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Can't load restart - pickling problems? #114
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I think this particular problem is addressed by d8b38a0
(When the extra frequencies were being estimated, the frequencies'value_siarray was extended but itsuncertaintyarray was not).
But so far nothing has been done to check for other errors of this type (eg. a check on set for value or value_si)The above commit does indeed solve the loading from restart problem, but now immediately after loading we fail to save the HTML output:
Loading previous restart file...
Saving current model to HTML file...Stack trace:
File "/nics/d/home/rwest/Code/RMG-Py/rmgpy/rmg/main.py", line 361, in execute self.saveEverything() File "/nics/d/home/rwest/Code/RMG-Py/rmgpy/rmg/main.py", line 517, in saveEverything self.saveOutputHTML() File "/nics/d/home/rwest/Code/RMG-Py/rmgpy/rmg/main.py", line 658, in saveOutputHTML saveOutputHTML(os.path.join(self.outputDirectory, 'output.html'), self.reactionModel) File "/nics/d/home/rwest/Code/RMG-Py/rmgpy/rmg/output.py", line 113, in saveOutputHTML family = rxn.getSource().label AttributeError: 'rmgpy.reaction.Reaction' object has no attribute 'getSource'
Seems we can't save reactions that came from a restart? Is the source being pickled correctly?
The source depends on the type of reaction being saved. I think in this case it's
rmgpy.rmg.pdep.PDepReactionthat is the issue; it is missing a specialized__reduce__()method, so it's using the one from the base class, which doesn't know how to save the source.- added a commit that references this issue
on May 2, 2013
I am getting this when I try to restart the methylformate example:
I'm not sure what the offending object is, but it's something with units of
cm^-1. I'm guessing vibrational frequencies (first four integer ones from Franklin's groups, last 3 floats from fitting to the Cp). Not sure why it only has 3 uncertainties (that are all zero!).Do we have a unit test on pickling and unpickling of frequencies?