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FRED-2 / Fred2

Python-based framework for computational immunomics
http://fred-2.github.io/
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EpitopeAssemblyWithSpacer with Cbc fails for more than 14 peptides #246

Open matdoering opened 3 years ago

matdoering commented 3 years ago

Cbc crashes for larger instances of the ILP for spacer design. Here's a minimal example that will crash after ~4 mins:

cleavage_predictor = CleavageSitePredictorFactory("PCM")
epitope_predictor = EpitopePredictorFactory("BIMAS")

opti_result = EpitopeAssemblyWithSpacer(
        peptides,
        cleavage_predictor,
        epitope_predictor,
        supported_alleles,
        solver="cbc",
        verbosity=1
    ).solve()

Please consider the log output.

Besides the crash, the python process also doesn't terminate since the crashed thread seems to be stuck. I tried to fix the problem by catching the exception and explicitly closing/terminating the thread pool but that didn't fix the problem either.