snap-python
snap-python copied to clipboard
snap-stanford
TNEANet memory leak
This was tested with snap-4.1.0-4.1-centos6.5-x64-py2.6
I took the tneanet.py test from the test folder and changed it so that to each edge an str attribute "attr5" with a fixed value is added. Then in an endless while loop, I go over all the edges and get that str attribute. using top, you will notice how the RES memory keeps increasing.
is this some sort of reference count problem, i.e. the object is not release/collected by gc?
import random
import sys
import snap
from time import sleep
def ManipulateAttributesIter():
"""
Test node, edge attribute functionality using iterators
"""
NNodes = 1000
NEdges = 1000
Graph = snap.TNEANet.New()
t = Graph.Empty()
# create the nodes
for i in range(0, NNodes):
Graph.AddNode(i)
t = Graph.Empty()
n = Graph.GetNodes()
# create random edges
NCount = NEdges
while NCount > 0:
x = int(random.random() * NNodes)
y = int(random.random() * NNodes)
# skip the loops in this test
if x != y and not Graph.IsEdge(x, y):
n = Graph.AddEdge(x, y)
NCount -= 1
print "Added nodes"
attr1 = "STR"
attr2 = "INT"
attr3 = "FLOAT"
attr4 = "DEFAULT"
attr5 = "TEST"
# Test column int iterator for node 3, 50, 700, 900
# Check if we can set defaults to 0 fordata.
Graph.AddIntAttrN(attr2, 0)
NI3 = Graph.GetNI(3)
NI50 = Graph.GetNI(50)
NI700 = Graph.GetNI(700)
NI900 = Graph.GetNI(900)
Graph.AddIntAttrDatN(NI3, 3 * 2, attr2)
Graph.AddIntAttrDatN(NI50, 50 * 2, attr2)
Graph.AddIntAttrDatN(NI700, 700 * 2, attr2)
Graph.AddIntAttrDatN(NI900, 900 * 2, attr2)
print "Added attributes"
NodeId = 0
NI = Graph.BegNAIntI(attr2)
while NI < Graph.EndNAIntI(attr2):
if NI.GetDat() != 0:
print "Attribute1: %s, Node: %i, Val: %d" % (attr2, NodeId, NI.GetDat())
# print "Attribute: %s, Node: %i, Val: %d" % (attr2(), NodeId, NI.GetDat())
NodeId += 1
NI.Next()
# Test column flt iterator for node 3, 50, 700, 900
NI5 = Graph.GetNI(5)
NI50 = Graph.GetNI(50)
NI300 = Graph.GetNI(300)
NI653 = Graph.GetNI(653)
Graph.AddFltAttrDatN(NI5, 3.41, attr3)
Graph.AddFltAttrDatN(NI50, 2.718, attr3)
Graph.AddFltAttrDatN(NI300, 150.0, attr3)
Graph.AddFltAttrDatN(NI653, 653, attr3)
NodeId = 0
NCount = 0
NI = Graph.BegNI()
while NI < Graph.EndNI():
NCount += 1
NI.Next()
NI = Graph.BegNAFltI(attr3)
NodeId = 0
while NI < Graph.EndNAFltI(attr3):
if NI.GetDat() != snap.TFlt.Mn:
print "Attribute2: %s, Node: %i, Val: %f" % (attr3, NodeId, NI.GetDat())
# print "Attribute: %s, Node: %i, Val: %f" % (attr3(), NodeId, NI.GetDat())
NodeId += 1
