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Fixing unreasonable memory usage when creating an InferenceData object from an emcee sampler #2215

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merged 4 commits into from
Feb 21, 2023
Merged

Fixing unreasonable memory usage when creating an InferenceData object from an emcee sampler #2215

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4f11090
Initializing the chain once in posterior_to_xarray
acpetit Feb 21, 2023
88722b5
Documenting fix
acpetit Feb 21, 2023
695218b
Apply suggestions from code review
OriolAbril Feb 21, 2023
03e6552
Merge branch 'main' into from_emcee-memoryspike
OriolAbril Feb 21, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
### New features

### Maintenance and fixes
- Fix memory usage and improve efficiency in `from_emcee` ([2215](https://github.com/arviz-devs/arviz/pull/2215))

### Deprecation

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11 changes: 6 additions & 5 deletions arviz/data/io_emcee.py
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Expand Up @@ -116,12 +116,13 @@ def __init__(
def posterior_to_xarray(self):
"""Convert the posterior to an xarray dataset."""
# Use emcee3 syntax, else use emcee2
if hasattr(self.sampler, "get_chain"):
samples_ary = self.sampler.get_chain().swapaxes(0, 1)
else:
samples_ary = self.sampler.chain

data = {
var_name: (
self.sampler.get_chain()[(..., idx)].swapaxes(0, 1)
if hasattr(self.sampler, "get_chain")
else self.sampler.chain[(..., idx)]
)
var_name: (samples_ary[(..., idx)])
for idx, var_name in zip(self.slices, self.var_names)
}
return dict_to_dataset(
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