[SciPy-User] Segmentation fault (core dumped)

Sema Atasever s.atasever at gmail.com
Thu Oct 12 09:34:31 EDT 2017

Dear scipy-users:

I am trying to write a python program which uses SciPy library that makes
hierarchical clustering.

After I type in my input at the "shell> " prompt:  *python
SciPy_clustering.py *

gives me the following error:

*Segmentation fault (core dumped)*

How can i fix this problem?

There is enough memory on my system (516 GB), python code uses just 21GB

My dataset includes 73.622 data samples (rows)  and 22 features (columns).
When i shrink dataset (31.000) it works fine correctly.

Thanks in Advance.

*python Clustering Code:*
# needed imports
import numpy as np
import time
from matplotlib import pyplot as plt
from scipy.cluster.hierarchy import dendrogram, linkage
from scipy.cluster.hierarchy import cophenet
from scipy.spatial.distance import pdist

start_time = time.clock()

X=np.loadtxt(open("dataset.txt", "rb"), delimiter=";")

print ('\nX.shape')
print (X.shape)

# generate the linkage matrix
Z = linkage(X, 'single')

np.savetxt('Z_output.txt', Z, fmt='%-7.5f')

c, coph_dists = cophenet(Z, pdist(X))

print("Cophenetic Correlation Coefficient : \n")

print("\nRunning Time:")
print (time.clock() - start_time, "seconds")
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