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[Bug 1813550] [NEW] FlowEngine memory leak - 600 Mb/hr

 

Public bug reported:

Running examples/oedometer.py with 8000 spheres, flow.useSolver=4 and
tracking RAM usage, I find we have a memory leak of 600 Mb/hr.

examples/oedometer.py with num_spheres=8000:

# -*- coding: utf-8 -*-

from yade import pack

num_spheres=8000# number of spheres
young=1e6
compFricDegree = 3 # initial contact friction during the confining phase
finalFricDegree = 30 # contact friction during the deviatoric loading
mn,mx=Vector3(0,0,0),Vector3(1,1,1) # corners of the initial packing

O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(compFricDegree),density=2600,label='spheres'))
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=0,density=0,label='walls'))
walls=aabbWalls([mn,mx],thickness=0,material='walls')
wallIds=O.bodies.append(walls)

sp=pack.SpherePack()
sp.makeCloud(mn,mx,-1,0.3333,num_spheres,False, 0.95,seed=1) #"seed" make the "random" generation always the same
sp.toSimulation(material='spheres')

triax=TriaxialStressController(
 maxMultiplier=1.+2e4/young, # spheres growing factor (fast growth)
 finalMaxMultiplier=1.+2e3/young, # spheres growing factor (slow growth)
 thickness = 0,
 stressMask = 7,
 max_vel = 0.005,
 internalCompaction=True, # If true the confining pressure is generated by growing particles
)

newton=NewtonIntegrator(damping=0.2)

O.engines=[
 ForceResetter(),
 InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
 InteractionLoop(
  [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
  [Ip2_FrictMat_FrictMat_FrictPhys()],
  [Law2_ScGeom_FrictPhys_CundallStrack()],label="iloop"
 ),
 FlowEngine(dead=1,label="flow"),#introduced as a dead engine for the moment, see 2nd section
 GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
 triax,
 newton
]

triax.goal1=triax.goal2=triax.goal3=-10000

while 1:
  O.run(1000, True)
  unb=unbalancedForce()
  if unb<0.001 and abs(-10000-triax.meanStress)/10000<0.001:
    break

setContactFriction(radians(finalFricDegree))

## ______________   Oedometer section   _________________

#A. Check bulk modulus of the dry material from load/unload cycles
triax.stressMask=2
triax.goal1=triax.goal3=0

triax.internalCompaction=False
triax.wall_bottom_activated=False
#load
triax.goal2=-11000; O.run(2000,1)
#unload
triax.goal2=-10000; O.run(2000,1)
#load
triax.goal2=-11000; O.run(2000,1)
e22=triax.strain[1]
#unload
triax.goal2=-10000; O.run(2000,1)

e22=e22-triax.strain[1]
modulus = 1000./abs(e22)

#B. Activate flow engine and set boundary conditions in order to get permeability
flow.dead=0
flow.defTolerance=0.3
flow.meshUpdateInterval=200
flow.fluidBulkModulus=2.2e9
flow.useSolver=4
flow.desiredPorosity=0
flow.permeabilityFactor=1
flow.viscosity=10
flow.bndCondIsPressure=[0,0,1,1,0,0]
flow.bndCondValue=[0,0,1,0,0,0]
flow.boundaryUseMaxMin=[0,0,0,0,0,0]
O.dt=0.1e-3
O.dynDt=False

O.run(1,1)
Qin = flow.getBoundaryFlux(2)
Qout = flow.getBoundaryFlux(3)
permeability = abs(Qin)/1.e-4 #size is one, we compute K=V/∇H
print "Qin=",Qin," Qout=",Qout," permeability=",permeability

#C. now the oedometer test, drained at the top, impermeable at the bottom plate
flow.bndCondIsPressure=[0,0,0,1,0,0]
flow.bndCondValue=[0,0,0,0,0,0]
flow.updateTriangulation=True #force remeshing to reflect new BC immediately
newton.damping=0

