TypeError: cannot serialize '_io.TextIOWrapper' while pickling conformer objects generated by HotBit

ReactionMechanismGenerator / AutoTST

AutoTST: A framework to perform automated transition state theory calculations

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TypeError: cannot serialize '_io.TextIOWrapper' while pickling conformer objects generated by HotBit #46

Closed skrsna closed 4 years ago

skrsna commented 4 years ago

Pickling Conformer objects generated by HotBit calculator leads to TypeError: cannot serialize '_io.TextIOWrapper' error. Googling this error resulted in several posts stating that this is unsolvable and inherent in multiprocessing and I don't know where I should look if I were to fix it. I'm just opening this issue to keep track of it.

rwest commented 4 years ago

What is the object you’re trying to serialize? Some part of Conformer?

rwest commented 4 years ago

https://docs.python.org/3/library/pickle.html#pickling-class-instances

skrsna commented 4 years ago

I'm trying to pickle the whole Conformer object to update the Mongo Collection. Using EMT or DFTB calculators doesn't give this error though. But I'll look into how to solve this.

rwest commented 4 years ago

Try to figure out which part of the conformer object is causing the problem. Presumably some attached Calculator or something.

skrsna commented 4 years ago

Fixed this by remaking the Conformer objects using _ase_molecule attribute.