NI.Next()
# Test column str iterator for node 3, 50, 700, 900
NI10 = Graph.GetNI(10)
NI20 = Graph.GetNI(20)
NI400 = Graph.GetNI(400)
Graph.AddStrAttrDatN(NI10, "abc", attr1)
Graph.AddStrAttrDatN(NI20, "def", attr1)
Graph.AddStrAttrDatN(NI400, "ghi", attr1)
# this does not show since ""=null
# Graph.AddStrAttrDatN(455, TStr(""), attr1)
# TODO Graph.AddStrAttrDatN(455, "", attr1)
NodeId = 0
NI = Graph.BegNAStrI(attr1)
NodeId = 0
while NI < Graph.EndNAStrI(attr1):
if NI.GetDat() != snap.TStr.GetNullStr():
print "Attribute3: %s, Node: %i, Val: %s" % (attr1, NodeId, NI.GetDat())
# print "Attribute: %s, Node: %i, Val: %s" % (attr1(), NodeId, NI.GetDat())
NodeId += 1
NI.Next()
# Test column iterator over many types (must skip default/deleted attr)
NId = 55
NI55 = Graph.GetNI(55)
NI80 = Graph.GetNI(80)
# Graph.AddStrAttrDatN(NId, TStr("aaa"), attr1)
Graph.AddStrAttrDatN(NI55, "aaa", attr1)
Graph.AddIntAttrDatN(NI55, 3 * 2, attr2)
Graph.AddFltAttrDatN(NI55, 3.41, attr3)
# Graph.AddStrAttrDatN(80, TStr("dont appear"), attr4) # should not show up
Graph.AddStrAttrDatN(NI80, "dont appear", attr4) # should not show up
attr1idx = Graph.GetAttrIndN(attr1)
attr2idx = Graph.GetAttrIndN(attr2)
attr3idx = Graph.GetAttrIndN(attr3)
attr4idx = Graph.GetAttrIndN(attr4)
print "Node attribute indexes: %s %d, %s %d, %s %d, %s %d" % (
attr1, attr1idx, attr2, attr2idx, attr3, attr3idx, attr4, attr4idx)
NI = Graph.GetNI(NId)
print "NI attributes: %i, %s %d %.2f" % (
NI.GetId(),
Graph.GetStrAttrDatN(NI, attr1),
Graph.GetIntAttrDatN(NI, attr2),
Graph.GetFltAttrDatN(NI, attr3))
print "ind attributes: %i, %s %d %.2f" % (
NI.GetId(),
Graph.GetStrAttrIndDatN(NI, attr1idx),
Graph.GetIntAttrIndDatN(NI, attr2idx),
Graph.GetFltAttrIndDatN(NI, attr3idx))
NIdAttrName = snap.TStrV()
NIdAttrValue = snap.TStrV()
NIdIntAttrValue = snap.TIntV()
NIdFltAttrValue = snap.TFltV()
NIdStrAttrValue = snap.TStrV()
Graph.AttrNameNI(NId, NIdAttrName)
AttrLen = NIdAttrName.Len()
for i in range(AttrLen):
print "Vertical Node1: %i, Attr: %s" % (NId, NIdAttrName.GetI(i)())
NIdAttrName = snap.TStrV()
Graph.IntAttrNameNI(NId, NIdAttrName)
AttrLen = NIdAttrName.Len()
for i in range(AttrLen):
print "Vertical Node11 (int): %i, Attr: %s" % (NId, NIdAttrName.GetI(i)())
NIdAttrName = snap.TStrV()
Graph.FltAttrNameNI(NId, NIdAttrName)
AttrLen = NIdAttrName.Len()
for i in range(AttrLen):
print "Vertical Node12 (flt): %i, Attr: %s" % (NId, NIdAttrName.GetI(i)())
NIdAttrName = snap.TStrV()
