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: ''.

[luciansmith]

Sorry for the delay, but I finally was able to investigate and fix the issue! If you need a fix right now, you can find binaries and wheel files at

https://github.com/sys-bio/roadrunner/actions/runs/18299641197

or you can just wait until Roadrunner's next release. Thank you again for reporting the issue!

[ZiyiiiLiu]

Hi Lucian, Thank you so much for the update! Does the upcoming new version solve the memory leaking and also can run successfully?

[luciansmith]

I found a memory leak that I fixed, so I think that's it, though I hope there aren't others. (I have tracked memory usage between calls to simulate, and it used to go up, and now stays the same.) I do know that this segmentation fault issue is definitely fixed. And yes, the next version will have both fixes.

[ZiyiiiLiu]

Hi Lucian,

I still met the segmentation error. I tried to use the patched wheel file sha256:24710521f9d6f3a533569f7f2805d3ddca70e6271bd3f818dc7d9d705285b921 with 3.10 python version linux in the link you provided above.

I did: I created a new env, installed the roadrunner and rrplugin within the whl file, and installed all other packages via pip.

Then, I tested the patched tool by the code you gave in Feb in this #1259 page. I met the segmentation fault error again.

Could you please let me know if I did something not correct? Thanks!

[luciansmith]

Oh, did you update both the rrplugins and libroadrunner? Both will need to be updated to fix the problem.

The latest files are at

https://github.com/sys-bio/roadrunner/actions/runs/19393934808

just in case you're running into a different problem with memory in Python that I also just fixed.

[ZiyiiiLiu]

Thanks. Do I use the roadrunner-2.8.0-python-wheels-manylinux_2_28-x86_64 in the link for python linux system?
There are rrplugin and libroadrunner, and I need to install these two in a new env, and I don't need to install the precious version right?