Hi, I’m relatively new to pymc3 but hope someone can help. I have a very large model. When I run it for most of my datasets, it works fine and samples without problems. However, with a few of my datasets, it works intermittently. It sometimes finishes successfully like the others, but often crashes…

Hi @junpenglao , thanks for the response. I read that thread. It appears to be giving a way to identify the RV causing the trouble, but I already know which it is (it’s in the error above). Also, it seems like the error he had was a “bad initial energy: nan”, whereas I have the one with “derivativ…

Hi, Yeah I think usually these errors relate to the same problems – NaN values or zeros somewhere, making the log of these values unidentifed (if I remember correctly). It’s hard to say without looking at the model, but have standardized your predictors / outcome variables? If they are on large sc…

Hey, yeah, unfortunately the model is very large at this point, fitting to a bunch of data, so it’s hard to provide a MWE :frowning: However, one clue is that it works for all the other data sets, but for the one that it fails with, that dataset doesn’t have one of the observables (i.e., a “column…

[image] hamburgled: What do you mean by standardized, do you mean normalizing them so that they have mean ~ 0 and SD ~ 1 or something? Yeah exactly – that can really do magic! Other than that, it’s difficult for me to say anything else without the model. Hope this helps anyway, and good luc…

ah yeah. I know that’s a standard for features is deep learning, but I hadn’t heard of using it here… it works well for MCMC too? thanks!

Definitely works like a charm – should be the default behavior!

"ValueError: Mass matrix contains zeros on the diagonal" error, how to debug?

Questions

junpenglao February 10, 2020, 8:04pm 2

You can find some pointer here: Frequently Asked Questions

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"ValueError: Mass matrix contains zeros on the diagonal" error, how to debug?

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