Error: Segmentation fault (core dumped)

[ZiyiiiLiu]

Hi, I updated my roadrunner to the newest version with 3.12 py, and I can only run one parameter set and got the results, and then meet the error. However, I can run many parameter sets with the previous roadrunner.

How can I fix that?

The error starts at

def autofunction(r):
    auto = Plugin("tel_auto2000")
    auto.setProperty("SBML", r.getCurrentSBML())
    auto.setProperty("ScanDirection", 'Positive')
    auto.setProperty("PrincipalContinuationParameter", "K_Y") #So the K_Y becomes PAR in the dataset
    auto.setProperty("PreSimulation", "True")
    auto.setProperty("PreSimulationDuration", 30)
    auto.setProperty("RL0", 0.001)
    auto.setProperty("RL1", 10)
    auto.setProperty("NMX", 8000) #8000
    auto.setProperty("NPR", 3) 
    auto.setProperty("KeepTempFiles", True) 
    auto.setProperty("DS", 0.001) #0.001
    auto.setProperty("DSMIN", 0.001) 
    auto.setProperty("DSMAX", 0.01) #0.01
    pts1 = auto.BifurcationPoints
    if 1:
        lbl1     = auto.BifurcationLabels
        biData1  = auto.BifurcationData

[ZiyiiiLiu]

Even when I changed the parameters in the autofunction(r) and it can't have a simulation result with different parameter sets in ODE, always with An unexpected error occurred: invalid literal for int() with base 10: ''

[luciansmith]

I was able to reproduce your problem! Here's the code I used:

import rrplugins
import tellurium as te

r = te.loads(r"https://www.ebi.ac.uk/biomodels/services/download/get-files/MODEL1708290005/5/BIOMD0000000648_url.xml")
sbmlModel = r.getSBML()

auto = rrplugins.Plugin("tel_auto2000")              
auto.setProperty("SBML", sbmlModel)
auto.execute()

auto2 = rrplugins.Plugin("tel_auto2000")              
auto2.setProperty("SBML", sbmlModel)
auto2.execute()

The first time auto.execute runs, it's fine; the second time it crashes.

@adelhpour : you investigated the memory leak earlier, and my guess is that a fix you made there caused this issue now. Would you mind looking into it?

[adelhpour]

Sure. I'll check it out.

[ZiyiiiLiu]

I can install the 3.8.0 roadrunner and run it succssefully with windows version in my own computer, but failed in linux system in school high performance computer. Not sure about the reason, but the linux should be better for running it.

I checked further, and the error is within auto.execute()---Segmentation fault (core dumped) , and pts1 = auto.BifurcationPoints---An unexpected error occurred: invalid literal for int() with base 10: ''.