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RuleWorld / nfsim

A general-purpose, stochastic, biochemical reaction simulator for large reaction networks
http://michaelsneddon.net/nfsim/
MIT License
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segfault on nfsim 1.14.1 #37

Closed alubbock closed 5 months ago

alubbock commented 8 months ago

Hi,

I've experienced a segfault trying to run a hybrid particle-population model on NFsim 1.14.1. This model runs successfully on NFsim 1.12.1.

Here's a link to the model:

hpptest.bngl.txt

This looks like it might be a bug in NFsim, but please let me know if you have any suggestions or advice.

Thanks for your help.

jrfaeder commented 8 months ago

Hi Alex,

We are aware of this issue in 1.14 and are actively working on a fix. I apologize that we had not created an issue for this already. It's a bug that cropped up in trying to identify the source of another problem (https://github.com/RuleWorld/PyBioNetGen/issues/55). Please note also that the current BioNetGen release (2.9.1) includes version 1.12.1 of NFsim, and so does not display the bug reported here.

jrfaeder commented 5 months ago

This bug was coming from new code supporting the rxnlog feature introduced in version 1.14 that could be triggered when species list in the seed species block were initialized with zero concentration. The fix is implemented on the issue37 branch that will soon be merged with master.

aadibiasi commented 5 months ago

This bug should be fixed with the release of v1.14.2!