBal opened this issue Jul 15, 2022 · 11 comments
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@rwmcintosh
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Version 11 Update 1

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@PavelBal
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Vehicle.zip

Probably an errorr in core.
When seeting all molecules as variable molecules in the attached simulation, runnning the batch produces the error that some molecules do not exist in the simulation.

# Load the simulation from file - adjust the path accordingly
simulation <- loadSimulation(file.path(getwd(), "../Models/Simulations", "Vehicle.pkml"))
# Get the paths of all molecules in the simulation
moleculePaths <- getAllMoleculePathsIn(container = simulation)
# Get the current intial values of all molecules
moleculesStartValues <- getQuantityValuesByPath(quantityPaths = moleculePaths,
                                                simulation = simulation)
# Create simulation batch and define all molecules as variable
simBatch <- createSimulationBatch(simulation = simulation,
                                  moleculesOrPaths = moleculePaths)
# Add run values
simBatch$addRunValues(initialValues = moleculesStartValues)
# Try to run
results <- runSimulationBatches(simBatch)

Error:

Error in rClr::clrCall(simulationRunner, "RunConcurrently") : 
  Type:    OSPSuite.Core.Domain.InvalidArgumentException
Message: Entities 'Organism|Kidney|Urine|ADC', 'Organism|Kidney|Urine|nAb', 'Organism|Kidney|Urine|Toxophore', 'Organism|Liver|Periportal|Intracellular|Undefined Liver', 'Organism|Liver|Pericentral|Intracellular|Undefined Liver', 'Organism|EndogenousIgG|Plasma|FcRn kinetics plasma', 'Organism|EndogenousIgG|Interstitial|FcRn kinetics interstitial', 'Organism|EndogenousIgG|Endosome|FcRn kinetics endosome', 'Applications|i.v. 0.3 mg/kg|Application_1|ADC' do not exist in the simulation
Method:  Void validate(System.Collections.Generic.IReadOnlyList`1[System.String], System.Collections.Generic.IReadOnlyList`1[System.String])
Stack trace:
   at OSPSuite.R.Domain.SimulationBatch.validate(IReadOnlyList`1 entitiesToVary, IReadOnlyList`1 entitiesThatWillBeVaried)
   at OSPSuite.R.Domain.SimulationBatch.validate(SimulationBatchOptions simulationBatchOptions)
   at OSPSuite.R.Domain.SimulationBatch.Initialize(IModelCoreSimulation simu
@PavelBal
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@abdelr Could you look into it when you have time? I can help you translating the example to .NET test if necessary.

@PavelBal PavelBal mentioned this issue Aug 25, 2022
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@PavelBal
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@rwmcintosh

@rwmcintosh
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https://github.com/Open-Systems-Pharmacology/OSPSuite.Core/blob/adf6f9f4c27928af05f75727a4dff2d7b3219c44/src/OSPSuite.Core/Domain/Services/SimModelManagerBase.cs#L84

For reference.

In the attached project there is a discrepancy at this line where the two lists are not perfectly 1 to 1.

Here is the list of paths in variableMoleculePaths that is not available from SpeciesProperties. Since this list of variableMoleculePaths comes from the simulation, I thought SpeciesProperties would contain them all.

"Organism|Kidney|Urine|ADC"
"Organism|Kidney|Urine|nAb"
"Organism|Kidney|Urine|Toxophore"
"Organism|Liver|Periportal|Intracellular|Undefined Liver"
"Organism|Liver|Pericentral|Intracellular|Undefined Liver"
"Organism|EndogenousIgG|Plasma|FcRn kinetics plasma"
"Organism|EndogenousIgG|Interstitial|FcRn kinetics interstitial"
"Organism|EndogenousIgG|Endosome|FcRn kinetics endosome"
"Applications|i.v. 0.3 mg/kg|Application_1|ADC"

The paths available in SpeciesProperties that are not in variableMoleculePaths are

