KarrLab / wc_sim

A multi-algorithmic simulator for whole-cell models
MIT License
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Enhance RunResults #83

Open artgoldberg opened 4 years ago

artgoldberg commented 4 years ago

(Includes unfinished parts of #70.)

  1. Investigate warning generated by random_states_s.to_hdf(self._hdf_file(), 'random_states') in __init__():

The warning is:

/usr/local/lib/python3.6/site-packages/pandas/core/generic.py:1996 PerformanceWarning:
your performance may suffer as PyTables will pickle object types that it cannot
map directly to c-types [inferred_type->mixed,key->values] [items->None]
  1. Speed up convert_checkpoints by using MakeDataFrame to build aggregate_states_df.

  2. Have hdf use disk more efficiently; for unknown reasons, in one example hdf uses 4.4M to store the data in 52 pickle files of 8K each, more than 10x less efficient than pickle.