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segfault on nfsim 1.14.1 #37

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alubbock opened this issue Feb 28, 2024 · 3 comments
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segfault on nfsim 1.14.1 #37

alubbock opened this issue Feb 28, 2024 · 3 comments
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@aadibiasi
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@alubbock
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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.
alubbock added a commit to alubbock/pysb that referenced this issue Feb 28, 2024
@alubbock
fix: CI failures with updated BNG/NFsim
eea4098 
Two CI failures have crept in with updates to BNG and NFsim.

This first is an error simulating a hybrid particle-population
model in our test suite. This looks like a bug in NFsim 1.14.1,
which generates a segfault on the model which worked in 1.12.1.
I've opened an issue with NFsim for this here:
RuleWorld/nfsim#37

In the meantime, I've pinned the test suite GitHub Actions CI
to NFsim 1.12.1.

The other is a test failure in a BNG model import, which looks
like it's just a consequence of the rule order parsing changing
between BNG versions. I've updated the test to test for the presence
of either of the two expected error messages, both regarding rate
laws.
@alubbock alubbock mentioned this issue Feb 28, 2024
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@jrfaeder
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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 (RuleWorld/PyBioNetGen#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 jrfaeder added the bug label Feb 28, 2024
alubbock added a commit to pysb/pysb that referenced this issue Feb 28, 2024
@alubbock
fix: CI failures with updated BNG/NFsim (#589)
6d850c2 
Two CI failures have crept in with updates to BNG and NFsim.

This first is an error simulating a hybrid particle-population
model in our test suite. This looks like a bug in NFsim 1.14.1,
which generates a segfault on the model which worked in 1.12.1.
I've opened an issue with NFsim for this here:
RuleWorld/nfsim#37

In the meantime, I've pinned the test suite GitHub Actions CI
to NFsim 1.12.1.

The other is a test failure in a BNG model import, which looks
like it's just a consequence of the rule order parsing changing
between BNG versions. I've updated the test to test for the presence
of either of the two expected error messages, both regarding rate
laws.
@alubbock alubbock mentioned this issue Mar 11, 2024
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@jrfaeder
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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
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This bug should be fixed with the release of v1.14.2!

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@alubbock @jrfaeder @aadibiasi