I'm trying to overwrite the pandas dataframe in hdf5 file. Each time I do this, the file size grows up while the stored frame content is the same. If I use mode='w' I lost all other records. Is this a bug or am I missing something? import pandas df = pandas.read_csv('1.csv') for i in range(100): store = pandas.HDFStore('tmp.h5') store.put('TMP', df) store.close() The tmp.h5 grows in size. Continue reading...