#we want the theoretical value from Terzaghi's solution
#keep in mind that we are not in an homogeneous material and the small strain
#assumption is not verified => we don't expect perfect match
#there can be also an overshoot of pressure in the very beginning due to dynamic effects
Cv=permeability*modulus/1e4
zeroTime=O.time
zeroe22 = - triax.strain[1]
dryFraction=0.05 #the top layer is affected by drainage on a certain depth, we account for it here
drye22 = 1000/modulus*dryFraction
wetHeight=1*(1-dryFraction)

def consolidation(Tv): #see your soil mechanics handbook...
 U=1
 for k in range(50):
  M=pi/2*(2*k+1)
  U=U-2/M**2*exp(-M**2*Tv)
 return U

triax.goal2=-11000

from yade import plot

## a function saving variables
def history():
   plot.addData(e22=-triax.strain[1]-zeroe22,e22_theory=drye22+(1-dryFraction)*consolidation((O.time-zeroTime)*Cv/wetHeight**2)*1000./modulus,t=O.time,p=flow.getPorePressure((0.5,0.1,0.5)),s22=-triax.stress(3)[1]-10000)
   #plot.addData(e22=-triax.strain[1],t=O.time,s22=-triax.stress(2)[1],p=flow.MeasurePorePressure((0.5,0.5,0.5)))

O.engines=O.engines+[PyRunner(iterPeriod=200,command='history()',label='recorder')]
##make nice animations:
#O.engines=O.engines+[PyRunner(iterPeriod=200,command='flow.saveVtk()')]

from yade import plot
plot.plots={'t':('e22','e22_theory',None,'s22','p')}
plot.plot()
O.saveTmp()
O.timingEnabled=1
from yade import timing
print "starting oedometer simulation"
O.run(200,1)
timing.stats()

## Make more steps to see the convergence to the stationnary solution

** Affects: yade
     Importance: High
     Assignee: Robert Caulk (rcaulk)
         Status: Fix Committed

** Description changed:

  Running examples/oedometer.py with 8000 spheres, flow.useSolver=4 and
  tracking RAM usage, I find we have a memory leak of 600 Mb/hr.
  
  examples/oedometer.py with num_spheres=8000:
  
  # -*- coding: utf-8 -*-
  
  from yade import pack
  
  num_spheres=8000# number of spheres
  young=1e6
  compFricDegree = 3 # initial contact friction during the confining phase
  finalFricDegree = 30 # contact friction during the deviatoric loading
  mn,mx=Vector3(0,0,0),Vector3(1,1,1) # corners of the initial packing
  
  O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(compFricDegree),density=2600,label='spheres'))
  O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=0,density=0,label='walls'))
  walls=aabbWalls([mn,mx],thickness=0,material='walls')
  wallIds=O.bodies.append(walls)
  
  sp=pack.SpherePack()
  sp.makeCloud(mn,mx,-1,0.3333,num_spheres,False, 0.95,seed=1) #"seed" make the "random" generation always the same
  sp.toSimulation(material='spheres')
  
  triax=TriaxialStressController(
- 	maxMultiplier=1.+2e4/young, # spheres growing factor (fast growth)
- 	finalMaxMultiplier=1.+2e3/young, # spheres growing factor (slow growth)
- 	thickness = 0,
- 	stressMask = 7,
- 	max_vel = 0.005,
- 	internalCompaction=True, # If true the confining pressure is generated by growing particles
+  maxMultiplier=1.+2e4/young, # spheres growing factor (fast growth)
+  finalMaxMultiplier=1.+2e3/young, # spheres growing factor (slow growth)
+  thickness = 0,
+  stressMask = 7,
+  max_vel = 0.005,
+  internalCompaction=True, # If true the confining pressure is generated by growing particles
  )
  
  newton=NewtonIntegrator(damping=0.2)
  
