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cdanielmachado / smetana

SMETANA: a tool to analyse interactions in microbial communities
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Segmentation fault #18

Closed pbelmann closed 3 years ago

pbelmann commented 3 years ago

Running Smetana (master branch, commit d2b10434d) with 4 models and with parameters --solver cplex -v --flavor bigg --detailed returns segmentation fault. Models were generated using carveme. Please let me know if I can help with debugging.

Output:

Loading community: all
Running SCS for community all on medium minimal...
Running MUS for community all on medium minimal...
Segmentation fault (core dumped)
pbelmann commented 3 years ago

I also noticed that sometimes for the same input segmentation fault is returned and sometimes not.

cdanielmachado commented 3 years ago

Hi, this is more likely an issue with cplex. Seg faults usually arise from pre-compiled binaries.

Did you install the correct cplex version for your python environment?

pbelmann commented 3 years ago

I installed python3.8 in an virtual environment and installed the cplex python library using setup.py that ships with cplex. (cplex/python/3.8/x86-64_linux/setup.py). However I noticed that if I set the use_bool flag to false it works just fine.

cdanielmachado commented 3 years ago

use_bool is not a flag in SMETANA... are you referring to the cplex installation ?

pbelmann commented 3 years ago

Sorry, I mean use_pool and not use_bool

cdanielmachado commented 3 years ago

No problem. That flag uses cplex solution pools for speeding up the enumeration of multiple solutions. Maybe there is a bug in this particular version of cplex when that option is used. Which version are you using?

pbelmann commented 3 years ago

No problem. That flag uses cplex solution pools for speeding up the enumeration of multiple solutions. Maybe there is a bug in this particular version of cplex when that option is used. Which version are you using?

20.1.0.0

pbelmann commented 3 years ago

I can confirm that cplex version 12.9.0 works without issues.

cdanielmachado commented 3 years ago

Perfect, thanks!