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This script was made to clean a table of rows that has no counterpart in another table (It must be made via arcpy because the table is a feature class with archiving enabled, from ESRI). I'm testing this script in production, so, instead actually erasing the rows, I'm just using a counter. However, when the counter 'excluidos' is about value 310000, the script just stops. There is some memory limit in arcpy update cursor? (normally I get some python memory error message, which is not the case here) Or there is some logic problem here that I'm missing?

# -*- encoding: utf-8 -*-
import os.path, sys, time
sys.path.append(os.path.join(os.path.dirname(__file__), '..'))

from arcpy import da

pasta = os.path.abspath(os.path.join( os.path.dirname(__file__), '..', 'modelos'))

fc = 'Database Connections/geodados em arcgissql01.sde/geodados.sigamgeo.fis_vistorias_aia_tcra'
fc2 = 'Database Connections/geodados em arcgissql01.sde/geodados.sigamgeo.tb_fis_vistorias_aia_tcra'
workspace = os.path.dirname(fc)

campos = [
 "NIS"
 ,"Sigla"]

campos2 = ["NIS", "DataElabRTV"]

print str(time.strftime('%x %X'))
print 'Iniciando busca de registros no workspace: ' + fc2

lista = 
listIg = 

with da.SearchCursor(fc2, (campos2)) as sc:
 for row in sc:
 if row[0] <> None:
 lista.append(row[0])

print str(time.strftime('%x %X'))
print 'Iniciando exclusao de registros no workspace: ' + fc

try:
 edit = da.Editor(workspace)
 print str(time.strftime('%x %X'))
 print 'Iniciando edicao.'
 edit.startEditing(False, False) #undo/multiuser
 print str(time.strftime('%x %X'))
 print 'Iniciando operacao.'
 edit.startOperation()
except Exception as e:
 print e
 sys.exit(0)

print str(time.strftime('%x %X'))
print 'Iniciando exclusao.'
excluidos = 0
ignorados = 0
multiplo = 100000
try:
 with da.UpdateCursor(fc, (campos)) as cursorExc:
 for row in cursorExc:
 if row[0] <> None:
 verifExcec = False
 for reg in lista:
 if reg == int(row[0]):
 verifExcec = True
 if verifExcec:
 listIg.append(reg)
 ignorados += 1
 continue
 else:
 #cursorExc.deleteRow()
 excluidos += 1
 else:
 ignorados += 1
 #verifica se o contador e igual ao multiplo definido para emitir o aviso
 if (excluidos % multiplo == 0):
 print u"0 - 1 ".format(time.strftime('%x %X'), excluidos) + u" registros excluídos até o momento."


except Exception as e:
 print e

print str(time.strftime('%x %X'))
print str(excluidos) + ' registros excluidos.'

print str(time.strftime('%x %X'))
print str(ignorados) + ' registros ignorados.'

try: 
 # Stop the edit operation.
 print str(time.strftime('%x %X'))
 print 'Encerrando operacao.'
 edit.stopOperation()

 # Stop the edit session and save the changes
 print str(time.strftime('%x %X'))
 print 'Encerrando edicao.'
 edit.stopEditing(True)
except Exception as e:
 print e

listIg.sort()
for nis in listIg:
 print nis

I think the limitation is on arcpy, so I should have made the question at GIS Stack Exchange. Anyway, I 'resolved' the issue with a much slower solution, starting and stopping edition for each exclusion:

print str(time.strftime('%x %X'))
print 'Iniciando busca de registros no workspace: ' + fc2

listAIA = 
listVist = 
listIg = 
adicionados = 0
ignorados = 0

with da.SearchCursor(fc2, (campos2)) as sc:
 for row in sc:
 if row[0] <> None:
 listVist.append(row[0])

with da.SearchCursor(fc, (campos)) as sc1:
 for row in sc1:
 verifExcec = False
 if row[0] <> None:
 for vist in listVist:
 if int(row[0]) == vist:
 verifExcec = True
 if verifExcec:
 ignorados += 1
 listIg.append(row[0])
 continue
 else:
 listAIA.append(row[0])
 adicionados += 1
 else:
 ignorados += 1
 listIg.append(row[0])

print str(time.strftime('%x %X'))
print 'Iniciando exclusao de registros no workspace: ' + fc

col_1 = 'NIS'
excluidos = 0
multiplo = 100000

for reg in listAIA: 
 expressao = '"' + col_1 + '" = ' + str(reg)
 try:
 edit = da.Editor(workspace)
 edit.startEditing(False, False) #undo/multiuser
 edit.startOperation()
 except Exception as e:
 print e
 sys.exit(0)

 try:
 with da.UpdateCursor(fc, (campos), expressao) as cursorExc:
 for row in cursorExc:
 #cursorExc.deleteRow()
 excluidos += 1
 print u"0 - 1 ".format(time.strftime('%x %X'), excluidos) + u" registros excluídos até o momento."

 except Exception as e:
 print e 

 try: 
 # Stop the edit operation.
 edit.stopOperation() 
 # Stop the edit session and save the changes
 edit.stopEditing(True)
 except Exception as e:
 print e

 if (excluidos % multiplo == 0):
 print u"0 - 1 ".format(time.strftime('%x %X'), excluidos) + u" registros excluídos até o momento."

print str(time.strftime('%x %X'))
print str(excluidos) + ' registros excluidos.'

print str(time.strftime('%x %X'))
print str(ignorados) + ' registros ignorados.'