Graph.StrAttrNameNI(NId, NIdAttrName)
AttrLen = NIdAttrName.Len()
for i in range(AttrLen):
print "Vertical Node13 (str): %i, Attr: %s" % (NId, NIdAttrName.GetI(i)())
Graph.IntAttrValueNI(NId, NIdIntAttrValue)
AttrLen = NIdIntAttrValue.Len()
for i in range(AttrLen):
print "Vertical Node14 (int): %i, Attr_Val: %d" % (NId, NIdIntAttrValue.GetI(i)())
Graph.FltAttrValueNI(NId, NIdFltAttrValue)
AttrLen = NIdFltAttrValue.Len()
for i in range(AttrLen):
print "Vertical Node15 (flt): %i, Attr_Val: %.2f" % (NId, NIdFltAttrValue.GetI(i)())
Graph.StrAttrValueNI(NId, NIdStrAttrValue)
AttrLen = NIdStrAttrValue.Len()
for i in range(AttrLen):
print "Vertical Node16 (str): %i, Attr_Val: %s" % (NId, NIdStrAttrValue.GetI(i)())
Graph.DelAttrDatN(NId, attr2)
Graph.AttrNameNI(NId, NIdAttrName)
AttrLen = NIdAttrName.Len()
for i in range(AttrLen):
print "Vertical Node2 (no int) : %i, Attr: %s" % (NId, NIdAttrName.GetI(i)())
Graph.AddIntAttrDatN(NId, 3 * 2, attr2)
Graph.DelAttrN(attr1)
Graph.AttrNameNI(NId, NIdAttrName)
AttrLen = NIdAttrName.Len()
for i in range(AttrLen):
print "Vertical Node3 (no str) : %i, Attr: %s" % (NId, NIdAttrName.GetI(i)())
Graph.AttrValueNI(NId, NIdAttrValue)
AttrLen = NIdAttrValue.Len()
for i in range(AttrLen):
print "Vertical Node4 (no str) : %i, Attr_Val: %s" % (NId, NIdAttrValue.GetI(i)())
for i in range(NNodes):
Graph.AddIntAttrDatN(i, 70, attr2)
total = 0
NI = Graph.BegNAIntI(attr2)
while NI < Graph.EndNAIntI(attr2):
total += NI.GetDat()
NI.Next()
print "Average: %i (should be 70)" % (total / NNodes)
if total / NNodes != 70:
print "*** Error3"
# Test column iterator for edge
EI3 = Graph.GetEI(3)
EI55 = Graph.GetEI(55)
EI705 = Graph.GetEI(705)
EI905 = Graph.GetEI(905)
Graph.AddIntAttrDatE(EI3, 3 * 2, attr2)
Graph.AddIntAttrDatE(EI55, 55 * 2, attr2)
Graph.AddIntAttrDatE(EI705, 705 * 2, attr2)
Graph.AddIntAttrDatE(EI905, 905 * 2, attr2)
EdgeId = 0
EI = Graph.BegEAIntI(attr2)
while EI < Graph.EndEAIntI(attr2):
if EI.GetDat() != snap.TInt.Mn:
print "E Attribute1: %s, Edge: %i, Val: %i" % (
attr2, EdgeId, EI.GetDat())
# % (attr2(), EdgeId, EI.GetDat())
EdgeId += 1
EI.Next()
# Test column flt iterator for edge
Graph.AddFltAttrE(attr3, 0.00)
EI5 = Graph.GetEI(5)
EI50 = Graph.GetEI(50)
EI300 = Graph.GetEI(300)
EI653 = Graph.GetEI(653)
Graph.AddFltAttrDatE(EI5, 4.41, attr3)
Graph.AddFltAttrDatE(EI50, 3.718, attr3)
Graph.AddFltAttrDatE(EI300, 151.0, attr3)
Graph.AddFltAttrDatE(EI653, 654, attr3)
EdgeId = 0
EI = Graph.BegEAFltI(attr3)
while EI < Graph.EndEAFltI(attr3):
