I'm new to python and ubuntu. i got killed after running python code. The file I'm using for the code is around 2.7 GB and I have 16 GB RAM with one tera hard ... what should I do to avoid this problem because I'm searching and found it seems to be out of memory problem
I used this command
free -mh
I got
total used free shared buff/cache available
Mem: 15G 2.5G 9.7G 148M 3.3G 12G
Swap: 4.0G 2.0G 2.0G
the code link I tried Link
import numpy as np
import matplotlib.pyplot as plt
class ProcessData(object):
def data_process(self, folder):
'''
:folder: data file path
:rtype: dict pair distance
MAX id number
'''
distance = dict()
max_pt = 0
with open(folder, 'r') as data:
for line in data:
i, j, dis = line.strip().split()
i, j, dis = int(i), int(j), float(dis)
distance[(i, j)] = dis
distance[(j, i)] = dis
max_pt = max(i, j, max_pt)
for num in range(1, max_pt + 1):
distance[(num, num)] = 0
return distance, max_pt
def entropy(self, distance, maxid, factor):
'''
:distance: dict with pair: dist
:factor: impact factor
:maxid: max elem number
:rtype: entropy H in data field
'''
potential = dict()
for i in range(1, maxid + 1):
tmp = 0
for j in range(1, maxid + 1):
tmp += np.exp(-pow(distance[(i, j)] / factor, 2))
potential[i] = tmp
z = sum(potential.values())
H = 0
for i in range(1, maxid + 1):
x = potential[i] / z
H += x * np.log(x)
return -H
def threshold(self, dist, max_id):
'''
:rtype: factor value makes H smallest
'''
entro = 10.0
# given data:
# 0.02139999999999999 7.203581306901208
# 0.02149999999999999 7.203577254067677
# 0.02159999999999999 7.203577734107922
# generate data:
# 0.367020, 6.943842
# 0.368959, 6.943840
# 0.370898, 6.943841
scape = np.linspace(0.330, 0.430, 50)
# 通用数据使用以下一行
# scape = np.linspace(0.001, 1.001, 100)
for factor in scape:
value = self.entropy(dist, max_id, factor)
print('factor: {0:.6f}, entropy: {1:.8f}'.format(factor, value))
# plt.scatter(factor, value, c='r', s=1)
if value and value < entro:
entro, thresh = value, factor
thresh = 3 * thresh / pow(2, 0.5)
"""
plt.xlabel(r'$\sigma$')
plt.ylabel(r'H')
plt.savefig('./images/Entropy test.png')
plt.close()
"""
print('current: ', entro, thresh)
# given data: 7.203577254067677 0.04560838738653229
# generate data: 6.943840312796875 0.7828967189629044
return thresh
def CutOff(self, distance, max_id, threshold):
'''
:rtype: list with Cut-off kernel values by desc
'''
cut_off = dict()
for i in range(1, max_id + 1):
tmp = 0
for j in range(1, max_id + 1):
gap = distance[(i, j)] - threshold
tmp += 0 if gap >= 0 else 1
cut_off[i] = tmp
sorted_cutoff = sorted(cut_off.items(), key=lambda k:k[1], reverse=True)
return sorted_cutoff
def Guasse(self, distance, max_id, threshold):
'''
:rtype: list with Gaussian kernel values by desc
'''
guasse = dict()
for i in range(1, max_id + 1):
tmp = 0
for j in range(1, max_id + 1):
tmp += np.exp(-pow((distance[(i, j)] / threshold), 2))
guasse[i] = tmp
sorted_guasse = sorted(guasse.items(), key=lambda k:k[1], reverse=True)
return sorted_guasse
def min_distance(self, distance, srt_dens, maxid):
'''
:srt_dens: desc sorted list with density values (point, density)
:rtype: min distance dict
min number dict
'''
min_distance = dict()
min_number = dict()
h_dens = srt_dens[0][0]
min_number[h_dens] = 0
max_dist = -1
for i in range(1, maxid + 1):
max_dist = max(distance[(h_dens, i)], max_dist)
min_distance[h_dens] = max_dist
for j in range(1, len(srt_dens)):
min_dist, min_num = 1, 0
current_num = srt_dens[j][0]
for k in srt_dens[0:j]:
current_dist = distance[(current_num, k[0])]
if current_dist < min_dist:
min_dist, min_num = current_dist, k[0]
min_distance[srt_dens[j][0]] = min_dist
min_number[current_num] = min_num
return min_distance, min_number
def make_pair(self, srt_dens, min_dist, maxid):
'''
:rtype: pair dict with {point: [density, min dist]}
refer factor dict with {point: density * dist}
'''
pair_dict = dict()
dens_dict = dict()
refer_dict = dict()
# convert list to dict
for elem in srt_dens:
dens_dict[elem[0]] = elem[1]
if len(dens_dict) == maxid:
for key in dens_dict.keys():
pair_dict[key] = [dens_dict[key], min_dist[key]]
refer_dict[key] = dens_dict[key] * min_dist[key]
else:
return print('missing %d value', maxid - dens_dict)
return pair_dict, refer_dict
def show_pair_info(self, pair, threshold):
show_dict = dict()
for p in pair.values():
show_dict[p[0]] = p[1]
tmp = sorted(show_dict.items())
dens, mdis = zip(*tmp)
plt.scatter(dens, mdis)
plt.xlabel(r'$\rho$')
plt.ylabel(r'$\delta$')
plt.title(r'$d_c=$' + str(threshold))
plt.savefig('./images/Decision Graph Cutoff test.png')
plt.close()
I tried to figure by using fil-profile and got a problem with line 11 which indicate this data_process
