Unable to process large data set??

[mkcedward]

I have a data set which is more than 100k records. When I try to fit into AutoSklearnRegressor, it always thrown an warning. It seems causing that I cannot get a expected output.

However, if number of records is small enough (says less than 20k), it can execute without any warming/ error. May you advise this situation? I am using 0.2 version

Sample code

import autosklearn.regression
import numpy as np

x = np.random.randint(2, size=(250000,100))
y = np.random.randint(2, size=(250000,1))


feature_types = (['numerical'] * 100)
automl = autosklearn.regression.AutoSklearnRegressor(
    time_left_for_this_task=120, per_run_time_limit=30
)
automl.fit(x, y, dataset_name='boston', feat_type=feature_types)

The exception is

WARNING] [2017-10-26 11:21:28,580:AutoMLSMBO(1)::boston] Could not find meta-data directory /home/anaconda3/lib/python3.5/site-packages/autosklearn/metalearning/files/r2_regression_dense

/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal

[mfeurer]

Thank you very much for reporting this, it seems like there is a bug. It appears that the bug is triggered from none of the evaluations of the machine learning algorithm actually succeeding. When you go from 20000 to 100000 samples, you should increase the time you give the ML algorithms to fit the data (increase per_run_time_limit).

[mkcedward]

Tried to increase both time_left_for_this_task and per_run_time_limit to 3000 but it cannot be applied. According to API for AutoSklearnRegressor, seems that there is no other value that I can change for time related param

The warning message is

Time limit for a single run is higher than total time limit. Capping the limit for a single run to the total time given to SMAC (2999.003905)

[mfeurer]

Try setting time_left_for_this_task to 3000 and per_run_time_limit to 600. The second one must be smaller than the first one, it is the time given to a single call of a machine learning algorithm.

[mkcedward]

import autosklearn.regression
import numpy as np
import datetime

x = np.random.randint(2, size=(250000,100))
y = np.random.randint(2, size=(250000,1))

print(datetime.datetime.now(), 'start')
feature_types = (['numerical'] * 100)

automl = autosklearn.regression.AutoSklearnRegressor(
    time_left_for_this_task=3000, per_run_time_limit=600
)

automl.fit(x, y, dataset_name='boston', feat_type=feature_types)

Tried the above code, but the warming is thrown after 1 ~ 2 mins.

[mfeurer]

I can neither reproduce this with autosklearn==0.2.0 or autosklearn==0.2.1. Could you please paste the full output of auto-sklearn?

[mkcedward]

2017-11-05 01:50:48.096598 start
[WARNING] [2017-11-05 01:50:49,322:AutoMLSMBO(1)::boston] Could not find meta-data directory /home/anaconda3/lib/python3.5/site-packages/autosklearn/metalearning/files/r2_regression_dense

/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():

/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():

/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():

/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
You are already timing task: index_run2
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():

You are already timing task: index_run2
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():

/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
You are already timing task: index_run2
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():

/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():

You are already timing task: index_run3
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():

/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: divide by zero encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:737: RuntimeWarning: invalid value encountered in true_divide
  (1. - dataset_minimum))
/home/anaconda3/lib/python3.5/site-packages/autosklearn/smbo.py:738: RuntimeWarning: invalid value encountered in greater
  Y_cfg[:, 0][Y_cfg[:, 0] > 2] = 2
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
  return (self.a < x) & (x < self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1735: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= self.b) & cond0
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in greater_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in less_equal
  return (self.a <= x) & (x <= self.b)
/home/anaconda3/lib/python3.5/site-packages/smac/optimizer/acquisition.py:164: RuntimeWarning: invalid value encountered in less
  if (f < 0).any():

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-1-439ee93732dd> in <module>()
     13 )
     14 
---> 15 automl.fit(x, y, dataset_name='boston', feat_type=feature_types)

/home/anaconda3/lib/python3.5/site-packages/autosklearn/estimators.py in fit(self, X, y, metric, feat_type, dataset_name)
    487         return super(AutoSklearnRegressor, self).fit(X=X, y=y, metric=metric,
    488                                                      feat_type=feat_type,
--> 489                                                      dataset_name=dataset_name)
    490 
    491     def predict(self, X, batch_size=None, n_jobs=1):

/home/anaconda3/lib/python3.5/site-packages/autosklearn/estimators.py in fit(self, *args, **kwargs)
    302     def fit(self, *args, **kwargs):
    303         self._automl = self.build_automl()
--> 304         super(AutoSklearnEstimator, self).fit(*args, **kwargs)
    305 
    306     def fit_ensemble(self, y, task=None, metric=None, precision='32',

/home/anaconda3/lib/python3.5/site-packages/autosklearn/estimators.py in fit(self, *args, **kwargs)
     21 
     22     def fit(self, *args, **kwargs):
---> 23         self._automl.fit(*args, **kwargs)
     24 
     25     def refit(self, X, y):

/home/anaconda3/lib/python3.5/site-packages/autosklearn/estimators.py in fit(self, X, y, metric, feat_type, dataset_name)
    619             metric = r2
    620         return self._automl.fit(X=X, y=y, task=REGRESSION, metric=metric,
--> 621                                 feat_type=feat_type, dataset_name=dataset_name)

