I have created a mathematical model in python. I want to make a standalone python executable for my model. The python script uses several python libraries like numpy, pandas, pymc3. I tried to make a python executable using pyinstaller and also auto-py-to-exe. In both cases, it failed to create the executable. The error occurs while importing the pymc3 module (theano library). My primary model is dependent on pymc3 module. I cannot bypass this module. Could anyone please help me to sort out this issue?
I am not at all experienced with creating executables - that is an interesting use case! What sort of error message are you seeing? I worry that you might find better help from the pyinstaller or auto-py-to-exe communities…
Here is the error message I get when I execute the converted .exe file,
WARNING (theano.tensor.blas): Using NumPy C-API based implementation for BLAS functions.
c:\python\lib\site-packages\PyInstaller\loader\pyimod03_importers.py:621: MatplotlibDeprecationWarning:
The MATPLOTLIBDATA environment variable was deprecated in Matplotlib 3.1 and will be removed in 3.3.
exec(bytecode, module.__dict__)
Traceback (most recent call last):
File "sample.py", line 46, in <module>
File "<frozen importlib._bootstrap>", line 983, in _find_and_load
File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
File "c:\python\lib\site-packages\PyInstaller\loader\pyimod03_importers.py", line 621, in exec_module
exec(bytecode, module.__dict__)
File "site-packages\pymc3\__init__.py", line 11, in <module>
File "<frozen importlib._bootstrap>", line 983, in _find_and_load
File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
File "c:\python\lib\site-packages\PyInstaller\loader\pyimod03_importers.py", line 621, in exec_module
exec(bytecode, module.__dict__)
File "site-packages\pymc3\stats.py", line 20, in <module>
File "site-packages\pkg_resources\__init__.py", line 481, in get_distribution
File "site-packages\pkg_resources\__init__.py", line 357, in get_provider
File "site-packages\pkg_resources\__init__.py", line 900, in require
File "site-packages\pkg_resources\__init__.py", line 786, in resolve
pkg_resources.DistributionNotFound: The 'scipy' distribution was not found and is required by the application
[13796] Failed to execute script sample
Here is the python script (sample.py)
class modelFit:
# Initialises the attributes
def __init__(self, x, y):
self.x = x
self.y = y
# Performs the Bayes estimation
def coeffEstimation(self):
X = np.array(self.x)
Y = np.array(self.y)
with pm.Model() as linearRegModel:
# Define priors
#regCoeff = pm.HalfNormal('regCoeff', sd = 20, shape=X.shape[1])
regCoeff = pm.Uniform('regCoeff', lower = 0, upper = 100, shape=X.shape[1])
# Standard deviation
sigma = pm.HalfNormal('sigma', sd = 5)
# Estimate of mean
mean = pm.math.dot(X, regCoeff)
# Likelihood estimate
likelihood = pm.Normal('Y_estimated', mu = mean, sd = sigma, observed = Y)
# Sampler
step = pm.NUTS()
# Posterior distribution
linearTrace = pm.sample(draws = 500, chains = 1,
tune = 500, nuts_kwargs=dict(target_accept=0.95))
with open('Summary.txt', 'w') as f:
print(pm.summary(linearTrace).round(3), file=f)
diverging = linearTrace['diverging']
print('Number of Divergent Chains: {}'.format(diverging.nonzero()[0].size), file=f)
divergingPer = diverging.nonzero()[0].size / len(linearTrace) * 100
print('Percentage of Divergent Chains: {:.1f}'.format(divergingPer), file=f)
print('Bayesian Inference Done! Exporting the results, Please hold on!')
return(linearTrace)
import theano.tensor.shared_randomstreams
import scipy
import pymc3 as pm
import numpy as np
import pandas as pd
dataLocation = './input/'
inputData = pd.read_excel(dataLocation + 'input.xlsx')
sizeInputData = inputData.shape
x = inputData.iloc[:,1:sizeInputData[1]]
y = inputData.iloc[:,0]
# Executes the Bayes method
linReg = modelFit(x, y)
regTrace = linReg.coeffEstimation()
It looks like the environment is missing scipy. Can you make sure it works without pymc3/theano?
Thank you.
Without pymc3 module, I could able to convert the script to standalone executable. It runs fine without any issues.
Problem comes only while importing pymc3.
Now, I could get rid of the import issues,
pkg_resources.DistributionNotFound: The 'scipy' distribution was not found and is required by the application
[13796] Failed to execute script sample
But now there is some issue with compilation. Could you please help me in this regard?
Thank you.
Here is the error message,
WARNING (theano.tensor.blas): Using NumPy C-API based implementation for BLAS functions.
c:\python\lib\site-packages\PyInstaller\loader\pyimod03_importers.py:621: MatplotlibDeprecationWarning:
The MATPLOTLIBDATA environment variable was deprecated in Matplotlib 3.1 and will be removed in 3.3.
exec(bytecode, module.__dict__)
You can find the C code in this temporary file: C:\Users\Vimal\AppData\Local\Temp\theano_compilation_error_tyojr99y
Traceback (most recent call last):
File "sample.py", line 66, in <module>
File "sample.py", line 15, in coeffEstimation
File "site-packages\pymc3\distributions\distribution.py", line 46, in __new__
File "site-packages\pymc3\model.py", line 833, in Var
File "site-packages\pymc3\model.py", line 1557, in __init__
File "site-packages\pymc3\distributions\transforms.py", line 95, in apply
File "site-packages\pymc3\distributions\distribution.py", line 56, in dist
File "site-packages\pymc3\distributions\transforms.py", line 125, in __init__
File "site-packages\pymc3\model.py", line 1274, in __init__
File "site-packages\pymc3\distributions\continuous.py", line 224, in logp
File "site-packages\theano\tensor\var.py", line 69, in __ge__
File "site-packages\theano\gof\op.py", line 615, in __call__
File "site-packages\theano\tensor\elemwise.py", line 482, in make_node
File "site-packages\theano\tensor\elemwise.py", line 438, in get_output_info
File "site-packages\theano\gof\op.py", line 670, in __call__
File "site-packages\theano\gof\op.py", line 955, in make_thunk
File "site-packages\theano\gof\op.py", line 858, in make_c_thunk
File "site-packages\theano\gof\cc.py", line 1217, in make_thunk
File "site-packages\theano\gof\cc.py", line 1157, in __compile__
File "site-packages\theano\gof\cc.py", line 1624, in cthunk_factory
File "site-packages\theano\gof\cmodule.py", line 1189, in module_from_key
File "site-packages\theano\gof\cc.py", line 1527, in compile_cmodule
File "site-packages\theano\gof\cmodule.py", line 2396, in compile_str
Exception: ('Compilation failed (return status=1): C:\\Users\\Vimal\\AppData\\Local\\Theano\\compiledir_Windows-10-10.0.17763-SP0-Intel64_Family_6_Model_142_Stepping_10_GenuineIntel-3.7.4-64\\tmp_yb6bb2e\\mod.cpp:1:10: fatal error: Python.h: No such file or directory. #include <Python.h>. ^~~~~~~~~~. compilation terminated.\r. ', '[InplaceDimShuffle{x}(TensorConstant{0.0})]')
[1820] Failed to execute script sample