# Check if defaults are set to 0.
if EI.GetDat() != 0:
print "E Attribute2: %s, Edge: %i, Val: %f" % (
attr3, EdgeId, EI.GetDat())
# (attr3(), EdgeId, EI.GetDat())
EdgeId += 1
EI.Next()
# Test column str iterator for edge
EI10 = Graph.GetEI(10)
EI20 = Graph.GetEI(20)
EI400 = Graph.GetEI(400)
Graph.AddStrAttrDatE(EI10, "abc", attr1)
Graph.AddStrAttrDatE(EI20, "def", attr1)
Graph.AddStrAttrDatE(EI400, "ghi", attr1)
# this does not show since ""=null
# Graph.AddStrAttrDatE(455, TStr(""), attr1)
# TODO Graph.AddStrAttrDatE(455, "", attr1)
EdgeId = 0
EI = Graph.BegEAStrI(attr1)
while EI < Graph.EndEAStrI(attr1):
if EI.GetDat() != snap.TStr.GetNullStr():
print "E Attribute3: %s, Edge: %i, Val: %s" % (
attr1, EdgeId, EI.GetDat())
# (attr1(), EdgeId, EI.GetDat())
EdgeId += 1
EI.Next()
# Test column iterator over many types (must skip default/deleted attr)
EId = 55
EI55 = Graph.GetEI(55)
EI80 = Graph.GetEI(80)
# Graph.AddStrAttrDatE(EId, TStr("aaa"), attr1)
Graph.AddStrAttrDatE(EI55, "aaa", attr1)
Graph.AddIntAttrDatE(EI55, 3 * 2, attr2)
Graph.AddFltAttrDatE(EI55, 3.41, attr3)
# Graph.AddStrAttrDatE(80, TStr("dont appear"), attr4) # should not show up
Graph.AddStrAttrDatE(EI80, "dont appear", attr4) # should not show up
attr1idx = Graph.GetAttrIndE(attr1)
attr2idx = Graph.GetAttrIndE(attr2)
attr3idx = Graph.GetAttrIndE(attr3)
attr4idx = Graph.GetAttrIndE(attr4)
print "Edge attribute indexes: %s %d, %s %d, %s %d, %s %d" % (
attr1, attr1idx, attr2, attr2idx, attr3, attr3idx, attr4, attr4idx)
EI = Graph.GetEI(EId)
print "EI attributes: %i, %s %d %.2f" % (
EI.GetId(),
Graph.GetStrAttrDatE(EI, attr1),
Graph.GetIntAttrDatE(EI, attr2),
Graph.GetFltAttrDatE(EI, attr3))
print "ind attributes: %i, %s %d %.2f" % (
EI.GetId(),
Graph.GetStrAttrIndDatE(EI, attr1idx),
Graph.GetIntAttrIndDatE(EI, attr2idx),
Graph.GetFltAttrIndDatE(EI, attr3idx))
EIdAttrName = snap.TStrV()
EIdAttrValue = snap.TStrV()
Graph.AttrNameEI(EId, EIdAttrName)
AttrLen = EIdAttrName.Len()
for i in range(AttrLen):
print "Vertical Edge1: %i, Attr: %s" % (EId, EIdAttrName.GetI(i)())
Graph.DelAttrDatE(EId, attr2)
Graph.AttrNameEI(EId, EIdAttrName)
AttrLen = EIdAttrName.Len()
for i in range(AttrLen):
print "Vertical Edge2 (no int) : %i, Attr: %s" % (EId, EIdAttrName.GetI(i)())
Graph.AddIntAttrDatE(EId, 3 * 2, attr2)
Graph.DelAttrE(attr1)
Graph.AttrNameEI(EId, EIdAttrName)
AttrLen = EIdAttrName.Len()
for i in range(AttrLen):
print "Vertical Edge3 (no str) : %i, Attr: %s" % (EId, EIdAttrName.GetI(i)())
Graph.AttrValueEI(EId, EIdAttrValue)
AttrLen = EIdAttrValue.Len()
for i in range(AttrLen):
print "Vertical Edge4 (no str) : %i, Attr_Val: %s" % (EId, EIdAttrValue.GetI(i)())
for i in range(NEdges):
Graph.AddIntAttrDatE(i, 70, attr2)
total = 0
EI = Graph.BegNAIntI(attr2)
while EI < Graph.EndNAIntI(attr2):
total += EI.GetDat()
EI.Next()
print "Average: %i (should be 70)" % (total / NEdges)
if total / NNodes != 70:
print "*** Error4"
EI = Graph.BegEI()
while EI < Graph.EndEI():
Eid = EI.GetId()
Graph.AddStrAttrDatE(Eid, "dummy_data", attr5)
EI.Next()
# test leak here
while True:
EI = Graph.BegEI()
while EI < Graph.EndEI():
Eid = EI.GetId()
attr1_val = Graph.GetStrAttrDatE(Eid, attr5)
EI.Next()
sleep(1)
Graph.Clr()
if __name__ == '__main__':
print "----- ManipulateAttributesIter -----"
ManipulateAttributesIter()