"Organism|Lumen|Stomach|Liquid"
"Organism|Lumen|Duodenum|Liquid"
"Organism|Lumen|Duodenum|ADC|Oral mass absorbed segment"
"Organism|Lumen|Duodenum|nAb|Oral mass absorbed segment"
"Organism|Lumen|Duodenum|Toxophore|Oral mass absorbed segment"
"Organism|Lumen|UpperJejunum|Liquid"
"Organism|Lumen|UpperJejunum|ADC|Oral mass absorbed segment"
"Organism|Lumen|UpperJejunum|nAb|Oral mass absorbed segment"
"Organism|Lumen|UpperJejunum|Toxophore|Oral mass absorbed segment"
"Organism|Lumen|LowerJejunum|Liquid"
"Organism|Lumen|LowerJejunum|ADC|Oral mass absorbed segment"
"Organism|Lumen|LowerJejunum|nAb|Oral mass absorbed segment"
"Organism|Lumen|LowerJejunum|Toxophore|Oral mass absorbed segment"
"Organism|Lumen|UpperIleum|Liquid"
"Organism|Lumen|UpperIleum|ADC|Oral mass absorbed segment"
"Organism|Lumen|UpperIleum|nAb|Oral mass absorbed segment"
"Organism|Lumen|UpperIleum|Toxophore|Oral mass absorbed segment"
"Organism|Lumen|LowerIleum|Liquid"
"Organism|Lumen|LowerIleum|ADC|Oral mass absorbed segment"
"Organism|Lumen|LowerIleum|nAb|Oral mass absorbed segment"
"Organism|Lumen|LowerIleum|Toxophore|Oral mass absorbed segment"
"Organism|Lumen|Caecum|Liquid"
"Organism|Lumen|Caecum|ADC|Oral mass absorbed segment"
"Organism|Lumen|Caecum|nAb|Oral mass absorbed segment"
"Organism|Lumen|Caecum|Toxophore|Oral mass absorbed segment"
"Organism|Lumen|ColonAscendens|Liquid"
"Organism|Lumen|ColonAscendens|ADC|Oral mass absorbed segment"
"Organism|Lumen|ColonAscendens|nAb|Oral mass absorbed segment"
"Organism|Lumen|ColonAscendens|Toxophore|Oral mass absorbed segment"
"Organism|Lumen|ColonTransversum|Liquid"
"Organism|Lumen|ColonTransversum|ADC|Oral mass absorbed segment"
"Organism|Lumen|ColonTransversum|nAb|Oral mass absorbed segment"
"Organism|Lumen|ColonTransversum|Toxophore|Oral mass absorbed segment"
"Organism|Lumen|ColonDescendens|Liquid"
"Organism|Lumen|ColonDescendens|ADC|Oral mass absorbed segment"
"Organism|Lumen|ColonDescendens|nAb|Oral mass absorbed segment"
"Organism|Lumen|ColonDescendens|Toxophore|Oral mass absorbed segment"
"Organism|Lumen|ColonSigmoid|Liquid"
"Organism|Lumen|ColonSigmoid|ADC|Oral mass absorbed segment"
"Organism|Lumen|ColonSigmoid|nAb|Oral mass absorbed segment"
"Organism|Lumen|ColonSigmoid|Toxophore|Oral mass absorbed segment"
"Organism|Lumen|Rectum|Liquid"
"Organism|Lumen|Rectum|ADC|Oral mass absorbed segment"
"Organism|Lumen|Rectum|nAb|Oral mass absorbed segment"
"Organism|Lumen|Rectum|Toxophore|Oral mass absorbed segment"
"Organism|Lumen|Feces|Liquid"
"Organism|Tumor|Intracellular|x1"
"Organism|Tumor|Intracellular|x2"
"Organism|Tumor|Intracellular|x3"
"Organism|Tumor|Intracellular|x4"

From the R code, the variableMoleculePaths are retrieved by

_containerTask.AllMoleculesPathsIn(_simulation);

@Yuri05 @msevestre Any idea why these two lists are not matching?

@rwmcintosh
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See my unit test which translates the R code

https://github.com/rwmcintosh/OSPSuite.Core/blob/3b152081707894657df5449668bf15021093c4a4/tests/OSPSuite.R.Tests/Services/ConcurrentSimulationRunnerSpecs.cs#L56

@rwmcintosh
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After discussion with @msevestre and @Yuri05 today, we decided that the bug itself can be fixed meaning - if the list of variable molecules is not a precise match we will only try to vary the intersection of the lists. The issue is caused because SimModel optimizes the molecules that won't be varied into parameters. The list in this example is created before the SimModel initialization, so there is no way for the application to know this will happen.