  O.engines=[
- 	ForceResetter(),
- 	InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
- 	InteractionLoop(
- 		[Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
- 		[Ip2_FrictMat_FrictMat_FrictPhys()],
- 		[Law2_ScGeom_FrictPhys_CundallStrack()],label="iloop"
- 	),
- 	FlowEngine(dead=1,label="flow"),#introduced as a dead engine for the moment, see 2nd section
- 	GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
- 	triax,
- 	newton
+  ForceResetter(),
+  InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
+  InteractionLoop(
+   [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
+   [Ip2_FrictMat_FrictMat_FrictPhys()],
+   [Law2_ScGeom_FrictPhys_CundallStrack()],label="iloop"
+  ),
+  FlowEngine(dead=1,label="flow"),#introduced as a dead engine for the moment, see 2nd section
+  GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
+  triax,
+  newton
  ]
  
  triax.goal1=triax.goal2=triax.goal3=-10000
  
  while 1:
-   O.run(1000, True)
-   unb=unbalancedForce()
-   if unb<0.001 and abs(-10000-triax.meanStress)/10000<0.001:
-     break
+   O.run(1000, True)
+   unb=unbalancedForce()
+   if unb<0.001 and abs(-10000-triax.meanStress)/10000<0.001:
+     break
  
  setContactFriction(radians(finalFricDegree))
  
  ## ______________   Oedometer section   _________________
  
  #A. Check bulk modulus of the dry material from load/unload cycles
  triax.stressMask=2
  triax.goal1=triax.goal3=0
  
  triax.internalCompaction=False
  triax.wall_bottom_activated=False
  #load
  triax.goal2=-11000; O.run(2000,1)
  #unload
  triax.goal2=-10000; O.run(2000,1)
  #load
  triax.goal2=-11000; O.run(2000,1)
  e22=triax.strain[1]
  #unload
  triax.goal2=-10000; O.run(2000,1)
  
  e22=e22-triax.strain[1]
  modulus = 1000./abs(e22)
  
  #B. Activate flow engine and set boundary conditions in order to get permeability
  flow.dead=0
  flow.defTolerance=0.3
  flow.meshUpdateInterval=200
  flow.fluidBulkModulus=2.2e9
  flow.useSolver=4
  flow.desiredPorosity=0
  flow.permeabilityFactor=1
  flow.viscosity=10
  flow.bndCondIsPressure=[0,0,1,1,0,0]
  flow.bndCondValue=[0,0,1,0,0,0]
  flow.boundaryUseMaxMin=[0,0,0,0,0,0]
  O.dt=0.1e-3
  O.dynDt=False
  
  O.run(1,1)
  Qin = flow.getBoundaryFlux(2)
  Qout = flow.getBoundaryFlux(3)
  permeability = abs(Qin)/1.e-4 #size is one, we compute K=V/∇H
  print "Qin=",Qin," Qout=",Qout," permeability=",permeability
  
  #C. now the oedometer test, drained at the top, impermeable at the bottom plate
  flow.bndCondIsPressure=[0,0,0,1,0,0]
  flow.bndCondValue=[0,0,0,0,0,0]
  flow.updateTriangulation=True #force remeshing to reflect new BC immediately
  newton.damping=0
  
  #we want the theoretical value from Terzaghi's solution
  #keep in mind that we are not in an homogeneous material and the small strain
  #assumption is not verified => we don't expect perfect match
  #there can be also an overshoot of pressure in the very beginning due to dynamic effects
  Cv=permeability*modulus/1e4
  zeroTime=O.time
  zeroe22 = - triax.strain[1]
  dryFraction=0.05 #the top layer is affected by drainage on a certain depth, we account for it here
  drye22 = 1000/modulus*dryFraction
  wetHeight=1*(1-dryFraction)
  
  def consolidation(Tv): #see your soil mechanics handbook...
- 	U=1
- 	for k in range(50):
- 		M=pi/2*(2*k+1)
- 		U=U-2/M**2*exp(-M**2*Tv)
- 	return U
+  U=1
+  for k in range(50):
+   M=pi/2*(2*k+1)
+   U=U-2/M**2*exp(-M**2*Tv)
+  return U
  