/home/anaconda3/lib/python3.5/site-packages/autosklearn/automl.py in fit(self, X, y, task, metric, feat_type, dataset_name)
    193                                             dataset_name=dataset_name)
    194 
--> 195         return self._fit(loaded_data_manager, metric)
    196 
    197     def fit_automl_dataset(self, dataset, metric):

/home/anaconda3/lib/python3.5/site-packages/autosklearn/automl.py in _fit(self, datamanager, metric)
    463 
    464         self._proc_ensemble = None
--> 465         self._load_models()
    466 
    467         return self

/home/anaconda3/lib/python3.5/site-packages/autosklearn/automl.py in _load_models(self)
    628         if self.ensemble_:
    629             identifiers = self.ensemble_.identifiers_
--> 630             self.models_ = self._backend.load_models_by_identifiers(identifiers)
    631             if len(self.models_) == 0 and self._resampling_strategy not in \
    632                     ['partial-cv', 'partial-cv-iterative-fit']:

/home/anaconda3/lib/python3.5/site-packages/autosklearn/util/backend.py in load_models_by_identifiers(self, identifiers)
    311         for identifier in identifiers:
    312             seed, idx = identifier
--> 313             models[identifier] = self.load_model_by_seed_and_id(seed, idx)
    314 
    315         return models

/home/anaconda3/lib/python3.5/site-packages/autosklearn/util/backend.py in load_model_by_seed_and_id(self, seed, idx)
    321         model_file_path = os.path.join(model_directory, model_file_name)
    322         with open(model_file_path, 'rb') as fh:
--> 323             return pickle.load(fh)
    324 
    325     def get_ensemble_dir(self):

/home/anaconda3/lib/python3.5/site-packages/sklearn/cluster/__init__.py in <module>()
      4 """
      5 
----> 6 from .spectral import spectral_clustering, SpectralClustering
      7 from .mean_shift_ import (mean_shift, MeanShift,
      8                           estimate_bandwidth, get_bin_seeds)

/home/anaconda3/lib/python3.5/site-packages/sklearn/cluster/spectral.py in <module>()
     15 from ..metrics.pairwise import pairwise_kernels
     16 from ..neighbors import kneighbors_graph
---> 17 from ..manifold import spectral_embedding
     18 from .k_means_ import k_means
     19 

/home/anaconda3/lib/python3.5/site-packages/sklearn/manifold/__init__.py in <module>()
      7 from .mds import MDS, smacof
      8 from .spectral_embedding_ import SpectralEmbedding, spectral_embedding
----> 9 from .t_sne import TSNE
     10 
     11 __all__ = ['locally_linear_embedding', 'LocallyLinearEmbedding', 'Isomap',

/home/anaconda3/lib/python3.5/site-packages/sklearn/manifold/t_sne.py in <module>()
     23 from ..metrics.pairwise import pairwise_distances
     24 from . import _utils
---> 25 from . import _barnes_hut_tsne
     26 from ..externals.six import string_types
     27 from ..utils import deprecated

sklearn/neighbors/quad_tree.pxd in init sklearn.manifold._barnes_hut_tsne()

sklearn/tree/_tree.pxd in init sklearn.neighbors.quad_tree()

ValueError: sklearn.tree._tree.TreeBuilder has the wrong size, try recompiling. Expected 72, got 80

[darxriggs]

In can reproduce the given example (boston dataset) with autosklearn==0.2.1 and sklearn==0.18.2.
I also get similar warnings with another dataset when the number of rows exceeds a certain amount.

[mkcedward]

Would like to supplement, my sklearn version is 0.19.1

[mfeurer]

I am surprised that you are able to auto-sklearn with scikit-learn 0.19.1, or are you using the development branch?

The issue with the tree builder looks weird. Is this on one machine after fitting is done? Or is fitting done on a different machine than you actually try to load the data? Anyway, it might be best if you open a new issue for that because it seems unrelated to the actual issue of this thread.

Regarding the actual issue, I come to believe that this is actually a bug. I will have a closer look with the current development version on Monday and will hopefully be able to fix this for the upcoming release.

[mkcedward]

scikit-learn 0.19.1 is released on Oct 2017. As I am eager to try new feature, i will also try the latest version. :)
http://scikit-learn.org/stable/whats_new.html#version-0-19-1

Currently, I am using single VM to execute those code.

[mkcedward]

Created another thread for tracking this issue. #390

[mfeurer]

Please excuse the delay with the promised release. I'm actually having problems to start on a big dataset myself at the moment and am hunting down a memory leak. @mkcedward did you ever encounter this?

[mfeurer]

Okay, I finally managed to push a new release. Could you please check if the issue is still there?

[darxriggs]

Good job. Running the example code given in the issue description with autosklearn==0.3.0 doesn't generate the given RuntimeWarnings anymore.

[mfeurer]

Does it give reasonable results? If yes, could you please close the issue?

[darxriggs]

I just tried auto-sklearn some months ago and run into this issue reported by @mkcedward.
Therefore I can just confirm that the warnings are gone but it's not possbile for me to assess the results.

[mfeurer]

I just pushed a new release - please reopen if this issue is still present with the latest version.