from pandas import (DataFrame, HDFStore) import pandas as pd import numpy as np import time d1 = np.random.random(size=(100000, 250000)) d2 = np.random.random(size=(100000, 250000)) timestr = time.strftime("%Y%m%d-%H%M%S") #hf = h5py.File('/gonzo/hdf5/'+timestr+'-data.h5', 'w') hf = HDFStore('/gonzo/hdf5/' + timestr + '-data.h5') df = DataFrame(np.random.randn(5, 3), columns['A', 'B', 'C']) store.put('d1', df, format='table', data_columns=True) hf.create_dataset('dataset_1', data=d1) hf.create_dataset('dataset_2', data=d2) hf.close()