  triax.goal2=-11000
- 
  
  from yade import plot
  
  ## a function saving variables
  def history():
-   	plot.addData(e22=-triax.strain[1]-zeroe22,e22_theory=drye22+(1-dryFraction)*consolidation((O.time-zeroTime)*Cv/wetHeight**2)*1000./modulus,t=O.time,p=flow.getPorePressure((0.5,0.1,0.5)),s22=-triax.stress(3)[1]-10000)
-   	#plot.addData(e22=-triax.strain[1],t=O.time,s22=-triax.stress(2)[1],p=flow.MeasurePorePressure((0.5,0.5,0.5)))
+    plot.addData(e22=-triax.strain[1]-zeroe22,e22_theory=drye22+(1-dryFraction)*consolidation((O.time-zeroTime)*Cv/wetHeight**2)*1000./modulus,t=O.time,p=flow.getPorePressure((0.5,0.1,0.5)),s22=-triax.stress(3)[1]-10000)
+    #plot.addData(e22=-triax.strain[1],t=O.time,s22=-triax.stress(2)[1],p=flow.MeasurePorePressure((0.5,0.5,0.5)))
  
  O.engines=O.engines+[PyRunner(iterPeriod=200,command='history()',label='recorder')]
  ##make nice animations:
  #O.engines=O.engines+[PyRunner(iterPeriod=200,command='flow.saveVtk()')]
  
  from yade import plot
  plot.plots={'t':('e22','e22_theory',None,'s22','p')}
  plot.plot()
  O.saveTmp()
  O.timingEnabled=1
  from yade import timing
  print "starting oedometer simulation"
  O.run(200,1)
  timing.stats()
  
  ## Make more steps to see the convergence to the stationnary solution

** Changed in: yade
   Importance: Undecided => High

** Changed in: yade
       Status: New => Fix Committed

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https://bugs.launchpad.net/bugs/1813550

Title:
  FlowEngine memory leak - 600 Mb/hr

Status in Yade:
  Fix Committed

Bug description:
  Running examples/oedometer.py with 8000 spheres, flow.useSolver=4 and
  tracking RAM usage, I find we have a memory leak of 600 Mb/hr.

  examples/oedometer.py with num_spheres=8000:

  # -*- coding: utf-8 -*-

  from yade import pack

  num_spheres=8000# number of spheres
  young=1e6
  compFricDegree = 3 # initial contact friction during the confining phase
  finalFricDegree = 30 # contact friction during the deviatoric loading
  mn,mx=Vector3(0,0,0),Vector3(1,1,1) # corners of the initial packing

  O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(compFricDegree),density=2600,label='spheres'))
  O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=0,density=0,label='walls'))
  walls=aabbWalls([mn,mx],thickness=0,material='walls')
  wallIds=O.bodies.append(walls)

  sp=pack.SpherePack()
  sp.makeCloud(mn,mx,-1,0.3333,num_spheres,False, 0.95,seed=1) #"seed" make the "random" generation always the same
  sp.toSimulation(material='spheres')

  triax=TriaxialStressController(
   maxMultiplier=1.+2e4/young, # spheres growing factor (fast growth)
   finalMaxMultiplier=1.+2e3/young, # spheres growing factor (slow growth)
   thickness = 0,
   stressMask = 7,
   max_vel = 0.005,
   internalCompaction=True, # If true the confining pressure is generated by growing particles
  )

  newton=NewtonIntegrator(damping=0.2)

  O.engines=[
   ForceResetter(),
   InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
   InteractionLoop(
    [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
    [Ip2_FrictMat_FrictMat_FrictPhys()],
    [Law2_ScGeom_FrictPhys_CundallStrack()],label="iloop"
   ),
   FlowEngine(dead=1,label="flow"),#introduced as a dead engine for the moment, see 2nd section
   GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
   triax,
   newton
  ]

  triax.goal1=triax.goal2=triax.goal3=-10000

  while 1:
    O.run(1000, True)
    unb=unbalancedForce()
    if unb<0.001 and abs(-10000-triax.meanStress)/10000<0.001:
      break

  setContactFriction(radians(finalFricDegree))

