[SciPy-User] Segmentation fault (core dumped)

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[SciPy-User] Segmentation fault (core dumped)

Sema Atasever
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 memory.

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(c)

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

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Re: Segmentation fault (core dumped)

Daπid
How far in your code do you reach? That will help narrowing down the problem.

Also, do you have the core dump? Can you run gdb on it?

On 12 October 2017 at 15:34, Sema Atasever <[hidden email]> wrote:
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 memory.

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(c)

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

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SciPy-User mailing list
[hidden email]
https://mail.python.org/mailman/listinfo/scipy-user



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SciPy-User mailing list
[hidden email]
https://mail.python.org/mailman/listinfo/scipy-user