Yuri05
commented
1 year ago not sure if the issue was fixed. @rwmcintosh
With ospsuite-R 11.1.115 I don't get any error, but the results are empty:
> simulation=loadSimulation("C:/Temp/Vehicle.pkml")
> moleculePaths <- getAllMoleculePathsIn(container = simulation)
> moleculesStartValues <- getQuantityValuesByPath(quantityPaths = moleculePaths,simulation = simulation)
> simBatch <- createSimulationBatch(simulation = simulation,moleculesOrPaths = moleculePaths)
> simBatch$addRunValues(initialValues = moleculesStartValues)
[1] "6278a07f-de5a-4d99-a35b-2820b36fe7aa"
> results <- runSimulationBatches(simBatch)
Warning message:
In .getConcurrentSimulationRunnerResults(results = results, resultsIdSimulationIdMap = resultsIdSimulationBatchIdMap, :
Initial value of Vehicle|Organism|Liver|Pericentral|Interstitial|TMEFF2 was not set
> results
$`d081efc9-56c6-486c-9659-353c7611f75c`
$`d081efc9-56c6-486c-9659-353c7611f75c`$`6278a07f-de5a-4d99-a35b-2820b36fe7aa`
NULL
> results$`d081efc9-56c6-486c-9659-353c7611f75c`
$`6278a07f-de5a-4d99-a35b-2820b36fe7aa`
NULL
results$
d081efc9-56c6-486c-9659-353c7611f75c$6278a07f-de5a-4d99-a35b-2820b36fe7aaNULL
PavelBal
@PavelBal commented on Fri Jul 15 2022
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.
Error:
@PavelBal commented on Fri Jul 15 2022
@abdelr Could you look into it when you have time? I can help you translating the example to .NET test if necessary.
@PavelBal commented on Thu Sep 22 2022
@rwmcintosh
@rwmcintosh commented on Thu Sep 22 2022
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.
The paths available in SpeciesProperties that are not in variableMoleculePaths are
From the R code, the variableMoleculePaths are retrieved by
@Yuri05 @msevestre Any idea why these two lists are not matching?
@rwmcintosh commented on Thu Sep 22 2022
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 commented on Fri Sep 23 2022
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 commented on Fri Sep 23 2022
Will have to revisit when SimModel supports the fix.