  ## ______________   Oedometer section   _________________

  #A. Check bulk modulus of the dry material from load/unload cycles
  triax.stressMask=2
  triax.goal1=triax.goal3=0

  triax.internalCompaction=False
  triax.wall_bottom_activated=False
  #load
  triax.goal2=-11000; O.run(2000,1)
  #unload
  triax.goal2=-10000; O.run(2000,1)
  #load
  triax.goal2=-11000; O.run(2000,1)
  e22=triax.strain[1]
  #unload
  triax.goal2=-10000; O.run(2000,1)

  e22=e22-triax.strain[1]
  modulus = 1000./abs(e22)

  #B. Activate flow engine and set boundary conditions in order to get permeability
  flow.dead=0
  flow.defTolerance=0.3
  flow.meshUpdateInterval=200
  flow.fluidBulkModulus=2.2e9
  flow.useSolver=4
  flow.desiredPorosity=0
  flow.permeabilityFactor=1
  flow.viscosity=10
  flow.bndCondIsPressure=[0,0,1,1,0,0]
  flow.bndCondValue=[0,0,1,0,0,0]
  flow.boundaryUseMaxMin=[0,0,0,0,0,0]
  O.dt=0.1e-3
  O.dynDt=False

  O.run(1,1)
  Qin = flow.getBoundaryFlux(2)
  Qout = flow.getBoundaryFlux(3)
  permeability = abs(Qin)/1.e-4 #size is one, we compute K=V/∇H
  print "Qin=",Qin," Qout=",Qout," permeability=",permeability

  #C. now the oedometer test, drained at the top, impermeable at the bottom plate
  flow.bndCondIsPressure=[0,0,0,1,0,0]
  flow.bndCondValue=[0,0,0,0,0,0]
  flow.updateTriangulation=True #force remeshing to reflect new BC immediately
  newton.damping=0

  #we want the theoretical value from Terzaghi's solution
  #keep in mind that we are not in an homogeneous material and the small strain
  #assumption is not verified => we don't expect perfect match
  #there can be also an overshoot of pressure in the very beginning due to dynamic effects
  Cv=permeability*modulus/1e4
  zeroTime=O.time
  zeroe22 = - triax.strain[1]
  dryFraction=0.05 #the top layer is affected by drainage on a certain depth, we account for it here
  drye22 = 1000/modulus*dryFraction
  wetHeight=1*(1-dryFraction)

  def consolidation(Tv): #see your soil mechanics handbook...
   U=1
   for k in range(50):
    M=pi/2*(2*k+1)
    U=U-2/M**2*exp(-M**2*Tv)
   return U

  triax.goal2=-11000

  from yade import plot

  ## a function saving variables
  def history():
     plot.addData(e22=-triax.strain[1]-zeroe22,e22_theory=drye22+(1-dryFraction)*consolidation((O.time-zeroTime)*Cv/wetHeight**2)*1000./modulus,t=O.time,p=flow.getPorePressure((0.5,0.1,0.5)),s22=-triax.stress(3)[1]-10000)
     #plot.addData(e22=-triax.strain[1],t=O.time,s22=-triax.stress(2)[1],p=flow.MeasurePorePressure((0.5,0.5,0.5)))

  O.engines=O.engines+[PyRunner(iterPeriod=200,command='history()',label='recorder')]
  ##make nice animations:
  #O.engines=O.engines+[PyRunner(iterPeriod=200,command='flow.saveVtk()')]

  from yade import plot
  plot.plots={'t':('e22','e22_theory',None,'s22','p')}
  plot.plot()
  O.saveTmp()
  O.timingEnabled=1
  from yade import timing
  print "starting oedometer simulation"
  O.run(200,1)
  timing.stats()

  ## Make more steps to see the convergence to the stationnary solution

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