To enable the steady state use case, some more reorganization will be required in SimModel and OSPSuite.Core so that the list of variable molecules and variable parameters are actually known by the caller.

@rwmcintosh rwmcintosh self-assigned this Sep 23, 2022
@rwmcintosh rwmcintosh mentioned this issue Sep 23, 2022
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@rwmcintosh
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Will have to revisit when SimModel supports the fix.

@rwmcintosh rwmcintosh mentioned this issue Sep 23, 2022
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rwmcintosh added a commit that referenced this issue Sep 29, 2022
@rwmcintosh
Fixes #1016 Error when running simulation batch
c326db6 
Update OSPSuite.Core
@PavelBal PavelBal mentioned this issue Oct 4, 2022
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@PavelBal
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Just tried it out with

sim <- loadTestSimulation("simple", loadFromCache = TRUE)

  # Get the paths of all molecules in the simulation
  moleculePaths <- getAllMoleculePathsIn(container = sim)
  # Get the current intial values of all molecules
  moleculesStartValues <- getQuantityValuesByPath(quantityPaths = moleculePaths,
                                                  simulation = sim)
  # Replace one value by NaN
  moleculesStartValues[[1]] <- NaN
  # Create simulation batch and define all molecules as variable
  simBatch <- createSimulationBatch(simulation = simulation,
                                    moleculesOrPaths = moleculePaths)
  # Add run values
  simBatch$addRunValues(initialValues = moleculesStartValues)
  
  results <- runSimulationBatches(simBatch)

and got the error again:

>   results <- runSimulationBatches(simBatch)
Error in rClr::clrCall(simulationRunner, "RunConcurrently") : 
  Type:    OSPSuite.Core.Domain.InvalidArgumentException
Message: Entities 'Organism|A', 'Organism|B', 'Organism|Liver|A', 'Organism|Liver|B' do not exist in the simulation
Method:  Void validate(System.Collections.Generic.IReadOnlyList`1[System.String], System.Collections.Generic.IReadOnlyList`1[System.String])
Stack trace:
   at OSPSuite.R.Domain.SimulationBatch.validate(IReadOnlyList`1 entitiesToVary, IReadOnlyList`1 entitiesThatWillBeVaried)
   at OSPSuite.R.Domain.SimulationBatch.validate(SimulationBatchOptions simulationBatchOptions)
   at OSPSuite.R.Domain.SimulationBatch.Initialize(IModelCoreSimulation simulation, SimulationBatchOptions simulationBatchOptions)
   at OSPSuite.R.Domain.SimulationBatchFactory.Create(IModelCoreSimulation modelCoreSimulation, SimulationBatchOptions simulationBatchOptions)
   at OSPSuite.R.Domain.ConcurrentRunSimulationBatch.AddNewBatch()
   at OSPSuite.R.Services.ConcurrentSimulationRunner.<>c.<initializeBatches>b__12_1(ConcurrentRunSimulatio

Something I forgot to update? This is the simulation: https://github.com/Open-Systems-Pharmacology/OSPSuite-R/blob/develop/tests/data/simple.pkml

@PavelBal PavelBal reopened this Oct 19, 2022
@PavelBal
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@rwmcintosh @msevestre

@PavelBal
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It works for the "Vehicle" simulation but not for this one..

@rwmcintosh
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The bug that won’t be squashed. Resilient.

@rwmcintosh rwmcintosh added this to the Version 11 Update 1 milestone Oct 20, 2022
@PavelBal
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Wrong alarm, my bad.

@PavelBal PavelBal moved this to Done in V11 - Update 1 Oct 20, 2022
@Yuri05 Yuri05 removed this from V11 - Update 1 Dec 27, 2022
@PavelBal PavelBal mentioned this issue Jun 22, 2023
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@PavelBal PavelBal mentioned this issue Feb 23, 2024
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